A commentary on coastal research in New

Zealand universities

Abstract:University research in coastal geomorphology, processes and management has made a

major contribution to the fundamental understanding of coastal systems in NewZealand over the
past 43 years. This article examines the growth in university-based coastalresearch since 1964 and
discusses the geographical pattern and themes of this research.Data indicate a significant
geographical concentration of research effort and focus on anarrow range of research themes.
Underlying reasons for these characteristics of NewZealand coastal research are explored and
challenges facing university based research arediscussed. Such challenges can be overcome
through a more coordinated research effortto realize the huge potential to undertake coastal
science of national relevance and internationalsignificance.Key words:coastal geomorphology,
coastal management, New Zealand, postgraduate research.

A comparison of different protocols for RAPD analysis of Littorina

Abstract
Randomly amplified polymorphic DNA (RAPD) is a fast and useful method of genome marking that is useful
for studies of, for example, parentage, mating patterns, taxonomy of sibling species and intra-specific
population genetic structures. Herewe compare three different procedures for extracting highmolecularweight
genomicDNA; phenol-chloroform, hexadecyltrimethyl ammonium-bromide (CTAB) and Chelex 100. Double
phenol-chloroform and CTAB extractions both generated high amounts of high quality DNA while Chelex
100 failed to do so.We also compared PCR-amplification with different concentrations of template DNA and
found that 1±2 ng per 25 rl of
amplification cocktail gave the best results. AmplifyingDNAprepared by the three extractionmethods revealed
that
DNA extracted with double phenol-chloroform gave the clearest bands. The double phenol-chloroform
extraction
seems thus the most suitable extraction method for RAPD in Littorina, however Chelex may be the only
method
useful for extracting DNA from very small individuals, for example, pre-hatching stages.

A historical perspective of the genus Mytilus (Bivalvia:

Mollusca) in New Zealand: multivariate morphometric
analyses of fossil, midden and contemporary blue mussels

The taxonomic status of smooth shelled blue mussels of the genus Mytilus has received considerable attention
in thelast 25 years. Despite this, the situation in the southern hemisphere remains uncertain and is in need of
clarification.
Recent work suggests that contemporary New Zealand mussels from two cool/cold temperate locations areM.
galloprovincialis. However, the distribution of Mytilus in New Zealand ranges from 35 Î to 52 Î south (

1800 km), meaning that large areas of the subtropical/warm temperate north and the subantarctic south remain
unsampled,
an important consideration when species of this genus exhibit pronounced macrogeographical differences in
their¿ distributions which are associated with environmental variables such as water temperature, salinity,
wave action and ice cover. This study employed multivariate morphometric analyses of one fossil, 83 valves
from middens, and 92 contemporary valves from sites spanning the distributional range of blue mussels to
determine a historical and
contemporary perspective of the taxonomic status of Mytilus in New Zealand. The findings indicated that all
fossil and midden mussels are best regarded as M. galloprovincialis and confirmed that contemporary
mussels, with one
possible regional exception, are also best regarded as M. galloprovincialis. Contemporary mussels from the
Bay of
Islands (warm temperate/subtropical) exhibited much greater affinity to M. edulis than they did to
M. galloprovincialis, indicating that mussels from this area require detailed genetic examination to determine
their
taxonomic status. The analyses revealed a significant difference between the fossil/midden mussels and the
contemporary
mussels, consistent with levels of present day differentiation among intraspecific populations and not
thought to reflect any substantive temporal change between mussels of the two groups. The continuous
distribution
of M. galloprovincialis in New Zealand from the warm north to the subantarctic south indicates that the
physiology
of this species is adapted to a wide range of water temperature conditions. Therefore, the distribution of this
species
on a worldwide scale is unlikely to be restricted by its adaptation to warm water alone, as has previously been
widely
assumed. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 329±
344.
ADDITIONAL KEYWORDS: distribution ± Mytilus galloprovincialis ± shell trait variation ± southern
hemisphere.

A multilocus allozyme discontinuity in the mussel

Mytilus galloprovincialis: the interaction of
ecological and life-history factors

ABSTRACT: Electrophoretically detectable genetic variability of the Mediterranean mussel Mytilus

galloprovincialis Lmk. was examined at 15 allozyme loci in 21 populations ranging from Santander
(northern Spain) to Livorno (northwestern Italy). A major genetic break between Almeria and Alicante
(southeastern Spain), as evidenced by 11 of 13 polymorphic loci examined, delimits 2 groups of populations
with a high internal homogeneity. Roughly 75% of the total genetic differentiation was attributable
to the divergence between these 2 groups of populations that displayed a genetic distance
between them (D â 0.03) in the range of conspecific populations. This genetic break in M. galloprovincialis
contrasts with earlier reports of genetic homogeneity among conspecific populations of the genus
Mytilus over vast geographical distances, and represents an uncommon result in manne organisms
with larval dispersal. The Zone of genetic divergence in M. galloprovincialis corresponds to a discontinuity
in the distribution of this mussel, and to tbe position of the well-defined Almeria-Oran oceanographic
front, with a distributional boundary between Atlantic and Mediterranean communities. In this
region, other manne species exhibit similar patterns of intraspecific divergence, suggesting the action
of common biogeographic processes. It is proposed that contemporary influences on gene flow related
to an ecological barrier, perhaps in combination with selective pressures associated to water mass differences,
maintain the abrupt change in southeastern Spain.
KEY WORDS: Mytilus . Allozyme . Genetic discontinuity . Larval dispersal . Ecological barrier

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Advances in marine conservation:
the role of marine protected areas
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Advances in molecular technology and their impact
on fisheries genetics
Introduction
The past six decades have seen increasing application
of genetics to fisheries management and
ecology (Waples et al. 2008), resulting in significant
insights into the organismal and population ecology
of marine exploited species, with consequent paradigm
shifts that changed our perception of the
Abstract
Although genetic approaches to questions in fisheries management have been very
useful in the past, they have encountered consistent hurdles despite the development
of new marker systems. However, recent technological advances in molecular
genetics will help to overcome many of these hurdles and are likely to revolutionize
fish and fisheries biology. DNA-sequencing costs have been decreasing exponentially,
and recent breakthroughs have led to rapid increase in throughput that allows
sequencing the entire expressed genome of a non-model organism with standard
project budgets. Increase in screening throughput and number of available markers,
reduction in costs and improved insights into gene function and control of gene
expression will allow applications that were impossible until recently. Here, we briefly
recount the recent history of fisheries genetics, provide an outlook on near-term and
long-term developments in genetic technology and consider their applications and
implications for fisheries science and education.
Keywords DNA sequencing, genome analysis, molecular genetics, single nucleotide
polymorphisms, technological developments

Responsible Approach to Marine Stock Enhancement‘



AFLP-based genetic linkage maps of the blue mussel
(Mytilus edulis)
Summary We report the construction of the first genetic linkage map in the blue mussel, Mytilus edulis.
AFLP markers were used in 86 full-sib progeny from a controlled pair mating, applying a
double pseudo-test cross strategy. Thirty-six primer pairs generated 2354 peaks, of which
791 (33.6%) were polymorphic in the mapping family. Among those, 341 segregated
through the female parent, 296 through the male parent (type 1:1) and 154 through both
parents (type 3:1). Chi-square goodness-of-fit tests revealed that 71% and 73% of type 1:1
and 3:1 markers respectively segregated according to Mendelian inheritance. Sex-specific
linkage maps were built with MAPMAKER 3.0 software. The female framework map consisted of
121 markers ordered into 14 linkage groups, spanning 862.8 cM, with an average marker
spacing of 8.0 cM. The male framework map consisted of 116 markers ordered into 14
linkage groups, spanning 825.2 cM, with an average marker spacing of 8.09 cM. Genome
coverage was estimated to be 76.7% and 75.9% for the female and male framework maps
respectively, rising to 85.8% (female) and 86.2% (male) when associated markers were
included. Twelve probable homologous linkage group pairs were identified and a consensus
map was built for nine of these homologous pairs based on multiple and parallel linkages of
3:1 markers, spanning 816 cM, with JOINMAP 4.0 software.

Larval Dispersal and Marine

Population Connectivity
Key Words
larval transport, biophysical modeling, complex life cycles, metapopulation,
self recruitment, population dynamics
Abstract
Connectivity, or the exchange of individuals among marine populations, is a
central topic in marine ecology. For most benthic marine species with complex
life cycles, this exchange occurs primarily during the pelagic larval stage.
The small size of larvae coupled with the vast and complex fluid environment
they occupy hamper our ability to quantify dispersal and connectivity. Evidence
from direct and indirect approaches using geochemical and genetic
techniques suggests that populations range from fully open to fully closed.
Understanding the biophysical processes that contribute to observed dispersal
patterns requires integrated interdisciplinary approaches that incorporate
high-resolution biophysical modeling and empirical data. Further, differential
postsettlement survival of larvae may add complexity to measurements of
connectivity. The degree to which populations self recruit or receive subsidy
from other populations has consequences for a number of fundamental ecological
processes that affect population regulation and persistence. Finally,
a full understanding of population connectivity has important applications
for management and conservation.

Application of DNA-Based Methods to Identify Fish and Seafood Substitution on the Commercial
Market
ABSTRACT: Fish and seafood substitution has become an important concern in domestic and international
marketplaces, in part due to increased international trade, per capita seafood consumption, and production of
processed foods. In many cases, seafood substitution is a form of economic deception, where highly prized
species are substituted with those of lesser value. To prevent illegal species substitution, a number of DNA-
basedmethods have been developed to detect fish and seafood species in commercial products. These
methods, alongwith commongene targets, have been reviewed previously in this journal. The current article is
meant to build upon earlier discussions by providing a comprehensive review of the application of these
DNA-based methods to the discovery of fish and seafood substitution on the commercialmarket. Popular food
uses, potential substitution cases, and peer-reviewed research articles published to date are discussed for
allmajor species groups of concern, including flatfish, gadoids,
scombroids, salmonids, percoids, sturgeons, sharks, eels, and bivalves. The use of DNA-based methods to
monitorcommercial whale meat products is also reviewed.
‘


‘ ‘
‘  ‘ ‘  ‘ ‘
‘
‘ ‘‘‘ ‘‘ ‘
 
The use of highly discriminatory methods for the identification and characterization of genotypes is essential
for plant protection and appropriate use. We utilized the RAPD method for the genetic fingerprinting of 11
plant species of desert origin (seven with known medicinal value). cndrachne telephioides, Zilla spinosa,
Caylusea hexagyna, cchillea fragrantissima, Lycium shawii, Moricandia sinaica, Rumex vesicarius, Bassia
eriophora, Zygophyllum propinquum subsp migahidii, Withania somnifera, and Sonchus oleraceus were
collected from various areas of Saudi Arabia. The five primers used were able to amplify the DNA from all
the plant species. The amplified products of the RAPD profiles ranged from 307 to 1772 bp. A total of 164
bands were observed for 11 plant species, using five primers. The number of well-defined and major bands
for a single plant species for a single primer ranged from 1 to 10. The highest pair-wise similarities (0.32)
were observed between c. fragrantissima and L. shawii, when five primers were combined. The lowest
similarities (0) were observed between c. telephioides and Z. spinosa; Z. spinosa and B. eriophora; B.
eriophora and Z. propinquum In conclusion, the RAPD method successfully discriminates among all the plant
species, therefore providing an easy and rapid tool for identification, conservation and sustainable use of these
plants.

Applications of random amplified polymorphic DNA

(RAPD) in molecular ecology
Abstract
Molecular genetic markers have been developed into powerful tools to analyse genetic
relationships and genetic diversity. c
an extension to the variety of existing techniques
using polymorphic DNA markers, the Random Amplified Polymorphic DNA (RAPD)
technique may be used in molecular ecology to determine taxonomic identity, assess
kinship relationships, analyse mixed genome samples, and create specific probes. Main
advantages of the c
technology include (i) suitability for work on anonymous
genomes, (ii) applicability to problems where only limited quantities of DNA are
available, (iii) efficiency and low expense.
¢eywords: DNA fingerprinting, DNA probes, kinship analysis, paternity determination, RAPD,
taxonomic identifications
Received 3 February 1992

Applied Environmental Economics. A GIS Approach

to Cost-Benefit Analysis
This book focuses on one of the most exciting and rapidly
evolving trends in environmental economics and natural resource
management: improving economic analyses of natural resource
planning and evaluation through the use of geographic information
system (GIS) technologies and data. The premise of the book is
that economic valuation approaches and cost-benefit analyses can
be substantially improved and made more relevant by incorporating
natural resource and socio-demographic data that are both more
detailed (site-specific) and spatially related to a variety of other data
and phenomena.
The book incorporates most of the contents of the Ph.D. thesis of
one of the authors, and many of its findings have been previously
published in various articles in the last decade, however it is
helpful to have the entirety of this material in one single medium.
The focus of the presented research is on a single case study:
the economic evaluation of converting agricultural land (primarily
in sheep production) to multipurpose woodland across the entire
country of Wales (United Kingdom) in the early 1990s.
The introductory chapter contains background material on both
GIS and cost-benefit analysis, but these treatments are very limited,
which encouraged me to skip ahead to chapter 9 (GIS and costbenefit
analyses) before beginning to read chapters 2±8. Chapter 2
summarizes recreation valuation methods used by economists to
capture both use and non-use values (the contingent and travel
cost approaches), while chapter 3 deals with recreation valuation
specific to woodlands. Chapter 4 covers the use of GIS for benefits
transfer (extrapolating prior valuation study results to another study
location). The focus of chapter 5 is timber yield forecasting and
estimating the productive values of woodlands, while chapter 6 deals
with estimating the net benefits of carbon sequestration. Chapter 8
focuses on the opportunity costs of converting agricultural land
to woodlands. Chapter 9 integrates economic analyses from all
the previous chapters, and the final chapter evaluates the policy
implications of this extensive research effort.
The strength of the book is in its detail and breadth, which make
it a very useful read for researchers or policy makers interested in
undertaking similar studies. The book also clearly demonstrates
the benefits to environmental and resource economists in taking
advantage of recently available GIS data and technologies.
A potential weakness of the book to some readers is that is difficult
to reference or locate specific technical topics, particularly GIS
procedures, using either the table of contents or index. On a related
note, there are several cases where insufficient detail is provided
regarding the µnuts and bolts¶ of GIS methods used and, in my
opinion, there are not enough caveats or warnings made regarding
the potential to misuse GIS techniques, particularly by economists
whomay have GIS training and experience. Therewere a few cases of
economics-based material being presented in too much detail, while
other topics were sorely missed, such as a discussion and analysis of

Aquaculture and environment from the perspective of a

Spanish fish farmer
F. Torrent Bravo and A. Sánchez Montañés
Aguaviva Azul S.L., San Martín de Porres 43, 1º P, 28035 Madrid, Spain
SUMMARY ± The Spanish marine aquaculture industry is here described as a new emerging
industry, although
with a sound background from the trout and mussel production industries. Its impact on the
environment is
considered not negative and even positive provided a good production and environmental
management system is
undertaken. A comparison with other industries such as fisheries and other human activities is here
described,
activities better socially accepted but in some cases more harmful for their negative impact on the
environment.
The necessity for a well scientifically based regulation by the Environmental Authorities is here
stated.
Key words: Aquaculture, environment, marine fish production.

Aquaculture in New Zealand

Aspects of the population genetics of Mytilus

(Mytilidae; Mollusca) in the British Isles
D. 0. F. SKIBINSKI, J. .A. BEARDMORE AAND ´
>
CROSS*
StLircIi gel electrophoi-esis was used to study \-ariation at I I loci in mussels sampled mainly from
British co'istal sites. Two types of mussel were identified, 2\f>sti"u |


tlie common mussel rind its
soutliern relatit e .\fvti/iir ga//n/~~,/,,or~iricSien\/ ie~r.a 1 partially dingnortic loci were used to miip tlie
distrihtition of tlie t\vo forms. .\fvti/riJ |


\\as present ;it all sites sampled in Britain and Ireland hut
as at low frequency in S England;

ga//ul,ioi'incia/ir vas detected in S England, tlie south and
west of Ireland. Scotland and S E England. hut was absent from soutli \Vales. the Irish sea co;ists of
tValt-s and Ireland. and SE England. Ap;irt fi-om tlie occurrence of . i f .á 
   in NE
England. this distribution conforms bvith tlie results of studies using morphological characters and
parallels the distrihution of many other soutlicrn species in Britain. At thc microgeographical l e d ,
.If. c d i i / i ~w as


to prcfrr more slieltered and rstiiarine conditions than `

,~a//opmr,iiiria/i.A~.n alysis
rising the hest diagnostic loci sliowed that tiybridizati(in is occurring between
V


and
.\I. gn/lopiur~in~-iaa/itr all localities where the) occiir sympatrically hut that tlie extent of hybridization
\aries considerahl) hetween localities. 'The distribution of localities ha ing Iiigli proportions of hybrid
individuals is hest interpreted hy assuming that 11) hrids ha e higher fitness than parental tyries at
these localities.
: stlid! v.is made o f \ ariation within and between those localities where only

~diiliri ndi\ iduals
Tvei-e ohser\.ed. Little significant geographic \.ariation in dlele frequency was detected, hut significcrnt
deficits of 1ieteroz)gotes  

with H;irdy-lVeinberg expectations nere seen for most loci.
.\n:ilysis suggests that the \Valilund effect is not involxd and that the most likely cause of tlie deficit
is low frequencies (if niill 'illeles. In .\I. p


no differences in phenotypic \.ariance in shell height and
width vwe ohserved hetween samples of multiply lietcrozygoiis and multiply liomozygoiis individuals
;ind no qriietic differences were found bet\vern juveniles and adults. Overall little evidence was found
that Iialnncing selectinn is responsible for m'rintrn;ince of the polymoi-phisms studied in .if. edulir.
1 lie ~iatterioi fgcogr;ipliic \.ariation in gene frequencies in d i f v t i /~iins the British Isles is discussed in
relation to variation in tlie south and north of F.rirope and Sorth . h e r i c a . It is concluded that steep
clines in gene li-eqiiencies in .\I.
VV
ohser\-ed h! otlier \viirkers in tlie Bnltir and in Long 1sl;ind
Sound cannot tie .ittribiited to the presencr of .\I. gn//ol"ui,incin/i.
KEYiV0RDS:- Poptilation genetics å .\!vfr/v~ å electrophoresis
I_
allozymes - geographic \.ariation
11) bridization speciation

ASSORTATI E MATING PREFERENCES

AMONG HYBRIDS OFFERS A ROUTE
TO HYBRID SPECIATION
Homoploid speciation generates species without a change in chromosome number via introgressive
hybridization and has been
considered rare in animals. u|


butterflies exhibit bright aposematic color patterns that also
act as cues in assortative
mating. u|


|V
has a color pattern that can be recreated by introgression of the u 
| |
|red band into an u 

genetic background. Wild u |V
males show assortative mating based on color pattern
and we here investigate the
origin of this preference by studying first-generation backcross hybrids between u | |
|and
u 
that resemble u 
|V
. These hybrids show assortative mating preferences, showing a strong preference for their
own color pattern over that
of either parental species. This is consistent with a genetic basis to wing pattern preference and
implies, first, that assortative
mating preferences would facilitate the initial establishment of a homozygous hybrid color pattern by
increasing the likelihood
that early generation hybrids mate among themselves. Second, once established such a lineage
would inherit assortative mating
preferences that would lead to partial reproductive isolation from parental lineages.
KEY WORDS: Homoploid speciation, introgression, mating preference, pleiotropy, transgressive
segregation.

Benthic mapping using local aerial photo interpretation and resident taxa
inventories for designing marine protected areas
SUMMARY
Given the frequent socioeconomic, political and
concomitant ecological failures of science-driven
marine protected area (MPA) programmes, it is now
important to design MPAs by integrating natural and
social science research more comprehensively. This
study shows how indigenous peoples assisted in the
design of MPAs by identifying marine substrates and
related resident taxa on aerial photos, information
which was then incorporated into a geographical
information system (GIS) database, along with dive
survey data. Two questions were asked: (1) Is indigenous
ecological knowledge accurate enough for
mapping the benthos and associated taxa? (2) Is such
an approach an appropriate way for assisting in the
biological and social design of MPAs in Oceania?
Conventional quadrat field dive surveys were used
to measure the accuracy of substrate identification
by local informants and a visual survey was used
to test hypotheses formulated from local knowledge
regarding the spatial distribution and relative
abundance of non-cryptic species within certain
benthic habitats. Equivalence rates between indigenous
aerial photo interpretations of dominant benthic
substrates and in situ dive surveys were 75±85%
for a moderately detailed classification scheme of
the benthos, which included nine locally-defined
abiotic and biotic benthic classes for the MPA
seabed. Similarly, the taxa inventory showed a strong
correspondence between the qualitative predictions of
local fisherfolk and the quantitative analysis of noncryptic
species distribution, including their relative
abundance and geophysical locations. Indigenous
people¶s predictions about the presence or absence of
fish in different benthic habitats corresponded77%and
92% of the time (depending on scoring schema)
with in situ visual measurements. These results
demonstrate how incorporating local knowledge of
benthic heterogeneity, existing biological communities,
and particular spatio-temporal events of biological
significance into a GIS database can corroborate
the production of scientifically reliable base resource
UCorrespondence: Dr Shankar Aswani Tel.: ß1 805 893 5285 Fax:
ß1 805 893 8707 e-mail: aswani@anth.ucsb.edu
maps for designing MPAs in an environmentally and
culturally sound fashion. This participatory approach
was used to design and then establish MPAs in
the Roviana and Vonavona region of the Western
Solomon Islands. Under appropriate conditions, interdisciplinary
work can complement the design
of scientific fishery management and biodiversity
conservation prescriptions for coastal Oceania.
¢eywords: benthic mapping, geographical information
systems (GIS), indigenous ecological knowledge, marine
protected areas, Oceania, taxa inventories
BIBLIOGRAFÍA

Biochemical-genetic variation in the green-lipped mussel

Ä|V


around New Zealand and
possible implications for mussel farming
Abstract Genetic variation was surveyed at 10
polymorphic enzyme loci in six samples of greenlipped
mussels, Äerna canaliculus, from around
New Zealand. There is a significant heterogeneity
at five loci and at four of these the heterogeneity
is produced by significant differences between
northern and southern samples. The differences may
be explained by limited genetic exchange owing to
current movements coupled with local selection.
Four loci were tested in spring and autumn seed
mussels from Marlborough Sounds and Ninety Mile
Beach. There is a significant difference between
spring and autumn seed at one locus. Seed mussels
show a significant excess of homozygotes at 6 out
of 16 tests whereas for adult mussels at the same
loci only 4 out of 24 tests are significant. It is suggested
that the differences between spring and
autumn seed and the greater homozygosity in seed
mussels may be produced by partial assortative
mating. For farming operations there may be
genetic disadvantages in transferring seed from one
water mass to another for ongrowing.
Keywords green-lipped mussel; Äerna canaliculus;
electrophoresis; genetic variation; mussel
farming

Biogeography of New Zealand¶s Coastal Marine Environment: Evaluation of Classification

Schemes for Systematic Conservation Planning
Key Words: benthic communities, biogeography, bioregions, macroalgae, marine reserves, New
Zealand, subtidal reefs, systematic conservation planning
2
Abstract: The scale of current global change in natural systems and initiatives to protect biodiversity
mean that biogeography has moved from the status of scholarly pursuit to an urgent requirement for
systematic conservation planning. In New Zealand, as for many coastal nations, several different
biogeographic classification schemes have been proposed for the marine environment. This poses a
major challenge for managers in choosing an appropriate spatial framework 5 for systematic
conservation planning. The aim of this study was to provide a systematic, robust approach for
evaluating and developing a biogeographic classification within a hierarchical spatial framework.
Systematically collected data for shallow subtidal (<12m depth) macroalgae (101 species) and mobile
macroinvertebrates (39) from 194 rocky reef sites at 33 locations throughout mainland New Zealand
10 were analysed to quantitatively evaluate six existing biogeographic classification schemes. These
were based on a variety of taxa and techniques including qualitative, delphic, quantitative and
phylogeographic. We found high concordance, particularly for macroalgae, between species
composition and these previously identified classification schemes (classification success of 63-92
%) justifying the use of algal assemblage data from shallow reefs as a surrogate for coastal
15 biodiversity. This provided a basis to develop a multivariate classification to identify large-scale
planning units within a hierarchical context. Cluster analysis based on presence-absence macroalgal
species composition data showed a general division between a Northern (warm-temperate) and
Southern (cold-temperate) biogeographic province (90% classification success). Nested within these
were 11 regional groups of spatially delineated locations (four Northern and seven Southern), termed
20 ³bioregions´ (81% classification success). Mobile macro-invertebrates also exhibited a division
between northern and southern locations but regional groupings were less distinctive. The
biogeographic data and analytical techniques used in this study provide an objective approach to
evaluating and choosing large-scale biogeographic frameworks necessary for systematic conservation
planning and the design of representative and comprehensive networks of marine protected areas.

Blue mussel - ‰p
| 


Mediterranean mussel -
‰  V 





Bridging the gap between the genotype and the phenotype:

linking genetic variation, selection and adaptation in fishes
Abstract
One of the most challenging problems in evolutionary biology is linking the evolution
of the phenotype with the underlying genotype, because most phenotypes are
encoded by many genes that interact with each other and with the environment.
Further, many phenotypes are correlated and selection on one can affect evolution of
the other. This challenge is especially important in fishes, because their evolutionary
response to harvest, global warming and conservation actions are among the least
understood aspects of their management. Here, we discuss two major genetic
approaches to studying the evolution of complex traits, multivariate quantitative
genetics and molecular genetics, and examine the increasing interaction between the
two fields. These interactions include using pedigree-based methods to study the
evolution of multivariate traits in natural populations, comparing neutral and
quantitative measures of population structure, and examining the contribution that
the two approaches have made to each other. We then explore the major role that
quantitative genetics is playing in two key issues in the conservation and
management of fish populations: the evolutionary effects of fishing and adaptation
to climate change. Throughout, we emphasize that it is important to anticipate the
availability of improvements in molecular technology and statistical analyses by
creating research populations such as inbred lines and families segregating at fitness
traits, developing approaches to measuring the full range of phenotypes related to
fitness, and collecting biological material and ecological data in natural populations.
These steps will facilitate studies of the evolution of complex traits over informative
temporal and spatial scales.
Keywords Climate change, fisheries-induced selection, genomics in fishes, multivariate
quantitative genetics, phenotypic evolution

BUSINESS PLANNING HANDBOOK

FOR THE
OCEAN AQUACULTURE OF BLUE MUSSELS

Can Developing Countries

Learn from Our Mistakes?
By ¢

 M. GWILLIAM
ABSTRACT: It is often asserted that developing countries can best
avoid the deterioration of the environment that is a consequence of
the unfettered increase of motorization by studying the failure of
industrialized countries to make the necessary political and resource
commitments to confront the issue. Such assertions usually fail to
recognize that differences in social objectives and both administrative
and fiscal capacity typically exclude the application in developing
countries of many of the restraining measures advocated for the
industrialized world. Instead, it is argued that the development of
efficient social and personal incentive systems, rather than the traditional
emphasis on systems of subsidy, public sector service provision,
and physical restraint, is the critical policy imperative for the
developing world.
Chapter 5

Characterization of single-nucleotide polymorphism

markers in the Mediterranean mussel,
Mytilus galloprovincialis
Manuel Vera1, Bele¤n G Pardo1, Ania Pino-Querido1, Jose¤ AntonioAŁ lvarez-Dios2, Jose¤ Fuentes3 &
Paulino Mart|¤nez1
r

 



   




 


 

 


   
    



 


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Abstract
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Keywords: 

 



 
   
 Mytilus galloprovincialis
Chromosomal markers

Chromosome polymorphism in Astyanax fasciatus

(Teleostei, Characidae), Part 3: Analysis of the
RAPD and ISSR molecular markers
Abstract
The Randomly Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSR) molecular
markers were used
to complement the study of chromosomal polymorphism in Astyanax fasciatus (Teleostei, Characidae) from
the Mogi-Guac¸u River
(Southeastern Brazil), analyzed in three collection sites along the river (Ouro Fino e MG, Cachoeira de Emas
e SP and Barrinha e
SP). Two cytotypes (or karyotypic types), denominated standard cytotypes, were previously characterized,
one including 2n ¼ 46
chromosomes and the other 2n ¼ 48 chromosomes, where all the chromosomes of the complement form
homologous pairs. Additionally,
variant karyotypic forms with 2n ¼ 45, 46 and 47 chromosomes were also detected, although with a lower
frequency in
relation to the standard cytotypes. RAPD turned out little informative in the analysis of the observed situation,
indicating a high
value of migrants per generation among the cytotypes. On the other hand, ISSR showed a small structure,
especially among the
standard cytotypes from the Barrinha region where the Nm was 0.4301 with a genetic identity of 0.6862 and
genetic distance
of 0.3765. However, the general results obtained do not discard the possibility of interbreeding between both
standard cytotypes
and/or their descendants as a source of chromosome variation. The association between the cytogenetic and
molecular markers
viabilized putative explanatory scenery for the origin and evolution of the forms seen in A. fasciatus.
_ 2007 Elsevier Ltd. All rights reserved.
Keywords: Astyanax fasciatus; ISSR marker; RAPD marker; Chromosome variation; Polymorphism

Clonality in the endangered Ambrosia pumila (Asteraceae)

inferred from RAPD markers; implications for conservation
and management

Abstract Clonal plants have the ability to spread and

survive over long periods of time by vegetative growth.

For endangered species, the occurrence of clonality can
have significant impacts on levels of genetic diversity,
population structure, recruitment, and the implementation
of appropriate conservation strategies. Here
we examine clone structure in three populations of
Ambrosia pumila (Nutt.) Gray (Asteraceae), a federally
endangered clonal species from southern California.
Ambrosia pumila is a perennial herbaceous species
spreading from a rhizome, and is frequently found in
dense patches of several hundred stems in a few square
meters. The primary habitat for this species is upper
terraces of rivers and drainages in areas that have been
heavily impacted by anthropogenic disturbances and
changing flood regimes. RAPD markers were employed
to document the number and distribution of
clones within multiple 0.25 m2 plots from each of three
populations. Thirty-one multi-locus genotypes were
identified from the 201 stems sampled. The spatial
distribution of clones was limited with no genotypes
shared between plots or populations. Mean clone size
was estimated at 9.10 ramets per genet. Genets in most
plots were intermingled, conforming to a guerrilla
growth form. The maximum genet spread was 0.59 m
suggesting that genets can be larger than the 0.25 m2 plots. Spatial autocorrelation analysis found a
lack of spatial genetic structure at short distances and
significant structure at large distances within populations.
Due to the occurrence of multiple genets within
each population, the limited spread of genets, and a
localized genetic structure, conservation activities
should focus on the maintenance of multiple populations
throughout the species range.
Keywords Ambrosia pumila Æ Asteraceae Æ
Clonality Æ Conservation genetics Æ RAPDssampled

Coastal oceanography and sedirnentology in New Zealand, 1967-91

Abstract This paper reviews research that has taken
place on physical oceanography and sedimentology
on New Zealand's estuaries and the inner shelf since
c. 1967. It includes estuarine sedimentation, tidal
inlets, beach morphodynamics, nearshore and inner
shelf sedimentation, tides and coastal currents,
numerical modelling, short-period waves, tsunamis,
and storm surges. An extensive reference list covering
both published and unpublished material is included.
Formal teaching and research programmes dealing
with coastal landforms and the processes that shape
them were only introduced to New Zealand
M91078
Keywords estuary; sediments; tidal inlets; beaches;
coastal erosion; inner shelf; tides; currents; waves;
tsunamis; storm surge; numerical modelling

Colonization and Connectivity of Habitat

Patches for Coastal Marine Species Distant
from Source Populations
Conectividad de Fragmentos de Hábitat y su Colonización por Especies Marinas Costeras Distantes de
Poblaciones
Fuente
Resumen:
l intercambio de propágulos o adultos móviles entre fragmentos de hábitat aislados es de importancia
crucial para algunos tipos de reservas, especialmente para especies que no se pueden propagar localmente.
Äara especies marinas, se puede estudiar el papel de la dispersión del plancton en el mantenimiento
de poblaciones locales viables examinando características de la historia de vida de especies que colonizan (o
que no logran colonizar) fragmentos de hábitat aislados. Comparamos las abundancias de especies
bentónicas
en un rompeolas rocoso expuesto rodeado de hábitats distintos en la costa de Washington ( .UU.) con
especies en sitios rocosos distantes dentro de áreas fuente potenciales. c pesar de su aislamiento, el
rompeolas
careció solo de una pequeña proporción de las especies de algas potenciales; estas ausencias podrían
deberse
al hecho de encontrarse a distancias de 40- a 100- km de áreas fuente más extensas o a diferencias sutiles de
hábitat en el rompeolas. Las algas coralinas tienen propágulos de vida corta y adultos que probablemente no
floten, lo que sugeriría que son malas propagadoras. stas algas no se encontraron en el rompeolas
estudiado,
sin embargo se encontraron en otros rompeolas aislados de la costa. xperimentos de transplante a
corto plazo indicaron que las coralinas pueden sobrevivir localmente una vez que hayan colonizado una
zona. Se notó la ausencia de pocos animales, uno de los cuales fue un quitón que se fija a algas coralinas y
se alimenta de las mismas. ran abundantes en el rompeolas los animales con dispersión obligada de crías
aún siendo incapaces de propagarse localmente y a pesar de la dilución de sus larvas dispersantes en el
plancton proveniente de fuentes lejanas. ambién se encontraban algunas especies animales sin fase
planctónica. Äor lo tanto, aquellos organismos con un amplio rango de atributos de historia de vida pueden
sobrevivir en este pequeño y distante fragmento de hábitat adecuado. l aislamiento a lo largo de la costa no
eliminó ni a los dispersores pobres ni a los dispersores obligados

Co-management Policy Can Reduce

Resilience in Traditionally Managed
Marine Ecosystems
ABSTRACT
Best-practice environmental policy often suggests
co-management of marine resources as a means of
achieving sustainable development. Here we consider
the impacts of superimposing co-management
policy, in the form of territorial user rights for
fishers over an existing traditional communitybased
natural-resource management system in
Chile. We consider a broad definition of co-management
that includes a spectrum of arrangements
between governments and user groups described
by different levels of devolution of power. We used
participatory rural appraisal techniques and questionnaires
to understand the mechanisms that
underpin the traditional management system for
the bull-kelp µµcochayuyo¶¶ (Durvillaea antarctica).
Traditional management was based on the allocation
of informal access rights through a lottery
system. This system was controlled by a complex
web of traditional institutions that were shown to
be successful in terms of equity and resilience.
Using a similar approach, we analyzed the effects of
superimposing a government-led co-management
policy into this traditional system. Two major effects
of the new policy were encountered. First,
traditional institutions were weakened, which had
negative effects on the levels of trust within the
community and intensified conflict among users.
Second, the management system¶s adaptive capacity
was reduced, thereby jeopardizing the ecosystem¶s
resilience. Our results suggest that the
devolution of power to this kind of fisher community
still has not reached the level required for
fishers to legally address the local deficiencies of the
Chilean co-management policy. Additionally, legal
adjustments must be made to accommodate traditionally
managed ecosystems that offer benefits
comparable to those mandated under the formal
policy. A fuller understanding of the interactions
between co-management and traditional institutions
can help us to identify ways to promote
resilience and facilitate equal access by mitigating
the potential negative effects of co-management
policy and informing its future implementation.
Key words: property rights; environmental entitlements;
sustainability; resilience; artisanal fishers;
traditional institutions; human dimension;
cochayuyo; bull-kelp; Chile

Comment on ³Impacts of Biodiversity

Loss on Ocean Ecosystem Services´
John Jaenike
Worm et al. (Research Articles, 3 November 2006, p. 787) used a power relation to predict a global
collapse of fisheries by the year 2048. However, a linear regression of the data for the past 40
years yields an excellent fit, with a predicted date of collapse of 2114. Thus, long-term projections
of fisheries collapse are highly dependent on the specific statistical model used.

Loss on Ocean Ecosystem Services´

Michael J. Wilberg* and Thomas J. Miller
Worm et al. (Research Articles, 3 November 2006, p. 787) reported an increasing proportion
of fisheries in a ³collapsed´ state. We show that this may be an artifact of their definition of
collapse as a fixed percentage of the maximum and that an increase in the number of
managed fisheries could produce similar patterns as an increase in fisheries with catches below
10% of the maximum.

Comment on ³Impacts of Biodiversity

Loss on Ocean Ecosystem Services´
Franz Hölker,1* Doug Beare,1 Hendrik Dörner,1 Antonio di Natale,2 Hans-Joachim Rätz,3
Axel Temming,4 John Casey5
Worm et al. (Research Articles, 3 November 2006, p. 787) investigated the importance of biodiversity
to marine ecosystem services across temporal and spatial scales. In projecting the extent of future
fisheries collapse, we argue that the authors inappropriately extrapolated beyond their available
observations and used data on marine reserves and fishery closures that are not representative of
global fisheries.

£

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Comparative analysis of genetic diversity in Indian bitter gourd

(Momordica charantia L.) using RAPD and ISSR markers for
developing crop improvement strategies
Abstract
A genetic analysis of 38 diverse Indian bitter gourd (Momordica charantia var. charantia, and var. muricata)
accessions was performed using 29
RAPD and 15 ISSR markers. RAPD primers yielded 208 amplicons of which 76 (36.5%) were polymorphic
providing an average of 2.6 amplicons
per primer. RAPD amplicons per primer ranged from 3 (OPE-19, OPW-09) to 15 (OPW-05), and varied in
size from 200 bp to 3000 bp. Fifteen
ISSR primers provided a total of 125 bands of which 94 (74.7%) were polymorphic. Polymorphic ISSR
markers ranged from 0 (UBC-841) to 12
(UBC-890) providing a mean of 6.3 amplicons per primer that ranged in size from 150 bp to 2700 bp.
Nevertheless, the concordance among bitter
gourd accession groupings after cluster analysis was relatively high (r = 0.77), indicating that RAPD- and
ISSR-based diversity assessments in this
germplasm array were generally consistent. The M. charantia var. charantia (domesticated) and var. muricata
(wild, free-living) accessions
examined were genetically distinct, and these differences provided for the development of strategies for
genetic analyses and crop improvement in
this species.
Complex larval connectivity patterns among marine
invertebrate populations
Based on the belief that marine larvae, which can spend days to
months in the planktonic stage, could be transported considerable
distances by ocean currents, it has long been assumed that populations
of coastal species with a planktonic larval stage are demographically
open and highly µµconnected.¶¶ Such assumptions about the
connectivity of coastal populations govern approaches to managing
marine resources and shape our fundamental understanding of population
dynamics and evolution, yet are rarely tested directly due to
the small size and high mortality of marine larvae in a physically
complex environment. Here, we document a successful application of
elemental fingerprinting as a tracking tool to determine sources of
settled invertebrates and show that coastal mussel larvae, previously
thought to be highly dispersed, can be retained within 20±30 km of
their natal origin. We compare two closely related and co-occurring
species, ‰p

 V


and ‰p
 V 



, and determine
that, despite expected similarities, they exhibit substantially
different connectivity patterns. Our use of an


plarval culturing
technique overcomes the previous challenge of applying microchemical
tracking methods to species with completely planktonic development.
The exchange of larvae and resulting connectivities among
marine populations have fundamental consequences for the evolution
and ecology of species and for the management of coastal
resources.
elemental fingerprinting _


plarval culturing _ larval retention _
larval transport _ ‰p


Defining µEvolutionarily Significant Units¶

for conservation
writing in the first issue of ˜


Ryder¶ brought the term µEvolutionarily
Significant Unit¶ (ESU) to the attention
of a broad audience of ecologists and
evolutionary biologists. The ESU concept
was developed to provide a rational basis
for prioritizing taxa for conservation
effort (e.g. captive breeding), given that
resources are limited and that existing
taxonomy may not adequately reflect
underlying genetic diversity*. With the
explicit recognition of the genetic component
of biodiversity in conservation
legislation of many countries and in the
Convention on Biological Diversity, the
ESU concept is set to become increasingly
significant for conservation of natural
as well as captive populations.
However, the ESU remains poorly defined,
both conceptually and operationally.
Most definitions suggest than an ESU
should be geographically discrete, but
genetic criteria range from significant divergence
of allele frequencies3 through
some level of genetic distance¶ to congruently
structured phylogenies among
gene+. Several authors have argued
that an ESU should display concordant
divergence for both molecular and nonmolecular
traitG6. Although all are trying
to achieve the same end, it seems
that the operational definitions vary
according to the biological and legislative
context. The purpose of this essay is
to revisit the ESU concept in relation to
recent developments in molecular population
genetics. The suggested definitions
and criteria are not supposed to
be proscriptive - rather, the intention is
to promote debate on the purpose and
practice of using genetic information to
define conservation units.

Designing Marine Reserves for

Fishery Management
Recent reports have raised serious concerns about the rapid declines of historically productive
marine fishery
resources and the degradation of essential fish habitats. This global crisis has spurred development
of innovative
management strategies to rebuild depleted fisheries and marine ecosystems. One highly touted
strategy
involves the design and creation of marine reserves (areas off limits to extractive uses) to rebuild
fisheries and
conserve marine biodiversity. In this paper, we propose an integrated sequence of methodologies
that provides
an objective, quantitative framework for the design of marine reserves in spatially heterogeneous
coastal ocean
environments.
The marine reserve designs proposed here satisfy the multiple, often-conflicting criteria of disparate
resource
user groups. This research is the first attempt to explicitly explore the trade-off between the
conservation goals
of fishery management and coral reef protection and the consumptive interests of commercial and
recreational
fishing fleets. The spatial distribution and size abundance of reef fish stocks throughout the Florida
Keys coral
reef ecosystem were estimated from a database consisting of more than 18,000 visual samples
taken from 1979
to 2002. These distributions of multispecies abundance and biomass, in conjunction with a
geographic database
of coral reef habitats, are used to demonstrate an integer goal programming methodology for the
design of
networks of marine reserves, called plans. Once multiple plans are proposed, a simulation model is
used to
assess the effects of reserve size and shape on select Florida Keys reef fish populations under
dynamic spatial
and temporal conditions.
¢| V : integer goal programming; simulation; fisheries management; marine reserves; Florida
Keys
u
p V: Accepted by Linda . Green, public sector applications; received July 18, 2003. This paper
was with
the authors 2 months for 1 revision

Development of EST-SSRs in the Mediterranean blue

mussel,
‰p
 V 




Abstract
Eight polymorphic microsatellite repeat markers were identified from
‰p
 V 




expressed sequence tags (EST) deposited in public sequence database. Number
of alleles per locus ranged from two to 10, and the observed and expected heterozygosities
ranged from 0.029 to 0.872 and from 0.031 to 0.811, respectively. Three additional Mytiloida
species assessed for cross-species amplification revealed four loci could give positive
amplifications. EST-derived simple sequence repeats provide robust, informative and potentially
transferable polymorphic markers suitable for population genetic, parentage, and
mapping studies of
‰  V 




DIFFERENTIAL GENE FLOW BETWEEN POPULATIONS
OF ‰
Ä
DISTRIBUTED ALONG
IBERIAN AND NORTH AFRICAN COASTS
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DIFFERENTIAL PATTERNS OF MALE AND FEMALE MTDNA EXCHANGE ACROSS

THE ATLANTIC OCEAN IN THE BLUE MUSSEL, MYILUS ULIS
cbstract. Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of
population
history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial
DNAs
(maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates
of gene
flow and population divergence. The blue mussel, Mytilus edulis, is distributed on both North American and
European
coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the
Atlantic
Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-
mtDNA
showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population
divergence
times to be greatly underestimated for these loci, although a single trans-Atlantic population divergence time
(1.2
MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The
apparent
lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female
mussels.
A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely
to
explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA
inheritance.
¢ey words. Coalescent, divergence population genetics, DUI, gene flow, interlocus contrasts,
phylogeography.

DNA polymorphisms amplified by arbitrary primers are

useful as genetic markers
ABSTRACT
Molecular genetic maps are commonly constructed by
analyzing the segregation of restriction fragment length
polymorphisms (RFLPs) among the progeny of a sexual
cross. Here we describe a new DNA polymorphism
assay based on the amplification of random DNA
segments with single primers of arbitrary nucleotide
sequence. These polymorphisms, simply detected as
DNA segments which amplify from one parent but not
the other, are inherited in a Mendelian fashion and can
be used to construct genetic maps in a variety of
species. We suggest that these polymorphisms be
called RAPD markers, after Random Amplified
Polymorphic DNA.

Driven by the West Wind Drift? A

synthesis of southern temperate marine
biogeography, with new directions for
dispersalism
ABSTRACT
Aim Twentieth century biogeographers developed intriguing hypotheses
involving West Wind Drift dispersal of Southern Hemisphere biota, but such
models were largely abandoned in favour of vicariance following the development
of plate tectonic theory. Here I present a synthesis of southern temperate marine
biogeography, and suggest some new directions for phylogeographic research.
Location The southern continents, formerly contiguous components of
Gondwana, are now linked only by ocean currents driven by the West Wind Drift.
Methods While vicariance theory certainly facilitates the development of testable
hypotheses, it does not necessarily follow that vicariance explains much of
contemporary southern marine biogeography. To overcome the limitations of
narratives that simply assume vicariance or dispersal, it is essential for analyses to
test biogeographic hypotheses by incorporating genetic, ecological and geological
data.
Results Recent molecular studies have provided strong evidence for dispersal,
but relatively little evidence for the biogeographic role of plate tectonics in
distributing southern marine taxa. Despite confident panbiogeographic claims to
the contrary, molecular and ecological studies of buoyant macroalgae, such as
Macrocystis, indicate that dispersal predominates. Ironically, some of the better
supported evidence for marine vicariance in southern waters has little or nothing
to do with plate tectonics. Rather, it involves far more localized and recent
vicariant models, such as the isolating effect of the Bassian Isthmus during
Pleistocene low sea-level stands (Nerita).
Main conclusions Recent phylogeographic studies of southern marine taxa (e.g.
Diloma and Parvulastra) imply that passive rafting cannot be ignored as an
important mechanism of long-distance dispersal. I outline a new direction for
southern hemisphere phylogeography, involving genetic analyses of bull-kelp
(Durvillaea) and its associated holdfast invertebrate communities.
Keywords
Historical biogeography, holdfast, kelp, macroalgae, oceanic dispersal, phylogeography,
rafting, vicariance.

Ecological and evolutionary

consequences of biotic
homogenization
Biotic homogenization, the gradual replacement of
native biotas by locally expanding non-natives, is a
global process that diminishes floral and faunal distinctions
among regions. Although patterns of homogenization
have been well studied, their specific ecological
and evolutionary consequences remain unexplored. We
argue that our current perspective on biotic homogenization
should be expanded beyond a simple recognition
of species diversity loss, towards a synthesis of higher
order effects. Here, we explore three distinct forms of
homogenization (genetic, taxonomic and functional),
and discuss their immediate and future impacts on ecological
and evolutionary processes. Our goal is to
initiate future research that investigates the broader
conservation implications of homogenization and to
promote a proactive style of adaptive management that
engages the human component of the anthropogenic
blender that is currently mixing the biota on Earth.

ECOLOGICAL DI ERGENCE ASSOCIATED

WITH MATING SYSTEM CAUSES NEARLY
COMPLETE REPRODUCTI E ISOLATION
BETWEEN SYMPATRIC ‰‰SPECIES
Speciation often involves the evolution of numerous prezygotic and postzygotic isolating barriers
between divergent populations.
Detailed knowledge of the strength and nature of those barriers provides insight into ecological and
genetic factors that directly or
indirectly influenced their origin, and may help predict whether they will be maintained in the face of
sympatric hybridization and
introgression. We estimated the magnitude of pre- and postzygotic barriers between naturally
occurring sympatric populations of
‰
pppand ‰ 
p. Prezygotic barriers, including divergent flowering phenologies,
differential pollen production,
mating system isolation, and conspecific pollen precedence, act asymmetrically to completely
prevent the formation of F1 hybrids
among seeds produced by ‰ ppp(F1g), and reduce F1 hybrid production among seeds
produced by ‰ 
p(F1n) to
only about 1%. Postzygotic isolation is also asymmetric: in field experiments, F1g but not F1n
hybrids had significantly reduced
germination rates and survivorship compared to parental species. Both hybrid classes had flower,
pollen, and seed production values
within the range of parental values. Despite the moderate degree of F1g hybrid inviability,
postzygotic isolation contributes very
little to the total isolation between these species in the wild. We also found that F1 hybrid flowering
phenology overlapped more
with ‰ pppthan ‰ 
p. These results, taken together, suggest greater potential for
introgression from ‰ 
pto ‰ 
pppthan for the reverse direction. We also address problems with commonly used indices of
isolation, discuss difficulties in
calculating meaningful measures of reproductive isolation when barriers are asymmetric, and
propose novel measures of prezygotic
isolation that are consistent with postzygotic measures.
KEY WORDS: Flowering phenology, introgression, natural hybridization, Phrymaceae, reproductive
asynchrony, Scrophulariaceae,
speciation.

Ecological interaction between sympatric Mytilus

species on the west coast of Canada investigated using
PCR markers
Abstract
M. californianus is the dominant marine mussel species on exposed rocky shores, while
M. trossulus is usually the dominant mussel species in more sheltered waters on the west
coast of North America. Since these species are physically indistinguishable when small
(< 10.0 mm), we developed two polymerase chain reaction (PCR) -based markers to discriminate
between them. Using these markers, we identified mussels taken from an
exposed coast (n = 114), a sheltered harbour (n = 80), and an upper-intertidal pool (n = 42)
on the west coast of Vancouver Island, British Columbia, Canada. M. californianus were
found only on the open coast. Small M. trossulus (< 20.0 mm) were common to all three
sample sites, but were extremely rare at larger sizes (> 20.0 mm) on the open coast. Our
results indicate that M. californianus are excluded from sheltered waters via early life factors,
while M. trossulus are excluded from the open coast due to mortality later in life.
¢eywords: competition, marine mussels, Mytilus californianus, Mytilus trossulus, open coast,
species markers

Ecological risk assessment using RAPD and distribution pattern

of a rare and endangered species
Abstract
Environmental and ecological risk assessment always provide useful evidence for characterisation
and conservation of the rare and
endangered species, e.g. seven-son flower (Heptacodium miconioides Rehd.). Seven-son flower is
a deciduous arbor species, but endangered,
with a restricted distribution in the subtropical forests of China. Genetic risk assessment of 56
samples of the flower from nine
main populations in Zhejiang (China) was carried out by using the RAPD analysis. This was to
study the ecological characteristics, spatial
distribution and genetic features of the seven-son flower communities and establish a feasible
conservation plan. Twenty-one primers
screened from 50 yielded 119 RAPD bands with 72 polymorphic products and 60.50% of total
bands. The genetic variation was found to
be partitioned mainly among rather than within populations. Percentages of genetic diversity among
populations were quantified by
Shannon index and the Nei¶s gene diversity coefficient. AMO A also demonstrated that these relict
populations were highly differentiated.
The high level of population variation observed is in contrast to that expected for a primarily
outcrossed woody perennial plant,
and suggests that there may be a degree of inbreeding. The dendrogram constructed from genetic
distances through UPGMA method
based on Nei¶s coefficients shows two groups among nine population clusters, which is further
supported by a principle components analysis
(PCA) of RAPD phenotypic data. The analysis showed that the biologic characteristics and habitat
fragmentation were the reasons
of the great genetic variation among populations. Some strategies of its genetic diversity
conservation were proposed in the fragmented habitats based on its genetic structure and its
biological characteristics in this study.

Ecological theories and indicators in economic models of

biodiversity loss and conservation: A critical review
We evaluate how well environmental-economic models describe biodiversity loss and
conservation issues. Four types of economic models turn out to dominate economic
research into biodiversity conservation. For each of these, we assess the extent to which
they integrate relevant ecological theories and indicators of biodiversity loss. A main
conclusion is that models with more economic detail contain less detailed descriptions of
the ecological dynamics of biodiversity change. We provide suggestions for improving
economic models of biodiversity conservation and discuss the advantages of using less
stylised representations of ecological processes.

Efecto de la temperatura en el desarrollo embrionario y larval

del mejillón, Mytilus galloprovincialis (Lamarck, 1819)
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E ect of pollution on genetic diversity in the bay

mussel Mytilus galloprovincialis and the acorn
barnacle Balanus glandula
Abstract
To test if environmental contamination acts as a selection force a ecting genetic diversity at
the population level, two intertidal invertebrate species, Mytilus galloprovincialis and Balanus
glandula, were collected from seven di erent bay sites in southern California. Collections were
made at three relatively pristine `clean' sites and four `impacted' sites exposed to heavy
industrial or boating activity, and which had previously been identi®ed as having measurable
levels of pollution. Genetic diversity at each site was assessed by comparing fragment poly-
morphisms generated from genomic DNA by randomly ampli®ed polymorphic DNA-
polymerase chain reaction (RAPD-PCR). All populations retained a large amount of genetic
diversity and were genetically similar to each other. However, several di erent measures
of diversity indicated that, for most primers, the populations of both species from impacted
sites had lower genetic diversity compared to those populations from clean sites. Individuals
at impacted sites were more likely to share the same haplotypes than were those from clean
sites. Few bands seen in the clean sites were absent from the impacted sites or vice versa, but a
number of bands in the clean site populations were signi®cantly less common in the impacted
populations, while a few bands uncommon in clean site populations were more common at
impacted sites. Together, these results suggest that pollution at the impacted sites may reduce
genetic diversity among the resident invertebrate populations. 5 2000 Elsevier Science Ltd.
All rights reserved.

Effects of ocean acidification on the immune

response of the blue mussel Mytilus edulis
ABSTRACT: The effects of medium term (32 d) hypercapnia on the immune response of ‰p

| 
were investigated in mussels exposed to acidified (using CO2) sea water (pH 7.7, 7.5 or 6.7;
control: pH 7.8). Levels of phagocytosis increased significantly during the exposure period,
suggesting
an immune response induced by the experimental set-up. However, this induced stress response
was suppressed when mussels were exposed to acidified sea water. Acidified sea water did not
have
any significant effects on other immuno-surveillance parameters measured (superoxide anion
production,
total and differential cell counts). These results suggest that ocean acidification may impact
the physiological condition and functionality of the haemocytes and could have a significant effect
on cellular signalling pathways, particularly those pathways that rely on specific concentrations of
calcium, and so may be disrupted by calcium carbonate shell dissolution.
KEY WORDS: ‰p
| 
· Ocean acidification · Carbon capture and storage · Seawater pH ·
Immune response · Phagocytosis

Environmental transformations in developing

countries: hybrid research and democratic
policy
This paper introduces a special edition of he GeographicalJournal on the theme of 'environmental
transformations in developing countries'. Geographical research into
human-environment relations is well established. However, many recent studies of political
ecology or constructivist approaches to environment either overlook biophysical
aspects of environmental change, or uncritically accept 'orthodox' explanations of physical
degradation without appreciating the social and political construction of such models.
This paper, and those following, attempt to outline ways in which environmental
research may remain sensitive to political and cultural debates, yet also give insights to
practical environmental management of biophysical resources 'externally real' to
human experience. It is argued that understanding human impacts on environment
may only be achieved through long-term environmental histories compiled using
locally-based 'hybrid' social and physical research methods; plus an awareness of the
social and political construction of environmental 'orthodoxies' by powerful domestic
and global agendas. As such, 'transformations' may be viewed as both physical changes
in factors such as land cover or health hazards; but also as the socio-economic transitions
in the driving forces of environmental degradation and perceptions of risk which
in turn fuel new orthodoxies in research and policy.
KEY SVORDS: environmental management, environment and development, desertification, deforestation,
industrialization, environmental policy.

Equivalence in yield from marine reserves and traditional fisheries management

Community structure of the macroinfauna in the sediments below an

intertidal mussel bed (Mytilus chilensis (Hupe)) of southern Chile
Estructura comunitaria de la macroinfauna en los sedimentos bajo un banco intermareal de
bivalvos (Mytilus chilensis (Hupe)) en el sur de Chile
ABSTRACT
The mytilid mussel Mytilus chilensis (Hupe) can form dense beds in sedimentary areas of the inland coast of
the Nord-Patagonic archipelagos of the Chilean coast (ca. 40-43V S). During the autumn of 2002, we collected
replicated samples at five intertidal stations in Panitao (Golfo de Reloncaví) ordered along a transect parallel
to the low tide level and extended from the center of the bank (stations one and two with 100 and ca. 25 % of
mussel cover, respectively) to the bare sediments of the intertidal (stations 3, 4 and 5, without mussels). The
macroinfauna was numerically dominated by Polychaeta, Oligochaeta and Crustacea Peracarida. The total
number of species collected was 14, being the most abundant the polychaete Äerinereis vallata, oligochaetes
from the family Tubificidae and the crustacean amphipod Corophium insidiosum. The number of species,
Shannon-Wiener diversity and total abundance of the macroinfauna did not differ significantly among
stations. However, the percent contribution of polychaetes was significantly higher at the sediments sampled
outside the mussel bed (stations three, four and five), while the percentual contribution of oligochaetes was
significantly higher at the sediments sampled in the mussel bed (stations one and two). No significant
differences were found between the percentual contribution of peracarid crustaceans between stations
sampled
in the mussel bed versus that sampled on the bare intertidal. The graphic results of NMMDS show that the
macroinfaunal assemblage of the stations located inside the mussel bed differed from that of stations located
outside the bed. Results of SIMPER and ANOSIM showed that the macroinfaunal composition of stations one
and two was significantly dissimilar (61-54 %) to that of the stations located outside the mussel bed, which
had similar composition. The graphic results of a NMMDS based upon sedimentological characteristics show
that most replicates of station one and some of station two separate from that of the other stations (i.e. located
outside the mussel bed). Results of ANOVA showed significant differences for all sediment variables, with
the exception of percentages of gravel particles and mean grain size of sands. The most noticeable difference
was that shown by station 1 (lower contents of sand and higher content of mud, biogenic aggregates and total
organic matter). The results of BIO-ENV routine showed that the best fit between the taxonomic composition
of the macroinfauna and single sediment variables, was reached with percentages of sand and mud. It is
concluded, that mussel beds of sedimentary bottoms of southern Chile have a significant role on the sediment
quality and community structure of the macroinfauna, a probable combined effect of physiological processes
(ingestion of larvae, biodeposition) and the complex physical matrix of the bed.
Key words: mussel beds, Mytilus chilensis, macroinfauna, southern Chile.

MARINE RESERVES AND OCEAN

NEIGHBORHOODS: The Spatial Scale of Marine
Populations and Their Management
‘ Abstract The movement of individuals defines a spatial neighborhood that can
help determine marine management strategies. Here, I briefly review four fields of
marine biology that each differentially illuminate the scale of marine neighborhoods:
effects of marine reserves, tagging studies, microchemistry, and population genetics.
These suggest adult neighborhood sizes for many demersal fish and invertebrates as
small as kilometers and up to 10 to 100 km. Larval dispersal may be shorter than
previously suspected: neighborhood sizes of 10 to 100 km for invertebrates and 50 to
200 km for fish are common in current compilations.
How can small reserves protect such species? One conceptual framework is to set
reserve size based on adult neighborhood sizes of highly fished species and determine
spacing of a reserve network based on larval neighborhoods. The multispecies nature
of fisheries demands that network designs accommodate different life histories and
take into account the way local human communities use marine resources.

Evolutionary Genetics of
Atlantic Salmon (Salmo salar L.)
- Molecular Markers and Applications Abstract
Vasemägi, A. 2004. volutionary Genetics of ctlantic salmon (Salmo salar L.) - Molecular
Markers and cpplications.
ISSN 1401-6230, ISBN 91-576-6708-X
This thesis deals with evolutionary genetics of Atlantic salmon populations, with the special
emphasis on the roles of migration, random genetic drift, mutation and natural selection
affecting the patterns of molecular variation across contemporary and historical time scales.
Studies of mitochondrial DNA variation supported the hypothesis of multiple post-glacial
colonization events of the Baltic Sea. The Eastern Atlantic populations differ from the
geographically close southern Baltic populations, indicating absence of inward and limited
outward gene flow through the Danish straits during the last 8000 years. Four common
European mitochondrial haplotypes derive from the ancestral ND1-BBBA haplotype by
one-step substitutions. Our results suggest that wild populations have an important role in
re-colonization processes of the former salmon rivers where populations have been driven
to extinction due to human activities. Spatio-temporal analysis over eighteen years provided
genetic evidence of immigration from compensatory hatchery releases into one of the
biggest wild Atlantic salmon population in the Gulf of Bothnia (R. Vindelälven) and
emphasize the genetic risks associated with current large-scale stocking practices in the
Baltic Sea. For restoration of former salmon rivers in the Gulf of Finland we recommend
that two closest native salmon populations should be preferred to help to fill in the currently
missing ³building blocks´ that are important for the persistence of genetic variation and
long-term survival of salmon populations in Estonia. We identified several expressed
sequence tag (EST) loci that are potentially affected by divergent selection demonstrating
that EST-scans may provide suitable strategy to discover functionally important genetic
variation both in model and non-model organisms.
¢eywords: population genetics, microsatellites, mitochondrial DNA, MHC,
adaptation, natural selection, migration, genetic drift, expressed sequence tags,
EST

Evolutionary Relationships among the Male and Female Mitochondrial DNA

Lineages in the 2Mytilus |
Species Complex
A novel form of mitochondrial DNA (mtDNA) inheritance has previously been documented for the blue
mussel
(Mytilus |
Female mussels inherit their mtDNA solely from their mother while males inherit mtDNA
from
both their mother and their father. In males, the paternal mtDNA is preferentially amplified so that the male
gonad is highly enriched for the paternal mtDNA that is then transmitted from fathers to sons. We
demonstrate
that this mode of mtDNA inheritance also operates in the closely related species M. 

  and M.
 

The evolutionary relationship between the male and female mtDNA lineages is estimated by
phylogenetic
analysis of 455 nucleotides from the large subunit ribosomal RNA gene. We have found that the male and
female
lineages are highly divergent; the divergence of these lineages began prior to the speciation of the three
species of
blue mussels. Further, the separation between the male and female lineages is estimated to have occurred
between
5.3 and 5.7 MYA.

Experimental evolution reveals natural selection on standing genetic variation

Evolution depends on genetic variation generated by mutation
or recombination from standing genetic variation. In sexual
organisms, little is known about the molecular population
genetics of adaptation and reverse evolution1±11. We carry
out 50 generations of experimental reverse evolution in
populations of Drosophila melanogaster, previously differentiated
by forward evolution, and follow changes in the
frequency of SNPs in both arms of the third chromosome. We
characterize the effects of sampling finite population sizes and
natural selection at the genotype level. We demonstrate that
selection has occurred at several loci and further that there is
no general loss or gain of allele diversity. We also observe that
despite the complete convergence to ancestral levels of
adaptation, allele frequencies only show partial return

Exploited marine invertebrates: genetics and fisheries

Abstract
The application of genetic techniques to invertebrate fisheries is in many ways essentially similar to that in
vertebrate
(i.e. finfish) fisheries, for which there is already an extensive body of published data. However, there
are also relative differences which lead to particular problems in the use of genetic data to study commercially
important invertebrate species. The main role for genetics of both vertebrates and invertebrates has been, and
is
likely to continue to be, the identification of groups of interbreeding individuals as the basis for a fishery. It is
in the identification of the breeding unit that the genetic differences between vertebrates and invertebrates can
be of practical significance. The genetic breeding unit, usually called a ¶stock¶ in fisheries biology, generally
shows a certain uniformity of size in most marine fish which have been studied. Smaller or less mobile fish
(e.g.
flatfish) may only range a few tens of kilometres to their breeding grounds, whilst in more mobile,
particularly
migratory pelagic species (e.g. Scombridae), the area occupied by a stock is likely to be far greater and for a
few (e.g. large pelagic elasmobranchs), a single unit of stock may be almost circumglobal. However, marine
fish
generally, particularly those large or plentiful enough to be of commercial interest, are likely to be fairly
mobile
and in many cases the order of mobility is likely to be in the region we might predict from our knowledge of
the biology and habits of the species. In the genetic assessment of µstocks¶ for invertebrate fisheries, we face a
number of additional problems, mostly related to the large evolutionary range of invertebrates exploited and
their
widely different biology. Although in Europe and North Americamarine invertebrate fisheries may be thought
of as
being mainly for decapod crustaceans and bivalve molluscs, globally commercially important marine
invertebrate
fisheries range from sponges to squid and include such diverse groups as sea cucumbers, barnacles, krill,
octopuses,
cuttlefish, sea anemones, ascidians, polychaetes, sea urchins, gastropods and jellyfish. An obvious feature of
many
of these invertebrates is that the adult (i.e. commercial) stage of the life cycle is sessile (e.g. barnacles,
sponges,
ascidians) or of very limited mobility (e.g. sea anemones, sea urchins, bivalves, gastropods), with the result
that
the dispersive phase of the life cycle is the larva. Other groups (e.g. krill, jellyfish) are planktonic or nektonic
and
may cover very large distances, but, unlike fish, have little control over the distance or direction of travel,
whilst
some of the open ocean pelagic squid are more mobile than most fish and may migrate thousands or
kilometres to
spawning grounds. The very low mobility of both larva and adult in some invertebrates indicates that
dispersal, and
hence stock size, is likely to be low and that, therefore, stocks are far more vulnerable to overfishing than in
most
fish species. An additional difficulty is that genetic studies to date indicate a remarkably high incidence of
cryptic
speciation in marine invertebrates, sometimes even in comparatively well studied commercially important
species.
Thus, although to date marine invertebrate fisheries have not received the same level of attention from
geneticist as
finfish fisheries, it is clear that for invertebrate fisheries genetic data are relatively far more important if a
fishery is
to be exploited without being endangered.

FAO SPECIES IDENTIFICATION GUIDE FOR FISHERY PURPOSES

THE LI ING MARINE RESOURCES OF THE
WESTERN CENTRAL PACIFIC

Feeding aquaculture growth through globalization: Exploitation of

marine ecosystems for fishmeal
Abstract
Like other animal production systems, aquaculture has developed into a highly globalized trade-
dependent industry. A major part of
aquaculture technology requires fishmeal to produce the feed for farmed species. By tracing and
mapping patterns of trade flows globally
for fishmeal we show the aquaculture industry¶s increasing use of marine ecosystems worldwide.
We provide an in-depth analysis of the
growth decades (1980±2000) of salmon farming in Norway and shrimp farming in Thailand. Both
countries, initially net exporters of
fishmeal, increased the number of import source nations of fishmeal, peaking in the mid-1990s.
Thailand started locally and expanded
into sources from all over the globe, including stocks from the North Sea through imports from
Denmark, while Norway predominantly
relied on northern region source nations to feed farmed salmon. In 2000, both have two
geographically alternate sources of fishmeal
supply: the combination of Chile and Peru in South America, and a regional complement. We find
that fishmeal trade for aquaculture is
not an issue of using ecosystems of the South for production in the North, but of trade between
nations with industrialized fisheries
linked to productive marine ecosystems. We discuss the expansion of marine ecosystem
appropriation for the global aquaculture industry
and observed shifts in the trade of fishmeal between marine areas over time. Globalization, through
information technology and
transport systems, has made it possible to rapidly switch between marine areas for fishmeal supply
in economically connected food
producing systems. But the stretching of the production chain from local to global and the ability to
switch between marine areas
worldwide seem to undermine the industry¶s incentives to respond to changes in the capacity of
ecosystems to supply fish. For example,
trade information does not reveal the species of fish that the fishmeal is made of much less its
origins and there is lack of feedback
between economic performance and impacts on marine ecosystem services. Responding to
environmental feedback is essential to avoid
the trap of mining the marine resources on which the aquaculture industry depends. There are
grounds to suggest the need for some
global rules and institutions that create incentives for seafood markets to account for ecosystem
support and capacity.
r 2006 Elsevier Ltd. All rights reserved.

Fisheries forensics: the use of DNA tools for improving

compliance, traceability and enforcement in the fishing
industry
Introduction
Fisheries management ideally aims to balance the
optimization of yield with the sustainability of
natural resources. Within this broad objective, the
science of fisheries biology has traditionally focused
on developing our understanding of the environmental
and biological parameters that influence
Abstract
There is an increasing requirement for traceability of fish and fish products, both for
consumer protection and for regulatory enforcement, in particular with respect to
illegal, unreported and unregulated (IUU) fishing. IUU fishing is a serious global
problem and one of the main impediments to the achievement of sustainable world
fisheries. Genetic markers are used for the identification of species and populations in
fisheries biology and can potentially also be used to support investigations and deter
IUU fishing and food fraud. This review examines the development and application of
non-human forensic genetic techniques for the purposes of species identification,
population assignment and supply chain traceability in world fisheries. Key issues in
the transfer from academic research to validated forensic methods are presented
highlighting differences in how data are produced and interpreted. The rapid increase
in genomic data production and subsequent future potential for greater spatial
resolution of fish stocks is discussed alongside the biological and practical limitations
of using DNA markers for fisheries enforcement.

Genetic and phylogenetic analyses of endangered species. Annual Review of

Genetics 28:467-89.
Keywords: Acinonyx jubatus/carnivore/cheetah/conservation/endangered species/homogeneous
state of genes/inbreeding/life history/management/population bottleneck/reproduction/sperm
abnormalities
Abstract: Several reviews have chronicled the application of genetic principles to conservation
management and summarized the state of genetic data on the few studied species. The goal
here is to review some lessons learned by applying empirical population genetic approaches to
define the factors that imperil fragile populations. Both the limitations of the inference and the
conclusions reached as a community of conservation scientists are summarized. Several
examples will illustrate the synthesis of genetic interpretation with demographic, ecological, and
life-history data to draw a cohesive picture of the threatened taxon. Most of the examples are
endangered large charismatic carnivore species selected for two reasons. First, large carnivore
species occupy the top position of a trophic chain for their ecosystem. They are often highly
specialized and provide a sensitive barometer of an ecosystem's condition. Second, charismatic
species attract long-term field studies that lay the groundwork for formulating falsifiable ecological
and life-history hypotheses. On of the presented examples is the cheetah.

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Genetic differentiation among common and selected hatchery

populations of flounder: Evidence from RAPD markers
Abstract
Randomly amplified polymorphism DNA (RAPD) analysis was performed in order to evaluate one common
population and two
selected hatchery populations of flounder Paralichthys olivaceus. A total of 90 individuals belonging to
three populations were
screened using 12 different RAPD primers. A total of 71 loci were produced in the three studied populations,
and 43.5%,
42.4% and 42.2% of these loci were polymorphic over all the genotypes tested in common, susceptible and
resistant populations,
respectively. The number of loci detected by single primers ranged from four to eight. The average
heterozygosites of common,
susceptible and resistant populations were 0.112, 0.103 and 0.111, respectively. Compared with the common
population, the
two selected hatchery populations, susceptible and resistant, showed some genetic differences including a
smaller number of
loci, a smaller number of polymorphic loci, a smaller number of genotypes and a smaller Shannon index. The
present study confirmed
that it is important to detect the genetic variability of the selected hatchery population for the conservation of
natural flounder
resources.

Blackwell Publishing Ltd

Genetic differentiation in relation to marine landscape in a broadcast-spawning bivalve mollusc (
Ä |p|
|

)
Abstract
Marine bivalves are sessile or sedentary as adults but have planktonic larvae which can
potentially disperse over large distances. Consequently larval transport is expected to play
a prominent role in facilitating gene flow and determining population structure. The sea
scallop (
Ä |p|
|


) is a dioecious species with high fecundity, broadcast
spawning and a

. 30-day planktonic larval stage, yet it forms discrete populations or µbeds¶
which have significantly different dynamics and characteristics. We analysed variation at
six microsatellite loci in 12 locations throughout the geographic range of the species from
Newfoundland, Canada, to New Jersey, USA. Significant differentiation was present and
the maximum pairwise ¨
value, between one of the Newfoundland samples in the north
and a sample from the southern portion of the range, was high at 0.061. Other proximate
pairs of samples had no detectable genetic differentiation. Mantel tests indicated a significant
isolation by distance, but only when one of the populations was excluded. A
landscape genetic approach was used to detect areas of low gene flow using a joint analysis
of spatial and genetic information. The two major putative barriers inferred by Monmonier¶s
algorithm were then used to define regions for an analysis of molecular variance (
AMOVA
).
That analysis showed a significant but low percentage (1.2%) of the variation to be partitioned
among regions, negligible variation among populations within regions, and the majority of
the variance distributed between individuals within populations. Prominent currents were
concordant with the demarcation of the regions, while a novel approach of using particle
tracking software to mimic scallop larval dispersal was employed to interpret within-region
genetic patterns.
¢| V 
: genetic differentiation, isolation by distance, landscape genetics, marine bivalve,
microsatellite DNA, scallop

GENETIC DIVERGENCE, REPRODUCTIVE ISOLATION, AND MARINE SPECIATION

cbstract
In marine species, high dispersal is often associated with only mild genetic
differentiation over large spatial scales. Despite this generalization, there are
numerous reasons for the accumulation of genetic differences between large,
semi-isolated marine populations. A suite of well-known evolutionary mechanisms
can operate within and between populations to result in genetic divergence,
and these mechanisms may well be augmented by newly discovered
genetic processes.
This variety of mechanisms for genetic divergence is paralleled by great
diversity in the types of reproductive isolation shown by recently diverged
marine species. Differences in spawning time, mate recognition, environmental
tolerance, and gamete compatibili~y have all been implicated in marine speciation
events. There is substantial evidence for rapid evolution of reproductive
isolation in strictly allopatric populations (e.g. across the Isthmus of Panama).
Evidence for the action of selection in increasing reproductive isolation in
sympatric populations is fragmentary.
Although a great deal of information is available on population genetics,
reproductive isolation, and cryptic or sibling species in marine environments, the
influence of particular genetic changes on reproductive isolation is poorly
understood for marine (or terrestrial) taxa. For a few systems, like the co-evolution
of gamete recognition proteins, changes in a small number of genes may give
rise to reproductive isolation. Such studies show how a focus on the physiology,
ecology, or sensory biology of reproductive isolation can help uncover the
548 PALUMBI
genetic changes associated with speciation and can also help provide a link
between the genetics of population divergence and the speciation process.

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Blackwell Publishing Ltd Genetic diversity and gene flow in collapsed and healthy abalone fisheries
Abstract
Overexploitation of marine species invariably results in population decline but can also
have indirect effects on ecological processes such as larval dispersal and recruitment that
ultimately affect genetic diversity and population resilience. We compared microsatellite
DNA variation among depleted and healthy populations of the black-lip abalone aliotis
rubra from Tasmania, Australia, to determine if over-fishing had affected genetic diversity.
We also used genetic data to assess whether variation in the scale and frequency of larval
dispersal was linked to greater population decline in some regions than in others, and if larval
dispersal was sufficient to facilitate natural recovery of depleted populations. Surprisingly,
allelic diversity was higher in depleted populations than in healthy populations (Ä < 0.05).
Significant subdivision across hundreds of metres among our sampling sites (FST = 0.026,
Ä < 0.01), coupled with assignment tests, indicated that larval dispersal is restricted in all
regions studied, and that abalone populations across Tasmania are largely self-recruiting.
Low levels of larval exchange appear to occur at the meso-scale (7±20 km), but age estimates
based on shell size indicated that successful migration of larvae between any two sites may
happen only once every few years. We suggest that genetic diversity may be higher in
depleted populations due to the higher relative ratio of migrant to self-recruiting larvae. In
addition, we expect that recovery of depleted abalone populations will be reliant on sources
of larvae at the meso-scale (tens of km), but that natural recovery is only likely to occur on
a timescale unacceptable to fishers and resource managers.
¢| V : connectivity, conservation, fisheries management, microsatellite DNA, larval dispersal,
self-recruitment

Genetic diversity within Sclerocarya birrea

populations in Kenya
Abstract
Knowledge on genetic diversity is important for the successful conservation and domestication of a
species. In order to determine the genetic diversity within different populations of Sclerocarya birrea
(A. Rich.) Hochst. (Anacardiaceae) (marula) in Kenya, leaf morphological characteristics and
random amplified polymorphic DNA (RAPD) profiles from 92 and 61 trees, respectively, collected
from six Kenyan stands and two reference populations from Tanzania, were investigated. Leaf
blade
lengths were measured, and whether leaf margins were serrated or entire was recorded. RAPD
analysis was applied to genomic DNA using 10 primers of 10 base pairs each. Both leaf
morphology
and DNA analysis clustered the eight populations of S. birrea into three groups. Group 1 (two
populations) consisted of plants with small sized leaves (average leaf blade length o3 cm) that had
entire or serrated leaf margins. Group 2 (two populations) comprised plants with large sized leaves
(average leaf blade length 43 cm) that, again, had entire or serrated leaf margins. Group 3 (four
populations) consisted of plants with large sized leaves (average leaf blade length 43 cm) but had
entire leaf margins only. RAPD analysis suggested that two Kenyan populations had particularly
high genetic diversity; these two stands could be of particular conservation and genetic
improvement
value.
r 2006 Elsevier Ltd. All rights reserved.
Keywords: African indigenous fruit tree; Genetic diversity; RAPD; Subspecies designation

GENETIC HETEROGENEITY ANALYSIS AND RAPD MARKER DETECTION AMONG FOUR

FORMS OF ATRINA PECTINATA LINNAEUS

Abstract
Background: Few models of genetic hitchhiking in subdivided populations have been developed
and the
rarity of empirical examples is even more striking. We here provide evidences of genetic hitchhiking
in a
subdivided population of the marine mussel ‰p
| 
. In the Bay of Biscay (France), a patch of
‰ | 

populations happens to be separated from its North Sea conspecifics by a wide region occupied
only by
the sister species ‰  V 



. Although genetic differentiation between the two ‰ | 

regions is
largely non-significant at ten marker loci (average FSTå0.007), a strong genetic differentiation is
observed
at a single locus (FST â 0.25). We validated the outlier status of this locus, and analysed DNA
sequence
polymorphism in order to identify the nature of the selection responsible for the unusual
differentiation.
Results: We first showed that introgression of ‰  V 



alleles was very weak in both
populations and did not significantly affect their differentiation. Secondly, we observed the genetic
signature of a selective sweep within both ‰ | 
populations in the form of a star-shaped clade
of alleles.
This clade was nearly fixed in the North Sea and was segregating at a moderate frequency in the
Bay of
Biscay, explaining their genetic differentiation. Incomplete fixation reveals that selection was not
direct on
the locus but that the studied sequence recombined with a positively selected allele at a linked
locus while
it was on its way to fixation. Finally, using a deterministic model we showed that the wave of
advance of a
favourable allele at a linked locus, when crossing a strong enough barrier to gene flow, generates a
step in
neutral allele frequencies comparable to the step observed between the two ‰ | 
populations
at the
outlier locus. In our case, the position of the barrier is now materialised by a large patch of
heterospecific
‰  V 



populations.
Conclusion: High FST outlier loci are usually interpreted as being the consequence of ongoing
divergent
local adaptation. Combining models and data we show that among-population differentiation can
also
dramatically increase following a selective sweep in a structured population. Our study illustrates
how a
striking geographical pattern of neutral diversity can emerge from past indirect hitchhiking selection
in a
structured population.
Note: Nucleotide sequences reported in this paper are available in the GenBankΠdatabase under
the
accession numbers EU684165 ± EU684228.
Published: 30 May 2008
º‰
 p

Vº
 2008, 8:164 doi:10.1186/1471-2148-8-164
Received: 7 February 2008
Accepted: 30 May 2008
This article is available from: http://www.biomedcentral.com/1471-2148/8/164
© 2008 Faure et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original
work is properly cited.
º‰
 p

Vº
 2008, 8:164 http://www.biomedcentral.com/1471-2148/8/164

Genetic relationship between cultured populations

of Pacific oyster revealed by RAPD analysis
Abstract. We developed random amplified polymorphic DNA (RAPD) analysis for the assessment of the
genetic
relationship between cultured populations of the Pacific oyster Crassostrea gigas Thunberg in Hiroshima
and Goseong, the largest oyster farming areas in Japan and Korea, respectively. Of 25 arbitrary primers
comprising
decamer nucleotides of random sequences, polymerase chain reaction amplifications with 5 different primers
gave reproducible electrophoretic patterns. A total of 49 RAPD markers were clearly identified for the
Hiroshima
and Goseong populations, and 46 markers were polymorphic presenting mean polymorphism rates of
the respective populations at 92.29% and 93.32%. Pairwise genetic distances of each 20 individuals from
these
populations served to produce a UPGMA dendrogram. The dendrogram comprised two main clusters, one of
which was a nested cluster including all individuals of the Hiroshima population along with 12 individuals of
the Goseong population, and the other cluster included the remaining individuals of the Goseong population.
Results
indicate that RAPD markers are useful for the assessment of the genetic relationships between populations
of the Pacific oyster and further that a significant portion of oysters imported from Korea could be genetically
related
to the Hiroshima population.
Key words: Crassostrea gigas, cultured population, genetic relationship, Pacific oyster, RAPD.

Genetic relationships of Mytilus galloprovincialis Lmk. populations worldwide: evidence

from nuclear -DNA markers

Abstract: Allozyme surveys of genetic variation in Mytilus galloprovincialis Lmk.

throughout the world have identified three groups within this species: a northeastern (NE)
Atlantic group that also includes the M. galloprovincialis population of South Africa, a
Mediterranean group that also includes the M. galloprovincialis populations from the eastern
and the western coasts of the North Pacific, and an Australasian g roup. Hypotheses that have
been proposed to account for the genetic differentiation patterns and disjunct, worldwide
distribution of M. galloprovincialis include the recent introduction of this species into the
Southern Hemisphere and the North Pacific through human agency, and an alternative
hypothesis that each of the three groups is endemic. We used two nuclear-DNA markers (the
polyphenolic adhesive protein gene Glu-5¶ and the first intron of the actin gene mac-1) to
investigate in more depth the genetic relationships among M. galloprovincialis populations.
Samples were taken between 1996 and 1999 from California, the NE Atlantic, the
Mediterranean Sea, South Africa, Korea, Western Australia, Tasmania, and New Zealand. NE
Atlantic M. edulis L. were used a s an outgroup. While all M. galloprovincialis samples were
fixed, or nearly so, for the diagnostic G allele at locus Glu-5¶, correspondence analysis of
mac-1 allele -frequency data highlighted the genetic distinctness of Australasian mussels
relative to other M. galloprovincialis populations. The latter consisted of two differentiated
groups (NE Atlantic and Mediterranean) as formerly reported at allozyme loci. Another
sample, from Chile, was nearly identical to Mediterranean M. galloprovincialis. Nuclear-DNA
data thus enforce the idea that M. galloprovincialis have probably been introduced from the
Mediterranean to the North Pacific (and now Chile), and from the NE Atlantic to South
Africa. We argue that Australasian mussels derive from a proto- M. galloprovincialis
population introgressed by M. edulis-like genes, and should be considered as a regional
subspecies of M. galloprovincialis.

GENETIC STRUCTURE OF NATURAL POPULATIONS IN THE RED ALGAE

GELIDIUM CANARIENSE (GELIDIALES, RHODOPHYTA) IN ESTIGATED BY RANDOM
AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS1
Random amplified polymorphic DNA (RAPD)
marker variation was analyzed in female gametophytes
in natural populations of Gelidium canariense
(Grunow)

Seoane-Camba ex Haroun, Gil-
Rodrı guez, Diaz de Castro et Prud¶Homme van
Reine from the Canary Islands to estimate the degree
and distribution of genetic variability and differentiation.
A total of 190 haploid individuals were
analyzed with 60 polymorphic RAPDs bands which
produced 190 distinct multilocus genotypes. A high
level of polymorphism was detected in all populations
analyzed. Within-population gene diversity
ranged from 0.156 to 0.264. The populations on
the island of Gran Canaria showed higher genetic
variation than the other populations analyzed. The
partitioning of molecular variance by analysis of
molecular variance showed that most genetic variation
resides within populations (68.85%). These results
suggest that sexual reproduction is the
predominant mode of reproduction for G. canariense
gametophytic populations, and the main determinant
in reaching high levels of genetic diversity.
The Neighbor-Joining tree and FCA analysis displayed
two subclusters that correspond to the populations
from the western islands (Tenerife, La
Palma, Gomera) and the eastern island (Gran Canaria).
In addition, we have detected a significant relationship
between FST/(1_FST) and geographical
distance consistent with data on water circulation
and age of islands. The results obtained agree with
an isolation by distance model, with gene flow from
eastern to the western islands, and a high level of
genetic differentiation between populations
(FST50.311, Po0.001).
Key index words: Canary Islands; Gelidium canariense;
genetic diversity; genetic structure; population
genetics; RAPD; Rhodophyta
Abbreviations: AMOVA, analysis of molecular variance;
FCA, factorial correspondence analysis; IBD,
isolation by distance; RAPD, random amplified polymorphic
DNA

Genetic structuring among populations of the

greenshell mussel Äerna canaliculus revealed by
analysis of randomly amplified polymorphic DNA
ABSTRACT: Allozyme analysis of 35 populations of the endemic New Zealand greenshell mussel
Ä|V


(Gmelin 1791) indicated an absence of genetic structuring, whereas
mitochondrial
DNA (mtDNA) single-strand conformation polymorphism (SSCP) analysis of 22 of the same
populations
indicated a pronounced genetic discontinuity between northern and southern mussels at å42° S
latitude. The present study examines the genetic structuring of a subset of 19 New Zealand mussel
populations using the randomly amplified polymorphic DNA (RAPD) technique. A genetic
discontinuity
was observed between northern and southern populations, which resulted from significant
allele frequency differences, but no absolute differences between populations of these regions.
Southern populations were genetically more diverse than northern populations, with the west coast
of the South Island being the most distinct from northern populations. The RAPD data are
consistent
with the mtDNA data, indicating that both studies have resolved the population structure of Ä 


at a higher level than previous allozyme studies. The location of the genetic
discontinuity
coincides with major hydrographic features at å42° S latitude. We hypothesise that restricted gene
flow (larval transport), a consequence of present day coastal surface circulation patterns, influences
the population genetic structuring of this species, an effect which is relatively recent in geological
time (within the last 12 000 yr).
KEY WORDS: Population genetics · Gene flow · Hydrography · RAPD · New Zealand · Ä|V



· Mussel

Genetic Variability at Neutral Markers, Quantitative Trait Loci and Trait in a Subdivided Population Under
Selection
ABSTRACT
Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated
at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with
additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an
analytical approach, we compared the diversity within deme (S) and the differentiation (FST) at the QTL
with the genetic variance within deme (VW) and the differentiation (QST) for the trait. The difference
between FST and QST was shown to depend on the relative amounts of covariance between QTL within and
between demes. Simulations were used to study the effect of selection intensity, variance of optima among
demes, and migration rate for an allogamous and predominantly selfing species. Contrasting dynamics
of the genetic variability at markers, QTL, and trait were observed as a function of the level of gene flow and
diversifying selection. The highest discrepancy among the three levels occurred under highly diversifying
selection and high gene flow. Furthermore, diversifying selection might cause substantial heterogeneity
among QTL, only a few of them showing allelic differentiation, while the others behave as neutral markers.

Genetic variation of the razor clam Ensis siliqua (Jeffreys, 1875) along the European coast based
on random amplified polymorphic DNA markers
Abstract
Ensis siliqua
 

  


  


 
 

 

  

    


   
  

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Keywords: Ensis siliqua  
  







Genetic variation ofRutilus rutilus caspicus (Jakowlew

1870) populations in Iran based on random amplified
polymorphic DNA markers: a preliminary study
Abstract
Rutilus rutilus caspicus
 

    




   
  

 
 
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Genetics and conservation biology

Abstract
Conservation genetics encompasses genetic management of small populations, resolution of taxonomic
uncertainties and
management units, and the use of molecular genetic analyses in forensics and to understanding species¶
biology. The role of
genetic factors in extinctions of wild populations has been controversial, but evidence now shows that they
make important
contributions to extinction risk. Inbreeding has been shown to cause extinctions of wild populations, computer
projections
indicate that inbreeding depression has important effects on extinction risk, and most threatened species show
signs of genetic
deterioration. Inappropriate management is likely to result if genetic factors are ignored in threatened species
management. o
cite this article: R. Frankham, C. R. Biologies 326 (2003).

Genetics and extinction

Abstract
The role of genetic factors in extinction has been a controversial issue, especially since Lande_s
paper [Genetics and demography in
biological conservation, Science 241 (1988) 1455±1460] paper in Science. Here I review the
evidence on the contribution of genetic
factors to extinction risk. Inbreeding depression, loss of genetic diversity and mutation accumulation
have been hypothesised to
increase extinction risk. There is now compelling evidence that inbreeding depression and loss of
genetic diversity increase extinction
risk in laboratory populations of naturally outbreeding species. There is now clear evidence for
inbreeding depression in wild species
of naturally outbreeding species and strong grounds from individual case studies and from
computer projections for believing that
this contributes to extinction risk. Further, most species are not driven to extinction before genetic
factors have time to impact. The
contributions of mutation accumulation to extinction risk in threatened taxa appear to be small and
to require very many generations.
Thus, there is now sufficient evidence to regard the controversies regarding the contribution of
genetic factors to extinction risk as
resolved. If genetic factors are ignored, extinction risk will be underestimated and inappropriate
recovery strategies may be used.
Keywords: Extinction risk; Genetic diversity; Inbreeding depression; Mutation accumulation; Self-
incompatibility

Genetics in fisheries management

Abstract
Genetic analyses have much to offer fisheries managers, especially in the provision of tools enabling
unequivocal
specimen identification and assessment of stock structure. The three commonly-used genetic tools ±
allozymes,
mitochondrial DNA and microsatellites ± differ in their properties. These differences must be born in mind,
especially when interpreting gene frequency data collected for stock structure research. Examples where
genetic
approaches have been used to identify specimens are given, with special attention being given to compliance
and
labelling issues. Treatment of stock structure focuses on Atlantic cod and on yellowfin, bigeye and albacore
tunas.
The different resolving powers of the various techniques are discussed. Marine fish typically show low levels
of
population genetic differentiation, and in such species the use of large sample sizes and, preferably, multiple
types
of markers are desirable to resolve stock structure issues.

Genetics of marine bioinvasions

¢ey words: ballast water, conservation, invasive species, population structure
Abstract
Anthropogenic biological introductions have captured the attention of marine scientists and resource
managers
in recent years. Human-mediated marine bioinvasions are presently acknowledged as often ecologically and
financially devastating events. Despite recent increases in scientific interest and financial resources devoted to
nonindigenous nuisance species globally, fundamental questions pertaining to taxonomic identity, geographic
source, introduction vector and invasive population dynamics frequently remain unanswered. Ecological
surveys
based on photometric and observational methods are unable to identify cryptogenic taxa, source populations,
multiple introductions, or genetic diversity. The twofold goal of this paper is to discuss the application of
molecular
genetic techniques to fundamental ecological questions pertaining to bioinvasions and to demonstrate the
utility of
DNA technology in providing data useful in the development of predictive models for marine bioinvasion
science.

Genome-Wide Association Studies: Quality Control

and Population-Based Measures
Genome-wide association studies, using hundreds of thousands of single-nucleotide polymorphism (SNP)
markers, have
become a standard approach for identifying disease susceptibility genes. The change in the technology poses
substantial
computational and statistical challenges that have been addressed in the quality control, imputation, and
population-based
measure groups of the Genetic Analysis Workshop 16. The computational challenges pertain to efficient
memory
management and computational speed of the statistical procedures, and we discuss an approach for efficient
SNP storage.
Accuracy and computational speed is relevant for genotype calling, and the results from a comparison of three
calling
algorithms are discussed. The first statistical challenge is related to statistical quality control, and we discuss
two novel
quality control procedures. These low-level analyses have an effect on subsequent preparatory steps for high-
level analyses,
e.g., the quality of genotype imputation approaches. After the conduct of a genome-wide association study
with successful
replication and/or validation, measures of diagnostic accuracy, including the area under the curve, are
investigated. The
area under the curve can be constructed from summary data in some situations. Finally, we discuss how the
populationattributable
risk of a genetic variant that is only measured in a reference data set can be determined. Genet. Epidemiol. 33.
Key words: genotype calling algorithm; data management; population attributable fraction; receiver-operating
characteristic curve; signal intensity plot

Genomic reticulation indicates mixed ancestry in

Southern-Hemisphere Mytilus spp. mussels
Previous surveys of allozyme variation in smooth-shell Mytilus spp. mussels have reported the presence in the
Southern Hemisphere of both Mytilus edulis and Mytilus galloprovincialis mussels. In the present study,
nuclear
DNA markers mac-1 and Glu-5/Glu-3, both diagnostic for Northern-Hemisphere M. edulis and M.
galloprovincialis,
were used to further characterize the nuclear genomes of M. edulis from Kerguelen and M. galloprovincialis
from Tasmania. Genomic reticulation was observed, with typical M. edulis allelomorphs fixed in both
populations
at locus mac-1 whereas, at locus Glu-5/Glu-3, allelomorphs characteristic of M. galloprovincialis were
present in
Kerguelen and nearly fixed in Tasmania. Kerguelen mussels had a genome of mixed M. edulis and M.
galloprovincialis
ancestry without evidence of barriers to merging as shown by Hardy±Weinberg and linkage equilibrium.
Tasmanian mussels possessed a predominantly M. galloprovincialis genomic background introgressed by M.
edulis
allelomorphs at locus mac-1. Genetic drift superimposed on ancient hybridization and introgression may
explain
the genomic reticulation observed in both Kerguelen and Tasmanian mussels. There was no evidence of a
recent
introduction of Northern-Hemisphere M. galloprovincialis or M. edulis to Kerguelen or Tasmania. © 2007
The
Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 747±754.
ADDITIONAL KEYWORDS: antitropical distribution, geographical structure ± hybridization ± introgression
± intron-length polymorphism ± nuclear DNA

Growth rate, condition, and shell shape of Mytilus

galloprovincialis: responses to wave exposure
ABSTRACT: Growth rates, condition indices and shell shapes of ‰p
 V 



, an
invasive
alien mussel that has colonised the west coast of South Africa, were measured at a series of sites
with different wave exposure regimes in 2 regions 500 km apart. Wave action at the sites was
determined
by maximum wave-force dynamometers. ‰  V 



grew faster and had higher condition
values on exposed than on sheltered shores, probably due to higher food availability at sites
with greater water flow. Growth rates and condition values, however, declined at sites experiencing
extreme wave action. This resulted in a polynomial relationship between the growth coefficient ¢,
and wave force. Mussels grew slower in the southern region, where food concentrations are lower.
The shells of ‰  V 



tended to be lower and narrower at exposed sites, perhaps
reducing
the effect of hydrodynamic forces. Mussel shells were thickest on sheltered and extremely
exposed shores. The results are discussed in the context of the impact that ‰  V 



is
likely to have on indigenous species. Because ‰  V 



is scarce and slow-growing at
sheltered sites, its competitive effects there are likely to be minimal, whereas on exposed sites its
density, growth and condition are highest and its effects will peak, diminishing again at extremely
exposed sites.
KEY WORDS: Growth rate · Condition · Mussels · Wave force · Rocky intertidal · South Africa

Short communication
Harmful algae and mariculture in New Zealand
Harmful algal blooms and their impacts on the Greenshell_ mussel industry in New
Zealand over the last decade are reviewed. The response of the regulatory authorities,
seafood industry, and scientists to the first significant toxic Gymnodinium blooms in the
summer of 1992/1993 has resulted in a well-organized interest group including
scientists, commercial interests, and public health regulators. Nearly all known toxic
species occur in New Zealand and unique and internationally accredited microalgal
monitoring programmes have been developed. New methods, such as DNA probes,
have been integrated into the system for rapid identification of species that are difficult
to differentiate morphologically. Monitoring is carried out weekly, with results being
dispatched within 24 h of sample receipt to enable risk assessments of toxicity by
shellfish harvesters. The introduction of this system has saved the shellfish industry
money and has reduced the amount of contaminated product being harvested and then
rejected. All the main marine biotoxins are monitored, including paralytic, neurotoxic,
diarrhetic, and amnesic shellfish toxins, and also compounds such as yessotoxin,
pectenotoxin, and gymnodimine. Blooms that could affect farmed finfish or wild
marine biota are also reported. Harmful algal monitoring is constantly reviewed in the
light of new research and incorporates local knowledge of oceanographic and climatic
conditions.
_ 2001 International Council for the Exploration of the Sea
Key words: DNA probes, HABs, marine biotoxins, phytoplankton monitoring, toxic
microalgae.

Heritability of body size in the Chilean blue mussel (Mytilus chilensis Hupe´ 1854): effects of
environment and ageing
Abstract






    


 
 





 

 
 











 

 

  






 


 





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 Mytilus chilensis

HETEROZYGOTE DEFICIENCY IN THE MUSSEL MYTILUS EDULIS SPECIES COMPLEX

REVISITED

HIGH FIDELITY OF MITOCHONDRIAL GENOME TRANSMISSION UNDER THE DOUBLY

UNIPARENTAL MODE OF INHERITANCE IN FRESHWATER MUSSELS(BIVALVIA: UNIONOIDEA)
cbstract. Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) has been demonstrated in
both
mytilid and unionid bivalves. Under DUI, females pass on their mtDNA to both sons and daughters, whereas
males
pass on their mtDNA to only sons. In mytilids, the loss of an original male (or M) mitotype, with its
subsequent
replacement by that lineage¶s female (or F) mitotype, has been called a role-reversal or, more specifically, a
masculinization
event. Multiple masculinization events have been inferred during the evolutionary history of mytilids but
not unionids. The perceived lack of role-reversal events in unionids may represent a significant difference in
the
evolutionary dynamics of DUI between the two bivalve taxa or simply a lack of sufficient taxon sampling in
unionids.
To evaluate these alternative hypotheses, six additional unionoidean bivalve genera were sampled for DUI
including
one genus from the sister taxon of the Unionidae, the Hyriidae. Phylogenetic analyses of 619 base pairs of
cytochrome
c oxidase I (COI) from eight genera (nine species) of unionoidean bivalves, plus the sister taxon to the
Unionoida,

eotrigonia, revealed that the M and F unionoidean mitotypes were contained in gender-specific,
topologically congruent
clades. This supports the hypothesis that either role-reversal events do not occur in unionoideans or, if they
do occur, their products are ephemeral in an evolutionary sense. Furthermore, the fact that the mantle-tissue-
derived

eotrigonia mitotype is the sister mitotype to the unionoidean F mitotype clade suggests that DUI has been
operating
with high fidelity in unionoids for at least 200 million years. A relatively low incidence of interspecific
hybridization
in unionoideans and a possibly obligate role for the M mitotype in unionoidean gender determination are
offered as
potential explanations for the disparate evolutionary dynamics of DUI observed between mytilid and
unionoidean
bivalves.
¢ey words. Bivalvia, cytochrome c oxidase I, doubly uniparental inheritance, mitochondrial DNA
transmission,
Paleoheterodonta, phylogenetics, Unionoidea.

Homoploid hybrid speciation in animals

Abstract
Among animals, evidence for homoploid hybrid speciation (HHS, i.e. the creation of a
hybrid lineage without a change in chromosome number) was limited until recently to the
virgin chub, Gila seminuda, and some controversial data in support of hybrid status for the
red wolf, Canis rufus. This scarcity of evidence, together with pessimistic attitudes among
zoologists about the evolutionary importance of hybridisation, prompted the view that HHS
is extremely rare among animals, especially as compared with plants. However, in recent
years, the literature on animal HHS has expanded to include several new putative examples
in butterflies, ants, flies and fishes. We argue that this evidence suggests that HHS is far
more common than previously thought and use it to provide insights into some of the
genetic and ecological aspects associated with this type of speciation among animals.
¢| V : animals, homoploid, hybridisation, introgression, molecular markers, speciation

How useful are the genetic markers in attempts to

understand and manage marine biodiversity?
Abstract
The genetics of marine populations is a subject that has made little progress compared with the
effort spent on the terrestrial environment. This is so despite µµapplied¶¶ aspects such as stock
management, marine aquaculture, creation of reserves, conservation of the coastal zones, taxonomy,
and protection of species. The crowded and dispersive marine environment, with its steep physical
gradients, favours the existence of a planktonic larval stage for most species. The attendant high
fecundity has important consequences for selection differentials and dispersal and therefore for the
evolution of genetic structures. These features must be taken into account in order to understand the
origin and maintenance of marine biodiversity and, in some cases, to manage it. In this article, after a
definition of genetic diversity among other aspects of biodiversity, special features of the marine
environment and processes governing genetic diversity are given together with the molecular tools
required to study it. Then, an overview of the interesting scientific questions in marine biodiversity
research is given concerning:Errorthe population structure as a function of dispersal systems and
spatial constraints: gene flow and speciation in a dispersive environment, Errorthe phylogeography
and historical biogeography of marine ecosystems; Errorthe functional and adaptive aspects of
polymorphism: larval phase and genetic control of recruitment. Some uses of genetic diversity for
assessment, conservation and protection purposes are also detailed. Organismal (specific) diversity
does not enter the scope of the article. D 2002 Elsevier Science B.V. All rights reserved.
Keywords: Assessment; Conservation; Evolution; Infra-specific biodiversity; Management; Molecular
ecology;
Monitoring

Hybridization in the Sea ****

Impacts of Biodiversity Loss on Ocean Ecosystem Services

Human-dominated marine ecosystems are experiencing accelerating loss of populations and
species, with largely unknown consequences. We analyzed local experiments, long-term regional
time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services
across temporal and spatial scales. Overall, rates of resource collapse increased and recovery
potential, stability, and water quality decreased exponentially with declining diversity. Restoration
of biodiversity, in contrast, increased productivity fourfold and decreased variability by 21%, on
average. We conclude that marine biodiversity loss is increasingly impairing the ocean's capacity to
provide food, maintain water quality, and recover from perturbations. Yet available data suggest
that at this point, these trends are still reversible.

Improving Marine Water Quality by

Mussel Farming: A Profitable Solution
for Swedish Society
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INBREEDING DEPRESSION IN
CONSERVATION BIOLOGY
Key Words endangered species, extinction, fitness, genetic restoration, purging
n Abstract Inbreeding depression is of major concern in the management and conservation
of endangered species. Inbreeding appears universally to reduce fitness, but
its magnitude and specific effects are highly variable because they depend on the genetic
constitution of the species or populations and on how these genotypes interact with
the environment. Recent natural experiments are consistent with greater inbreeding
depression in more stressful environments. In small populations of randomly mating
individuals, such as are characteristic of many endangered species, all individuals may
suffer from inbreeding depression because of the cumulative effects of genetic drift
that decrease the fitness of all individuals in the population. In three recent cases, introductions
into populations with low fitness appeared to restore fitness to levels similar
to those before the effects of genetic drift. Inbreeding depression may potentially be
reduced, or purged, by breeding related individuals. However, the Speke¶s gazelle
example, often cited as a demonstration of reduction of inbreeding depression, appears
to be the result of a temporal change in fitness in inbred individuals and not a reduction
in inbreeding depression.

Inbreeding effects in wild populations

Whether inbreeding affects the demography and persistence of natural

populations has been questioned. However, new pedigree data from field
populations and molecular and analytical tools for tracing patterns of
relationship and inbreeding have now enhanced our ability to detect
inbreeding depression within and among wild populations. This work reveals
that levels of inbreeding depression vary across taxa, populations and
environments, but are usually substantial enough to affect both individual and
population performance.Data from bird and mammal populations suggest
that inbreeding depression often significantly affects birth weight, survival,
reproduction and resistance to disease, predation and environmental stress.
Plant studies, based mostly on comparing populations that differ in size or
levels of genetic variation, also reveal significant inbreeding effects on seed set,
germination, survival and resistance to stress.Data from butterflies, birds and
plants demonstrate that populations with reduced genetic diversity often
experience reduced growth and increased extinction rates. Crosses between
such populations often result in heterosis. Such a genetic rescue effect might
reflect the masking of fixed deleterious mutations. Thus, it might be necessary
to retain gene flow among increasingly fragmented habitat patches to sustain
populations that are sensitive to inbreeding.

Influence of genotype and geography on shell shape

and morphometric trait variation among North Atlantic
blue mussel (Mytilus spp.) populations
The influence of geography and genotype on shell shape (outline) and trait (morphometric) variation among
North
Atlantic blue mussels and their hybrids has been examined. Shape differences among reference taxa (Mytilus
trossulus, Mytilus edulis and Mytilus galloprovincialis) were consistent with an association between taxon-
specific
genes and shape genes. Newfoundland M. edulis ¥ M. trossulus populations and northern Quebec M.
trossulus
populations exhibited an uncoupling of taxon-specific genes from shape genes, whereas Nova Scotia M.
trossulus
populations and SW England M. edulis ¥ M. galloprovincialis populations exhibited an association between
taxon-specific genes and shape genes. We found no evidence of a geographic effect (NE versus NW Atlantic)
for
shape variation, indicating that the genotype effect is stronger than any geographic effect at macrogeographic
scales. Pronounced differences were observed in trait variability consistent with an association between
taxonspecific
genes and trait genes in European populations, and trait divergence of New York M. edulis from all
European mussels. Trait variability in mussels from Newfoundland, Nova Scotia and northern Quebec
indicated
an uncoupling of taxon genes from trait genes, whereas trait variability in SW England M. edulis ¥ M.
galloprovincialis
populations was consistent with background genotype, indicating a strong association between taxon
genes and trait genes. A pronounced macrogeographic split (NE versus NW Atlantic) regardless of taxonomy
was
observed, indicating that geography exerts a greater influence than genotype on trait variation at the
macrogeographic
scale. This is consistent with pronounced within-taxon genetic divergence, indicative of different selection
regimes or more likely of different evolutionary histories of mussels on either side of the North Atlantic. ©
2009
The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 875±897.

Integrated management of land and water resources based on a collective approach to fragmented
international conventions
Interlinked crises of land degradation, food security, ecosystem decline, water quality and water flow
depletion stand in the way of poverty reduction and sustainable development. These crises are made worse
by increased fluctuations in climatic regimes. Single-purpose international conventions address these crises
in a piecemeal, sectoral fashion and may not meet their objectives without greater attention to policy,
legal, and institutional reforms related to: (i) balancing competing uses of land and water resources within
hydrologic units; (ii) adopting integrated approaches to management; and (iii) establishing effective
governance institutions for adaptive management within transboundary basins. This paper describes this
global challenge and argues that peace, stability and security are all at stake when integrated approaches
are not used. The paper presents encouraging results from a decade of transboundary water projects
supported by the Global Environment Facility in developing countries that test practical applications of
processes for facilitating reforms related to land and water that are underpinned by science-based
approaches. Case studies of using these participative processes are described that collectively assist in the
transition to integrated management. A new imperative for incorporatiing interlinkages among food, water,
and environment security at the basin level is identified.
Keywords: integrated land and water management; water security; transboundary basins;
stakeholder participation; water governance; Global Environment Facility

Integrating genetic data into management of marine resources: how can we do it better?
Abstract
Molecular genetic data have found widespread application in the identification of
population and conservation units for aquatic species. However, integration of
genetic information into actual management has been slow, and explicit and
quantitative inclusion of genetic data into fisheries models is rare. In part, this reflects
the inherent difficulty in using genetic markers to draw inferences about demographic
independence, which is generally the information of the greatest short-term
interest to fishery managers. However, practical management constraints, institutional
structures and communication issues have also contributed to the lack of
integration. This paper identifies some of the organizational, conceptual and technical
barriers that have hampered full use of genetics data in stock assessment and hence
fishery management and outlines how such use could be enhanced.
Keywords Demographic independence, fish stock assessment, fisheries management,
mixed-stock fisheries, stock identification

Interspecific variability of RAPD and fatty acid composition of

some pomegranate cultivars (Punica granatum L.) growing in
Southern Anatolia Region in Turkey
Abstract
The interspecific variability of fatty acid (FA) composition and RAPD profiles was used to examine
biochemical and genetic
relationships among six pomegranate cultivars, which dominate pomegranate production in Southern Anatolia
Region of Turkey.
Fatty acid composition of pomegranate leaves was determined by using gas chromatography. Differences in
the FA composition
were found among cultivars. In particular, cv. kirli hanim had a distinct fatty acid profile that differs from the
other cultivars.
Linoleic acid was not detected in this cultivar, whereas the other cultivars had various levels of linoleic acid.
RAPD data also
showed that this cultivar formed a unique pattern. The differences in the composition of fatty acids among
pomegranate cultivars
suggested that fatty acid profiles could be used to differentiate among some of the pomegranate cultivars.
RAPD analysis was also
useful for grouping the pomegranate cultivars.
_ 2007 Elsevier Ltd. All rights reserved.
Keywords: Genetic diversity; FAMEs; Punica granatum; RAPD

Intraespecific phylogeography of lasmigona subviridis bivalvia unionidae, conservation implications of range

discontinuity

Introgression patterns in the mosaic hybrid zone between

‰p
| 

and
‰  V 




N. BIERNE,
Abstract
Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine
hybrid zones deserve more investigation because of the generally high dispersion potential
of planktonic larvae which allows migration on scales unrivalled by terrestrial species.
Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels
‰p
| 
and‰  V 




, using three length-polymorphic PCR loci as
neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead
of a single genetic gradient from
‰  V 




on the Iberian Peninsula to
‰ | 

populations in the North Sea, three successive transitions were observed in France. From
South to North, the frequency of alleles typical of
‰  V 




first decreases in the
southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains
high in most of Brittany, and finally decreases again in South Normandy. The two enclosed
patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although
predominantly
‰ | 

-like and
‰  V 




-like, respectively, are genetically
original in two respects. First, considering only the various alleles typical of one species, the
patches show differentiated frequencies compared to the reference external populations.
Second, each patch is partly introgressed by alleles of the other species. When introgression
is taken into account, linkage disequilibria appear close to their maximum possible values,
indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation
mechanisms (habitat specialization, spawning asynchrony, assortative fertilization
and hybrid depression) have been documented in previous studies, although their relative
importance remains to be evaluated. We also provided evidence for a recent migratory Ôshortcut
Õ connecting
‰ | 

-like populations of the Charente patch to an external
‰ | 

population in Normandy and thought to reflect artificial transfer of spat for aquaculture.


 ‰Ä

ĉÄ

 
uÄ

  

 ‰  
º


Is Good Policy Unimplementable? Reflections on the Ethnography of Aid Policy and Practice
ABSTRACT
Despite the enormous energy devoted to generating the right policy models in
development, strangely little attention is given to the relationship between
these models and the practices and events that they are expected to generate
or legitimize. Focusing on the unfolding activities of a development project
over more than ten years as it falls under different policy regimes, this article
challenges the assumption that development practice is driven by policy,
suggesting that the things that make for µgood policy¶ ² policy which legitimizes
and mobilizes political support ² in reality make it rather unimplementable
within its chosen institutions and regions. But although
development practice is driven by a multi-layered complex of relationships
and the culture of organizations rather than policy, development actors work
hardest of all to maintain coherent representations of their actions as
instances of authorized policy, because it is always in their interest to do so.
The article places these observations within the wider context of the anthropology
of development and reflects on the place, method and contribution of
development ethnography.


   
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LARVAL ECOLOGY AND MACROEVOLUTION IN MARINE INVERTEBRATES

ABSTRACT
In marine mollusks, planktotrophic and nonplanktotrophic modes of development generally
confer different scales of larval dispersal, which in turn influence species' geographic
ranges and genetic population structures. In Late Cretaceous gastropods, planktotrophic species
(as inferred from larval shell morphologies) exhibit significantly broader geographic ranges,
longer species durations, and lower speciation and extinction rates than nonplanktotrophic
species; these effects outweigh a variety of adult traits. Nor are the effects of these specieslevel
larval traits reducible to selection at the organismic level, but instead evidently fulfill
the requirements of true species selection: differences in genetic populations structuremediated
by modes ofIarval development-affect the multiplication and survival of species,
vary among species but rarely within species, and are heritable at the species level. The
geographic and stratigraphic pattern of first appearance of species with respect to other
members of their clade suggests that larval types affect modes as well as rates of evolution,
with the genetically-subdivided nonplanktotrophs subjected to a greater variety of processes
than the potentially more panmictic planktotrophs. Nonplanktotrophs have the appropriate
population structure for the operation of shifting balance mechanisms, and their fossil record
is consistent with this possibility, with first occurrences nested in, but stratigraphically abutting,
the ranges of related species. However, survival of genera during the end-Cretaceous
mass extinction is unrelated to larval development and several other traits (e.g., species
richness) that were influential during times of normal, background levels of extinction. Instead,
taxonomic survivorship is related to the magnitude of the clades' geographic ranges-regardless
of the geographic range of constituent species. This change in selectivity indicates
that mass extinctions are not simply intensifications or extrapolations of background processes,
but may be indifferent to the quality of adaptation, fitness values, or clade configurations
achieved during background times. The results presented here suggest that evolutionary
theory (1) should be more explicitly hierarchical (as argued by Gould, Eldredge, Vrba,
Salthe, and others), with selection, drift, and other processes occurring at a series of focal
levels that are neither wholly extrapolations nor wholly independent of processes at adjacent
levels; and (2) must take into account the alternation of background and mass extinction
regimes.

LEGALSIZEBLUEMUSSEL

Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic
Sea
Abstract
Marginal populations are often isolated and under extreme selection pressures resulting
in anomalous genetics. Consequently, ecosystems that are geographically and ecologically
marginal might have a large share of genetically atypical populations, in need of particular
concern in management of these ecosystems. To test this prediction, we analysed genetic
data from 29 species inhabiting the low saline Baltic Sea, a geographically and ecologically
marginal ecosystem. On average Baltic populations had lost genetic diversity compared
to Atlantic populations: a pattern unrelated to dispersal capacity, generation time of
species and taxonomic group of organism, but strongly related to type of genetic marker
(mitochondrial DNA loci had lost

. 50% diversity, and nuclear loci 10%). Analyses of
genetic isolation by geographic distance revealed clinal patterns of differentiation between
Baltic and Atlantic regions. For a majority of species, clines were sigmoid with a sharp slope
around the Baltic Sea entrance, indicating impeded gene flows between Baltic and Atlantic
populations. Some species showed signs of allele frequencies being perturbed at the edge
of their distribution inside the Baltic Sea. Despite the short geological history of the Baltic
Sea (8000 years), populations inhabiting the Baltic have evolved substantially different
from Atlantic populations, probably as a consequence of isolation and bottlenecks, as well
as selection on adaptive traits. In addition, the Baltic Sea also acts a refuge for unique
evolutionary lineages. This marginal ecosystem is thus vulnerable but also exceedingly
valuable, housing unique genes, genotypes and populations that constitute an important
genetic resource for management and conservation.

Limiting abuse: marine protected areas, a limited solution

Abstract
Designation of marine protected areas (MPAs) is increasing as humans seek to combat overexploitation of
marine
resources and preserve the integrity of the ocean¶s unique biodiversity. At present there are over 1300 MPAs.
The
primary legal responsibility for the designation of MPAs falls to individual countries, but protection of the
marine
environment at large scales is also critical because ocean circulation does not honor legal boundaries and
often
exceeds the influence of any one nation or group of nations. There are many reasons for establishing MPAs;
the
papers we surveyed principally referred to scientific, economic, cultural, and ethical factors. Two approaches
predominated: fisheries management and habitat protection. Although the major threat to terrestrial systems is
habitat loss, the major threats to the world¶s oceans are fisheries overexploitation, coastal development, and
chemical
and biological pollution. MPAs may provide conservation of formerly exploited species as well as benefits to
the
fishery through leakage of µsurplus¶ adults (spillover) and larvae (larval replenishment) across reserve
boundaries.
Higher order effects, such as changes in species richness or changes in community structure and function,
have only
been superficially explored. Because many MPAs are along coastlines, within shipping lanes, and near human
centers
of activity, the chance of chemical and biological pollution is high. Use of MPAs to combat development and
pollution is not appropriate, because MPAs do not have functional boundaries. The ocean is a living matrix
carrying
organisms as well as particles and therefore even relatively environmentally sensitive uses of coastal
ecosystems can
degrade ecosystem structure and function via increasing service demands (e.g. nutrient and toxics
transformation) and
visitation. Whether an MPA is effective is a function of the initial objectives, the level of enforcement, and its
design.
Single reserves need to be large and networked to accommodate bio-physical patterns of larval dispersal and
recruitment. Some authors have suggested that reserve size needs to be extremely large ² 50±90% of total
habitat
² to hedge against the uncertainties of overexploitation. On a local scale, marine protected areas can be
effective
conservation tools. On a global scale, MPAs can only be effective if they are substantively representative of
all
biogeographic zones, single reserves are networked within biogeographic zones, and the total amount of area
reserved
per zone is 20% or greater. The current size and placement of protected areas falls far short of comprehensive
or even
adequate conservation objectives. © 1999 Elsevier Science B.V. All rights reserved.

LINKING LARVAL SETTLEMENT TO LARVAL

TRANSPORT: ASSUMPTIONS, POTENTIALS,
AND PITFALLS
I ABSTRACT
Settlement rate time series of nearshore invertebrate taxa can be helpful for posing
questions about larval transport processes. However, the potential of these time series
remains mostly unexplored, and the assumptions in this inquiring process are rarely
identified. This contribution discusses the potentials and pitfalls of using settlement
rate time series in posing questions about larval transport. I discuss why physical
processes are distinct in the nearshore, up to ~30 m depth, as compared to the offshore,
and briefly consider the likely problems in uncritically transferring meso-scale (~100¶s
km) arguments to nearshore discussions. I consider the assumptions of available and
shared larval pools often used in shoreward larval transport studies, and then the
hierarchical nature of the different processes influencing settlement-rate, developing
an argument about their relative importance. Large-scale offshore processes operate
first on more larvae than small-scale nearshore processes, which operate last on fewer
larvae; it is argued that large-scale offshore processes are disproportionally important
in determining population fluctuations. Many field studies using settlement plates or
larval collectors assume that settlement rate is only influenced by the rate of arrival of
larvae. I discuss how the sampling interval, and the ³settlement environment´, the
background where plates or larval collectors are installed, can influence settlement
rate. Settlement often does not correlate directly with larval supply, and settlement
interval should be kept as short as possible as settlement and time do not scale
proportionally. Finally, I discuss the processes that generate smooth and peaked
settlement time series, and the use of settlement time-series in identifying the temporal
and spatial scales of physical transport.

Local adaptation and species segregation in two mussel(‰p
| 
 ‰p
pV ) hybrid
zones
Abstract
Few marine hybrid zones have been studied extensively, the major exception being the
hybrid zone between the mussels
‰p
| 

and
‰p
 V 




in southwestern
Europe. Here, we focus on two less studied hybrid zones that also involve
‰p

spp.;
‰p
| 

and
‰p
pV 
are sympatric and hybridize on both western
and eastern coasts of the Atlantic Ocean. We review the dynamics of hybridization in these two
hybrid zones and evaluate the role of local adaptation for maintaining species boundaries.
In Scandinavia, hybridization and gene introgression is so extensive that no individuals with
pure
‰ pV 
genotypes have been found. However,
‰ pV 
alleles are maintained at
high frequencies in the extremely low salinity Baltic Sea for some allozyme genes. A synthesis
of reciprocal transplantation experiments between different salinity regimes shows that
unlinked


and
Ä
alleles change frequency following transplantation, such that posttransplantation
allelic composition resembles native populations found in the same salinity.
These experiments provide strong evidence for salinity adaptation at


and
Ä
or genes
linked to them). In the Canadian Maritimes, pure
‰ | 

and
‰ pV 
individuals are
abundant, and limited data suggest that
‰ | 

predominates in low salinity and sheltered
conditions, whereas
‰ pV 
are more abundant on the wave-exposed open coasts. We
suggest that these conflicting patterns of species segregation are, in part, caused by local
adaptation of Scandinavian
‰ pV 
to the extremely low salinity Baltic Sea environment.
¢| V 
: allozyme, hybrid zone,
 
, mussel, selection, speciation
||
| 
|V|


V||
| | p| |V| p| | p| |V

Maintenance of genetic diversity: challenges for management of marine resources

There are three general classes of threat to biodiversity at the gene level: 1) extinction, which results in
complete and irreversible loss of genes; 2) hybridization, which may cause re-arrangement of co-adapted
genes and loss of adaptability to local conditions, and 3) reduction of genetic variability within populations.
While extinction avoidance is a fundamental management objective and hybridization can usually be
dismissed in marine populations, the reduction of genetic variability within populations is a plausible threat
and can occur in two ways. First, a decrease in population size may result in inbreeding. Normally, marine
fish have very large population sizes, and commercial extinction is likely to occur long before populations are
reduced to the level required for losses of genetic diversity due to inbreeding. However, when populations are
very severely over-fished to small numbers, concerns associated with small population sizes and disruptions
of migration between populations may become prominent. In particular, undetected populations within
management units may be fished to this level before the situation is properly evaluated and remedied. Second,
a reduction of genetic variability within populations may occur in a directed way, due to, e.g., selective
fishing. Fishing is expected to generate selection on life history traits such as age and size at maturation;
changes in life history traits influence the dynamics of fish populations, energy flows in the ecosystem, and
ultimately, sustainable yield. We discuss management objectives designed to ameliorate genetic
complications associated with small population size and fisheries-induced selection, and outline a
management approach that may be useful when developing advice for maintaining genetic diversity.
Keywords: biodiversity, inbreeding, management objectives, selection

Managing marine genetic diversity: time for action?

Marine Reserves and Fisheries Management

Mechanisms of habitat segregation between an invasive

and an indigenous mussel: settlement, post-settlement
mortality and recruitment
Abstract The mussel Mytilus galloprovincialis is highly
invasive worldwide, but displays varying degrees of local
and regional coexistence with indigenous mussels through
spatial habitat segregation. We investigated the roles of
settlement, post-settlement mortality, juvenile growth and
recruitment in partial habitat segregation between the invasive
M. galloprovincialis and the indigenous mussel Äerna
perna on the south coast of South Africa. We used two
study locations, Plettenberg Bay and Tsitsikamma, 70 km
apart, with two sites (separated by 300±400 m) per location,
each divided into three vertical zones. There were no signiWcant
e ects in Tsitsikamma, where daily settlement and
monthly recruitment were signiWcantly lower than in Plettenberg
Bay. In Plettenberg Bay, settlement (primary and
secondary) and recruitment of both species decreased
upshore. Post-settlement mortality was measured over two
consecutive 6-day periods during a spring tide and a neap
tide. For both species mortality was low on the low-shore.
High-shore mortality was consistently low for M. galloprovincialis,
but increased dramatically for Ä. perna during
spring tide. No data were obtained for growth of Ä. perna,
but juvenile M. galloprovincialis grew more slowly farther
upshore. Ä. perna recruited mainly in spring and summer,
with a peak in summer far greater than for M. galloprovincialis.
Recruitment of M. galloprovincialis was more protracted,
continuing through autumn and winter. Thus local
coexistence is due to a combination of pre- and postrecruitment
factors di ering in importance for each species.
Ä. perna is excluded from the high-shore by recruitment
failure (low settlement, high mortality). High survival and
slow growth in juveniles may allow large densities of
M. galloprovincialis to accumulate there, despite low settlement
rates. With no di erences between species in
settlement or mortality on the low-shore, exclusion of
M. galloprovincialis from that zone is likely to be by postrecruitment
processes, possibly strengthened by periodic
heavy recruitments of Ä. perna. At larger scales, larval
retention and protracted recruitment contribute to the success
of M. galloprovincialis at Plettenberg Bay, while
recruitment limitation may explain why M. galloprovincialis
is less successful at other sites.
METAPOPULATION
DYNAMICS AND GENETICS
Abstract
Metapopulation dynamics as originally defined by Levins consists of the
extinction and colonization of local populations. Theory suggests that these
processes can profoundly affect demographic persistence. the coexistence of
interacting species, genetic variation, and evolution. However, a review of
empirical studies illustrates the limitations of the Levins definition and indicates
the need for a more complex view of metapopulation dynamics. We
describe a modeling approach that can incorporate a greater range of ecological
and genetic processes within local populations. We discuss uses of this general
formulation, its connections to other modeling frameworks, and directions for
the future integration of ecological and genetic studies of metapopulations

Microgeographic allozyme differentiation in the hybrid zone of MFtilus galloprovincialis Lmk. And M. edulis
L. on the continental European coast
ABSTRACT: The European Mytilus gafloprovinciafis Link. and [vl. edulis L. coexist and hybridize in
different proportions in extended areas of the British and Atlantic French coasts. I. galloprovincialis
typical allozymes seem to predominate in wave exposed areas, at high levels of attachment
and in larger mussels in the British hybrid zone. Mussel samples from exposed and sheltered areas,
200 m apart, and from high and low levels of attachment were collected from a location of the French
hybrid zone in 1988-92. Pure M. gafloprovincialis and M. edu]is populations were also taken as controls.
Diagnostic enzyme loci for both
lytilus ( S-', LcÄ-I ", MÄI', o') and cÄ-I ", LcÄ.2 ~
and ÄGM" loci were studied. The frequencies of the M. galloprownciaiis typical alleles were significantly
greater in exposed pol)ulations than in sheltered samples (e.g. 0.729 to 0.803 vs 0.192 to
0.581 for S- "90), and at high level of attachment than at low level for the sheltered area (e.g.
0.581 vs 0.192 for S- "90). Putative lVl. galloprovinc~ahs was more abundant on the exposed coast
(0.591 and t).702) than on the sheltered shore, where it predominated at the high shore but not
at the low shore location (0.371 vs 0.045). Significantly posihve correlations between shell length and
typical M. galloprovincialis compound allele frequencies were found only for populations from
exposed areas. Relationships between the Mytilus genehc differentiation and ecological factors are
discussed.

Migration and Genetic Structure of Salmo salar and Salmo trutta in Northern Swedish Rivers
Abstract
Östergren, J. 2006. Migration and Genetic Structure of Salmo salar and Salmo trutta in
Northern Swedish Rivers. Doctor¶s dissertation. ISSN: 1652-6880. ISBN: 91-576-7261-
X.
This thesis focuses on the migration of Atlantic salmon (Salmo salar L.) and sea trout
(Salmo trutta L.) before, during and after spawning in two northern Swedish rivers and
influence of habitats and environmental factors on these activities. In addition, genetic
structure of brown trout and genetic impact of stocked salmon and sea trout juveniles from
foreign populations on native stocks was studied. Migrations and genetics are related to
anthropogenic factors as historical log-floating and hydropower production.
On their spawning migration, radio-tagged salmon (n=128) and sea trout (n=86) showed
that salmon mainly migrated directly to their spawning area, while sea trout exhibited
several up- and downstream migrations. Migration speeds was lowered or delayed at steep
sections and was higher (25 kmd-1) later in the migration period compared to early in the
run (8 kmd-1) and negatively correlated with water flow. Salmon and sea trout spawned in
the main stem in the river Vindelälven, 230 km and 60 km upstream, respectively, while sea
trout in the river Piteälven spawned in various tributaries. A majority (90%) of the sea trout
survived after spawning and overwintered in the rivers. These kelts migrated seaward in
spring at water temperatures of 4±6°C whereafter 69% and 25% was lost at power-station
passage in the rivers Vindelälven and Piteälven, respectively.
Genetic differentiation among brown trout with different life histories was high
(FST=0.09) while weak differentiation among sea migrating populations was revealed
(maximum FST of 0.03). There was no correlation between genetic and geographic distance
among all samples while among samples within the Vindelälven such relationship was
significant. Within the Piteälven a subpopulation of sea trout was found in one tributary.
Genetic assignment supported that tagged sea trout was homing to this stream. Despite
longterm stocking of foreign salmon stocks in the river Sävarån mixed-stock analysis were
unable to detect genetic introgression. Likewise, genetic impact of stocking sea trout in the
Sävarån seemed low, however, with overlap in genotypes genetic introgression could not be
ruled out.
Restorations of connectivity and river habitats were hypothesized to positively influence
salmon and sea trout production and gene flow among populations.
¢eywords: spawning migration, genetic structure, homing, genetic assignment, powerstation,
radio tag, stocking, kelt.

MINI-REVIEW: DISTRIBUTION OF THE MEDITERRANEAN MUSSEL MYILUS

GcLLoÄRoVI
CIcLIS (BIVALVIA: MYTILIDAE) AND HYBRIDS IN THE
NORTHEAST PACIFIC
cBSRcC The non-native Mediterranean mussel Mytilus galloprovincialis is broadly established in the
northeast Pacific. Until
recently, the coast north of Humboldt Bay, California, USA, was not considered a major zone of sympatry
and hybridization with the
native sibling species M. trossulus. However, M. galloprovincialis has been introduced in Washington, USA,
and British Columbia,
Canada, for aquaculture, has been collected from ballast water in-bound to Oregon, USA, and is now reported
widely in Puget Sound,
Washington. Here I review published reports of M. galloprovincialis alleles in the Northeast Pacific,
including recent data showing that
these alleles are more widespread and abundant in Washington than previously known. These results indicate
the presence of a major
zone of sympatry and hybridization in Washington waters that may be contiguous with the California zone.
Because M. galloprovincialis
has likely been introduced to the region on multiple occasions via multiple routes, it is unlikely that a sole
source can be
identified. Factors influencing the success and impacts of this now widespread invader remain to be
investigated.
¢ Y WoRS: introduced marine species, hybridization, Pacific Northwest, Mytilus galloprovincialis

Mitochondrial DNA variation in a species with

two mitochondrial genomes: the case of ‰p
 V 



from the Atlantic, the
Mediterraneanand the Black Sea
We have examined mitochondrial DNA (mtDNA) variation in samples of the mussel
‰p
 V 



from the Black Sea, the Mediterranean and the Spanish Atlantic coast
by scoring for presence or absence of cleavage at 20 restriction sites of a fragment of the
COIII gene and at four restriction sites of the 16S RNA gene. This species contains two types
of mtDNA genomes, one that is transmitted maternally (the F type) and one that is transmitted
paternally (the M type). The M genome evolves at a higher rate than the F genome. Normally,
females are homoplasmic for an F type and males are heteroplasmic for an F and an M type.
Occasionally molecules from the F lineage invade the paternal transmission route, resulting
in males that carry two F-type mtDNA genomes. These features of the mussel mtDNA system
give rise to a new set of questions when using mtDNA variation in population studies and
phylogeny. We show here that the two mtDNA types provide different information with
regard to amounts of variation and genetic distances among populations. The F genome
exhibits higher degrees of diversity within populations, while the M genome produces higher
degrees of differentiation among populations. There is a strong differentiation between
the Atlantic and the Black Sea. The Mediterranean samples have intermediate haplotype
frequencies, yet are much closer to the Black Sea than to the Atlantic. We conclude that in this
species gene flow among the three Seas is restricted and not enough to erase the combined
effect of mutation and random drift. In one sample, that from the Black Sea, the majority
of males did not contain an M mtDNA type. This suggests that a molecule of the maternal
lineage has recently invaded the paternal route and has increased its frequency in the
population to the point that the present pool of paternally transmitted mtDNA molecules
is highly heterogeneous and cannot be used to read the population¶s history. This liability
of the paternal route means that in species with doubly uniparental inheritance, the maternal
lineage provides more reliable information for population and phylogenetic studies.
¢| V : Doubly Uniparental Inheritance, mtDNA variation, mussels
||
| !pV|


V||
| "|| |V| p| #
V

Molecular genetic analyses of species boundaries in the sea

Abstract
The tools of molecular genetics have enormous potential for clarifying the nature and age of species
boundaries
in marine organisms. Below I summarize the genetic implications of various species concepts, and review the
results of recent molecular genetic analyses of species boundaries in marine microbes, plants, invertebrates
and
vertebrates. Excessive lumping, rather than excessive splitting, characterizes the current systematic situation
in
many groups. Morphologically similar species are often quite distinct genetically, suggesting that
conservative
systematic traditions or morphological stasis may be involved. Some reproductively isolated taxa exhibit only
small levels of genetic differentiation, however. In these cases, large population sizes, slow rates of molecular
evolution, and relatively recent origins may contribute to the difficulty in finding fixed genetic markers
associated
with barriers to gene exchange. The extent to which hybridization blurs species boundaries of marine
organisms
remains a subject of real disagreement in some groups (e.g. corals). The ages of recently diverged species are
largely unknown; many appear to be older than 3 million years, but snails and fishes provide several examples
of more recent divergences. Increasingly sophisticated genetic analyses make it easier to distinguish allopatric
taxa, but criteria for recognition at the species level are highly inconsistent across studies. Future molecular
genetic analyses should help to resolve many of these issues, particularly if coupled with other biological and
paleontological approaches.

Molecular genetics and the management and

conservation of marine organisms
Abstract
Biochemical and molecular species identification techniques have a broad range of applications in the
management
and conservation of marine organisms. While species boundaries are not always clearly defined,
phylogeneticists
utilise autapomorphic characters to distinguish phylogenetic species. Genetic markers discriminate between
marine
taxa when traditional morphological distinctions are unclear. The applications of these techniques can be
divided
into four general categories. Firstly, compliance enforcement, which often depends on genetic identification
techniques
to enable officials to identify the species to which regulations pertain. Secondly, quality control applications,
to allow for the testing of marine products to guard against fraudulent substitution with less valuable species,
which
is particularly pertinent since processing often obliterates identifiable features. Thirdly, a variety of
applications
to ecological and life-history studies and conservation management are reported. Here, the genetic
identification
techniques of species from cryptic life-cycle stages or of morphologically indistinct species are an
indispensable
tool for marine scientists, conservators and managers. Lastly, the application of genetic techniques for
sourcing
population origin is briefly discussed. The biochemical and molecular techniques applied to species
identification
all exploit phenotypic or genotypic polymorphisms that are sampled using either tertiary level protein based
methods
or primary level DNA based methods. In this review, examples of the applications along with the total
protein,
allozyme, serological, PCR and other DNA based methodologies are briefly described and some generalities
with
regard to their use are presented.

Molecular genetics in fisheries: current and hmre

perspectives
In the 40 years since the introduction of starch gel electrophoresis, genetic polymorphisms
have been increasingly studied in fish. In many cases such polymorphisms
have been used as markers to draw wider inferences on the genetics of the unit of study
rather than simply involving the polymorphic locus itself. While initial studies involved
proteins such as haemoglobin and transferrin, attention quickly turned to enzymatic
proteins (allozyme variation). In the past decade, increasing emphasis has been given to
direct DNA examination, first mitochondrial DNA and then as molecular techniques
developed, nuclear DNA. Technological developments leading to new genetic
approaches have generally come about from studies of organisms other than fish although
often fine-tuning of techniques has been necessary for application to fish. Fish geneticists
require to keep abreast of genetic developments in humans, laboratory mammals,
rosophila and other model organisms. This can avoid wasteful 'reinvention of the
wheel' as well as pitfalls of interpretation. There are occasions when this approach can be
misleading. As pointed out by Park and Moran (1994), the mtDNA D-loop has been
targeted for sequencing studies because it is highly variable in mammals, but in fish such
as the salmonids it shows little variability. However, too often it is apparent in
manuscripts that the authors have little familiarity with the literature outside their own
topic. It is also often apparent that authors have limited knowledge of theoretical
population genetics, a greater appreciation of which would have improved their
experimental design and analysis or, in some cases, would have indicated that their goal
was unrealistic.
One of the first goals of molecular genetics work in fish was to find stock-specific
markers. In many cases, while interpopulation differences in allozyme frequency have
been revealed, fixed or high-frequency diagnostic alleles have not been found. In spite of
this, many workers continue to search for the 'holy grail' of the perfect stock marker by
eagerly embracing each new technical development. In the Northern Hemisphere many
populations of freshwater and anadromous species have only existed since the end of the
last Ice Age, a period of some 10000 to 15000 years. An elementary consideration of
population genetic models shows that substantial differences in allele frequencies will not
occur in this time period except in very small isolated populations or as a result of
selection.
Substantial debate has taken place over the past 25 years on whether protein
polymorphisms are neutral or subject to natural selection. There is increasing evidence
for selection operating on at least some protein-coding loci. Also evidence is now
appearing that microsateUite 'allele' size may affect gene regulation (Epplen et aL, 1993)
and such polymorphisms may not be selectively neutral. All markers are potentially

Molecular Markers, Natural History,and Conservation of Marine Animals

Molecular genetic techniques have found broad utility in modern marine ecology, and applications continue
to grow. atabases of 
c sequences
now permit iwtiexpertí to identify eggi ami larval stages of many marine atiirnah that were prevmisly
mysteries. Molecular identifications officUcottccteti
organisms ami tissues tire used lo help iisscss popuhitioii conncdivily, iiivcsügale mariiw food wchs, and
identify marketed commodities.
cdvances in technology already include prototype development of in situ robotic instrumentation for sampling
and molecular identification of
animal larvae. Smdies of population connectivity, once limited to a few gene loci, are slowly giving way to
new genomic arrays of markers and
high-throughput methodologies for scoring genotypes. Äopulation genetic theory is providing new
computational techniques to assess patterns of
population structure, estimate effective population sizes, and infer aspects of demographic history. In this
article I review a subset of recent work in
this growing area of molecular marine ecology.
¢eywords: molecular ecology, population structure, species identification, marine ecology, historical
demography

Molecular population genetics of male and female mitochondrial

genomes in European mussels Mytilus
Abstract The doubly uniparental system of mitochondrial
inheritance (DUI) is best known in marine mussels
Mytilus. Under DUI there are two types of mitochondrial
DNA (mtDNA). The female type (F) is transmitted to
o spring of both genders and the male type (M) exclusively
to sons; consequently two distinct mtDNA lineages exist.
The M lineage evolves under more relaxed selection than
the F lineage resulting in higher polymorphism within the
M lineage. Though this polymorphism is expected to make
inferences on Wne population structure easier using M
instead of F data, no comprehensive comparative data exist
to support this claim. We sequenced a 1,205 bp fragment of
M and F mtDNA comprising parts of the CoIII and
2
genes, and analysed 204 individuals representing three
Mytilus species: M. edulis, M. galloprovincialis and
M. trossulus from 13 European sampling sites. A clear distinction
between Mediterranean and Atlantic populations
was found with both M and F data, but much better geographic
di erentiation was found within the Atlantic using
F rather than M data. In particular, Atlantic M. galloprovincialis
can be di erentiated from Atlantic M. edulis, and further
subdivision of Atlantic M. edulis is possible using the
F data but not the M data. Multiple tests of selection were
carried out to attempt to explain this paradox. We concluded
that the overall pattern of polymorphism is consistent
with strong purifying selection; not only is this
selection relaxed in the M lineage in comparison with the F
lineage, but it is also more frequently interrupted by periodic
selective sweeps within the M lineage.

Morphostructure and evolution of submarine canyons across an active margin: Cook

Strait sector of the Hikurangi Margin, New Zealand
The Cook Strait sector of the Hikurangi Margin contains several canyons including New Zealand's largest
canyon, the multi-branched shelf-indenting Cook Strait Canyon. The morphology of the canyons reflects the
transition from subduction related thrust faulting to oblique collision and strike±slip faulting. High resolution
EM300 multibeam and multichannel seismic reflection data reveal: i) widespread, deep-seated bedrock
landsliding as a principal control on canyon enlargement; ii) a retrogressive entrenchment of tributary
submarine catchments in response to a base-level perturbation which has rejuvenated canyons inferred to
have been inactive as top to bottom sediment conduits since the last glaciation; and iii) the control of
structurally generated bathymetric relief on both the routing of sediment pathways and the erosion of
intercanyon
slopes. The models of canyon evolution demonstrated here have widespread implications for canyon
development and evolution on other tectonically actively continental margins

Most species are not driven to extinction before genetic factors impact them
There is controversy concerning the role of genetic factors in
species extinctions. Many authors have asserted that species are
usually driven to extinction before genetic factors have time to
impact them, but few studies have seriously addressed this issue.
If this assertion is true, there will be little difference in genetic
diversity between threatened and taxonomically related nonthreatened
species. We compared average heterozygosities in 170
threatened taxa with those in taxonomically related nonthreatened
taxa in a comprehensive metaanalysis. Heterozygosity was
lower in threatened taxa in 77% of comparisons, a highly significant
departure from the predictions of the no genetic impact
hypothesis. Heterozygosity was on average 35% lower (median
40%) in threatened taxa than in related nonthreatened ones. These
differences in heterozygosity indicate lowered evolutionary potential,
compromised reproductive fitness, and elevated extinction
risk in the wild. Independent evidence from stochastic computer
projections has demonstrated that inbreeding depression elevates
extinction risk for threatened species in natural habitats when all
other threatening processes are included in the models. Thus, most
taxa are not driven to extinction before genetic factors affect them
adversely.

Naturally low seston concentration and the net energy balance

of the greenshell mussel (Ä|V


) at Island Bay,
Cook Strait, New Zealand
Abstract This paper describes an investigation
of the physiological energetics of the New Zealand
greenshell mussel, Äerna canaliculus (Gmelin,
1791), which is aimed at determining if mussels
are absent from many shores of Cook Strait as a
consequence of a negative energy balance resulting
from ambient low seston quantity and quality.
Seston characteristics and mussel physiological
functions were measured under ambient summer
conditions at Island Bay, a site in Cook Strait.
Estimates of total particulate matter (TPM in
mg litre-1), particulate organic matter (POM in
mg litre-1), and particulate organic carbon (POC in
|ig litre-1) were low but of a similar magnitude to
values reported for many comparable temperate
regions. However, seston % organic matter (% OM)
values were consistently low (<25%) and resulted
in negative net absorption efficiency (AE) values
and concomitant negative scope for growth (SFG
= net energy balance) values. We suggest that the
ongoing costs of energy loss associated with extraand
intracellular digestion (termed metabolic faecal
loss) are greater than the energy derived from seston
M99061
Received 29 october 1999; accepted 20 ecember 2000
of such low organic matter. Our data indicate that
ambient levels of seston % OM of 25% are
insufficient to promote a positive net energy balance
in Ä. canaliculus, and as such probably play a major
role in explaining the almost complete absence of
mussels from many Cook Strait shores.
Keywords greenshell mussel; Äerna canaliculus;
physiological energetics; seston; scope for growth;
net energy balance; ecological distribution

New Zealand coastal system boundaries,

connections and management
Abstract:
Understanding coastal boundaries, connections and drivers of landscape change
is integral to effective coastal planning and management. This concept is explored here
through case studies representing two very different New Zealand systems: embayed sand
beaches in eastern and western open-coast settings; and mixed sand and gravel coast river-mouth
lagoons. When framed within a resource and environmental management context these
studies indicate that national recognition of the dynamic and interactive nature of coastal
environments is a relatively new and amorphous phenomenon in New Zealand and, as such,
has been ineffective in driving integrated regional management practices and sustainable
coastal outcomes.
Key words:
beach connectivity, catchments, coastal systems, lagoons, sediment bypassing,
wetlands.

Nutrient Biogeochemistry of the Coastal Zone

The coastal seas are one of the most valuable and vulnerable
of Earth¶s habitats. Significant inputs of nutrients to the
coastal zone arrive via rivers, groundwater, and the atmosphere.
Nutrient fluxes through these routes have been increased
by human activity. In addition, the N:P:Si ratios of
these inputs have been perturbed, and many coastal management
practices exacerbate these perturbations. There is
evidence of impacts arising from these changes (in phytoplankton
numbers and relative species abundance, and deepwater
oxygen declines) in areas of restricted water exchange.
Elsewhere, the nutrient fluxes through the coastal zone appear
to be still dominated by large inputs from the open ocean,
and there is little evidence of anthropogenic perturbations.

On the roles of selection, mutation and drift in the evolution of mitochondria1 DNA diversity in British My
tilus edulis (M ytilidae ; Mollusc a)populations
Species of the marine mussel genus ‰
possess two distinct mtDNA genomes. The F
genome is inherited maternally, the M genome is inherited paternally. This mode of
inheritance provides a unique opportunity for studying evolutionary forces and phylogeny
within the genus, because patterns of variation at the two genomes can be cross compared.
Previous studies of evolutionary forces acting on Mytilus mtDNA have been carried out by
analysing sequence data from relatively small numbers of individuals, often comparing
different species. In the present study we use an RELP approach to study population variation
in a single species Mytilus edulzi from five localities in Britain. These localities lie within an area
in which previous allozyme studies had failed to detect significant geographic differentiation. In
the present study, significant mtDNA differentiation is observed for both genomes both for
haplotype frequencies and for nucleotide divergence. Nucleotide diversity within and divergence
between populations is greater for the M genome consistent with a higher mutation
rate and/or lower purifying selection for this genome. Application of the Ewens-Watterson
test provides evidence for excess µhomozygosity¶ much greater in magnitude for the F genome
consistent with the stronger action of purifying selection on this genome. The distribution
of painvise nucleotide divergence values within populations was compared with theoretical
distributions obtained by computer simulation. Much better fit of the empirical results is
observed to a purifying selection model than to an equilibrium neutral or population
expansion model. The results are in agreement with those of previous studies of DNA
sequences, adopting different tests, in providing evidence for the action of purifying selection
on both genomes but of greater intensity on the F genome. It is concluded that the results
are explained well by the nearly neutral theory of evolution giving important roles to selection,
drift and mutation as causes of the observed patterns of variation.

Origin of the antitropical distribution pattern in marine mussels (Mytilus spp.): routes and timing of
transequatorial migration
Abstract Many marine species, including mussels in the
Mytilus edulis species group (i.e. M. edulis L., M. gal-
loprovincialis Lamarck, and M. trossulus Gould), have
an antitropical distribution pattern, with closely related
taxa occurring in high latitudes of the northern and
southern hemispheres but being absent from the tropics.
We tested four hypotheses to explain the timing and
route of transequatorial migration by species with anti-
tropical distributions. These hypotheses yield di erent
predictions for the phylogenetic relationship of southern
hemisphere taxa relative to their northern counter-parts.
The three Mytilus species were used to test these hy-
potheses since they exhibit a typical antitropical distri-
bution and representative taxa occur in both the Paci®c
and Atlantic. Two types of mtDNA lineages were found
among populations of mussels collected from the
southern hemisphere between 1988 and 1996; over 90%
of the mtDNA lineages formed a distinct subclade
which, on average, had 1.4% divergence from haplo-
types found exclusively in northern Atlantic populations
of M. galloprovincialis. These data indicate that southern
hemisphere mussels arose from a migration event from
the northern hemisphere during the Pleistocene via an
Atlantic route. The remainder of the southern hemi-
sphere lineages (<10%) were very closely related to
mtDNA haplotypes found in both M. edulis and
M. galloprovincialis in the northern hemisphere, sug-
gesting a second, more recent migration to the southern
hemisphere. There was no evidence that southern
hemisphere mussels arose from Paci®c populations of
mussels.

Paradigm shifts in marine fisheries genetics: ugly hypotheses

slain by beautiful facts
Abstract
By providing new approaches to the investigation of demographic and evolutionary
dynamics of wild populations, molecular genetics has led to fundamental changes in
our understanding of marine ecology. In particular, genetic approaches have
revolutionized our understanding in three areas: (i) most importantly, they have
contributed to the discovery of extensive genetic population structure in many
marine species, overturning the notion of large, essentially homogenous marine
populations limiting local adaptation and speciation. (ii) Concomitant differences in
ecologically important traits now indicate extensive adaptive differentiation and
biocomplexity, potentially increasing the resilience to exploitation and disturbance.
Evidence for rapid adaptive change in many populations underlies recent concerns
about fisheries-induced evolution affecting life-history traits. (iii) A compilation of
recent published research shows estimated effective population sizes that are 2±6
orders of magnitude smaller than census sizes, suggesting more complex recruitment
dynamics in marine species than previously assumed. Studies on Atlantic cod are
used to illustrate these paradigm shifts. In our synthesis, we emphasize the
implications of these discoveries for marine ecology and evolution as well as the
management and conservation of exploited marine fish populations. An important
implication of genetic structuring and the potential for adaptive divergence is that
locally adapted populations are unlikely to be replaced through immigration, with
potentially detrimental consequences for the resilience to environmental change ±
a key consideration for sustainable fisheries management.
Keywords Atlantic cod, effective population size, local adaptation, marine fishes,
population connectivity, population structure

Parasites and Symbionts From Mytilus galloprovincialis (Lamark, 1819)

(Bivalves: Mytilidae) of the Aveiro Estuary Portugal
ABSTRACT: The primary aim of the present study was to conduct a 1-yr
parasitological survey of a Mytilus galloprovincialis mussel population
from the Aveiro Estuary, Portugal. In addition, we attempted to assess the
host response to parasites by examining host histopathology, including an
evaluation of hemocyte infiltration and parasite encapsulation. The
parasites present (prevalence) included the following: 1 protozoan,
Nematopsis sp. (70%); 1 turbellarian, Urastoma cyprinae, (39%); 2
trematodes, Diphtherostomum sp. (58%) and Prosorhynchus crucibulum
(0.3%); 3 crustaceans, Bathylaophonte azorica (0.3%); and 2 species of
Mytilicola sp. (3.5%), M. intestinalis and M. orientalis. Highest
prevalences for the most abundant species occurred in summer and
autumn. Histological sections of the mantle of infected mussels revealed a
marked reduction in the reproductive tissue, indicating that P. crucibulum
invades the mussel and promotes a severe damage to its reproductive
capacity.

Patterns of polymorphism and gene flow of genderassociated

mitochondrial DNA lineages in European
mussel populations
Abstract
Mussels of the genus ‰p
have two types of mitochondrial DNA (mtDNA). The M
type is transmitted paternally and the F type is transmitted maternally. RFLP analysis is
used to assess phylogenetic relationships and nucleotide diversity and divergence for
both mtDNA genomes in European populations of ‰ | 
and Atlantic and
Mediterranean forms of ‰  V 



 Ten restriction endonucleases were used to
assay variation in regions of the and
genes for a total of 77 individuals. F and
M genomes show a concordant phylogenetic split into two major divergent clades, one
specific to Mediterranean ‰  V 



and the other containing haplotypes from
the three taxa. For both genomes, the geographical distribution of mtDNA variation
suggests: (i) extensive levels of mtDNA introgression; (ii) asymmetric mtDNA gene flow
from Atlantic to Mediterranean populations; and (iii) recurrent historical hybridization
events. Significantly higher mtDNA diversity and divergence are observed for the M than
F genome in all three ‰p
taxa, although the evolutionary forces responsible for these
differences cannot be resolved. The extensive mtDNA gene flow between European
‰p
taxa conflicts with the restricted mtDNA introgression observed in American
musselsimplying geographical variation in the nature of nuclear/mtDNA interactions
regulating biparental inheritance.
¢| V : asymmetric introgression, diversity, heteroplasmy, mitochondrial DNA, ‰p
,
paternal inheritance
||
| D|| |V""$V|


V||
| %| VV""!| p| D| VV""!

PCR based nuclear and mtDNA markers and shell morphology as an approach to study the taxonomic status
of the Chilean mussel mytilus chilensis

PCR Technique for Identification of Mussel Species

Random amplified polymorphic DNA (RAPD) analysis has been applied to the identification of four
mussels species: Mytilus edulis, Mytilus chilensis, Mytilus galloprovincialis, and Perna canaliculus.
Amplifications of DNA from mussel were carried out using random primers. The most distinctive
bands
were then isolated, cloned, and sequenced to design specific primers. Finally, DNA from different
mussels was amplified with these specific primers, and results allow genetic identification of M.
galloprovincialis from the rest of the mussel species.
KEYWORDS: Mussels; Mytilus; RAPD; species identification

PCR-based methods for fish and fishery products authentication

This work intends to provide an updated and extensive overview
on the PCR-based methods for fish and fishery products
authentication. arious techniques such as PCR-sequencing,
Multiplex-PCR, PCR-RFLP, PCR-SSCP, RAPD, Real-Time PCR
and PCR lab-on-a-chip are described and discussed. Moreover,
commercial PCR kits for fish species identification are
provided in this review. These methods could allow consumers
protection against fraudulent practices in the fishery industry
and enforce national and trans-national laws and regulations

Perishing blue mussels and invading aliens ± What are the reasons for ecological turnover in the
Wadden Sea ?

Phenotypic and genotypic population

differentiation in the bivalve mollusc crctica
islandica: results from RAPD analysis

ABSTRACT: The bivalve mollusc Vp



is an important commercial species with a
presumed
panmictic dispersal strategy, and is widely distributed throughout much of the soft sediment benthos
of
the North Atlantic continental shelf. Previous studies have shown that there can be gross
morphological
differences between populations, which has led to the suggestion that this may be reflected in
genotype.
So far, only one study has examined the population genetics of this species, revealing, depending
upon location, that populations are only genetically distinct at a macroscale (>1000 km), thereby
supporting the assumption of panmixia. Examination of the quantitative morphological traits
between
5 different populations (4 North Sea and 1 Canadian) determined that all populations could be
readily
identified from their unique morphologies (shapes/growth patterns) derived from 2 factors resulting
from
a principal components analysis. Investigation, using random amplified polymorphic DNA (RAPD)
analysis, into the genetics of the populations, to indirectly assess whether the observed phenotypic
differences could be related to potential differences in genotype, revealed that all populations were
genetically distinct (between populations overall phiST â 0.662) from each other even at a
microscale
(<25 km) (phiST â 0.719). However, no correlation between genetic distance, morphological
distance
and/or geographical distance, whatever metric was applied, could be obtained. It is concluded that
although phenotypic differences can be used to distinguish between populations of  


, it
should
not and cannot be used to infer genetic differences in the absence of further studies. What is
interesting
is that the results from the genetic analysis dispute the presumption that the dispersal patterns of  



is in any shape or form panmictic. This has very important consequences for the
management
of the species. The results are discussed with reference to the possible mechanisms responsible for
maintaining a high degree of genetic diversity between the populations that were studied.
KEY WORDS: Vp



· Dispersal · Genotypic · Panmixia · Phenotypic · RAPD

31P-nuclear-magnetic-resonance study of muscles from Mytilus edulis

Phosphorus-31 nuclear magnetic resonance (NMR) spectra were recorded from freshly excised and resting
anterior byssus rectractor muscles of the mussel Mytilus edulis.
The absolute concentrations of phosphometabolites measured by NMR compare well with the values obtained
by a biochemical method. Quantitative measurements were achieved in several minutes by applying to the
observed
NMR signals a correction taking the saturation effects into account.
The time evolution of the phosphometabolite concentrations reveals that the hydrolysis of phosphoarginine
is a first-order reaction producing inorganic phosphate, whilst the adenosine triphosphate level remains
constant
for more than 10 h.
The phosphoarginine hydrolysis rate varies as a function of the season and reaches a maximum during the
reproduction period of the mussel. This increase in phosphoarginine consumption could be bound up with the
higher excitability of the muscles during spring. The activation energy of the phosphoarginine hydrolysis
reaction
also depends on the season and the difference between the value determined in winter and that measured in
spring
is explained by a modification of the mode of action or of the proportions of the enzymes involved in the
muscular
metabolism.

Population dynamics and genetic differentiation in

the bivalve mollusc cbra tenuis: aplanic dispersal

ABSTRACT: The bivalve mollusc  Vp|


is an aplanic (directly developing) species occupying
a
discontinuous (fragmented) habitat in the high intertidal area of mudflats. In view of its mode of
reproduction and habitat, populations of  p|

should exhibit temporal stability and be
genetically
dissimilar. Examination of the population dynamics of  p|

, at 2 sites in the Dutch Western
Wadden Sea over the last 29 yr, has revealed that population densities fluctuate wildly from year to
year, and that there have been 2 µapparent¶ local extinction events, one of which lasted for 3 yr.
Investigation
into the population genetics of  Vp|

in the Dutch Western Wadden Sea, using random
amplified polymorphic DNA (RAPD) analysis, both at the macro (*2 km) and microscale (*30 m),
determined that 6 of the 7 studied populations formed 3 groups that were genetically homogenous
within a group, but genetically distinct from each other. This included a group pair where the
distance
of geographical separation was å3 km. The 7th population was genetically distinct from all
other population groups. While there is some degree of genetic differentiation among populations,
given both the population genetics and dynamics results, it is evident that dispersal has occurred
among some populations.
KEY WORDS: Aplanic ·  Vp|

· Dispersal · Metapopulation · Panmixia · Population dynamics ·
RAPD · Reproduction

ÄÄ
 


 &
ĉ 
u Äu '

 
uº  

POPULATION GENETICS, DEMOGRAPHIC CONNECTIVITY, AND THE

DESIGN OF MARINE RESERVES
cbstract. Genetic analyses of marine population structure often find only slight geographic
differentiation in species with high dispersal potential. Interpreting the significance
of this slight genetic signal has been difficult because even mild genetic structure implies
very limited demographic exchange between populations, but slight differentiation could
also be due to sampling error. Examination of genetic isolation by distance, in which close
populations are more similar than distant ones, has the potential to increase confidence in
the significance of slight genetic differentiation. Simulations of one-dimensional stepping
stone populations with particular larval dispersal regimes shows that isolation by distance
is most obvious when comparing populations separated by 2±5 times the mean larval
dispersal distance. Available data on fish and invertebrates can be calibrated with this
simulation approach and suggest mean dispersal distances of 25±150 km.
Design of marine reserve systems requires an understanding of larval transport in and
out of reserves, whether reserves will be self-seeding, whether they will accumulate recruits
from surrounding exploited areas, and whether reserve networks can exchange recruits.
Direct measurements of mean larval dispersal are needed to understand connectivity in a
reserve system, but such measurements are extremely difficult. Genetic patterns of isolation
by distance have the potential to add to direct measurement of larval dispersal distance
and can help set the appropriate geographic scales on which marine reserve systems will
function well.
¢ey words: connectivity; dispersal; isolation by distance; larvae; population structure.

Ä

‰ &



‰


 ‰
º
 

POPULATION GENETICS, DEMOGRAPHIC CONNECTIVITY, AND THE

DESIGN OF MARINE RESERVES

PROPERTY RIGHT AND NATURAL REOURCE MANAGEMENT IN DEVELOPING COUNTRIES

Protected marine reserves as ®sheries management tools:

a bioeconomic analysis
This paper develops a dynamic computational bioeconomic model with the objective of assessing protected
marine reserves as
®sheries management tools. Data on the North East Atlantic cod stock are used to determine the
bioeconomically optimal size
of a marine reserve for the Barents Sea cod ®shery, as a function of the net transfer rate between the protected
and unprotected
areas of the marine habitat. The single agent model developed, allows for the occurrence of a shock to the
system in the form
of severe recruitment failure in the non-protected area. Two key results emerge from the study. First,
establishment of marine
reserves are bioeconomically bene®cial when net transfer rates for cod are `reasonably' high and reserve sizes
are large: large
reserves provide good protection for the stock in the face of the shock, while high transfer rates make the
protected ®sh
available for harvesting after the shock has occurred. Further, optimally chosen reserve size when net transfer
rates are high,
also mitigates against biological losses. Second, when net transfer rates are low, the establishment of marine
reserves does not
mitigate against losses in the discounted economic rent, while they tend to be ef®cient in mitigating against
biological losses.
5 1998 Elsevier Science B.V. All rights reserved.
Keywords: Uncertainty; Net transfer rates; No-®shing areas; Biological; Economic; Trade-offs

Range-wide genetic homogeneity in the California sea

mussel (Mytilus californianus): a comparison of allozymes, nuclear DNA markers, and mitochondrial DNA
sequences

We tested for genetic differentiation among six populations of California sea mussels
(Mytilus californianus) sampled across 4000 km of its geographical range by comparing
patterns of variation at four independent types of genetic markers: allozymes, single-copy
nuclear DNA markers, and DNA sequences from the male and female mitochondrial
genomes. Despite our extensive sampling and genotyping efforts, we detected no significant
differences among localities and no signal of isolation by distance suggesting that M.
californianus is genetically homogeneous throughout its range. This concordance differs
from similar studies on other mytilids, especially in the role of postsettlement selection
generating differences between exposed coastal and estuarine habitats. To assess if this
homogeneity was due to M. californianus not inhabiting estuarine environments, we
reviewed studies comparing allozymes with other classes of nuclear DNA markers.
Although both types of markers gave broadly consistent results, there was a bias favouring
studies in which allozymes were more divergent than DNA markers (nine to three) and a
disproportionate number of these cases involved marine taxa (seven). Furthermore, allozymes
were significantly more heterogeneous than DNA markers in three of the four studies that
sampled coastal and estuarine habitats. We conclude that the genetic uniformity exhibited
by M. californianus may result from a combination of extensive gene flow and the lack of
exposure to strong selective gradients across its range.
¢| V : allozymes, female mitochondrial DNA, gene flow, male mitochondrial DNA, natural
selection, population structure, scnDNA markers
||
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Recent developments in conservation genetics

Because of the new molecular genetics information from various genome projects, new applications and
insights for genetics
studies in endangered species are forthcoming. Neutral variants are generally used for conservation
applications and estimating
evolutionary parameters, and with highly variable loci, many more markers, or extensive sequence data, these
approaches should
become much more informative. Detrimental and adaptive variation is of importance in conservation genetics
but identification
and characterization of such variation is more difficult. Neutral variants might be used to identify adaptive
variants but the
overlay of different mutational processes and selective regimes suggests that great caution should be used in
making such
predictions. Examples in endangered species discussed below are (1) estimation of long-term effective
population size using
neutral markers in three fishes of the lower Colorado River; (2) genetic restoration of the Florida panther by
the introduction of
Texas cougars; (3) impact of pathogens and adaptive variation on the winter-run chinook salmon; (4)
examination of the adaptive
variation for a major histocompatibility complex (MHC) gene in red wolves. Although these examples are all
from animals, the
techniques and approaches used should prove equally useful in endangered plant species.
5 2004 Elsevier B.V. All rights reserved.
Keywords: Effective population size; Florida panthers; Inbreeding depression; Lethals; Neutrality; MHC; Red
wolves; Winter-run chinook
Salmon

Regional patterns of microsatellite variation in Mytilus

galloprovincialis from the Iberian Peninsula

Abstract The Almerı a-Oran Oceanographic Front
(AOOF) has been proposed as an effective marine barrier
to gene flow between the NE Atlantic Ocean and the
Mediterranean Sea for several species. Previous studies
using allozymes and mitochondrial DNA have reported a
scenario of secondary intergradation between populations
of Mytilus galloprovincialis from those basins, with the
allelic frequencies of some loci showing abrupt clinal
patterns across the AOOF. In this study, we aimed at
testing the congruence between six neutral polymorphic
microsatellites versus previous data on allozymes and
mtDNA-RFLPs, at depicting the population structure of
this species in the Iberian Peninsula. Microsatellite genotyping
was scored on 17 samples of mussels collected in
the Iberian coast, including some areas not sampled before.
Microsatellites exhibited larger intrabasin diversity
(FSC = 1.72%, HE _ SD ¼ 0:772 _ 0:154), similar interbasin
differentiation (FCT = 2.81%) and fewer allelic
clines than allozymes or mtDNA haplotypes. These results
fully support the scenario of secondary intergradation with

Response to Comments on
³Impacts of Biodiversity Loss on
Ocean Ecosystem Services´
We show that globally declining fisheries catch trends cannot be explained by random processes
and are consistent with declining stock abundance trends. Future projections are inherently
uncertain but may provide a benchmark against which to assess the effectiveness of conservation
measures. Marine reserves and fisheries closures are among those measures and can be equally
effective in tropical and temperate areas²but must be combined with catch-, effort-, and gear
restrictions to meet global conservation objectives.

Restocking and stock enhancement of coastal fisheries:

Potential, problems and progress
The demand for fish is expected to rise substantially by 2020. Although aquaculture must provide much of the
additional fish, it remains to
be seen whether restored or enhanced capture fisheries can also help fill the projected gap in supply. The key
challenges for capture fisheries
involve reducing fishing effort, removing excess fishing capacity and building the institutional arrangements
needed to restore spawning
biomass to more productive levels, and to reverse degradation of the supporting habitats. Two interventions,
based largely on hatchery
technology, have the potential to reduce the time needed to rebuild some severely over-exploited fisheries, or
improve the productivity of
other µhealthy¶ fisheries. These interventions are µrestocking¶, which involves releasing cultured juveniles to
restore spawning biomass to
levels where the fishery can once again support regular harvests, and µstock enhancement¶, which involves
release of cultured juveniles to
overcome recruitment limitation. However, despite the potential of these interventions, few restocking and
stock enhancement programmes
have met expectations. The main problems have been a pre-occupation with bio-technical research at the
expense of objective analysis of the
need for the intervention, and failure to integrate the technology within an appropriate management scheme
that has the participation and
understanding of the users. The papers presented at the Special Symposium on this subject at the Seventh
Asian Fisheries Forum provide
a series of valuable lessons to guide objective assessment of the potential for restocking and stock
enhancement. They also show how to
implement these interventions responsibly and effectively where they are deemed to add value to other forms
of management. Above all,
these studies demonstrate that restocking and stock enhancement programmes are applied in complex human±
environment systems, involving
dynamic interactions between the resource, the technical intervention and the people who use it.
Crown Copyright © 2006 Published by Elsevier B.V. All rights reserved.
¢eywords: Restocking; Stock Enhancement; Fisheries management; Fisheries potential; Spawning biomass;
Recruitment limitation

Scaling properties in landscape patterns: New Zealand experience

Abstract
In this paper we present a case study of spatial structure in landscape patterns for the North and South Islands
of New Zealand. The aim was to characterise quantitatively landscape heterogeneity and investigate its
possible
scaling properties. The study examines spatial heterogeneity, in particular patchiness, at a range of spatial
scales, to
help build understanding on the effects of landscape heterogeneity on water movement in particular, and
landscape
ecology in general.
We used spatial information on various landscape properties (soils, hydrogeology, vegetation, topography)
generated from the New Zealand Land Resource Inventory. To analyse this data set we applied various
methods
of fractal analyses following the hypothesis that patchiness in selected landscape properties demonstrates
fractal
scaling behaviour at two structural levels: (1) individual patches; and (2) mosaics (sets) of patches.
Individual patches revealed scaling behaviour for both patch shape and boundary. We found self-affinity in
patch shape with Hurst exponent ufrom 0.75 to 0.95. We also showed that patch boundaries in most cases
were
self-similar and in a few cases of large patches were self-affine. The degree of self-affinity was lower for finer
patches. Similarly, when patch scale decreases the orientation of patches tends to be uniformly distributed,
though
patch orientation on average is clearly correlated with broad scale geological structures. These results reflect a
tendency to isotropic behaviour of individual patches from broad to finer scales. Mosaics of patches also
revealed
fractal scaling in the total patch boundaries, patch centers of mass, and in patch area distribution. All these
reflect a
special organisation in patchiness represented in fractal patch clustering. General relationships which
interconnect
fractal scaling exponents were derived and tested. These relationships show how scaling properties of
individual
patches affect those for mosaics of patches and vice-versa. To explain similarity in scaling behaviour in
patchiness
of different types we suggest that the Self-OrganisedCriticality concept should be used. Also, potential
applications

Scope for growth of Mytilus galloprovincialis (Lmk., 1819)

in oligotrophic coastal waters (Southern Tyrrhenian Sea, Italy)
Abstract The µscope for growth¶ (SFG) tool was used to
study the growth performance of cultivated populations of
Mytilus galloprovincialis (Lmk., 1819) in an oligotrophic
area of the Southern Mediterranean Sea. The study was
carried out between 1993 and 1996 by using data from four
seasonal oceanographic cruises and from growth experiments.
Water samples were collected and analysed for total
suspended matter (TSM), particulate organic carbon (POC)
and nitrogen (PON), particulate lipids, proteins and carbohydrates
and chloropigments. The sum of the carbon
equivalents of carbohydrates, proteins and lipids is indicated
as the total biopolymeric particulate organic carbon
(BPC) and was converted into a unit of energy in order to
calculate the SFG of a theoretical mussel of 5 cm length. In
order to test the performance of mussel growth at two
depths (5 and 15 m water depth), mussel body size [as ash
free dry weight (AFDW)] and the actual concentrations
of BPC were used to calculate the monthly SFG using
the physiological energetic relationships suggested in the
current literature. Data from the field cruises led us to
characterise the study site as ultra-oligotrophic (annual
average of chloropigment concentration approximately
0.5 lg L-1). SFG calculations allowed us to identify a site
where mussels grown successively were found to reach a
commercial size in approximately 12 months. The good
agreement obtained between energetic response and subsequent
production response suggests that the available
energy from particulate food could be fully available for
organic production for maintaining µµproportionate¶¶ growth
trajectories, even in a ultra-oligotrophic system.

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Settlement, growth and production of the mussel

Mytil us gallopro vin cialis
ABSTRACT: Abundance, growth, survival and production of Mytilus galloprovincialis Lamk. were
investigated in a subtidal bed on the muddy bottom of a deltaic lagoon of the Adriatic coast (Italy) from
1977 to 1979. Observations on recruitment timing were integrated by checking larval settlement on
semiartificial substrata during 1980. Reconstruction of the cohort composition of the mussel-bed
population was derived from size-class analysis of samples. The Bertalanffy growth curve was fitted on
size-class data. Incorporating temperature as day-degrees into the length-growth curve, and using the
results of lengthldry weight conversions, estimates were made of seasonal variations in weight.
Mortality rates were estimated from density variations of cohorts. Settlement shows a fairly well
defined seasonal pattern with a May-June peak, following the main late winter spawning of mussel
populations of that region. Individual length growth is rapid, reaching 50.0 mm in about 14.5 mo after
settlement. Weight growth shows large seasonal variations mainly due to winter spawning and
starvation. Mortality rates are higher for old, larger mussels, year round, and for all specimens during
spring-summer. Annual production, starting from 0' recruits surviving in autumn after settlement, was
estimated from 0.30 to 0.53 kg m-' of dry flesh weight. It is highly probable that both growth and
production benefit from abundant food in the environment but are hindered mainly by the excessive
amount of suspended inorganic detritus coming from the deltaic river branches, which

Sharp genetic breaks among populations of u p (
 |(Stomatopoda) indicate limits to

larval transport:patterns, causes, and consequences
Abstract
To help stem the precipitous decline of coral reef ecosystems world-wide, conservation
efforts are focused on establishing interconnected reserve networks to protect threatened
populations. Because many coral reef organisms have a planktonic or pelagic larval dispersal
phase, it is critical to understand the patterns of ecological connectivity between
reserve populations that result from larval dispersal. We used genetics to infer dispersal
patterns among 24 Indo-West Pacific populations of the mantis shrimp, u p (

|. Contrary to predictions of high dispersal facilitated by the strong currents of the
Indonesian throughflow, mitochondrial DNA sequences from 393 individuals displayed
striking patterns of regional genetic differentiation concordant with ocean basins isolated
during periods of lowered sea level. Patterns of genetic structuring indicate that although
dispersal within geographical regions with semicontiguous coastlines spanning thousands
of kilometres may be common, ecologically meaningful connections can be rare among
populations separated by as little as 300 km of open ocean. Strong genetic mosaics in a
species with high dispersal potential highlight the utility of genetics for identifying regional
patterns of genetic connectivity between marine populations and show that the assumption
that ocean currents will provide ecological connectivity among marine populations must
be empirically tested in the design of marine reserve networks.
¢| V : dispersal, genetics, larvae, marine, reserves, Stomatopod
||
| %V|


V||
| D|| |V| p| D|| |V

Shore-level induced variations in condition and feeding of the mussel Ä|V



from the
east coast of the South Island, New Zealand
Abstract Mussels (Äerna canaliculus) (Gmelin,
1791) collected from mid and low tide rocky platforms
along the east coast of the South Island of New
Zealand differed in dry weight condition index between
shore levels. Mussel condition was c. 15%
lower at mid tide level than the low tide level and
there was greater variation between shore level than
between sites. Feeding experiments were conducted
at 15°C with mussels collected from mid and low
tide levels using Isochrysis galbana as the food.
Clearance rate depended upon body size, shore level,
and season. During summer clearance rates of mid
and low tide mussels were similar. However in winter,
increased filtration rates were recorded in mussels
from the mid tide level compared with those
from the low tide. In addition, for mussels from both
shore levels, winter rates were higher than those
recorded in the summer. Nitrogen excretion by
mussels also showed seasonal and shore level differences.
High values for ammonia excretion of
mussels collected from the mid tide during winter
suggests they utilise metabolic reserves to maintain
their basal metabolism. Although our results suggest
that increased filtration rates for mid tide mussels
might compensate for reduced feeding time, in the
winter, larger mussels from the mid tide level would
M98077
Received 30 october 1998; accepted 29 cpril 1999
be unlikely to obtain sufficient energy for maintenance
or growth. Large mussels were infrequent in
the mid tide population, where the mean length was
62.5 mm compared with 75.1 mm from the low tide.
It is concluded that nutrient limitation, as a result of
reduced feeding time can act as a significant stress
factor limiting the growth potential of mussels settled
at the mid tide level.
Keywords mussel; Äerna canaliculus; clearance
rate; condition index; nitrogen excretion; tidal level

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular
traits
Abstract
Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in
evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being
at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in
which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval
phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral
molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is
expected to be hindered by the putatively high gene flow. We determined the geographical distribution of
molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.)
in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of
this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory
starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at
23%. The proportion of total genetic variation that is between sites is much larger for the morphological
additive genetic variation (QST ¼ 0.416) than for allozyme (FST ¼ 0.000±0.022) and mitochondrial DNA
cytochrome-c-oxidase-1 sequence variation (UST ¼ 0.017). Divergent selection must be involved and
intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low
levels of isolation.

Spatially-Explicit Individual Based Modeling of Marine Populations: A Review of the Advances in the
1990's
The utility of individual based models (IBMs) is that properties of ecological systems can be derived by
considering the properties of individuals constituting them. Individual differences may be physiological,
behavioral or may arise from interactions among individuals. The differences result in unique life histories,
which when considered as a whole give rise to growth and size distributions that provide a measure of the
state of the population. Early IBMs generally did not consider the effect of a spatially variable physical
environment. Recent advances in ocean circulation models that include realistic temporal and spatial variation
of currents, turbulence, light, prey, etc., have enabled IBMs to be embedded in model flow fields and for
unique, sometimes behaviorally modified, Lagrangian trajectories to be computed. The explicit consideration
of realistic spatial heterogeneity provides an additional factor that contributes to the differentiation among
individuals, to variances in population structure, and ultimately to our understanding of the recruitment
process. This is particularly important in marine environments where fronts, boundary layers, pycnoclines,
gyres and other smaller spatial features have been hypothesized to play a significant role in determining vital
rates and population structure. In this paper we will review the status of research on spatially-explicit IBMs,
their successes, limitations and future developments. Examples will be drawn from approaches used in the
past decade in GLOBEC, FOCI, SABRE and other programs.

Spatio-temporal patterns in the genetic structure of recently settled blue mussels (Mytilus spp.)
across a hybrid zone
Abstract Previous studies of a hybrid zone between the
mussels Mytilus edulis Linnaeus and M. galloprovincialis
Lamarck have not resolved the relative importance of
the genetic composition of settling larval cohorts versus
post-settlement selection in determining the distribution
of the parental species and their hybrids. In the present
study, recently settled mussels (spat) were collected from
20 sites in southwest England throughout the summer
and fall (May±October) in 1998 and 1999. This study
investigated the spatio-temporal patterns of settlement
and genetics of mussel spat by genetically identifying M.
edulis, M. galloprovincialis and their hybrids using the
diagnostic PCR marker Glu-5¢. Settlement was observed
earlier in populations of M. edulis than in populations of
M. galloprovincialis. Settlement occurred in hybrid
populations at times intermediate to and overlapping
with both of the parental populations. Temporal genetic
variation within years was rare at most sites, while there
was some variation between the two years. Spatial genetic
variation, however, was common among spat settling
within the hybrid populations and matched that
observed in small, sub-adults at the same sites. No
consistent directional changes in allele frequency were
observed over the course of several weeks after settlement.
These data suggest that the observed spatial variation
in the adult populations is the result of spatial
variation in settling larval cohorts and not of either
temporal genetic variation or of selection soon after
settlement.

Symbionts and diseases of farmed mussels

Mytilus galloprovincialis throughout the culture
process in the Rias of Galicia (NW Spain)
ABSTRACT: Mediterranean mussels Mytilus galloprovincialis were experi~nentallyc ultured from 5
rafts located in 4 Galician Rias, following the established industrial procedure. Cultures were sampled
monthly until mussels exceeded market slze. Observation of histological sections of sampled mussels
by light microscopy demonstrated symbionts which could be classified into 3 groups according to their
pathogenicity. The first group consisted of symbionts with unnoticeable pathogenic effects including:
prokaryotic inclusion bodies (PlB) in digestive gland and gills, an unidentified protistan in digestive
primary ducts, a kidney coccidian, intracytoplasmic ciliates in digestive tubules, gill ciliates and a
turbellarian in the ~ntestinal lumen. The second group comprised syn~bionts that could damage the
host, although unlikely to be lethal, including: the microsporidian Steinhausia mytilovum, the flatworm
Urastoma cyprinae, and the copepod Mytilicola intestinahs. The third group included the protistan
Marteilia refringens and the trematode Proctoeces rnaculatus, potentially lethal pathogens. In addition,
mussels with haemocytic infiltration of tissues and granulocytomas and a few cases of disseminated
neoplasia were detected. The qualitative composition of mussel symbiont community was similar at the
5 study sites, except for 3 symbionts which were not detected at some sites Quantitatively, symbiont
loads were higher and histological signs of stress more abundant in Moana and Vilagarcia (the most
inner sites in the Rias), intermediate in Illa de Arousa and Muros, and lower in Lorbe. Symbionts
increased in prevalence as mussels grew. Some of the symbionts were detected in mussel seed at the
beginning of the experimental cultures.
KEY WORDS: Mytilus galloprovincialis . Symbionts Parasites Prokaryota Protista . Metazoa
Pathological conditions .

Techniques and statistical data analysis in molecular population genetics

Abstract
Following the development of PCR methods, molecular techniques have become widely used for detecting
genetic
variation in natural populations. Most nucleotide changes can be detected by these techniques. Many of these
changes probably reflect silent substitutions that are likely to be selectively neutral, making them particularly
suitable to population genetic studies. In this paper, we review the published literature on molecular
population
genetics, with respect to the genome assayed (nuclear, mitochondrial or chloroplast), the organisms studied,
the molecular techniques used, and the biological problems addressed. Severalmolecular techniques are then
comparedusing experimental results obtained from a population genetic study of the Mytilus complex in the
North AtlanticandMediterranean. Finally, the most appropriate theoretical tools to analyse molecular
population genetic data arediscussed.

The coastal module of the Global Ocean Observing System (GOOS): an assessment of current
capabilities to detect change

Two related topics are addressed in this paper. The first is the challenging and difficult task of
producing scientifically crediblequantitative assessments of the status, condition or health of coastal
marine and estuarine ecosystems on regional to global scales.The second is the current capacity to
provide the data required to produce such assessments in a routine and repeatable fashion, a
purpose of the Global Ocean Observing System (GOOS). It is concluded that there is an immediate
need to develop a coastal moduleof GOOS that will enable periodic ecosystem assessments and
significantly improve the ability of participating nations to achieve thegoals of international
agreements and conventions for environmental protection, sustainable resources, healthy marine
andestuarine ecosystems, and safe and efficient marine operations.

The ecology of ecosystem services: introduction to the special

Issue

THE ECOLOGY OF RAFTING IN THE MARINE ENVIRONMENT. III. BIOGEOGRAPHICAL AND

EVOLUTIONARY CONSEQUENCES
Abstract
Rafting of marine and terrestrial organisms has important ecological, biogeographical and evolutionary
implications. Herein the general principles of rafting are described and how they contribute to population
connectivity. Rafting dispersal has particular characteristics, which may differ substantially from those of
species with planktonic larval dispersal. Dispersal distances achieved via rafting can vary considerably:
journeys may be very short or in some cases extremely long, depending on currents and wind. Accumulation
of rafts in convergence zones facilitates cohesion of travelling groups, possibly reducing the risk of founder
populations being very small. This becomes particularly important over long distances where singular founder
events could provoke strong reduction of the genetic variability in the founded population. The frequency of
transport affects the degree of connectivity between local populations. Three important rafting routes are
distinguished: frequent, intermittent and episodic. Frequent rafting routes are found in bays, lagoons and
estuaries, and they are typically facilitated by substrata of biotic origin (seagrass,saltmarsh vegetation,
intermediate-sized algae and mangroves). Intermittent rafting routes are found
along temperate continental shores where they are facilitated primarily by giant kelps. In the
subtropics and the Arctic intermittent rafting routes facilitated by wood are particularly important.
Episodic rafting routes, which often cross vast areas of open ocean (biogeographic barriers), are
facilitated by volcanic pumice, floating trees and occasionally by giant kelps when these are pushed
beyond intermittent routes by strong winds or currents. Dispersal events occur in a highly sporadic
manner in this latter category of rafting route, but when they happen, large amounts of floating
substrata and rafters may be dispersed simultaneously. Intervals between events can be decades,
centuries or even millennia, and consequently populations resulting from these events may be
isolated from each other for long time periods. Population connectivity on frequent, intermittent
and episodic rafting routes is high, intermediate and low, respectively. Genetic studies support these
predictions, and furthermore underline that rafting may contribute to population connectivity over
a wide range of geographic scales, from <100 km up to >5000 km. Rafting also has a strong effect
on evolutionary processes of the organisms dispersed by this means. It is suggested that local
recruitment (consequence of direct development) contributes to enhanced rates of population divergence
among local populations of common rafters, but occasionally high genetic diversity may
result from secondary admixture. Isolation of colonisers after singular episodic rafting events
facilitates allopatric speciation. Through these processes rafting dispersal may support local species
richness and thus have an influence on local biogeography and biodiversity. Human activities affect
rafting connections in the oceans either by reducing or enhancing the possibility of transport and
landfall. In many cases it cannot be safely decided whether the appearance of a species in a new
habitat is due to rafting or to other transport mechanisms, and genetic studies can help to identify
the most likely causes. Future field and laboratory studies on the ecology of potential rafters in
combination with genetic studies on different spatial and temporal scales will contribute to a better
understanding of the mechanisms of rafting dispersal, consideration of which is crucial in developing
efficient conservation measures in the marine environment.

The effects of coastal and estuarine conditions on

the physiology and survivorship of the mussels
Mytilus edulis, M. trossulus and their hybrids
Abstract
Among the three taxa of smooth-shelled blue mussels, it is widely believed that Mytilus
trossulus is the best adapted to conditions of low andror fluctuating salinity. We examined the
affect of two contrasting environmental regimes on aspects of the biology of M. edulis, M.
trossulus and their hybrids from Newfoundland, Atlantic Canada. We employed two experimental
treatments, AcoastalB ênatural, unfiltered coastal seawater pumped directly into the laboratory. and
AestuarineB ênatural, unfiltered freshwater from a nearby pond added to ambient sea water., and
for both treatments we measured temperature, salinity, total particulate matter êTPM mg ly1., and
particulate organic matter êPOM mg ly1.. We compared the mortality rate, energy acquisition,
biochemical composition and specific growth rate êSGR. of M. edulis, M. trossulus and their
hybrids under both sets of experimental conditions. Under coastal conditions, mussels from two
sites êBellevue, an open coast, non-estuarine site: Traytown, an estuarine site. exhibited mortality
rates which were so low that they precluded meaningful statistical comparison. Under estuarine
conditions, mortality occurred among M. trossulus mussels from both sites before it occurred
among the M. edulis mussels. Consistent with the mortality data we also observed greater
utilisation of non-protein energy reserves in M. trossulus than in M. edulis. Our data therefore do
not support the hypothesis that M. trossulus is better adapted to estuarine conditions than is M.
edulis. Although there was some limited evidence of taxon-specific effects for the other variables
investigated êSGR, soft body C:N ratio, absolute C and N values êmg per mg dry body weight.,
weight standardised clearance rate êCRS., faecal production rate êmg dry weight dayy1 and mg
ash-free dry weight êAFDW. dayy1., and absorption efficiency êAE.., these were almost completely
obscured by the effects of the experimental treatment. We conclude that the lack of
taxon-specific differences in physiological responses êSGR, CRS, faecal production rates, AE.
indicates that the higher mortality rate of M. trossulus in the estuarine regime did not result from
a reduction in energy intake. This interpretation is consistent with findings for the same taxa from
northern Europe, and suggests that other factors at the cellular or biochemical levels êfor example,
a failure to control intracellular ionic balance. warrant attention as possible explanations for
ecological differences between the two hybridising taxa. We suggest that detailed study of the
micro-scale distributions of these mussels is required to examine further the influence of low
salinity, and associated environmental variability, on the geographic distributions of both taxa and
their hybrids in Atlantic Canada. q2001 Elsevier Science B.V. All rights reserved.

The genetic structure of Mytilus chilensis (Hupe´ 1854) populations along the Chilean coast based
on RAPDs analysis
Abstract
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THE HUMBOLDT CURRENT SYSTEM OF NORTHERN AND CENTRAL CHILE OCEANOGRAPHIC

PROCESSES, ECOLOGICAL INTERACTIONS AND SOCIOECONOMIC FEEDBACK
Abstract
The Humboldt Current System (HCS) is one of the most productive marine ecosystems
on earth. It extends along the west coast of South America from southern Chile (~42VS) up to
Ecuador and the Galapagos Islands near the equator. The general oceanography of the HCS is
characterised by a predominant northward flow of surface waters of subantarctic origin and by
strong upwelling of cool nutrient-rich subsurface waters of equatorial origin. Along the coast of
northern and central Chile, upwelling is localised and its occurrence changes from being mostly
continuous (aseasonal) in northern Chile to a more seasonal pattern in southern-central Chile.
Several important upwelling centres along the Chilean coast are interspersed with long stretches
of coast without or with sporadic and less intense upwelling. Large-scale climatic phenomena
(El Niño Southern Oscillation, ENSO) are superimposed onto this regional pattern, which results
in a high spatiotemporal heterogeneity, complicating the prediction of ecological processes along
the Chilean coast. This limited predictability becomes particularly critical in light of increasing
human activities during the past decades, at present mainly in the form of exploitation of renewable
resources (fish, invertebrates and macroalgae). This review examines current knowledge of ecological
processes in the HCS of northern and central Chile, with a particular focus on oceanographic
factors and the influence of human activities, and further suggests conservation strategies for this
high-priority large marine ecosystem. Along the Chilean coast, the injection of nutrients into surface
waters through upwelling events results in extremely high primary production. This fuels zooplankton
and fish production over extensive areas, which also supports higher trophic levels,
including large populations of seabirds and marine mammals. Pelagic fisheries, typically concentrated
near main upwelling centres (20±22VS, 32±34VS, 36±38VS), take an important share of the
fish production, thereby affecting trophic interactions in the HCS. Interestingly, El Niño (EN) events
in northern Chile do not appear to cause a dramatic decline in primary or zooplankton production
but rather a shift in species composition, which affects trophic efficiency of and interactions among
higher-level consumers. The low oxygen concentrations in subsurface waters of the HCS (oxygenminimum
zone, OMZ) influence predator-prey interactions in the plankton by preventing some
species from migrating to deeper waters. The OMZ also has a strong effect on the bathymetric
distribution of sublittoral soft-bottom communities along the Chilean coast. The few long-term
studies available from sublittoral soft-bottom communities in northern and central Chile suggest
that temporal dynamics in abundance and community composition are driven by interannual phenomena
(EN and the extent and intensity of the OMZ) rather than by intra-annual (seasonal) patterns.
Macrobenthic communities within the OMZ are often dominated in biomass by sulphide-oxidising,
mat-forming bacteria. Though the contribution of these microbial communities to the total primary
production of the system and their function in structuring OMZ communities is still scarcely known,
they presumably play a key role, also in sustaining large populations of economically valuable
crustaceans. Sublittoral hard bottoms in shallow waters are dominated by macroalgae and suspension
feeder reefs, which concentrate planktonic resources (nutrients and suspended matter) and
channel them into benthic food webs. These communities persist for many years and local extinctions
appear to be mainly driven by large-scale events such as EN, which causes direct mortality
of benthic organisms due to lack of nutrients/food, high water temperatures, or burial under
terrigenous sediments from river runoff. Historic extinctions in combination with local conditions
(e.g., vicinity to upwelling centres or substratum availability) produce a heterogeneous distribution
pattern of benthic communities, which is also reflected in the diffuse biogeographic limits along
the coast of northern-central Chile. Studies of population connectivity suggest that species with
highly mobile planktonic dispersal stages maintain relatively continuous populations throughout
most of the HCS, while populations of species with limited planktonic dispersal appear to feature
high genetic structure over small spatial scales. The population dynamics of most species in the
HCS are further influenced by geographic variation in propagule production (apparently caused by
local differences in primary production), by temporal variation in recruit supply (caused by upwelling
events, frontal systems and eddies), and topographically driven propagule retention (behind headlands,
in bay systems and upwelling shadows). Adults as well as larval stages show a wide range
of different physiological, ecological and reproductive adaptations. This diversity in life-history
strategies in combination with the high variability in environmental conditions (currents, food
availability, predation risk, environmental stress) causes strong fluctuations in stocks of both
planktonic and benthic resources. At present, it remains difficult to predict many of these fluctuations,
which poses particular challenges for the management of exploited resources and the conservation
of biodiversity in the HCS. The high spatiotemporal variability in factors affecting
ecological processes and the often-unpredictable outcome call for fine-scale monitoring of recruitment
and stock dynamics. In order to translate this ecological information into sustainable use of
resources, adaptive and co-participative management plans are recommended. Identification of areas
with high biodiversity, source and sink regions for propagules and connectivity among local
populations together with developing a systematic conservation planning, which incorporates decision
support systems, are important tasks that need to be resolved in order to create an efficient
network of Marine Protected Areas along the coast of northern-central Chile. Farther offshore, the
continental shelf and the deep-sea trenches off the Chilean coast play an important role in biogeochemical
cycles, which may be highly sensitive to climatic change. Research in this area should
be intensified, for which modern research vessels are required. Biodiversity inventories must be
accompanied by efforts to foster taxonomic expertise and museum collections (which should
integrate morphological and molecular information). Conservation goals set for the next decade
can only be achieved with the incorporation of local stakeholders and the establishment of efficient
administrative structures. The dynamic system of the HCS in northern-central Chile can only be
understood and managed efficiently if a fluent communication between stakeholders, administrators,
scientists and politicians is guaranteed.

The Management of Fisheries and Marine Ecosystems

The global marine fish catch is approaching its upper limit. The number of overfished
populations, as well as the indirect effects of fisheries on marine ecosystems, indicate
that management has failed to achieve a principal goal, sustainability. This failure is
primarily due to continually increasing harvest rates in response to incessant sociopolitical
pressure for greater harvests and the intrinsic uncertainty in predicting the harvest
that will cause population collapse. A more holistic approach incorporating interspecific
interactions and physical environmental influences would contribute to greater sustainability
by reducing the uncertainty in predictions. However, transforming the management
process to reduce the influence of pressure for greater harvest holds more immediate
promise.

The Role of Economics in Climate Change Policy

Many policy problems have frustratingly long histories of inefficient regulation that can be difficult or
impossible to reverse, even where large efficiency gains might be had from doing so. Climate change is an
exception, however, because little real action has been undertaken to date. It presents an unusual opportunity
for an efficient economic policy to be employed right from the beginning. However, the opportunity could
easily be lost. Ongoing negotiations conducted under the auspices of the United Nations Framework
Convention on Climate Change have so far produced the Kyoto Protocol, a deeply flawed agreement that
manages to be both economically inefficient and politically impractical.
In this article we examine the key economic characteristics of climate change and argue that economic theory
provides good guidance on the design of an efficient and politically realistic policy. Because climate change
involves vast uncertainties and has potentially enormous distributional effects, neither of the standard market-
based instruments is a viable approach: a tradable permit system would be inefficient and an emissions tax
would be politically unrealistic. However, a hybrid policy, combining the best features of the two, would be
an efficient and practical approach. We then compare our hybrid proposal to the Kyoto Protocol and argue
that it overcomes the Protocol¶s shortcomings.

The role of genetics in shellfish restoration

Abstract ± Restoration of shellfish populations is becoming an increasingly common practice worldwide, as
natural
fisheries succumb to pressures of overharvesting, habitat loss or degradation, and challenges from invasive
competitors
and pathogens. Primary genetic concerns relevant to shellfish restoration projects are reviewed, using the
cupped oysters
Crassostrea gigas and Crassostrea virginica as case studies. Molecular genetic tools can be used to delineate
the
geographic distribution of germ plasm diversity at the species and intraspecific levels, enabling more
informed selection
of genetic material for hatchery breeding and production. Maintenance of genetic variability and prevention of
excessive
inbreeding in hatchery stocks may be facilitated by the use of genetic markers for regular pedigree
monitoring. The
effect of hatchery supplementation on the effective population size of a recipient wild population (Ryman-
Laikre effect)
is reviewed in light of the population biology of bivalve molluscs, and appears to be minimal. Deployment of
selected
enhancement stocks may be a valuable tool for improvement of degraded wild populations, reversing the
negative effects
of generations of selective harvesting. Molecular genetic tools can be used effectively to monitor restoration
programs,
when the discriminatory power of the marker(s) is high and high-throughput scoring methods currently
available are
used.
Key words: Effective population size / Genetic diversity / Restoration / Genetic monitoring / Crassostrea
virginica /
Crassostrea gigas

Enchantment and Disenchantment: The Role of Community in Natural Resource Conservation

Summary.ÐThe poor conservation outcomes that followed decades of intrusive resource
management strategies and planned development have forced policy makers and
scholars to reconsider the role of community in resource use and conservation. In a
break from previous work on development which considered communities a hindrance
to progressive social change, current writings champion the role of community in
bringing about decentralization, meaningful participation, and conservation. But despite
its recent popularity, the concept of community is rarely de®ned or carefully examined
by those concerned with resource use and management. We seek to redress this
omission by investigating ``community'' in work concerning resource conservation and
management. We explore the conceptual origins of the community, and the ways the
term has been deployed in writings on resource use. We then analyze those aspects of
community most important to advocates for community's role in resource management
Ð community as a small spatial unit, as a homogeneous social structure, and as shared
norms Ð and indicate the weaknesses of these approaches. Finally, we suggest a more
political approach: community must be examined in the context of development and
conservation by focusing on the multiple interests and actors within communities, on
how these actors in¯uence decision-making, and on the internal and external institutions
that shape the decision-making process. A focus on institutions rather than ``community''
is likely to be more fruitful for those interested in community-based natural resource management.

The utility and limitations of genetic data for stock identification and management of North Pacific rockfish
(Sebastes spp.)
Abstract Rockfishes (Sebastes spp.) represent a
speciose and ecologically important group of marine
fishes found in both the Pacific and Atlantic oceans,
with approximately 105 species found world-wide
(Hyde and Vetter 2007). They also comprise the
majority of species found in the Pacific groundfish
fishery. Thorough species assessments in terms of
harvest management have been done for only 11
species, and of the 11 species, seven have been
declared overfished. Having accurate genetic information
is critical to the continuing effort at stock
assessments, but sampling is often difficult in marine
fishes. Genetic techniques are a powerful tool in the
effort to better characterize the ecology of these
species. These techniques can be used to investigate
multiple biological traits, including species identity,
intra- and interspecific genetic variation, migration
patterns, and effective population size. There are
important caveats and limitations when applying
specific genetic methods, especially in marine species
that lack discrete spawning aggregates. Nevertheless,
it is clear from a review of recent literature that
genetic tools have already provided very specific
insight regarding rockfish population dynamics. The
results are diverse and difficult to synthesize;
however, existing studies show five primary patterns
to population groupings in rockfishes: no obvious
pattern of structure, structure consistent with isolation
by distance, structure evident but inconsistent with
isolation by distance, structure that correlates to
oceanographic features, and potential genetic introgression.
Clearly the study of rockfish population
genetics is poised for rapid expansion that will
unquestionably aid management of the rockfish
fisheries and general understanding of rockfish evolutionary
systematics. A principle challenge at this
point is to derive generalized inferences from such a
diverse array of study results across the vast North
Pacific range of Sebastes. This review summarizes
existing genetic studies in Sebastes spp. in the North
Pacific to assist in identifying knowledge gaps for this
ecologically important and diverse group.
Keywords Rockfish _ Sebastes _

The zone of sympatry and hybridization of Mytilus edulis and M. galloprovincialis, as described by
intron length polymorphism at locus mac-1
Intron-size variation at the actin gene locus mac-1 was used to characterize mussel, Mytilus spp.,
populations in the å2000-km wide zone of contact and hybridization (`hybrid zone') between
M. edulis and M. galloprovincialis in western Europe. Twenty-®ve samples were collected in
1995 99 in locations within the hybrid zone and from reference populations of each species. We
used correspondence analysis on the matrix of allelic frequencies to determine which alleles are
characteristic of each species, and to characterize samples along the genetic gradient between
M. edulis and M. galloprovincialis. In the hybrid zone, some samples exhibited mac-1 allele
Frequencies that were typical of M. edulis; other samples were distributed along the M. edulis/M.
galloprovincialis gradient and displayed variable levels of intergradation that were not correlated
with geography. Some of the latter samples exhibited signi®cant heterozygote de®ciencies. The
simple admixture hypothesis (Wahlund e ect) could not be rejected for two-®fths of the samples.
The hybrid zone thus appeared as a mosaic of populations which are either pure M. edulis, or
hybrid between M. galloprovincialis and M. edulis, or a mixture of the foregoing with M.
galloprovincialis individuals.These results were consistent with published allozyme data, suggesting
that they can be extended to
the entire nuclear genome. M. edulis mac-1 alleles were present at moderate frequency in Atlantic
M. galloprovincialis, and at signi®cantly lower frequency in some Mediterranean samples. This
pattern was homogeneous over a broad geographical range within each basin. It was not evident
that
introgression of M. edulis into M. galloprovincialis presently occurs south of the zone of contact. We
propose that the distinctness of the Atlantic M. galloprovincialis population results from past
introgression by M. edulis alleles.

˜    
culacomya maoriana, Mytilus galloprovincialis  Äerna
canaliculus 


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Tissue-specific expression of male-transmitted mitochondrial DNA and its implications for ratesof
molecular evolution in ‰p
mussels (Bivalvia: Mytilidae)

Abstract: Mytilus and other bivalves exhibit an unusual system of mitochondrial DNA (mtDNA) transmission
termed
doubly uniparental inheritance (DUI). Specifically, males transmit the mtDNA they have received from their
fathers to
their sons. Females transmit their mother¶s mtDNA to both sons and daughters. Males are normally
heteroplasmic and
females are normally homoplasmic, but not exclusively. This system is associated with an unusual pattern of
molecular
evolution. Male-transmitted mtDNA (M type) evolves faster than female-transmitted (F type) mtDNA.
Relatively relaxed
selection on the M type has been proposed as an explanation for this phenomenon. To further evaluate the
selective
forces acting upon the M-type genome, we used RT-PCR to determine where it is expressed. M-type mtDNA
expression was detected in all gonad samples and in 50% of somatic tissues of males, and in a single female
tissue. Ftype
mtDNA expression was detected in all female tissues, all male somatic tissues, and all but one male gonad
sample.
We argue that the expression of M-type mtDNA in male somatic and male gonad tissues has implications for
the
strength of selection acting upon it.
¢ey words: gender-associated mitochondrial DNA, doubly uniparental inheritance of mtDNA, Mytilus edulis,
molecular
evolution.

Trypanosoma cruzi: Subtractive hybridization as a molecular strategy to generate new targets to

distinguish groups and hybrids
Abstract
RAPD analysis and sequences of the mini-exon and ribosomal genes show that Trypanosoma cruzi
can be clustered into two phylogenetic
groups²T. cruzi I and II. Herein, the Representational Difference Analysis (RDA) method was
used, providing new targets specific
for each group. After three rounds of RDA hybridizing F strain (tester) with Y strain (driver) and vice-
versa, an F-specific (F#30)
and Y-specific (Y#22) clone were obtained specifically recognizing isolates from Amazonas (T. cruzi
I) and Piauı´ (T. cruzi II). These
segments corresponded to an unspecified protein (F#30) and a trans-sialidase (Y#22). Analysis of
the F#30 sequence in T. cruzi I,
T. cruzi II and zymodeme 3 samples displayed negligible specific differences that distinguished
each group. In addition this F#30 gene
has great potential as a hybrid marker.
_ 2007 Elsevier Inc. All rights reserved.
Index Descriptors and Abbreviations: RDA, representational difference analysis; DNA,
deoxyribonucleic acid; LIT, liver infusion tryptose; PBS, phosphate
buffer saline; TE, 10 mM Tris±HCl pH 8.0, 10 mM EDTA, pH 8.0; SDS, sodium dodecyl sulphate;
SSC, Saline sodium citrate; Trypanosoma cruzi;
Phylogenetic lineages; RDA; Hybrids; Protozoa; Molecular markers

Two Events Are Responsible for an Insertion in a Paternally Inherited Mitochondrial Genome of the Mussel
Mytilus galloprovindalis
ABSTRACT
Frequent nonhoniologous recombination has been previously postulated to explain the 1045-bp insertion
in one mitochondrial spemi-transmitted haplotype oi Mytilus galtoprovincialis. Stich recombination
would lead to the disrtiption of gene order and so the existence ofa specific mechanism for maintaining
the same gene order in both mitochondrial genomes of Mytilus has been proposed. Here the simpler
explanation ofthe observed structtne, involving a tandem duplication atid a deletioti, is presented. Their
occasional occurrence in Mytilus mtDNA proves the similarity, not the difference, between animals with
and without DUI,

Two to tango: the role of government in fisheries co-management

Use of molecular markers and major genes in the genetic improvement of livestock
Recent developments in molecular biology and statistics have
opened the possibility of identifying and using genomic
variation and major genes for the genetic improvement of
livestock. Information concerning the basis of these techniques
and their application to the genetic improvement of animals is
reviewed. Main marker molecular marker systems in animals
(RFPL and microsatellites), genome maps, methods for
detecting marker-QTL linkages and use of marker assisted
selection, genetic fingerprinting and mixture models based on
segregation analysis are analyzed. The characteristics in
where the application of marker assisted selection can be more
effective are those that are expressed late in the life of the
animal, or controlled by a few pairs of genes. The first
example corresponds to the longevity and carcass
characteristics in meat producing animals, the second, to the
resistance to certain diseases or defects of simple inheritance.
The detection of major genes using mixture models with
segregation analysis can direct the work of identification of
DNA marker genotypes towards populations and
characteristics with greater probability of detecting a QTL.
The present trend indicates that molecular, pedigree and
phenotypic information will be integrated in the future
through mixture models of segregation analysis that might
contain QTL effects through the markers, polygenic
inheritance and uses powerful and flexible methods of
 estimation such as Gibbs Sampling

‘ ‘‘  ‘‘‘‘ ‘ ‘ ‘

1. Introduction This manual provides a brief introduction to the use and manipulation of the Marine
Environment Classification using various software, including ESRI¶s ArcView 3.2 GIS software. There are
two classifications on the DVD. The first classification is a low resolution (1 km grid) of the whole of New
Zealand¶s exclusive economic zone (EEZ). The second classification is a higher resolution (200m grid) of the
Hauraki Gulf region. This manual assumes that the user has a reasonable understanding of ArcView, eg. how
to add layers, join tables and display maps.

Using Discourses for Policy Evaluation: The Case of Marine Common Property Rights in Chile
In an attempt to combine marine conservation and economic development, the Chilean
government introduced a policy that gives formal property rights over defined
areas of seabed to artisanal fishers. This study used discourse analysis to understand
the impacts and consequences of this policy. Story lines based on sustainability,
livelihood maintenance, and historical right claims are mechanisms by which three
different groups of fishers adopted postures toward the policy and each other. These
act as a means of legitimizing claims when adapting to conditions generated by the
policy and also vindicate poaching between syndicates, thereby jeopardizing the
whole system. Results show the fishing groups studied adopt the policy for different
reasons than those espoused by government during its development. Discourse
analysis assists the understanding of actors¶ policy responses and provides an insightful
tool to investigate incentives and dominance of particular sets of ideas in a comanagement
framework.

Using simplified watershed hydrology to define spatially explicit µzones of influence¶

Abstract Riparian areas represent dynamic spatial
gradients characterized by a varying degree of
terrestrial±aquatic interaction. Many studies have
considered riparian zones to be discrete watershed
sub-portions (e.g., 100-m riparian buffers), whereas I
introduce µzones of influence¶ that are subsets of the
riparian zone. The purpose of this study is to
introduce the concept of hydrologically defined
influence zones using a simple hydrologic model to
delimit land-cover. I describe a method for identifying
zones of influence using watershed hydrologic
patterns to delimit zones along a near-stream continuum
between a downstream point (e.g., sample reach)
and the watershed boundary. Using hydrologic modeling
equations and GIS, travel time was calculated
for every 30 9 30-m cell in 10 watersheds providing
spatially explicit estimates of watershed hydrology
and enabling us to calculate the travel time required
for rainfall in any watershed cell to reach the
watershed terminus. Shorter-duration travel times
(i.e., 30±60 min) described smaller areas than
longer-duration travel times (i.e., 210±300 min). This
method is an alternative method to delimit near
stream areas when quantifying watershed influence.
Keywords Riparian ecology _ Runoff _
Watershed management _ Hydrology _
Land use/land-cover change

Virus-like particles associated with marine mussel

mortalities in New Zealand
ABSTRACT. Green-lip mussel Perna canaliculus spat (15 to 30 mm length) in the outer Marlborough
Sounds, New Zealand, suffered 50 to 100% mortal~t)!d uring January to April 1994 (summer/autumn)
following thinning and reseeding of the mussel lines by farmers Adult mussel ~nortalities of 2 to 5 %
continued from February to early h4ay 1994 Histolog~cael xamination showed extensive haemocytosis
and multifocal liquefact~onn ecrosls of int e r s t~t~caell ls, basal cells and diges t~vetu bule ep~thel iacl ells.
Sloughed pyknot~c0 1-k aryolyt~cd igestive tubule epithelia1 cells formed charactens t~cr ounded granular
b o d ~ e s1 0 to 15 pm diameter both In digestive tubules and free in lesions. No v ~ r ailn clusion bodies
were observed Ultrastructural examination showed highly mod~fied rough endoplasn~ic reticulum
assoc~atedw ith small, 25 to 45 nm diameter, electron-dense uncoated virus-like particles Identical cell
damage and virus-like particles were subsequently found In moribund adult (75 to 110 mm length)
P canallculus and stunted (25 to 47 mm length) subtidal 12-li'tilusg alloprov~ncial~frso m the same area.
Following purification of extracts of the moribund spat b}! isopycnlc centl-ifugation in CsCI, large
numbers of 25 nm diameter, unenveloped, virus pal-t~clesw ere scvn by electron mlcroscopy These
part~cles had a density of 1.364 g cm-3 A broad band at a dens~ty c~xpected for enveloped particles
(1 21 to 1 24 g cm ' ) was also observed but contained few v~rus-likep articles Cell damage and mussel
mortalit~es are thus likely due to a small unenveloped virus.
KEY WORDS. Bivalve . Perna . Mytilus . Endoplasmic reticulum . Histology . Ultrastructure . Virus

What is a genetic marker?

A genetic marker is an easily identifiable piece of genetic

material, usually DNA, that can be used in the laboratory
to tell apart cells, individuals, populations, or species.
The use of genetic markers begins with extracting
proteins or chemicals (for biochemical markers) or DNA
(for molecular markers) from tissues of the plant (for
example, seeds, foliage, pollen, sometimes woody tissues).
Laboratory protocols (often well developed, but may
need adjustments for certain species) are then applied,
resulting typically in visual representations from staining
or tagging techniques, which are then converted into
data ² usually allele types and frequencies, or presence/
absence data. Genetic markers thus allow us to characterize genetic diversity.

What role for genomics in fisheries management

and aquaculture?
Abstract ± The development and application of genomics has been facilitated in a number of fields by the
availability
of new methodologies and tools, such as high throughput DNA sequencing and complementary DNA (cDNA)
microarrays.
Genomic tools are already used in research on commercially important fish and shellfish species. Thousands
of
expressed sequence tags (EST) are now available for some of these species, and the sequencing of complete
genomes
of tilapia, cod, salmonids, flatfishes, sea bass and Pacific oyster has been proposed. Microarray technology
through
simultaneous analysis of the expression of thousands of genes allows the identification of candidate genes
involved in
the function of multiple physiological, morphological and behavioural traits of interests in organisms and
populations
from different environments. This paper reviews the current development of genomic technologies, and
pinpoints their
potential beneficial applications as well as implications for fisheries management and aquaculture.
Key words: Genomics / Genetics / Fisheries / Mariculture / Quantitative trait loci / Fish / Oyster

Where are the mussels on Cook Strait (New Zealand) shores? Low seston quality as a possible factor limiting
multi-species distributions
ABSTRACT: Exammation of the physiological ecology of 3 sympatncally occurring mytilids (the ribbed,
blue and greenshell mussels, Aulacomya maoriana, ivlytilus galloprovincialis and Perna canalicdus,
respectively) was carned out during summer and winter at 2 sites which differ markedly in their
environmental
characteristics (Mahanga Bay inside Wellington Harbour, where mussels are abundant, and
Island Bay on the exposed Cook Strait shore, where mussels are absent). Seston components (particle
counts per rnl in the size range 2.5 to 63 pm, total particulate matter [TPbI], particulate organic matter
[POM], and percent organic matter [PCOM]) all varied significantly between sites and between seasons.
Mahanga Bay seston exhibited characteristics typical of productive temperate coastal waters.
whereas Island Bay seston was characterised by low POM and low PCOM values. Weight-standardised
clearance rate (CRS), net absorption efficiency (AE) and Scope for Growth (SFG) values were determined
for all 3 mussel species at both sites during both seasons. At Island Bay there was no evidence of
seasonal differences in CRs whereas at Mahanga Bay species-specific CRs values were all highest in
the winter. Regardless of season, CRs estimates for all 3 species were higher at Mahanga Bay than at
Island Bay. At both sites, AE estimates were highest in the w~ntera, nd AE estimates were higher at
Mahanga Bay than at Island Bay during each season SFG estlrnates mirrored AE estimates, with SFG
at both sites being highest in winter, and higher at Mahanga Ray than at Island Bay dunng each season.
The SFG data support the hypothesis that mussels are absent from sites along Cook Strait shores
because they do not enjoy a positive energy balance for long periods of time, consistent wlth the low
seston organic matter levels at such locations. The SFG data also indicate that mussels lnside Wellington
Harbour can maintain a large, positive net energy balance throughout the year, consistent with the
considerable biomass and very large size of all 3 species in this environment.
KEY WORDS: Aulacomya maoriana . Mytilus galloprovincialis . Perna canaLiculus - Mussels -
Ecological distribution . Physiological energetics - Seston . Scope for Growth

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