PERSPECTIVES
but could have switched on quickly in ice-free in ice cover in summer 2007 (16). Very warm
areas. In contrast, biomass burning sources
were stable, showing little change between
cool and warm times (7). As a warming event
is sustained, decomposing northern methane
hydrates (clathrates) may inject fossil methane
into the air, with wetland, thawing permafrost,
and clathrate emissions reinforcing each other
in a feedback loop (8). Petrenko et al.’s data
leave such a scenario unconstrained but imply
that wetlands were the main driver.
A possible explanation for the sudden end
of the Younger Dryas is that, at a time of high
Arctic insolation, an initial outburst of
methane—perhaps from a geological source
such as methane clathrates—triggered global
warming, initiating both strong wetland emis-
sion in the tropics and north (8), and further
hydrate responses as the thermal shock pene-
trated the permafrost (9, 10), freeing methane
from decomposing clathrate hydrates and
releasing gas pools trapped beneath them. The
clathrate gun hypothesis (11) postulates the
dominant role of hydrate decomposition, as
opposed to wetland emission, as the principal
driver of change. Organic matter in thawing
permafrost can also generate large emissions
of methane (12). Detailed comparison in
Greenland ice cores between the methane
record and warming, as shown in nitrogen and
argon isotopic signals (13, 14), suggests that
warmer air reached Greenland before the
main rise in methane, thus challenging the
clathrate gun scenario (11).
δD results (5) have been used to argue
against the hypothesis that an outburst of
methane from clathrate hydrates drove the
change. However, although marine hydrates
supplied by gas from deep geological sources
are enriched in deuterium relative to terrestrial
methane sources, shallow hydrate and decay-
ing permafrost sources can be depleted.
Moreover, the interpretation of the D/H signa-
ture during the decades of most sharply rising
atmospheric methane is complex, because the
global methane budget is not in equilibrium.
The jury thus remains out on the initial
trigger, but it is clear that a very rapid wetland
response plays a major role in driving the
main methane increase. In addition, the end of
the Younger Dryas is accompanied by a large
increase of another greenhouse gas: N2O (15),
produced, for example, in soils and marine
upwelling areas.
There are clear analogies with the modern
Arctic, especially because global warming is
expected to be strongest in the Arctic. Within
the next few decades, reduced summer ice
cover, earlier springs, and later freeze-up may
cause radical change in Arctic wetland and per-
mafrost regions. There was a sudden decrease
478 24 APRIL 2009
other factors influencing methane, such as bio-
summer weather, possibly driven by global
warming, has occurred recently in the Arctic.
This may trigger new wetland sources (17, 18)
as well as fossil and thermokarst methane emis-
sions (12, 19).
Could the Arctic be preparing to shift gear
again? If a shift on the scale and rapidity of past
changes were to happen tomorrow— including
intensified methane emissions from wetlands,
decaying permafrost, and hydrate breakdown
on Arctic continental margins and slopes—
then the consequences for humanity could be
very severe. Far from the Arctic, crops could
fail and nations crumble. It is thus essential to
decipher what took place in the past.
The hard labors of Petrenko et al. in mining
tons of ice show the way, as there is plenty
more ice to extract on outcropping blue ice
fields at both poles. There is now a strong case
for horizontal ice mining at the right depths in
polar ice caps, far from surface cosmic ray in
situ production. Large-sample ice collection
from vanishing tropical ice caps is also
urgently needed to assess the past history of
GENETICS
It’s a Bull’s Market
Harris A. Lewin
Research on domesticated livestock heralds new advances in evolutionary biology, animal
breeding, and animal models for human diseases.
F
rom Darwin to Dolly, domesticated
livestock have guided our understand-
ing of evolution and biology. Moreover,
for the past 10,000 years, livestock have pro-
vided sustenance to humans with their hides,
hair, meat, milk, strength, speed, and compan-
ionship. Now, livestock are poised to give us
even more, thanks to new insights from
genomics and molecular phylogenetics. Five
articles in this issue deal with the biogeogra-
phy of domestication (1, 2), the development
of modern breeds (1, 3), the genes responsible
for agriculturally important traits (3, 4), and
the potential use of livestock species as mod-
els for human diseases (5).
The publication by the Bovine Genome
Sequencing and Analysis Consortium de-
scribing the sequence, annotation, and com-
parative analysis of the cattle genome marks a
major milestone in animal genetics (3). The
Institute for Genomic Biology and Department of Animal
Sciences, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA. E-mail: h-lewin@uiuc.edu
VOL 324 SCIENCE www.sciencemag.org
Published by AAAS
mass burning. Humanity is triggering great
changes; it would be wise to document and
understand the past before we face the future.
References
1. J. Chappellaz et al., Nature 366, 443 (1993).
2. J. P. Steffensen et al., Science 321, 680 (2008); pub-
lished online 19 June 2008 (10.1126/science.1157707).
3. V. V. Petrenko et al., Science 324, 506 (2009).
4. J. Chappellaz et al., J. Geophys. Res. 102, 15987 (1997).
5. T. Sowers, Science 311, 838 (2006).
6. H. Schaefer et al., Science 313, 1109 (2006).
7. H. Fischer et al., Nature 452, 864 (2008).
8. E. G. Nisbet, J. Geophys. Res. 97, 12859 (1992).
9. E. G. Nisbet, Can. J. Earth Sci. 26, 1603 (1989).
10. E. G. Nisbet, Can. J. Earth Sci. 27, 148 (1990).
11. J. P. Kennett, K. G. Cannariato, I. L. Hendy, R. J. Behl,
Science 288, 128 (2000).
12. K. M. Walter, M. E. Edwards, G. Grosse, S. A. Zimov,
F. S. Chapin III, Science 318, 633 (2007).
13. J. Severinghaus et al., Nature 391, 141 (1998).
Downloaded from www.sciencemag.org on April 27, 2009
14. E. J. Brook et al., Global Biogeochem. Cycles 14, 559
(2000).
15. J. Flückiger et al., Science 285, 227 (1999).
16. R. W. Lindsay et al., J. Clim. 22, 165 (2009).
17. M. Rigby et al., Geophys. Res. Lett. 35, L22805 (2008).
18. E. J. Dlugokencky et al., Eos 89 (fall meet. suppl.), A12A-
05 (2008).
19. N. Shakhova et al., Eos 89 (fall meet. suppl.), U23D-
0081 (2008).
10.1126/science.1172001
Cetartiodactyl order of mammals, to which
cattle and all other ruminants belong, is phylo-
genetically distant from the primates, and thus
contains invaluable information for under-
standing human genome evolution. Cattle
have numerous adaptive traits that underlie
their unique biology, including a four-cham-
bered stomach for digesting fiber, as well as
specialized immune, endocrine, and repro-
ductive system functions and architectures.
Comparison of the cattle genome to that of
other mammals was thus expected to yield
exciting new information on how mammalian
genomes evolve, mechanisms of gene regula-
tion, genetic control of complex traits, and
host-microbe interactions. The cows have not
disappointed us.
At the gene level, there are tantalizing
clues to explain the “essence of bovinity.”
Seventy-one genes show evidence of positive
selection. Several immune function–related
genes are expanded in copy number, such as
the β-defensin and interferon genes, and
rearrangements occur in key genes involved
 PERSPECTIVES

in lactation. The bacteria-bust-
ing lysozyme genes used by
white blood cells have been
expanded in copy number and
adapted to a similar function in
the ruminant abomasum, the
glandular stomach (similar to
the human stomach) where
microbes that digest cellulose
and ferment complex sugars in
the rumen are broken down.
(The rumen is also an excellent
source of cellulytic bacteria
that may be important for bio-
fuels production.) As with
rodents and dogs, cattle have
about 1000 genes not found in
INTEGRATED GENOMIC STRATEGIES cated horses found in Siberia and Eastern and
FOR ANIMAL AGRICULTURE Central Europe were homozygous for all six
coat-color genes, which likely made these
Genomic technologies for ancient animals “bay” colored. However, coat-
animal production and health color variants rapidly increased during and
after the Bronze Age, which coincides with the
Biomedical models timing of domestication proposed by Outram
et al. (10), suggesting a human hand in their
spread. Apparently, a horse of a different color
Genomic analysis of was a thing to be cherished by our ancestors.
Systems biology
complex traits The barnyard door is now open. We can
expect that any animal with medically or agri-
culturally useful traits will be sequenced and
resequenced. Similar to the primate-human
Comparative and evolutionary genomics comparisons geneticists are making to under-
stand the origins of human intelligence, com-
parative genomic studies of cattle, pigs, sheep,

Downloaded from www.sciencemag.org on April 27, 2009

the human genome, and 1217 Research roadmap. An integrated approach to animal studies will sup- and goats, may help us to better understand
genes occur only in eutherian port advances in sustainable agriculture and animal and human health. the genetics of wool production, lactation,
(placental) mammals. These growth, metabolism, and environmental adap-
intriguing genes complement the large num- those found in human and dog populations tation. This will further accelerate the devel-
ber of variants in promoter sequences and (7, 8). The greatest diversity was found in opment of new technologies for sustainable
transcription factors that are thought to con- indicine Brahman cattle, with one SNP animal agriculture (see the figure). Moreover,
tribute to differences in mammalian develop- (single-nucleotide polymorphism, a DNA as outlined by Roberts et al. (5), cattle and
ment and physiology. sequence variation) every 285 base pairs of other livestock have played important roles in
The high quality of the cattle genome DNA. That’s more than twice the number advancing biomedical research, leading to
assembly enabled a detailed multispecies for the taurine Holstein and Angus breeds, new technologies including assisted repro-
comparison of chromosome organization that thus indicating that more individuals were duction and organ transplants. With the
produced novel insights into mammalian involved in forming indicine cattle before genome sequence of cattle in hand, and that of
chromosome evolution. A major finding was domestication. Following domestication, the other livestock species soon to follow, we can
that higher densities of segmental duplica- genetic evidence suggests that cattle breeds for the first time select animal models of
tions, retroposons, and retrovirus long termi- went through mild bottlenecks, possibly due human diseases on the basis of trait homology
nal repeats are present in chromosome regions to a limited number of founder individuals or as well as gene structure, chromosome organ-
that were rearranged during the last 80 million selection for production traits. Furthermore, ization, and transcription factor binding sites.
years, leading to the Bos taurus karyotype. several regions of the genome were differenti- This will help increase the reliability of ani-
Thus, specific kinds of repetitive elements ated in breeds used for milk and meat pro- mal models, because common genomic archi-
and segmental duplications appear to directly duction, and many of these regions contain tecture may more accurately predict the regu-
promote the chromosome rearrangements genes responsible for quantitative variation in lation of disease-related genes. The antici-
associated with speciation in multiple mam- milk production and meat-quality traits. This pated rapid advances in comparative and
malian lineages. With additional mapped and reveals a fascinating linkage between tradi- functional genomics will make genome-
sequenced genomes on the horizon, it will be tional animal breeding and genomic archi- enabled livestock models an increasingly
possible to explore further the relationship tecture and suggests that genetic diversity valuable resource for biomedical research. In
between chromosome rearrangements and should be carefully monitored as genomic a bull’s market, everyone wins.
adaptive evolution of mammals (6). selection for quantitative traits (9) takes its
In his1868 opus The Variation of Animals place as a routine technology for animal References and Notes
1. B. Chessa et al., Science 324, 532 (2009).
and Plants Under Domestication, Charles genetic improvement. 2. A. Ludwig et al., Science 324, 485 (2009).
Darwin wrote: “I have often speculated on the Genome analyses, coupled with molecular 3. The Bovine Genome Sequencing and Analysis
probable causes through which each separate phylogenetic techniques, have also revealed Consortium, C. G. Elsik, R. L. Tellam, K. C. Worley, Science
district in Great Britain came to possess in for- new historical insights into the domestication 324, 522 (2009).
4. The Bovine HapMap Consortium, Science 324, 528
mer times its own peculiar breed of cattle….” of other livestock species, such as sheep and (2009).
What Darwin was trying to distinguish were horses. It is now clear that sheep were domes- 5. R. M. Roberts et al., Science 324, 468 (2009).
the roles of common ancestry, natural selec- ticated in Southwest Asia and then spread to 6. D. M. Larkin et al., Genome Res. 10.1101/gr.086546.108
(2009).
tion, and artificial (human-assisted) selection Europe in two distinct waves. Most modern-
7. E. A. Ostrander, R. K. Wayne, Genome Res. 15, 1706
in the extraordinary diversity of cattle pheno- day sheep breeds appear to be a result of this (2005).
types. The Bovine HapMap Consortium de- second migration (1). Horse domestication has 8. G. Marth et al. Proc. Natl. Acad. Sci. U.S.A. 100, 376
scribe (4) the genetic structure of modern proved difficult to pin down, but Ludwig et al. (2003).
9. B. J. Hayes et al., J. Dairy Sci. 92, 433 (2009).
taurine and indicine (humped) breeds and the (2), using six coat-color genes, provide strong 10. A. K. Outram et al., Science 323, 1332 (2009).
factors that may have shaped the breeds’ support for an earlier conclusion (10) that 11. I thank G. E. Robinson and R. Oliveira for their helpful
genetic diversity, thus addressing Darwin’s links horse domestication to the Botai cul- suggestions.
muse. High levels of genetic diversity were ture, which flourished in Kazakhstan in the
found in all cattle breeds, even higher than fourth millennium B.C.E.. Wild predomesti- 10.1126/science.1173880

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