Report On Spiny Lobster Abundance and Fishing Mortality and Preliminary Analysis of Existing Fisheries Data at Glover's Reef Research Station

GLOVERS REEF ANNUAL REPORT
REPORT ON SPINY LOBSTER ABUNDANCE AND FISHING MORTALITY AND PRELIMINARY ANALYSIS OF EXISTING FISHERIES DATA AT GLOVERS REEF RESEARCH STATION
March 2011
This publication was produced for review by the United States Agency for International Development. It was prepared by Dr. Elizabeth Babcock and Dr. Robin Coleman; Wildlife Conservation Society

REPORT ON SPINY LOBSTER ABUNDANCE AND FISHING MORTALITY AND PRELIMINARY ANALYSIS OF EXISTING FISHERIES DATA AT GLOVERS REEF RESEARCH STATION
Contract No.: EPP-I-00-04-0020-00 Task Order No. 5 Subcontract No.: EPP-I-05-04-0020-00-WCS Period of Performance: November 24, 2010 to September 15, 2014
The authors views expressed in this publication do not necessarily reflect the views of the United States Agency for International Development or the United States Government.
The authors views expressed in this publication do not necessarily reflect the views of the United States Agency for International Development or the United States Government.
CONTENTS
List of Acronyms and Abbreviations ............................................................................... iiiv Preface................................................................................................................................ ix Introduction .........................................................................................................................1 Part I: Spiny Lobster Abundance and Fishing Mortality at Glovers Reef Marine Reserve Abstract ................................................................................................................................3 Method ........................................................................................................................................... 3
Length based metrics of fishing pressure ........................................................................ 3 Abundance trends from the WCS catch per unit effort data set .......................................... 5 Abundance trends from the LAMP fishery-independent data set ....................................... 7 Abundance trends from the LAMP fishery-independent data set ....................................... 8
Bayesian DeLury state-space model fitted to catch.9 Bayesian DeLury regression model based on effort..10 Results ...............................................................................................................................11 Length - based metrics of fishing pressure ............................................................11 Abundance trends from the WCS catch per unit effort data set ............................12 Abundance trends from the LAMP fishery-independent data set ..........................13 Estimates of total abundance and fishing mortality from depletion analysis ........13 Bayesian DeLury state-space model fitted to catch ....................................14 Bayesian DeLury regression model based on effort ...................................15 Discussion ..........................................................................................................................15 References ..........................................................................................................................18 Table and Figures ...............................................................................................................20 PART II: Preliminary Analysis of Existing Fisheries Data at Glovers Reef Marine Reserve Abstract ..............................................................................................................................33 Methods..............................................................................................................................33 WCS Catch and Effort Data ...................................................................................33 LAMP data .............................................................................................................35 Catch and Effort from Fisheries .............................................................................36
vi GLOVERS REEF ANNUAL REPORT
Results ................................................................................................................................36 WCS Catch and Effort Data ...................................................................................36 LAMP Data ............................................................................................................37 Fisheries Data.........................................................................................................38 Discussion ..........................................................................................................................38 References ..........................................................................................................................39 Tables and Figures .............................................................................................................41
vii
LIST OF ACRONYMS AND ABBREVIATIONS

AIC BIC CITES CL CPUE CZ DIC F0.1 FAO Fmax GLM GLMM GUZ LAMP Lopt MCMC MSY SL TL WCS Akaike information criterion Bayesian information criterion Convention on International Trade in Endangered Species of Wild Fauna and Flora Carapace Length Catch Per Unit Effort Conservation Zone Deviance Information Criterion Fishing mortality rate that corresponds to a slope of the yield per recruit function 10% of its level for an unexploited stock Food and Agriculture Organization of the United Nations Fishing mortality rate that maximizes yield per recruit Generalized Linear Model Generalized Linear Mixed Model General Use Zone Long-term Atoll Monitoring Program Length that Optimizes Yield per Recruit Markov Chain Monte Carlo Maximum Sustainable Yield Shell Length Total Length Wildlife Conservation Society
viii
PREFACE
The Management of Aquatic Resources and Economic Alternatives program, financed by the United States Agency for International Development (USAID) and implemented by Chemonics International, with the Wildlife Conservation Society as a subcontractor, builds on previous projects in Central America to support and promote marine and coastal conservation through rights-based access and market-driven mechanisms in concert with local partners from both the private and public sectors. The USAID program will achieve these goals with a focus on four key trans-boundary watershed areas and seven key focal species. The four trans-boundary regions are the Gulf of Honduras, the Moskitia Coast, Cahuita-Gandoca-Bocas del Toro, and the Gulf of Fonseca. The focal species for the USAID program are divided into species with commercial importance: mangrove cockles, queen conch, grouper, snapper, and spiny lobsters; as well as two groups of endangered species: sharks and sea turtles. The USAID program will employ multiple strategies to positively affect its target species within its regional points of focus including the promotion of rights-based legislation and programs, establishment of managed protected areas and no-take reserves, promoting specific protections and management regimes for threatened species and by providing economic alternatives to local communities where resource extraction threatens marine and coastal natural resources. This Glovers Reef Annual Report provides long term analysis of spiny lobster and queen conch fishery independent surveys and catch per unit effort surveys to provide stock and catch information necessary to implement and manage an ecosystem approach to rights based fisheries at Glovers Reef.
ix
INTRODUCTION
Caribbean spiny lobster (Panulirus argus) is the most economically important species in the fisheries of Belize. According to an age-based stock assessment of spiny lobster in Belize (Gongora 2010), the spawning stock biomass declined by 8.7% between 1999 and 2009 and fishing mortality increased 46% to 1.3, because of increasing fishing effort. Although the biomass appears to be fairly stable in recent years, the fishing mortality rate is higher than the optimal level. According to yield per recruit analysis, the fishing mortality rate that would maximize yield (Fmax) is 0.85, while the more precautionary F0.1 reference point is 0.49 (Gongora 2010). A reduction in fishing mortality nationwide would be required to achieve either of these targets. Lobsters are also the most important fishery at Glovers Reef Marine Reserve. Conch are also an important fishery at the marine reserve (Acosta 2006). At Glovers Reef, WCS, with the support of USAID Program, has been interviewing fishermen to collect data on lobster and conch length, weight, catches and fishing effort from 2004 through the present (Grant 2004). The WCS LAMP data set, from a fishery independent underwater census focusing on conch, lobster and select finfish, was also available from 2004 through the present, including length and abundance of lobsters and conch at fixed sites in both the Conservation Zone and the General Use Zone. The National and Northern fisheries Cooperatives also report catches of spiny lobsters and conch to the Fisheries Department by month for the Glovers Reef region (Region 3); these data were available from 2002 through the present. Queen conch (Strombus gigas) is the second only to lobster as an economically important species in the fisheries of Belize. Queen conch are depleted throughout the Caribbean and are listed on Appendix II of CITES (FAO 2007). In Belize, conch production has increased over the last decade but is still below the national total allowable catch quota, and recent assessments have shown in increase in the population (Belize national report in FAO 2007, Carcamo 2008). The objectives of this paper are to evaluate the available data on size and abundance of spiny lobsters at Glovers Reef and to determine the level of fishing mortality, population size and trends in population size. It is not known what fraction of the lobsters recruiting at Glovers Reef are offspring of the local spawning stock and what fraction come from elsewhere in the Meso-American Barrier Reef system. Therefore, we did not apply stock assessment methods that assume a relationship between spawning stock and recruitment, as such models would require the assumption that Glovers Reef is a self-sustaining population. Instead, we used length-based indicators and depletion methods to estimate the abundance and fishing mortality of post-recruitment lobsters at Glovers Reef. Given this information, an appropriate sustainable catch level at Glovers Reef could be determined by applying the national target fishing mortality rate (Gongora 2010) to the lobsters at Glovers Reef. Another objective is to evaluate the available data on size and abundance of conch at Glovers Reef and to determine whether these data will be useful in estimating the level of fishing mortality, population size and trends in population size.
PART I: SPINY LOBSTER ABUNDANCE AND FISHING MORTALITY AT GLOVERS REEF MARINE RESERVE ABSTRACT
Data available on spiny lobsters at Glovers Reef Marine Reserve include the reported catch and fishing effort from the fishing Cooperatives, data on sizes, catches and fishing effort collected from fishermen at Glovers Reef, and a fishery independent visual survey (LAMP). Most of the harvested lobsters at Glovers Reef were above the size at maturity, but many were below the optimal size for harvest. The fishing mortality rate estimated from the length frequencies was less than the current national fishing mortality rate. The abundance data from the LAMP survey shows a generally increasing abundance trend across the time series, which combined with the fact that the LAMP survey found that lobsters tend to be bigger and more abundant inside the Conservation Zone, demonstrates that the Conservation Zone provides significant protection for lobsters. The catch per vessel day (from the Cooperative data) and the catch per fisherman hour showed a decline in relative abundance during the fishing season in most years. The WCS CPUE trend appeared to decline across years, while there was no clear trend in the Cooperative CPUE. Catches at Glovers Reef (those reported as region 3 by the National and Northern Cooperatives) were lower in recent years than in 2002-2004; however, it is unknown what fraction of catch from Glovers is inaccurately reported as catch from other regions. Delury population depletion models fitted to the CPUE data, combined with either catch or effort data from the Cooperatives gave extremely variable results depending on the model formulation and whether catch or effort data were used. More reliable catch and effort data would be needed to use these methods to estimate stock status and reference points. Recommendations are made for the improvement of data collection under new licensing scheme.
METHOD
Length based metrics of fishing pressure
Froese (2004) proposed three simple indictors to determine whether a population was being harvested in a sustainable fashion, based on the length distribution of fish in the catch. To avoid recruitment overfishing, he suggested that the fraction of fish in the catch that are above the length of maturity (Lm) should be high, preferably 100%, so that each individual has a chance to spawn at least once before being harvested. To prevent growth overfishing, all or most of the fish caught should be within plus or minus 10% of the optimal length of harvest (Lopt) based on yield per recruit analysis. The optimal length is the length at which the number of fish in a year class multiplied by their average weight is maximized; allowing the fish to grow to this size before harvesting them maximizes the weight of fish that can be caught. The third indicator proposed by Froese (2004), is the number of mega spawners which he defined as fish that are more than 10% above Lopt. A fishery management plan that included a maximum size limit and so avoided capturing any of these mega spawners would be ideal because the large fish are a
GLOVERS REEF ANNUAL REPORT 3
critical source of fecundity. In the absence of a maximum size limit in the fishery, the fraction of mega spawners in the population should be greater than 20%, consistent with a population with a healthy age distribution (Froese 2004). To calculate the Froese (2004) indicators for spiny lobster, we assumed the size at maturity was 70 to 80 mm carapace length (CL, FAO 2000). The minimum legal size for lobsters in Belize is 3 inches CL (76 mm), which is around the age at maturity, so that we expect most lobsters caught to be above this length. The optimal length (Lopt) was calculated as the length at which the numbers at age (assuming only natural mortality) multiplied by the weight at age reached a maximum using the von Bertalaffy growth curve [L=L(1-exp(-K(t-t0)))], using parameter values from Gongora (2010), a weight length relationship from FAO (2001) (W = 0.00460 CL ^2.630) and exponential decline in numbers, with a natural mortality rate of 0.34. Average length data can also be used to estimate total mortality (Z) based on average length and life history parameters taken from the literature, using the method of Beverton and Holt (1957) as modified by Ehrhardt and Ault (1992) and Ault et al. (2008, 2005). The original Beverton and Holt (1957) method makes the following assumptions: recruitment has been relatively constant in recent years; fish growth follows the von Bertalanffy growth model, with parameters K (growth rate) and L (asymptotic length); the total mortality rate (Z) is relatively constant over time and fish ages; and there is knife edge recruitment into the fishery at length Lc, and all fish above this size are equally likely to be captured.
Given these assumptions, the total mortality can be calculated as: K ( L L ) (1) Z = ( L Lc ) Ehrhardt and Ault (1992) showed that this method can be biased if the fishery does not exploit all older age classes of fish (for example if older individuals move into deeper water). They proposed the following formulation that also includes a maximum size of capture ( L ) assumed to be less than L. L L (2) L L c Z ( Lc L ) + K ( L L ) = Z (L L ) + K (L L )
Z K
Given these estimates of total mortality (Z) for each species, we calculated fishing mortality rate (F) by subtracting the natural mortality rate (M) taken from the literature. Any population for which F is much larger than M has probably experienced overfishing in its recent history. The method of Ehrhardt and Ault (1992) has previously been applied to spiny lobsters in the Caribbean (FAO 2001).
Lengths were reported in mm carapace length (CL) in both the LAMP data and the WCS catch data. The catch data also included tail length (TL) and second segment width (SW). Both TL and SW were recorded more often than CL in the WCS catch data set because the data recorders often had no access to lobster tails before they were processed by the fishermen. Nevertheless, the available life history data and the LAMP data used CL, so we used CL for all calculations, converting TL to CL using the linear relation between CL and TL calculated from the lobsters for which both lengths were available. There are many published growth curves for spiny lobster. We used a von Bertalanffy growth curve, with values of L =183 mm CL, K = 0.24, and t0=0.44, consistent with the most recent national assessment (Gongora 2010). We estimated total mortality from the WCS CPUE data set, as well as the LAMP visual survey data both in the General Use Zone and in the Conservation Zone.
Abundance trends from the WCS catch per unit effort data set
WCS researchers collected data on the number and size of lobsters caught from fishermen on the fishing grounds at Glovers Reef between 2004 and the present. For each fisherman, we calculated catch per unit of effort (CPUE) in whole weight of lobsters caught per fisherman hour. For more than 60% of the lobsters that were observed in the catch data set, whole weights were recorded. For lobsters for which tail weights had been recorded, we converted to whole weight using the conversion of tail weight to total weight from FAO (2001) (WTotal=2.97Wtail - 0.000327 in kg for females, WTotal= 3.38Wtail - 0.0238 for males). For individual lobsters for which no weights were recorded, we converted carapace length (WTotal = 0.00460CL2.630) to total weight using relationships from FAO (2001). It was necessary to exclude data for which the fishermans name was not recorded because it was not possible to determine how many lobsters had been captured by each individual fisherman. There were 641 unique combinations of fisherman, boat and date for which these data were collected. For each of these, we calculated CPUE as the weight of Caribbean spiny lobsters caught per hour fishing. There were a few cases (10 out of 641) in which the individual fisherman were interviewed twice in one day; we calculated only one value of the CPUE in this case, counting all the lobsters they had caught that day and using the largest reported value for hours fished. Lobster CPUE is expected to be proportional to abundance. However, catch rates can also vary depending on fishing location, environmental conditions and the relative effectiveness of different fishermen. Provided that data are available, a generalized linear model (GLM) can be used to estimate the impact of environmental conditions and other explanatory variables on the catch rates so that these effects can be removed from the estimated temporal trend. The GLM estimated trend should reflect only changes in abundance over time without being biased by any of the confounding factors (Maunder and Punt 2004). The data collected along with the lobster catches, biological data and hours fishing include the name of the boat, the name of the fisherman, the location, date, time and
depth fished. We classified the data into fishing seasons, assuming that lobster season started on June 15 and ended February 14 of every year, so that, for example, fishing season 2005 would begin on June 15, 2005, and include all fishing through the following February. Month within each fishing season was included in the model as a factor, so that the change in abundance during each fishing season could be tracked. We also included the moon phase (full: within 4 days of full, new: within 4 days of new, mid: otherwise) as a factor in case moon phase influenced catch rates. We did not include time of day in the analysis because most fishermen reported fishing six hours or more, so that the time each individual lobster was captured was not precisely known. Also, most data were collected between noon and 3:00 PM, so that the fishermen were all fishing around the same time of day (morning and early afternoon). We also did not include depth in the analysis because, although the fishermen were asked to report the depth range at which they were fishing, most had fished for 6 hours or more, so that it seemed unlikely that they had stayed within one depth zone. Of the 18 boats for which lobster catch and effort data were recorded, only 12 were sampled on 3 or more days. For the models in which boat name was included as a factor, we included only the 12 boats that had been sampled on three or more occasions. Locations were described with different categories in 2004-2005 than in 2006-2010. From 2006 to 20010, the majority of the lobsters (61%) were taken in the central lagoon north of the conservation zone (areas G5-G7). It was not possible to include both boat and location in the model, because most combinations of boat and location contained zero data points. Because there appeared to be more variability between boats than between locations, we chose to include boat in the model and ignore location. Using only data from the 12 boats with multiple samples, for the 2005through 2010 fishing seasons, the number of CPUE records was 641. There were no zero observations because the data recorder did not fill out a data sheet for fishermen who did not catch any lobsters. The lack of zero observations may introduce a bias into the estimated time trend of abundance because fishermen are more likely to catch zero lobsters when lobster abundance is low. The GLM model was: (3)
log(CPUEi , j ,k ,l ) = Ti + M j + Vk + 2way + i , j ,k ,l
where Ti is the effect of fishing year and month (i) for the 37 months between June, 2005 and July, 2010 for which data were collected, Mj is the effect of moon phase (j=full, mid or new), and Vk is the effect of individual boat (k = boat 1 through 12), and i , j ,k ,l is a normally distributed error term. All of the second order interactions between the terms are included. To determine which of these factors and their interaction significantly improve the model, we used Akaikes Information Criterion (AIC, Akaike 1974):
6 GLOVERS REEF ANNUAL REPORT
(4)
AIC=-2log(L)+2n
where log(L) is the natural log of the likelihood of the model and n is the number of parameters. The model with the lowest AIC thus optimizes the tradeoff between achieving a good fit between the GLM model and the CPUE data, and minimizing the number of parameters. We allowed the stepAIC function in the MASS library for R to choose the model that minimized AIC (Venables and Ripley 2002). In the case where boat or any of the two way interactions with boat were included in the AIC best model, we treated these parameters as random effects, using the function glmer in R (Bates 2010, Ortiz and Arocha 2004, R Development Core Team 2010). The AIC and the BIC (Bayesian information criterion; Bates 2010) were used to choose the best model with random effects. The time period (year and month) effect calculated by the mixed model was used to predict the log-CPUE for month and year and the predicted values and their standard errors were transformed from normal to lognormal to extract the temporal trend in abundance. Finally, to determine whether there was a significant decreasing trend in abundance within each fishing season, we repeated the GLM model with day within fishing season as a numerical variable to estimate the linear regression between day and CPUE within season: (5)
log(CPUEi , j ,k ,l ) = Yi + Di + M j + Vk + 2way + i , j ,k ,l
where Yi is the effect of fishing year i, and Di is the slope of the linear relationship between day since the beginning of fishing season i and log-CPUE.
Abundance trends from the LAMP fishery-independent data set
For lobster observations in the fishery independent LAMP data set, we used a similar generalized linear modeling approach. In the LAMP case, the sampling unit was one dive, so that the number of lobsters seen per dive is assumed to be an index of lobster abundance. For each lobster seen, the divers recorded the date, site, carapace length (CL), sex, whether eggs were visible, start time, number of minutes spent searching, depth, visibility and other physical variables. The LAMP data were collected at 11 fixed sampling locations that were either inside the conservation zone or in the general use zone near the boundary between zones. To test for an effect of management zone on lobster abundance, we included distance from the Conservation Zone boundary as a numerical variable (with negative values inside the Conservation Zone). An alternative formulation included management zone as factor with three levels: (1) general use zone more than 500 m from the conservation zone, (2) general use zone less than 500 m from the conservation zone, and (3) in the conservation
zone, in case the relationship between management zone and lobster abundance was nonlinear. Of the 207 dives in the dataset, 40% recorded zero lobsters. Therefore, we used a delta lognormal modeling approach, in which the number of lobsters in dives in which lobsters were seen was modeled as lognormal, while presence or absence was modeled as a binomial process (Ortiz and Arocha 2004). As in the fisheries CPUE analysis, we included potential explanatory variables in the model, to remove any effects of environmental conditions that may influence the count of lobsters. The potential explanatory variables we considered were the time period (year and month), the linear effect of distance from the management zone boundary, moon phase (full, new or mid), and the linear effects of time of day, visibility and depth. The GLM models were: (6)
log(Ci , j ,k ) = Ti + M j + Z + v + t + d + 2 way + i , j ,k
for positive sets, and : (7)
logit( Pi , j ,k ) = Ti + M j + Z + v + t + d + 2way
for presence or absence (P), where Ti is the effect of time period i, Mj is the effect of moon phase (j=full, new or mid), Z is the linear effect of distance from the Conservation Zone boundary (km), v is the linear effect of visibility (m), t is the effect time of day (in decimal 24 hour time), d is the linear effect of depth (m) and i , j ,k is a normally distributed error term. Some 2 way interaction terms were also included, although it was not possible to include all interactions given the relatively small sample sizes. To determine which of these factors significantly improve the model, we used Akaikes Information Criterion (AIC, Akaike 1974). The index of abundance was calculated by multiplying the inverse logit of the time period effect from the binomial model by the exponent of the time period effect from the lognormal model (with bias correction). Standard errors were calculated using the method of Lo et al. (1992). All factors were treated as fixed effects.
Catches and fishing effort (in vessel days) for region 3 (Glovers Reef) were provided by the Belize Fisheries Department by month, as reported by the National and Northern Cooperatives. The catches were reported as lobster tail weight and lobster head weight. We calculated total weights from tail weight as WTotal= 3.175 Wtail- 0.01206 (FAO 2001). The CPUE in lobster weight per fishing vessel day appeared to decline during most fishing seasons. Therefore we used several modifications of the DeLury depletion model
(Robert et al. 2010, Quinn and Deriso 1999, Bataille and Quinn 2006) to estimate the biomass of lobsters in the open area at the beginning of each fishing season, using a Bayesian method to estimate the parameters of each model.
Bayesian DeLury state-space model fitted to catch
We assumed that all recruitment occurred between fishing seasons, so that no lobsters would grow from sub-legal to legal size during the fishing season. During each month of the fishing season, the number of lobsters can be calculated as (Robert et al. 2010): (8)
N i ,t +1 = N i ,t e M 12 C iN e M 24 ,t
where Ni,t is number of legal sized lobsters in the General Use Zone at the beginning of month t in fishing season i, CNi,t is the catch in numbers during month t assumed to take place in the middle of the month, M is the instantaneous natural mortality rate, assumed to constant across years; M is in annual terms, so it is divided by 12 for a monthly time step in Equation 8. Assuming that the average weight of lobsters is constant, so that biomass is proportional to numbers: (9)
Bi ,t +1 = Bi ,t e M 12 C i ,t e M 24
where Bi,t is biomass of legal sized lobsters in the General Use Zone and Cit is catch in weight. We used Equation 9 rather than Equation 8 because the catch data were available in weight not numbers. Bi,1, the biomass at the beginning of the fishing season i, is a parameter that must be estimated; biomass in each subsequent month can be calculated from the starting biomass, natural mortality rates and catches using Equation 9. To estimate the model parameters, the predicted abundance trend from Equation 9 was fitted to catch per unit of effort as an index of abundance. The abundance indices used were the CPUE index derived from the Cooperative data (i.e. the average of the weight of lobster caught per vessel day in each month), and the standardized index of abundance derived above for the WCS catch and effort data described above. The standardize LAMP series could also be used as an index of abundance, but it was only available for two or three months in every year, so the we did not use it for the depletion model. The catch per unit effort from either the fishing Cooperative data or the WCS CPUE data was assumed to be proportional to abundance in the middle of the month, approximated by the average of abundance at the beginning and end of the month:
B + Bi ,t +1 (10) I j ,i ,t = q j i ,t e 2
where Ij,i,t is the value of the jth CPUE index of abundance in month t of fishing season i, qj is the constant of proportionality for abundance index j and is a normally distributed error (with variance j2). Both qj and j2 are assumed to be constant across months within a year; we ran some model formulations where they varied by year and some where they
were constant across all eight years (2002-2009). The fishing mortality rate in each monthly time step was approximated as Ft=-log(1-Ct/Bt), and the annual fishing mortality rate was the sum of the monthly rates. We used a Bayesian method to estimate the model parameters, implemented in the WinBUGS software (Sturtz et al. 2010, Lunn et al. 2000), which uses a Markov Chain Monte Carlo (MCMC) algorithm to approximate the posterior distributions of the parameters. Several alternative model structures were used (Table 1a). For models A through D, we fit the two abundance series for all eight years simultaneously. In models A and B, the model estimated a common catchability and variance across years for each series and a common natural mortality rate, along with the starting biomasses in each year. Models C and D allowed the model to estimate a different catchability and variance in each year for each series. The models also differed in how the starting biomass in each season (i= 2002 to 2009) was estimated. In models A and C, each years starting biomass was given an independent non-informative prior (Table 1). In models B and D a Bayesian hierarchical modeling framework was used, so that the starting biomasses in each fishing season was assumed to be randomly drawn from a lognormal distribution, with log-mean and log-standard deviation estimated by the model (Table 1a and b). This hierarchical structure allows the data from multiple years to inform the estimate of starting biomass in each year, thus increasing the precision of the estimates for each year (Royle and Dorazio 2008). The four multi-year models (A through D) were compared using the Deviance Information Criterion (DIC, Royle and Dorazio 2008), which is the equivalent of the AIC for Bayesian models, and allows us to pick the model that optimizes the trade-off between the number of parameters and goodness of fit to the CPUE data. Note that the hierarchical models have a lower number of effective parameters than do the nonhierarchical models, because there is a correlation between starting biomasses in each year. As an additional sensitivity analysis, we fit the model to the CPUE data to each series in each year independently, using the same priors as in the multi-year models (model E). The prior distributions of the estimated parameters (Table 1b) were non-informative , except for the prior for M, which was normally distributed with a mean of 0.34, and standard deviation of 0.04 (Gongora 2010, FAO 2001). This prior distribution constrained the value of M to be within a biologically plausible range. To ensure adequate convergence of the MCMC, we ran three chains, with 450,000 iterations after a burn-in of 50,000 iterations, and a thin rate of 10. With these settings, all the models converged adequately according to the Gelman-Rubin diagnostic (Lunn et al. 2000).
Bayesian DeLury regression model based on effort
The decline in abundance during a fishing season can also be modeled using effort rather than catch: (11)
10
N i ,t +1 = N i ,t e M qU t
where Ut is the effort in month t. Therefore, the log of the abundance index (I) in each time period can be modeled as: (12) log(I t ) = log(qB1 ) M (t 0.5) qEt + t where Et is cumulative effort up to the middle of month t and is a normally distributed error term (Quinn and Deriso 1999, Battaile and Quinn 2006). This is the classical DeLury regression method, with the addition of natural mortality. The model was fitted to the average CPUE per vessel trip from the Cooperative data and the Cooperative effort data in vessel days. We used a Bayesian method to estimate the parameters for this model, with the same priors for M, q and the error variance that were used in the statespace model (Table 1). The prior for q only allowed positive values of this parameter; we also re-ran the model with an unrestricted prior for q to determine whether the data support a relationship between cumulative effort and CPUE (i.e. whether the value of q was positive and significant). The annual fishing mortality rate was calculated as F=qEt at the end of the season.
RESULTS
Length - based metrics of fishing pressure
Of the 3309 lobsters recorded in the WCS catch dataset, TL was measured for all, but CL was measured for only 2113. For the 2089 lobsters for which both CL and TL data were measured and the two values were consistent with each other, the regression was CL=14.6+0.54TL (R2=0.47). We used this equation to convert TL to CL. The optimal length (Lopt) was 119 mm CL, corresponding to an age of 4.8 years. The values of the Froese (2004) indicators were: (1) 78-96% of the catch was mature individuals; (2) 15% were near the optimal length; and (3) 4% were mega-spawners. These values indicate that there is some potential to harvest a higher yield of lobsters from Glovers Reef if they were allowed to grow somewhat bigger before they are harvested. In general, the average sizes within the size range most commonly taken in the fishery (between 89 and 180 cm CL) were slightly higher in the conservation zone LAMP data than in the general use zone LAMP data, and both were larger than in the fisheries data (Table 2, Figure 1). The distribution of sizes for male and female lobsters was fairly similar to each other in each data set (Figure 1). Because of the difference in average size, the estimated fishing mortality rate was higher for the fishery data than for the LAMP data in the fished zone, which was higher than the estimate in the unfished zone. The estimated value of F from the fishery data was 0.88, which is considerably lower than the national average fishing mortality rate of 1.3, but higher than the Fmax of 0.85 (Gongora 2010). The higher average size in the LAMP data may be in part explained by spillover from the marine reserve. The size distribution of lobsters seen in the LAMP survey more than 500 m from the Conservation Zone (Figure 1b) is similar to the length
distribution in the fishery (Figure 1a), while there are many more lobsters greater than 100mm CL within 500 m of the boundary (Figure 1c). The annual average size of individuals above the minimum size in the LAMP data appear to have increased and then decreased again between 2002 and 2009 (Figure 2), while the average size in the fisheries data seems to be fairly constant. The lack of change in average size between years is consistent with relatively stable recruitment and relatively similar fishing mortality rates in each year. Within the fisheries data, the average sizes are fairly constant across months in most years (Figure 3), the exception being a decline in average size in 2006 and an increase in 2005.
Abundance trends from the WCS catch per unit effort data set
The unstandardized log-CPUE data (Figure 4) appear to show a downward trend in logCPUE with time within most fishing seasons. Log-CPUE also appears to be lower in the new moon, and variable between fishing boats. Fishing location shows no obvious patterns in the raw data. In the GLM, all of the direct effects of time period, boat and moon phase were highly significant (Table 3a). The interactions between boat and moon phase and boat and time period were also included in the AIC best fit model with fixed effects. This model explained about 47% of the variability in the log CPUE data. The diagnostics showed a good fit between the model and the data (Figure 5). When boat and the 2-way interactions were treated as random effects, both the BIC and the AIC found that the best model was the one that included the three main effects plus the time period x boat and time period x moon phase interactions (Table 3b). This model was used to calculate the standardized CPUE trend. The standardized CPUE by month (Figure 6) is highest in the first month of the season for all seasons, while the last month of each season has the lowest CPUE. If the fishing mortality remained at a sustainable level, we would expect CPUE to decline during the fishing season, and increase again at the beginning of the next season. While the CPUE at the beginning of each season is higher than that at the end of the first season, there also appears to be a declining trend across the entire time series. When a linear trend was estimated for CPUE across days within the fishing season (rather than including month as a factor), there was a decline in CPUE during every fishing seasons except 2006. Unfortunately, the data set includes catch and effort from only fishermen who caught lobster; fishermen who went out looking for lobsters and did not find any on the day when they were interviewed are not included in the dataset (i.e. no zero data are recorded). A histogram of the count of lobsters caught per fishermen in the dataset (Figure 7) shows that it is quite common for fishermen to catch only one or two lobsters; thus, it is probably common for fishermen to catch zero lobsters. This lack of zero observations can introduce bias into the use of CPUE as an index of abundance. For example, if low abundance of lobster causes fishermen to spend more time searching for lobsters without finding any, the lack of zero observations in the data would cause the
CPUE method to overestimate abundance at times when abundance was low, thus reducing the estimated change in abundance.
In the LAMP data set, about 39% of dives recorded zero spiny lobsters, although some reported as many as twenty (Figure 8). A total of 579 lobsters were observed, of which 67% were above the legal size. The natural log of lobsters seen per dive appeared to vary by time period, visibility, depth, time of day, sampling site, management zone, moon phase and whether lobster season is open (Figure 9). Estimating the impact of these variables on the number of lobsters seen would thus improve the estimate of changes in abundance over time. For both GLM of the log of positive CPUE and the presence/absence GLM, the AIC best fit models (Table 4, Figure 10) included time period and distance from the Conservation Zone. The best model also included visibility and depth for the presence/absence model. The interaction between distance from the Conservation Zone and time period was not significant and was not included in the AIC best model; implying that the temporal trend in abundance was the same both inside and outside of the Conservation Zone. In both models, distance from the Conservation Zone had a negative effect on abundance, although the effect was only significant in presence/absence model. These models explained 24% of the deviance in the presence/absence data and 71% of the deviance in the abundance if present. The diagnostics (Figure 10) showed a good fit to the positive CPUE model (Figure 10b), although the qq-normal plot of the presence/absence GLM (Figure 10a) shows some departure from normality. When an abundance index was calculated as the product of the predicted fraction of dives to see a lobster, times the expected number of lobsters, from the AIC best fit models, the abundance of lobsters is quite variable but shows a generally increasing trend (Figure 11). Despite the fact that more lobsters are seen in the Conservation Zone than the General Use Zone (Figure 9), the temporal trend is the same both inside and outside the Conservation Zone. There is also a tendency for abundance to be higher around the beginning of lobster season in most years (Figure 11).
Estimates of total abundance and fishing mortality from depletion analysis
The reported catch of spiny lobster at Glovers Reef, from the Northern and Central Cooperatives, has been lower in 2005 through 2009 than in 2002 through 2004; reported catches also declined between the beginning and end of the lobster season in most years (Figure 12). The CPUE (i.e. average of catch per vessel-day as reported to the Cooperatives) also declined during the first few months of the lobster season every year (Figure 12b), although there are also some high CPUE values late in the year in 2004 and especially 2008. The low reported catches in recent years are not consistent with the WCS data (Figure 12c). Although WCS has consistently been sampling on 10-20% of the days in each month, there are some months when WCS sampled a larger catch than
was reported to the cooperatives (fraction of catch greater than 1 in Figure 12c). This implies that some of the decline in Glovers Reef catches reported to the cooperatives is likely an error, perhaps caused by incorrect allocation of catches from area 3 (Glovers Reef) to other regions.
Bayesian DeLury state-space model fitted to catch
The Bayesian depletion models, whether fitted to data from only one year, or to all years simultaneously were able to fit the declining trends in CPUE during each year (Figure 13). For the single year models in 2008, the trend estimated with the only the Cooperative CPUE data was different from that estimated with only the WCS CPUE data, because in that year, the WCS data showed a decline while the Cooperative data showed an increase in CPUE throughout the fishing season. The multiyear models and the single year models produced similar trends every year except 2009. In 2009, the multi-year models showed very little decline throughout the fishing season while the single year model showed a decline. The posterior distributions of the biomass at the beginning of the fishing season (Figure 14) implied that the biomass was very poorly estimated in most years. Although there was a distinct peak in the posterior distribution at biomass levels on the order of 100 t in most years, implying that values in this range were the most likely, the posterior distribution had a long tail to the right, implying that even very high biomass levels had posterior probabilities greater than zero. Of the four multi-year models, the DIC preferred the models with separately estimated variances and catchabilities in each year over the models with fixed catchability and variance (Table 5). The DIC best model was the one with time-varying q and variance and without hierarchical structure in the starting biomasses in each year (Model C, Table 5). Model C estimated an increase in both catchability and variance in the Cooperative series; both catchability and variance were variable but decreasing for the WCS series (Figure 16). The reason for these estimated trends in catches is not clear. The catchability for the Cooperative CPUE series, based on catches per vessel day, could change between years if trip length or number of fishermen per boat changed, or if there were changes in how data are recorded. Catchability may be more constant between years in the WCS series based on catch per fishermen hour, if fishing methodologies have not changed. It is also possible that catchability changes over time within fishing season, for example if lobsters are easier to find earlier in the season or that there is non-linear relationship between catch rates and abundance. The hierarchical models across all years (B and D) gave a more precise estimate of the starting year biomass than the non-hierarchical models (A and C), and models that allowed variance and catchability to vary across years (C and D) were more precise than those with catchability and variance fixed across years (A and B) (Figure 15). All of the multi-year models except model D give more precise results than did the single year models (Figure 14, Figure 15a). Model D, which allowed q and variance and starting year biomass to vary freely between years was, as expected, nearly identical to the results
obtained by fitting data from each year separately. The hierarchical models, as expected, estimated more similar abundance levels in each year than did the year by year models. Interestingly, the non-hierarchical multi-year model with time-varying q and variance (model C) also gave more similar starting biomass estimates across years than did the single year models, implying that whether or not catchability and error variance are allowed to vary across time periods has a significant influence on the results. The year by year models give a reasonably precise estimate of the starting year biomass in years when the CPUE appeared to decline exponentially over the course of the season (e.g. 2002 for the Cooperative series, 2007 for the WCS series). For years in which the CPUE increased during the fishing season (e.g. 2008 for the Cooperative data series), the yearby-year model estimated an extremely broad credibility interval for starting year biomass. The models estimated starting biomass levels from about 20 to 200 t live weight of lobsters in the General Use Zone (Figure 15a). The lobster biomass was depleted to about 55-75% of starting biomass in each fishing year (Figure 13). The fishing mortality rates estimated by the models ranged from 0.05 to 0.5 (Figure 15b). Like the biomass estimates, the F estimates are more precise for the multi-year models than for the year by year models. Because the multi-year models (except for model D) estimate relatively constant starting biomasses across the year, they estimate a declining trend in fishing mortality rate. The year to year trend in biomass and fishing mortality also varies with model structure.
Bayesian DeLury regression model based on effort
The Leslie regression methods were able to estimate beginning year biomass levels from the Cooperative effort data in every year (Figure 17, Figure 15). Because of the informative prior for M, and the fact that q and was constrained to be positive, the model estimated a declining trend in each year, even when CPUE appeared to increase with cumulative effort in 2008. An alternative run in which negative q was allowed estimated a negative starting biomass in 2008, but produced identical results in every other year. The regression methods generally estimated a starting biomass in each season in the lower range of the posterior distribution estimated by the Bayesian models and also estimated that starting biomass declined between 2002 through 2009 (Figure 15a). Because of the decline in biomass, these models implied an increase in fishing mortality rate between 2002 and 2009 (Figure 15b), and the estimated fishing mortality rates were much lower than those estimated by the state-space models.
DISCUSSION
The analysis presented here provides a somewhat complex picture of the status and trends in abundance of spiny lobsters at Glovers Reef marine reserve (Table 6). According to the size based indicators, most of the harvested lobsters at Glovers Reef are above the size at maturity, but many are below the optimal size for harvest. The fishing mortality rate based on the length data from the fisheries (F=0.88) is just above Fmax , and well
above both F0.1 and M; it is also less than the current national fishing mortality rate (F=1.3) (Figure 18). There are no obvious trends in average length over time, which would indicate a change in fishing mortality rate. The abundance data from the LAMP survey shows a generally increasing trend across the time series, although abundance seems to be higher around the beginning of the lobster season than it is later in the season. This increase in abundance, combined with the fact that the LAMP survey found that lobsters tend to be bigger and more abundant inside the Conservation Zone is consistent with the Conservation Zone providing significant protection for lobsters. All but two of the LAMP survey sites for lobster are either inside the Conservation Zone or within 500 m of the boundary, so that it is to be expected that the LAMP survey trend would be dominated by the Conservation Zone where lobsters are more abundant. The two CPUE indices of abundance (from the Cooperative data and from the WCS data) show a decline in relative abundance during the fishing season in most years, and no obvious trend between years except a slight decline in the WCS data. The CPUE in catch per fisherman hour (the WCS data) is more likely to be an accurate measure of abundance than the catch per vessel day (the Cooperative data), because effort is measured more precisely. The CPUE in terms of vessel day can be biased if, for example, the number of fishermen associated with a vessel changes, or if the vessel loses a days fishing due to weather. Some measure of catch (or effort) is necessary to estimate sustainable catch levels. Unfortunately, the region 3 catches reported by the National and Northern Cooperatives do not appear to include a significant fraction of catches from Glovers Reef, particularly after 2005. In part because the catch and effort data are inconsistent with the CPUE data, the results of the Bayesian depletion estimates are quite variable. The state-space model (using catch data) estimated very low fishing mortality rates, ranging from 0.05 to 0.5 depending on the structure of the model (Figure 18). These mortality rates are quite low compared to the current national averaging fishing mortality rate of 1.3 (Gongora 2010). On the other hand, the regression model fitted to the effort time series estimated fishing mortality rates very similar to those from Gongora (2010), with a current (2009) median F of 1.5. Which of these two sets of estimates is more accurate is difficult to say; both are based on the same CPUE indices of abundance, but the regression method uses effort data while the state-space method uses catch data. Also, the different model structures imply different error structures, which can influence the results. It would be worthwhile to determine what fraction of Glovers Reef lobster catch is reported at the National and Northern Cooperatives. If fishermen sell some of their catch elsewhere, especially if the fraction of catch sold elsewhere has changed over time, the catch and effort data may be very misleading. It should also be noted that, because these analyses are based on data from lobsters that were caught by fishermen, the estimated biomass at the beginning of the season is only the biomass that is available to the fishery, corresponding to the biomass of legal sized lobsters in the General Use Zone within free-diving depths at the beginning of the lobster
season. Spillover of lobsters from the Conservation Zone during the lobster season would be interpreted by the models as lower fishing mortality rates, because such spillover would prevent the CPUE indices from declining as rapidly as they would otherwise. Also, the models assume that no lobsters grow to the legal size during the fishing season; such growth would be interpreted as lower fishing mortality by the model. Assuming that the National and Northern Cooperative data capture all or most of the lobsters taken from Glovers Reef, it would be possible to set a total allowable catch (TAC) for Glovers Reef based on these data. For example, using F0.1 as a target fishing mortality rate, and using the biomass estimates from the same models shown in Figure 18, the appropriate target catches range from much lower than the current catch, to as high as catches used to be in 2002 through 2004 (Figure 19). Given the uncertainty of the catch and effort data, these values should probably not be used. Alternatively, an ad hoc management system could be developed using the indicators that we have calculated, for example using a decision tree in which the population is considered overfished if several indicators show a negative trend (e.g. Prince 2008). Finally, relative densities inside and outside the no-take zone could be used to determine an appropriate level of harvest. For any management strategy, it is critical to be able to document the total catch and/or total effort at Glovers Reef, either by improving the reliability of the area designations in the Cooperative data, or by gathering complete catch and effort data from the fishermen while they are at Glovers Reef.
17
REFERENCES
Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control. 19:716 723 Ault, J.S., Smith, S.G. & Bohnsack, J.A. 2005. Evaluation of average length as an indicator of exploitation status for the Florida coral reef fish community. ICES Journal of Marine Science 62:417423. Ault, J. S. S. G. Smith, J. Luo, M. E. Monaco and R. S. Appeldoorn. 2008. Length-based assessment of sustainability benchmarks for coral reef fishes in Puerto Rico. Environmental Conservation 35 (3): 221231. Battaile, B. C. and T. J. Quinn. 2006. A Delury depletion estimator for walleye pollock (Theragra chalcogramma) in the Eastern Bering Sea. Natural Resources Modeling 19: 655-674. Bates, D. 2010. Package LME4: Linear mixed-effects models using S4 classes. http://lme4.r-forge.r-project.org/. Beverton, R.J.H. and Holt, S.J. 1957. On the Dynamics of Exploited Fish Populations. Ministry of Agriculture, Fisheries and Food, Fishery Investigations Series II, Volume 19. Cope, J. M. and A. E. Punt. 2009. Length-based reference points for data-limited situations: Applications and restrictions. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 1:118, 2009 Ehrhardt, N.M. & Ault, J.S. 1992. Analysis of two length-based mortality models applied to bounded catch length frequencies. Transactions of the American Fisheries Society 121: 115122. FAO. 2001. Report on the FAO/DANIDA/CFRAMP/WECAFC Regional Workshops on the Assessment of the Caribbean Spiny lobster (Panulirus argus). FAO Fisheries Report No. 619. Froese, R. 2004. Keep it simple: three indicators to deal with overfishing. Journal of Fish Biology 56: 758773. Gongora, M. 2010. Assessment of the spiny lobster (Panulirus argus) of Belize based on fishery-dependent data. Belize Fisheries Department. March, 2010. Grant, S. 2004. Glovers Reef Marine Reserve Fisheries Boat Census 2004 (Part 1). Wildlife Conservation Society.
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Lo, N. C. H., L. D. Jacobson, and J. L. Squire. 1992. Indices of relative abundance from fish spotter data based on delta-lognormal models. Canadian Journal of Fisheries and Aquatic Sciences 49: 251 5-2526. Lunn, D.J., Thomas, A., Best, N., and Spiegelhalter, D. (2000) WinBUGS -- a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing, 10:325--337. Maunder, M.N. and A. E. Punt. 2004. Standardizing catch and effort data: a review of recent approaches. Fisheries Research 70:141159. Ortiz, M. and F. Arocha. 2004. Alternative error distribution models for standardization of catch rates of non-target species from a pelagic longline fishery: billfish species in the Venezuelan tuna longline fishery. Fisheries Research 70: 275297. Prince, J. D., H. Peeters, H. Gorfinec and R. W Dayc. 2008. The novel use of harvest policies and rapid visual assessment to manage spatially complex abalone resources (Genus Haliotis). Fisheries Research 94:330338 Quinn, T.J., II, and Deriso, R.B. 1999. Quantitative Fishery Dynamics. Oxford, New York. R Development Core Team. 2010. R: A Language and Environment for Statistical Computing, Vienna, Austria http://www.R-project.org. Robert, M., A Faraj, M. K. McAllister and E. Rivot. 2010. Bayesian state-space modeling of the DeLury depletion model: strengths and limitations of the method, and application to the Moroccan octopus fishery. ICES journal of Marine Science . Royle, J.A. and R. M. Dorazio. 2008. Hierarchical Modeling and Inference in Ecology: The Analysis of Data from Populations, Metapopulations and Communities. Elsevier. Sturtz, S., U. Liggesy and A. Gelman. 2010. R2WinBUGS: A Package for Running WinBUGS from R. www.cran.org Shin, Y. J. ,M.J. Rochet, S. Jennings,J. G. Field, and H. Gislason. 2005. Using size-based indicators to evaluate the ecosystem effects of fishing. ICES Journal of Marine Science: 62: 384-396. Venables, W.N. and B. D. Ripley. 2002. Modern Applied Statistics with S. 4th Edition. Springer.
19
TABLES AND FIGURES

Table 1. Parameters and their prior distributions for the Bayesian depletion models. (a) Model parameters
Model configuration A. All years, both series, constant q and 2 B. Same, but hierarchical model of Bi,1 C. All years, both series, variable q and 2 D. Same, but hierarchical model of Bi,1 E. Each individual series (12 runs) Parameters M q1, q2 M q1, q2 M q1- q12 M q1- q12 M q
2 2
1 , 2 2 2 1 , 2 2 2 1 - 12 2 2 1 - 12 2
Bi,1 for 8 years Bi,1 for 8 years Bi,1 for 8 years Bi,1 for 8 years B1
B, B B, B
(b) Priors for the model parameters

Parameter M B B
2
Description Natural mortality rate Average across years of starting biomass Variance between years of starting biomass Exploitable biomass of lobsters at the beginning of the lobster season i
Prior M=Normal(=0.34, =0.04) log(B)=Normal(=0, =1000) 1/ B =Gamma(0.01,0.01) log(Bi,1)=Normal(= B, = B) for the hierarchical models, log(Bi,1)=Normal(= 0, =1000) for non-hierarchical models
2
Range - - 10001.0E7 0- 0- 10001.0E7 1.0E-71.0 0.001100
Bi,1
qj j
2
Catchability for abundance index j Observation error variance for abundance index j
log(qj)=Normal(=0, =0.01) 1/ j =Gamma(0.01,0.01)

2
Table 2. Fishing mortality rate estimated from average length using the method of Ehrhardt and Ault (1992).
Data source Catch data LAMP general use zone LAMP conservation zone n 3293 228 341 Lc 90 90 90 n in range 1859 89 214
L
105.3 117.8 120.3
se 0.33 2.51 1.69
Z 1.22 0.56 0.49
M 0.34 0.34 0.34
F 0.88 0.22 0.15
Table 3. GLM of lobster log CPUE in whole weight of legal sized lobsters per fisherman-hour, as a function of time period (T), boat (B) and moon phase (M), for (a) the AIC best model with fixed effects, and (b) random effects models with all
possible second order interactions. The best random effects model according to the AIC and the BIC is in bold. (a) For AIC best model with fixed effects
Df NULL T B M TxB TxM BxM 36 11 2 38 8 2 Deviance 155.4 29.4 5.0 47.1 17.8 11.2 Resid. Df 614 578 567 565 527 519 517 Resid. Dev 558.3 402.9 373.5 368.5 321.4 303.6 292.5 F 7.63 4.72 4.40 2.19 3.94 9.86 Pr(>F) 0.0000 0.0000 0.0128 0.0001 0.0002 0.0001 % deviance 0.28 0.05 0.01 0.08 0.03 0.02
(b) With random effects.

Model T+M+B T+M+B+TxB T+M+B+TxM T+M+B+BxM T+M+B+TxB+TxM T+M+B+TxB+BxM T+M+B+TxM+BxM T+M+B+TxB+TxM+BxM AIC 1590.25 1577.84 1581.12 1591.67 1572.01 1579.82 1581.42 1573.29 BIC 1771.53 1763.55 1766.83 1777.38 1762.14 1769.95 1771.55 1767.84 deviance 1463.39 1477.21 1507.77 1465.41 1502.30 1477.59 1509.36 1504.66
Table 4. Analysis of deviance table for AIC best fit model of log of the count of lobsters per dive in the LAMP survey (T=time period[month and year], Z=distance from conservation zone boundary, v=visibility and d=depth). (a) presence/absence
Df NULL T v d Z 20 1 1 1 Deviance 43.4 11 9.4 9.5 Resid. Df 220 200 199 198 197 Resid. Dev 305 261.6 250.6 241.2 231.7 P(>|Chi|) 0.0018 0.0009 0.0022 0.0021 % deviance 0.14 0.04 0.03 0.03
(b) log count of lobsters for positive dives.

Df NULL T Z 20 1 Deviance 176.7 1.5 Resid. Df 133 113 112 Resid. Dev 248.6 71.9 70.5 F 14.04 2.31 Pr(>F) 0 0.1314 % deviance 0.71 0.01
21
Table 5. DIC results for the Bayesian state space models. Model C (catchability and variance different in each year, no hierarchical structure for starting biomass) has the lowest DIC.
Model A B C D Dbar 144.20 144.76 100.25 99.99 Dhat 134.84 137.68 83.21 73.50 pD 9.36 7.08 17.04 26.50 DIC 153.56 151.84 117.28 126.49 Delta DIC 36.27 34.56 0.00 9.21
Table 6. Summary of results for spiny lobster

Analysis Froese indicators F from ave. length Catches WCS CPUE CPUE from Coop LAMP abundance B from depletion models F from depletion models Status Most are mature, but too few large lobsters F above F0.1 and close to Fmax Lower in 2005-2009 then in 2002-2004 Declines during season, between years Declines during season, no trend between years Decrease during seasons, increase between years Stable or decreasing depending on model Increasing or decreasing depending on model
Figure 1. Length frequency distributions of spiny lobster in the LAMP and WCS catch data. Lobsters mature at 70-80 mm CL (Gongora 2010), and the legal minimum size is 78 mm CL.
(a) Fishery
Female Male Unknown 600
(b) LAMP General Use Zone far from boundary
Count
400
200
20
40
60
80 100
130
160
190
220
250
0 0
8 10
20
40
60
80 100
130
160
190
220
250
(c) LAMP General Use Zone near boundary

20 40 0 20 40 60 80 100 130 160 190 220 250 0 10 20 30
(d) LAMP Conservation Zone
Count
10
15
20
40
60
80 100
130
160
190
220
250
Carapace length (mm)
Carapace length (mm)
22
Figure 2. Average lengths plus or minus one standard error for the LAMP data in both unfished and fished zones and for the WCS fisheries data, for all lobsters for which carapace length (CL) was greater than the minimum size limit.
(a) LAMP Conservation Zone
150 150
(b) LAMP General Use Zone

120 CL(mm) 2004 2005 2006 Year 2007 2008 2009 0 20 40 60 80 100
(c) Catch CL
100
CL(mm)
50
CL(mm) 0 2004 2005 2006 Year 2007 2008 2009
50
100
2004
2005
2006 Year
2007
2008
2009
Figure 3. Average lengths by months within years, in WCS catch data set. (a) Fisheries
150 CL(mm) 50 100
2004 2005
2006 2007
2008 2009
6 Month
10
12
Figure 4. Raw log-CPUE (in kg) data summary, showing the trend in log-CPUE (a) by month within each fishing season (i.e. 2005.01 means the first month in the 2005 fishing season),(b) by moon phase, (c) by boat and (d) by location.
(a) Month in season
9 8 8 5 6 7 9 log CPUE
(b) Days after full moon
log CPUE
(c) Boat
9 8 8 5 1 2 3 4 5 6 7 8 9 10 11 12 6 7 9 log CPUE
2005.01 2005.02 2005.03 2005.04 2005.07 2005.08 2006.01 2006.03 2006.04 2006.05 2006.06 2006.08 2007.01 2007.02 2007.03 2007.04 2007.05 2007.06 2007.07 2007.08 2008.01 2008.02 2008.03 2008.04 2008.06 2008.07 2008.08 2009.01 2009.02 2009.03 2009.04 2009.05 2009.06 2009.08 2009.09 2010.01 2010.02
(d) Location
log CPUE
Eastern Reef
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 25 26 27 28 29 G3 G4 G5 G6 G7 G8 North Point
23
Figure 5. Residuals versus fitted values, and qq normal plot, for the AIC best fit mixed effects model (Table 3.2b) for lobster log-CPUE.
Residuals versus fitted

2 Sample Quantiles 2
Normal Q-Q Plot
Residuals
-2 -1
5.0
5.5
6.0
6.5 Predicted values
7.0
7.5
8.0
-2 -1 -3
-2
-1
Theoretical Quantiles
Figure 6. Trend in CPUE (solid line) during each fishing season from the AIC best fit model (Table 3.2), plus and minus one standard error (dashed line), along with unstandardized CPUE values (points).
CPUE
0 2005
2006
2007 Year
2008
2009
2010
24
Figure 7. Histogram of number of lobsters caught per fisherman in the WCS catch data.
Count
10
20
30
40
50
60
70
11
13
15
17
19
21
23
25
27
29
31
33
35
37
39
41
43
45
Lobsters per fisherman
Figure 8. Histogram of lobsters observed per dive in the LAMP data set.
Legal All sizes
Number of dives
20
40
60
80
100
10
11
12
13
14
15
16
17
18
19
20
Number of lobsters
25
Figure 9. Log number of lobsters observed per dive [log(Count+0.01)] in the LAMP data, by month, visibility, depth, time of day, sampling site, distance from the conservation zone boundary, management zone, days from full moon and whether lobster season is open, including dives for which no lobsters were observed.
Time period
0 2 4 6 8 0 2
Visisbility
5
Depth
log-count
log-count
log-count 5 10 Visibility(m) 15 20
-6 -4 -2
2004.08 2004.10 2005.03 2005.05 2005.11 2006.03 2006.07 2006.09 2007.02 2007.05 2007.08 2007.11 2008.02 2008.05 2008.08 2008.11 2009.02 2009.06 2009.08 2010.05
-10
-4
-5
10 Depth(m)
15
Start time
0 2 4 0 2
Site
4
Distance from conservation zone
log-count
log-count
log-count prC10AB prC1AB prC3AB prC6AB prC8AB
-6 -4 -2
-4
-8
10
12 Time
14
16
-8
-4
-2
-1
0 Distance (km)
Management zone
2 6 0 4
Days from full moon

0 2
Fishing season
log-count
log-count
-6 -4 -2
log-count 0 5 10 15 Day 20 25 30
CZ
Line
GUZ
-4 -2 0
-6 -4 -2
1 fishseason
Figure 10. Residuals and qq-normal plot of the AIC best fit model of (a) presence or absence of lobsters and (b) log lobster sightings per minute in the LAMP observations for dives in which lobsters were seen. (a) Presence/absence
Residuals vs Fitted
3 Std. deviance resid.
6
Normal Q-Q
3
6
Residuals
-1
-2
65
-2
-1
57
57
18
-4
-2
0 Predicted values
-3
-2
-1
0 Theoretical Quantiles
(b) Positive log-lobsters per dive

Residuals vs Fitted
Std. deviance resid. 1 2
183
Normal Q-Q
183
Residuals
-1
-2
38 29
-2
-1
38 29
0.5
1.0 Predicted values
1.5
-2
-1
26
Figure 11. LAMP lobster standardized trend (liness), plus and minus one standard error, from the AIC best fit models (Table 4). The CPUE abundance index is the product of the predicted fraction of dives seeing a lobster times the predicted number of lobsters seen given that any were seen. Unstandardized average count for sites in the General Use Zone is also shown (points). The index and the raw data have been divided by their means. Vertical lines indicate the beginning (at the tick mark) and end of the fishing season.
Lobster abundance index
2004
2005
2006
2007 Fishing season
2008
2009
2010
Figure 12. Lobster (a) catches and (b) catch per unit of effort from area 3 (Glovers Reef) from the Belize fisheries data set by month, for Northern and National Cooperatives combined, and (c) comparison between catch and effort sampled by WCS and catch and effort reported to the cooperatives. (a)
Whole weight (kg)
5000 10000
2002
2003
2004
2005
2006
2007
2008
2009
27
28
(b)
(c)
CPUE 5 10 15 20 25 (b) Average catch per vessel day
0.0
2004.04 2005.01
0.2
0.4
0.6
0.8
1.0
Fraction of catch sampled Fraction of days sampled
2002
2005.02 2005.03 2005.04 2005.07 2006.01 2006.03 2006.04 2006.05 2006.06 2007.01 2007.02 2007.03 2007.04 2007.05 2007.06 2007.07
2003 2004 2005
Year
2008.01 2008.02 2008.03 2008.04 2008.06 2008.07 2009.01 2009.02 2009.03 2009.04 2009.05 2009.06
2006 2007 2008 2009
Figure 13. CPUE data points from the Cooperative data (by vessel-trip) and from the WCS catch and effort data (by fisherman-hour), along with the median values of the fitted biomass trends from the depletion model fitted to the data from each year separately (fitted to each index independently and to the two together), as well as the biomass trend from the models fitted to data from all years simultaneously.
3.0 2.5 2.0 1.5 1.0 0.5 0.0 3.0 2.5
2002
2003
2004
2005
2006
2007
CPUE
2.0 1.5 1.0 0.5 0.0 3.0 2.5 2.0 1.5 1.0 0.5 0.0 2 4 6 8 10 12 2 4 6 8 10 2 4 6 8 10 Coop CPUE WCS CPUE Trend Coop 1 yr Trend WCS 1 yr Trend Both 1 yr Trend multiyear
2008
2009
Month
Figure 14. Posterior distributions of starting exploitable biomass of lobsters at Glovers Reef, from the Bayesian depletion model with catchability and variance different in each year (Model C), compared to the models fit to data from one year at a time.
0.4
2002
2003
2004
0.3
0.2
0.1
0.0 0.4
2005
2006
2007
Probability
0.3
0.2
0.1
0.0 0.4
2008
2009
0.3
0.2
All years: Model C By year, Coop By year, WCS By year, both
0.1
0.0 0 200 400 600 800 1000 0 200 400 600 800 1000 0 200 400 600 800 1000
Biomass (t)
29
Figure 15. Comparison of depletion model results for the Bayesian state space models described in Table 1, and the DeLury regression model fitted to effort. (a) Starting biomass
1000
- - -
Starting biomass (t)
All years:A All years:B All years:C All years:D By year:Coop By year:WCS By year:Both Regression
600
800
200
- ----- 2002
------ 2003
--
----- --- 2006 Year
----- -- --- 2007
400
-- - -- -- 2008
- ---- 2004
- -- -- --- 2005
-- -- - - 2009
(b) Fishing mortality rate

2.0 All years:A All years:B All years:C All years:D By year:Coop By year:WCS By year:Both Regression
Fishing mortality rate
1.5
- --- --- --2005
1.0
- -- - --- --2006 Year
- - -
- -- -- - -2002
-- - ---- 2003
0.5
-- - - -- 2004
- ----- ---2007
0.0
- -- - - - --- -2008
-- ---- 2009
30
Figure 16. Catchability (q) and error variance by year for the non hierarchical models with and without time-varying q and variance (Table 1, models A and C).
0.12 0.06 q (*1000) 2005 2006 2007 2008 2009 0.00 2002 2003 2004 2005.0 0.02 0.04
(a) q for Coop series
(b) q for WCS series
q (*1000)
0.00
0.04
0.08
2005.5
2006.0
2006.5 Year
2007.0
2007.5
2008.0
Year
(c) Variance for Coop series

0.6
(d) Variance for WCS series
0.0
2002
2003
2004
2005
2006
2007
2008
2009
0 2005.0
200 400 600 800
Variance
0.2
Variance
0.4
2005.5
2006.0
2006.5 Year
2007.0
2007.5
2008.0
Year
Figure 17. Observed (points) and predicted (lines) log-CPUE from the Cooperative data versus cumulative effort from the Cooperative data, from the Delury regression.
2002
2003
2004
0 4
2005
2006
2007
Log(CPUE)
0 4
2008
2009
0 100 200 300 400 500 0 200 400 600 800 0 200 400 600 800
Cumulative effort (vessel days)
31
Figure 18. Fishing mortality rates estimated from Glovers Reef data (methods on y-axis), compared to the values computed for the whole of Belize in 2009, and Fmax and F0.1 (Gongora 2010). The value of M is also shown for comparison.
M F0.1 Fmax Belize F-2009
Model A, all years Model A, 2009 Model C, all years Model C, 2009
| | || | | | |
| | | | | | | X
0.5 1.0 Fishing mortality 1.5 2.0
| | |
Regression, all years Regression, 2009 From ave. length 0.0
Figure 19. Expected catches with a F0.1 harvest strategy, applied to the biomass estimates from the models specified in the y-axis.
C-2007 C-2009 C-2006 C-2005 C-2008 C-2003 C-2002 C-2004
Model A, all years
| | | | | | | ||| | | | |
Model A, 2009
Model C, all years
Model C, 2009
Regression, all years
Regression, 2009
10000
20000
30000 Catch (kg live wt)
40000
50000
60000
32
PART II: PRELIMINARY ANALYSIS OF EXISTING FISHERIES DATA FOR QUEEN CONCH AT GLOVERS REEF MARINE RESERVE ABSTRACT
Data available on queen conch at Glovers Reef Marine Reserve include the reported catch and fishing effort from the fishing Cooperatives, data on sizes, catches and fishing effort collected from fishermen at Glovers Reef, and a fishery independent visual survey (LAMP). Conch are larger, more likely to be mature, and more abundant in the Conservation Zone than in the General Use Zone. The catch per unit of effort from the fishery and the number of conchs seen in fishery independent visual surveys were both standardized using GLM methods. The resulting abundance indices were highly variable and showed no trend over time. The catches reported to the fishing Cooperatives were lower than expected, particularly after 2005, implying that catches from Glovers Reef may not be recorded as being from Region 3 on the Cooperative data sheets. The catch per unit vessel trip from the Cooperative data was also highly variable.
METHODS
WCS Catch and Effort Data
Catch and effort of conch (Strombus gigas) at Glovers Reef were analyzed in the same way as the lobster catch and effort. For conch, there were 952 unique combinations of fisherman, boat and date for which data were collected between 2005 and 2010. In some cases, the number of conchs caught was reported for more than one fisherman who fished together; we calculated CPUE as the unprocessed weight of conchs captured per fisherman hour. WCS data collectors weighed the conchs and recorded how thoroughly they had been processed (UN=Unprocessed, PF=meat 50% processed, PS=meat 65% processed, PE=meat 85% processed, PR=meat 100% processed). We converted all weights to unprocessed weights using the conversions in Table 1 (Aspra et al. 2009). Conchs for which no weight type was recorded were assumed to unprocessed, as this was the most common weight type. For 4 individuals for which length was recorded but not weight, we converted length to weight using the equation log10 (W)=2.286+3.459log10(L), for shell length in cm and unprocessed weight in grams (Ehrhardt and Valle-Esquivel 2008). To extract an unbiased index of conch abundance, we used a generalized linear mixed model (GLMM) approach in which the effects of factors which might bias the estimated biomass trend are removed from the time trend. The potential explanatory variables were the factors of fishing year and month within fishing year (from March 2005 through July 2010), moon phase (full: within 4 days of full, new: within 4 days of new, mid: otherwise), and boat name (treated as either a fixed or a random effect). In an alterative model run, days since the beginning of the fishing season (October 1 of each year) was
included as a numerical variable instead of months, to test for a linear trend within each fishing season. We did not include time of day or depth in the analysis because most fishermen reported fishing six hours or more, so that the time and depth at which each conch was captured was not precisely known. Of the 26 boats for which conch catch and effort data were recorded, 19 were sampled on 3 or more days and were included in the analysis. There was much less variability in catch rates between locations than there was between boats, so we included boat as a factor in the model but not location. Using only data from the 19 boats with multiple samples, the number of CPUE records was 906. The GLM model was: (1) log(CPUEi , j ,k ,l ) = Ti + M j + Vk + 2way + i , j ,k ,l where Ti is the effect of fishing year and month (i) for the 45 months between March, 2005 and July 2010 for which data were collected, Mj is the effect of moon phase (j=full, mid or new), and Vk is the effect of individual boat (k = boat 1 through 19), and i , j ,k ,l is a normally distributed error term. All of the second order interactions between the terms are included. To determine which of these factors and their interaction significantly improve the model, we used Akaikes Information Criterion (AIC, Akaike 1974): (2) AIC=-2log(L)+2n where L is Likelihood and n is the number of parameters. The percent of model deviance explained by the factor in the model was also considered, and factors that explained less than 1% of deviance were excluded. We used the stepAIC function in the MASS library for R to choose the model that minimized AIC (Venables and Ripley 2002). In the case where boat or any of the two way interactions with boat were included in the AIC best model, we treated these parameters as random effects, using the function glmer in R (Bates 2010, Ortiz and Arocha 2004, R Development Core Team 2010). The AIC and the BIC (Bayesian information criterion; Bates 2010) were used to choose the best model with random effects. The time period (year and month) effect calculated by the mixed model was used to predict the log-CPUE for month and year and the predicted values and their standard errors were transformed from normal to lognormal to extract the temporal trend in abundance. Finally, to determine whether there was a significant decreasing trend in abundance within each fishing season, we repeated the GLM model with day within fishing season as a numerical variable to estimate the linear regression between day and CPUE within season:
(3) log(CPUEi , j ,k ,l ) = Yi + Di + M j + Vk + 2 way + i , j ,k ,l where Yi is the effect of fishing year i, and Di is the slope of the linear relationship between day since the beginning of the fishing season and log-CPUE.
LAMP Data
For conch observations in the fishery independent LAMP data set, we used a similar generalized linear modeling approach. In the LAMP case, the sampling unit was one dive, so that the number of conchs seen per dive is assumed to be an index of conch abundance. For each conch seen, the divers recorded the date, site, type of transect, shell length and other morphometrics and physical variables. The LAMP data were collected at 33 fixed sampling locations, including 11 patch reefs sampled with a timed survey and 22 sand flat sites sampled with transects. In some years there were duplicate transects and timed surveys at the sand flat sites but these were excluded from the analysis for consistency across the time series. Of the 616 dives recorded, about 54% of the transects and 27% of the timed surveys recorded zero conchs. Therefore, we used a delta lognormal modeling approach, in which the number of conchs in dives in which conchs were seen was modeled as lognormal, while presence or absence was modeled as a binomial process (Ortiz and Arocha 2004). The potential explanatory variables considered were the time period (year and month), management zone category (Conservation Zone, General Use Zone within 500 m of the boundary, GUZ zone more than 500 m from the boundary), moon phase (full, new or mid), site type (patch reef versus sand-flat) and the linear effects of time of day and visibility as a categorical variable (low:<10 m; high:>=10 m). Depth was not included in the model because the majority of dives were around the same depth (<5 m). The GLM models were: (4) log(Ci , j ,k ,l ,m,n ) = Ti + M j + Sk + Z l + vm + t + 2way + i , j ,k ,l ,m,n for count (C) in positive sets, and : (5) logit( Pi , j ,k ,l ,m ) = Ti + M j + S k + Z l + vm + t + 2 way for presence or absence (P), where Ti is the effect of time period i, Mj is the effect of moon phase (j=full, new or mid), Sk is the effect of site type (k =patch reef or sand flat), Zl is the management zone (l is the three levels), v is the effect of visibility (m=low or high), t is the linear effect time of day (in decimal 24 hour time) and i , j ,k ,l is a normally distributed error term for dive n. All 2-way interactions were included. To determine which of these factors significantly improve the model, we used Akaikes Information Criterion (AIC, Akaike 1974). Some factors were removed from the model
because they explained only a small amount (<3%) of the model deviance. The index of abundance was calculated by multiplying the inverse logit of the time period effect from the binomial model by the exponent of the time period effect from the lognormal model (with bias correction). Standard errors were calculated using the method of Lo et al. (1992). In the case where any of the two way interactions with the time trend were included in the AIC best model, we treated these interactions as random effects, using the function glmer in R (Bates 2010, Ortiz and Arocha 2004, R Development Core Team 2010).
Catch and Effort from Fisheries
Catches and fishing effort (in vessel days) for region 3 (Glovers Reef) were provided by the Belize Fisheries Department by month, as reported by the National and Northern cooperatives. Landings were reported either as conch fillets or as conch. We converted to unprocessed (without shell) weight by assuming that conch was 85% processed, and fillets were 100% processed, and using the conversions of Aspra et al. (2009, Table 1). Catch per unit of effort was calculated as the average value of total unprocessed weight divided by days fishing.
RESULTS
WCS Catch and Effort Data
The WCS catch and effort survey has weighed more than 35,000 individual conchs between 2004 and 2009. The size distribution (Figure 1) showed an average weight between 100 and 200 g depending on the degree of processing. This implies that most conchs are around the legal size limit of 78 g fillet weight. Catch per unit of effort was calculated in weight per fishermen hour. The number of conchs caught in a record in the data set is expected to be higher for longer fishing excursions and for greater numbers of fishermen. This does not appear to be the case, as the largest number of conchs per trip is caught by single fishermen in short trips (Figure 2). It seems likely that fishermen spend more time searching for conchs when they are less abundant, so that longer fishing episodes are likely to have fewer conchs. Catch per fishermen hour in weight and catch per fishermen hour in numbers of conchs were 86% correlated, but there was a tendency for the CPUE in weight to be more variable than in numbers (Figure 3); both appeared to be lognormally distributed. For the remainder of this analysis, CPUE is in terms of unprocessed weight per fisherman hour. The unstandardized log-CPUE data (Figure 4) are quite variable across months, moon phase and fishing boat. In the log-normal GLM with fixed effects (Table 2a), the AIC best fit model included time period, moon phase and boat, as well as the interactions between time period and both moon phase and boat, although the interaction between moon phase and boat. This model explained 76% of the model deviance. When boat and
the time period x boat interaction were modeled as random effects (Table 2b), the best model chosen by both the BIC and the AIC included only time period, boat and their interaction. The diagnostics for this model showed a good model fit (Figure 5). The standardized CPUE index of abundance showed no clear trend over time. In particular, there did not seem to be a decline in catch per unit of effort during each fishing season. . Conch is known for having hyper-stable CPUE. That is, the catch per fisherman hour doesnt necessarily decline linearly with abundance, so that CPUE can remain constant while abundance is declining (Ehrhardt and Valle-Esquivel 2009). When fishing year and day of the fishing season were included in the model (rather than year and month as a factor), fishing year was significant but day within the season was not, implying that there is no linear trend within fishing seasons. The high variability and lack of trend within fishing seasons implies that CPUE may not strongly correlated with abundance.
LAMP Data
The LAMP survey has observed a total of 7,999 queen conchs between 2004 and 2010. Length frequencies (Figure 7) show that there are many more conchs above the legal size limit of 178 mm inside the Conservation Zone than in the General Use Zone, but large conch are as common in the GUZ near the CZ boundary as they are in the GUZ. This implies that the Conservation Zone is effective at protecting conchs, and there is probably some spillover of individuals from the CZ into the GUZ. The mean length in each zone does not appear to have changed over time (Figure 7d). The fraction of conchs that were mature as indicated by the presence of a thickened shell lip was higher in the Conservation Zone (27%) versus the General Use Zone more than 500m from the Conservation Zone (11%). The number of conchs seen per dive varied with many of the explanatory variables (Figure 9), particularly distance from the Conservation Zone and site type. For the GLM model of presence/absence the AIC best model included all the main effects and some interactions; however, time and moon phase explained very little deviance (Table 4a). The best model without moon phase or time of day (Table 4b, Figure 10) explained 15% of the model deviance, as compared to 16% in the AIC model (Table 4a). We therefore chose the model without moon phase or time for the standardized index. For the GLM models of log of positive counts (Table 4c), the AIC best model with fixed effects included time period, transect type, management zone, visibility and time of day, as well as the interaction between management zone and site type, and visibility and time of day. The model provided a reasonably good fit to the data (Figure 10) and explained 67% of the deviance in the presence/absence data. The standardized index showed no trend between 2004 and 2010 (Figure 11).
37
Fisheries Data
Catches of conchs from Glovers Reef are quite variable (Figure 12) and were lower in recent years than they were in 2005-2007. Catches are often highest in the first month of the season; however, in most years, the CPUE is quite variable and does not show a clear decline with time throughout the season.
DISCUSSION
The size data from the LAMP survey show that there are more large conchs inside the Conservation Zone than in the General Use Zone, and some large conchs also spill over into the GUZ near the CZ. The fraction of mature conchs is higher in the Conservation Zone than the General Use Zone. Conchs are also more abundant in the Conservation Zone as shown by the significant effect of management zone in the GLM analysis of the LAMP abundance data. The sizes of conchs in the fishery seem to be rather small, with a mean of 200g unprocessed weight, which would be about 70 mm fillet weight. Both the fisheries CPUE and the LAMP index of abundance were highly variable, showing no clear trend over time. Also, given that the number of conchs caught by fishermen doesnt seem to increase with number of fishermen or number of hours spent fishing, CPUE is probably not a good index of abundance. It is very common for CPUE of conch to be unrelated to abundance (Ehrhardt and Valle-Esquivel 2009), so this is not surprising. Future research will involve calculating the density of the conchs both in the Conservation Zone and in the General Use Zone. Because conchs have internal fertilization, it is necessary for densities to remain high enough that male and female individuals are able to find each other (Ehrhardt and Valle-Esquival 2008). For this reason, many conch fisheries are managed to maintain densities above a target reference point. Comparing the density of conchs and the density of mature conchs between the two management zones is probably the best way to calculate fisheries reference points such as the level of depletion of spawning stock biomass (e.g. Acosta 2006, Carcamo 2008).
38
REFERENCES
Acosta, C. A. 2006. Impending trade suspensions of Caribbean Queen Conch under CITES: A case study on fisheries impacts and potential for stock recovery. Fisheries 31: 601-606. Aspra, B.; Barnutty, R.; Mateo, J.; Marttin. F.; Scalisi, M. Conversion factors for processed queen conch to nominal weight. FAO Fisheries and Aquaculture Circular 1042. Rome. Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control. 19:716 723 Bates, D. 2010. Package LME4: Linear mixed-effects models using S4 classes. http://lme4.r-forge.r-project.org/. Beverton, R.J.H. and Holt, S.J. 1957. On the Dynamics of Exploited Fish Populations. Ministry of Agriculture, Fisheries and Food, Fishery Investigations Series II, Volume 19. Carcamo, R. 2008. Stock assessment of the queen (Strombus gigas) conch population of Belize 2008. Belize Fisheries Department. Cope, J. M. and A. E. Punt. 2009. Length-based reference points for data-limited situations: Applications and restrictions. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 1:118, 2009 Ehrhardt, N.M. and M. Valle-Esquivel. 2008. Conch (Strombus gigas) Assessment Manual. Caribbean Fishery Management Council. FAO. 2007. Regional Workshop on the Monitoring and Management of Queen Conch, Strombus gigas. Kingston, Jamaica, 15 May 2006. FAO Fisheries Report. No. 832. Rome, FAO. Gongora, M. 2005. Conch Standard Weights Study. Grant, S. 2004. Glovers Reef Marine Reserve Fisheries Boat Census 2004 (Part 1). Wildlife Conservation Society. Lo, N. C. H., L. D. Jacobson, and J. L. Squire. 1992. Indices of relative abundance from fish spotter data based on delta-lognormal models. Canadian Journal of Fisheries and Aquatic Sciences 49: 251 5-2526. Lunn, D.J., Thomas, A., Best, N., and Spiegelhalter, D. (2000) WinBUGS -- a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing, 10:325--337.
39
Maunder, M.N. and A. E. Punt. 2004. Standardizing catch and effort data: a review of recent approaches. Fisheries Research 70:141159. Ortiz, M. and F. Arocha. 2004. Alternative error distribution models for standardization of catch rates of non-target species from a pelagic longline fishery: billfish species in the Venezuelan tuna longline fishery. Fisheries Research 70: 275297. R Development Core Team. 2010. R: A Language and Environment for Statistical Computing, Vienna, Austria http://www.R-project.org. Venables, W.N. and B. D. Ripley. 2002. Modern Applied Statistics with S. 4th Edition. Springer.
40
TABLES AND FIGURES

Table 1. Conch weight conversions. The conversion to whole (with shell) weight was taken from Aspra (2009); conversion to unprocessed (without shell) was calculated by dividing by 5.7.
Code Percent processed Conversion to whole Conversion to unprocessed UN 0 5.7 1 PF 50 9.5 1.67 PS 60 NA 1.88 PE 85 13.7 2.4 PR 100 16.3 2.86 WC w/ shell 1 0.18
Table 2. GLM of conch log-CPUE in unprocessed weight per fisherman-hour, as a function of time period (T), boat (B) and moon phase (M), for (a) the AIC best model with fixed effects, and (b) random effects models with all possible second order interactions. The best random effects model according to both the AIC and the BIC is in bold. (a) For AIC best model with fixed effects including moon phase
Df
NULL T B M TxB TxM 44 18 2 113 25
Resid. Deviance Df
471.7 270.3 1.7 125.3 22 905 861 843 841 728 703
Resid. Dev
1185 713.3 443 441.3 316 294
F
25.64 35.92 2.03 2.65 2.11
Pr(>F)
0.0000 0.0000 0.1328 0.0000 0.0013
% Deviance
0.40 0.23 0.00 0.11 0.02
(b) With random effects.

Model
T+B T+B+TxB T+M+B T+M+B+TxB T+M+B+TxM T+M+B+BxM T+M+B+TxB+TxM T+M+B+TxB+BxM T+M+B+TxM+BxM T+M+B+TxB+TxM+BxM
AIC
2176.92 2115.96 2183.06 2124.7 2147.12 2182.84 2118.7 2126.7 2148.85 2120.7
BIC
2402.94 2346.8 2418.71 2365.15 2387.57 2423.29 2363.96 2371.96 2394.11 2370.77
deviance
2019.42 1999.11 2014.86 1996.67 2035.05 2016.49 2008.99 1996.67 2035.71 2008.99
Table 4. GLM results for LAMP data (a) AIC best model for presence/absence
Df
NULL T S Z M t S:M 20 1 2 2 1 2 26.9 49.5 63.3 0.4 2.8 4
Deviance
Resid. Df
653 633 632 630 628 627 625
Resid. Dev
905.3 878.3 828.8 765.6 765.2 762.4 758.4
P(>|Chi|)
0.1378 0.0000 0.0000 0.8377 0.0944 0.1338
% Deviance
0.03 0.05 0.07 0.00 0.00 0.00
(b) Best model without M or t for presence/absence Df Deviance

NULL T S Z 20 1 2 23.7 47.2 64.4
Resid. Df Resid. Dev P(>|Chi|) % Deviance

661 641 640 638 916.3 892.6 845.4 781.0 0.2539 0.0000 0.0000 0.03 0.05 0.07
(c) AIC best model of log CPUE of positive dives

Df
NULL T S Z v t S:Z v:t 20 1 2 1 1 2 1 708.4 0.2 10.7 0.1 2.5 31.4 11.7
Deviance
Resid. Df
360 340 339 337 336 335 333 332
Resid. Dev
1140.1 431.6 431.4 420.7 420.6 418.1 386.7 374.9
F
0.0000 0.6533 0.0086 0.8060 0.1332 0.0000 0.0013
Pr(>F)
0.62 0.00 0.01 0.00 0.00 0.03 0.01
% Deviance
20 1 2 1 1 2 1
42
Figure 1. Histograms of weight by weight type from the WCS catch and effort data set. The minimum size limit is 78 g fillet weight.
1000 Count 300 Weight (g) 400 500 600 0 0 100 200 0 200 600 800
(a) 50% processed weight
(b) 60% processed weight
Count
200
400
600
200
400 Weight (g)
600
800
100 200 300 400
Count
Count
200
400 Weight (g)
600
800
0 1000 0
3000
5000
(c) 85% processed
(d) Unprocessed weight
200
400 Weight (g)
600
800
1000
Figure 2. Number of conch caught per record in the WCS catch and effort data (a and c), and number caught per fisherman hour (b) or per hour irrespective of the number of fishermen working together (d)
(a) Number of conch versus hours fishing by crew size
70 1 Mean CPUE 1 50 1 1 1 1 2 4 6 8 Hours fished 10 12 14 1 1 1 1 1 1 2 2 1 2 3 2 2 3 3 3 3 3 2 2 3 2 2 3 3 2 2 2 2 15 Mean count of conch
(b) Catch per fisher hour versus hours fishing

1
10
1 1 1 1 1 2 3 2 4 1 1 1 1 1 1 1
30
2 1 3
1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 6 8 Hours fished
10
2 3 10
2 3 12
2 14
(c) Number of conch versus hours fishing

Mean count of conch 40
(d) Catch per hour versus hours fishing
Mean CPUE 2 4 6 8 Hours fished 10 12 14
30
20
10
10
15
8 Hours fished
10
12
14
Figure 3. Histograms of conch weight, log-CPUE in both weights and numbers per fisherman hour, and CPUE in weights plotted against CPUE in numbers.
Number of records
Number of conchs
200
400
600
800
1000
20 40
2000
60 80 100
(a) Histogram of conch weights

6000
(b) Log-CPUE in numbers
-2
-1
Unprocessed weight (kg)
CPUE in weight
70
(c) Log-CPUE in weight

Log-CPUE in weight 15000 0 2 4 6 Log-CPUE 8 10 5000
(d) Conch CPUE in weight versus in numbers
Number of records
0 10
30
50
10
20
30
40
50
Log-CPUE in numbers
Figure 4. Raw log-CPUE in unprocessed weight of conchs per fisherman-hour, by month, day, boat and location.
10 10 log CPUE 2 log CPUE 1 2 3 4 5 6 7 8 9 11 13 15 17 19 2 Eastern Reef G2 G3 G4 G5 G6 G7 G8 4 6 8 10 4 6 8
(a) Month in season
(b) Days after full moon
log CPUE
log CPUE
10
(c) Boat
2004.06 2004.08 2004.09 2005.01 2005.02 2005.03 2005.04 2005.05 2005.06 2005.07 2005.08 2005.09 2006.01 2006.02 2006.03 2006.04 2006.05 2006.06 2006.07 2006.08 2006.09 2007.01 2007.02 2007.03 2007.04 2007.05 2007.07 2007.08 2007.09 2008.02 2008.03 2008.04 2008.05 2008.06 2008.07 2008.08 2008.09 2009.01 2009.02 2009.04 2009.05 2009.06 2009.07 2009.08 2009.09
(d) Location
Figure 5. Diagnostics for the mixed effects lognormal GLM including time period, boat and their interaction.
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 N W Reef Western Reef
Residuals versus fitted

2 2
Normal Q-Q Plot
Sample Quantiles 5 6 7 8
Residuals
-1
-2
-3
-3
-2
-1
-3
-2
-1
Figure 6. Trend by month for catch in weight per fisherman-hour from the mixed effects model including time period as a fixed effect and boat and the interaction between time period and boat as random effects. The x-axis refers to the year when the fishing season started (in October). Points are unstandardized CPUE.
4 CPUE 0 1 2 3
2005
2006
2007
2008
2009
Figure 7. Conch shell length by management zone from the LAMP survey.
45
(a) LAMP conch Conservation Zone

10 15 20 25 30 0 0 100 200 Shell length(mm) 400 300 5 200
(b) LAMP conch General Use Zone near the Conservation Zone
Count
50 100
Count
100
200 Shell length(mm)
300
(c) LAMP General Use Zone

200
(d) Average by year and zone

-
300
Mean SL (mm)
Count
200
100
150
100
100
200 Shell length(mm)
300
50
CZ GUZ
2004
2005
2006
2007 Year
2008
2009
2010
Figure 8. Conch shell lip presence and thickness by management zone.

(a) Fraction with lip by zone
3000 Without lip With lip Count 80 GUZ far from CZ 0 Conservation GUZ near CZ 0 20 40 60
(b) Lip thickness Conservation Zone
Count
1000
2000
10
15
20
25
30
35
Shell lip thickness (mm) 40 Count 0 0 5 10 15 20 25 30 35 0 10 20 30
(c) Lip thickness General Use Zone near the Conservation Zone
10 12
(d) Lip thickness General Use Zone
Count
10
15
20
25
30
35
Shell lip thickness (mm)
Shell lip thickness (mm)
Figure 9. Raw log-count of conchs per dive (log-Count+0.01 so zeroes can be included) compared to potential explanatory variables
46
Time period
2 4 2
Visisbility
0 2
Depth
log-count
-2
-2
2004.08 2004.10 2005.03 2005.05 2005.11 2006.03 2006.07 2006.09 2007.02 2007.05 2007.08 2007.11 2008.02 2008.05 2008.08 2008.11 2009.02 2009.06 2009.08 2010.05
10
15 Visibility(m)
20
25
30
-8 -6
0
-4
-4
-4 -2
10 Depth(m)
15
Start time
0 1 2 4 2
Site
2 3
Distance from conservation zone
log-count
-2
-2
-4
10 Time
15
prC10AB
prC4AB
sf12
sf16
sf21
sf25
sf29
sf33
-2 -1
-4
-4
-2
0 Distance (km)
Days from full moon

4 0.5 2
Fishing season
2 4
Patch reef or sand flat and transect type
-0.5
-2
-4
-1.5
10
15
20
25
30
1 fishseason
-4
-2
pr
sf
Figure 10. Residuals for the selected models, which were the AIC preferred models once visibility was removed. (a) presence/absence binomial model
Residuals vs Fitted
2 Std. deviance resid. 2
Normal Q-Q
Residuals
-1
-2
85 196
-2
-1
196 85 82
82
-3
-1
1 Predicted values
-3
-2
-1
(b) for log count of conch given they were observed in a dive
Residuals vs Fitted
602
Normal Q-Q
3 Std. deviance resid.
602 326 603
326 603
Residuals
-1
-2
0.0
0.5
1.0
1.5
2.0
2.5
-2 -3
-1
-2
-1
Predicted values
Figure 11. Standardized trend in conch catch rates from the AIC best models, with unstandardized values (points). The solid vertical lines are the beginning and end of conch fishing season, the years are labeled at the beginning of the season (October 1st).
47
conch abundance index
2004
2005
2006 Fishing season
2007
2008
2009
Figure 12. Conch catches (in unprocessed weight without shell) and catch per unit of effort from area 3 (Glovers Reef) from the Belize fisheries data set by month, for Northern and National cooperatives combined.
Unprocessed weight(kg) 15000 0 5000 10000 (a) Area 3 catches
2002
2003
2004
2005
2006
2007
2008
2009
(b) Average catch per vessel day 35 CPUE 5 15 25
2002
2003
2004
2005
2006
2007
2008
2009
Year
48

Report On Spiny Lobster Abundance and Fishing Mortality and Preliminary Analysis of Existing Fisheries Data at Glover's Reef Research Station

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Report On Spiny Lobster Abundance and Fishing Mortality and Preliminary Analysis of Existing Fisheries Data at Glover's Reef Research Station

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GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

LIST OF ACRONYMS AND ABBREVIATIONS

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

for positive sets, and : (7)

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

GLOVERS REEF ANNUAL REPORT

TABLES AND FIGURES

(b) Priors for the model parameters

Range - - 10001.0E7 0- 0- 10001.0E7 1.0E-71.0 0.001100

log(qj)=Normal(=0, =0.01) 1/ j =Gamma(0.01,0.01)

se 0.33 2.51 1.69

Z 1.22 0.56 0.49

M 0.34 0.34 0.34

F 0.88 0.22 0.15

(b) With random effects.

(b) log count of lobsters for positive dives.

GLOVERS REEF ANNUAL REPORT

Table 6. Summary of results for spiny lobster

(b) LAMP General Use Zone far from boundary

(c) LAMP General Use Zone near boundary

(d) LAMP Conservation Zone

Carapace length (mm)

Carapace length (mm)

GLOVERS REEF ANNUAL REPORT

(b) LAMP General Use Zone

CL(mm) 0 2004 2005 2006 Year 2007 2008 2009

(b) Days after full moon

GLOVERS REEF ANNUAL REPORT

Residuals versus fitted

Normal Q-Q Plot

6.5 Predicted values

GLOVERS REEF ANNUAL REPORT

Lobsters per fisherman

Legal All sizes

GLOVERS REEF ANNUAL REPORT

Distance from conservation zone

log-count prC10AB prC1AB prC3AB prC6AB prC8AB

Days from full moon

(b) Positive log-lobsters per dive

1.0 Predicted values

GLOVERS REEF ANNUAL REPORT

Lobster abundance index

2007 Fishing season

Whole weight (kg)

GLOVERS REEF ANNUAL REPORT

CPUE 5 10 15 20 25 (b) Average catch per vessel day

Fraction of catch sampled Fraction of days sampled

2003 2004 2005

2006 2007 2008 2009

All years: Model C By year, Coop By year, WCS By year, both

GLOVERS REEF ANNUAL REPORT

Starting biomass (t)

----- --- 2006 Year

----- -- --- 2007

(b) Fishing mortality rate