Population genetics of Cobia (Rachycentron canadum): implications for fishery management along the coast of the southeastern United States

Cobia (Rachycentron canadum) is a pelagic, migratory species with a transoceanic distribution in tropical and subtropical waters. Recreational fishing pressure on Cobia in the United States has increased substantially during the last decade, especially in areas of its annual inshore aggregations, making this species potentially susceptible to overfishing. Although Cobia along the Atlantic and Gulf coasts of the southeastern United States are currently managed as a single fishery, the genetic composition of Cobias in these areas is unclear. On the basis of a robust microsatellite data set from collections along the U.S. Atlantic coast (2008–09), offshore groups were genetically homogenous. However, the 2 sampled inshore aggregations (South Carolina and Virginia) were genetically distinct from each other, as well as from the offshore group. The recapture of stocked fish within their release estuary 2 years after release indicates that some degree of estuarine fidelity occurs within these inshore aggregations and supports the detection of their unique genetic structure at the population level. These results complement the observed high site fidelity of Cobias in South Carolina and support a recent study that confirms that Cobia spawn in the inshore aggregations. Our increased understanding of Cobia life history will be beneficial for determining the appropriate scale of fishery management for Cobia.

Population structure of island-associated dolphins: evidence from photo-identification of common bottlenose dolphins (Tursiops truncatus) in the main Hawaiian Islands

Management agencies often use geopolitical boundaries as proxies for biological boundaries. In Hawaiian waters a single stock is recognized of common bottlenose dolphins, Tursiops truncatus, a species that is found both in open water and near-shore among the main Hawaiian Islands. To assess population structure, we photo-identified 336 distinctive individuals from the main Hawaiian Islands, from 2000 to 2006. Their generally shallow-water distribution, and numerous within-year and between-year resightings within island areas suggest that individuals are resident to the islands, rather than part of an offshore population moving through the area. Comparisons of identifications obtained from Kaua‘i/Ni‘ihau, O‘ahu, the “4-island area,” and the island of Hawai‘i showed no evidence of movements among these island groups, although movements from Kaua‘i to Ni‘ihau and among the “4-islands” were documented. A Bayesian analysis examining the probability of missing movements among island groups, given our sample sizes for different areas, indicates that interisland movement rates are less than 1% per year with 95% probability. Our results suggest the existence of multiple demographically independent populations of island-associated common bottlenose dolphins around the main Hawaiian islands.

Age validation, growth, mortality, and additional population parameters of the goldband snapper (Pristipomoides multidens) off the Kimberley coast of northwestern Australia

Goldband snapper (Pristipomoides multidens) collected from commercial trap and line fishermen off the Kimberley coast of northwestern Australia were aged by examination of sectioned otoliths (sagittae).A total of 3833 P. multidens, 80–701 mm fork length (98–805 mm total length), were examined from commercial catches from 1995 to 1999. The oldest fish was estimated to be age 30+ years. Validation of age estimates was achieved with marginal increment analysis. The opaque and translucent zones were each formed once per year and are considered valid annual growth increments (the translucent zone was formed once per year between January and May). A strong link between water temperature and translucent zone formation was evident in P. multidens. The von Bertalanffy growth function was used to describe growth from length-at-age data derived from sectioned otoliths.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Biology and population dynamics of cowcod (Sebastes levis) in the southern California Bight

Cowcod (Sebastes levis) is a large (100-cm-FL), long-lived (maximum observed age 55 yr) demersal rockfish taken in multispecies commercial and recreational fisheries off southern and central California. It lives at 20–500 m depth: adults (>44 cm TL) inhabit rocky areas at 90–300 m and juveniles inhabit fine sand and clay at 40–100 m. Both sexes have similar growth and maturity. Both sexes recruit to the fishery before reaching full maturity. Based on age and growth data, the natural mortality rate is about M =0.055/yr, but the estimate is uncertain. Biomass, recruitment, and mortality during 1951–98 were estimated in a delay-difference model with catch data and abundance indices. The same model gave less precise estimates for 1916–50 based on catch data and assumptions about virgin biomass and recruitment such as used in stock reduction analysis. Abundance indices, based on rare event data, included a habitat-area–weighted index of recreational catch per unit of fishing effort (CPUE index values were 0.003–0.07 fish per angler hour), a standardized index of proportion of positive tows in CalCOFI ichthyoplankton survey data (binomial errors, 0–13% positive tows/yr), and proportion of positive tows for juveniles in bottom trawl surveys (binomial errors, 0–30% positive tows/yr). Cowcod are overfished in the southern California Bight; biomass during the 1998 season was about 7% of the virgin level and recent catches have been near 20 metric tons (t)/yr. Projections based on recent recruitment levels indicate that biomass will decline at catch levels > 5 t/yr. Trend data indicate that recruitment will be poor in the near future. Recreational fishing effort in deep water has increased and has become more effective for catching cowcod. Areas with relatively high catch rates for cowcod are fewer and are farther offshore. Cowcod die after capture and cannot be released alive. Two areas recently closed to bottom fishing will help rebuild the cowcod stock.

Life history and population dynamics of the finetooth shark (Carcharhinus isodon) in the northeastern Gulf of Mexico

The life history and population dynamics of the finetooth shark (Carcharhinus isodon) in the north-eastern Gulf of Mexico were studied by determining age, growth, size-at-maturity, natural mortality, productivity, and elasticity of vital rates of the population. The von Bertalanffy growth model was estimated as Lt=1559 mm TL (1–e–0.24 (t+2.07)) for females and Lt = 1337 mm TL (1–e–0.41 (t+1.39)) for males. For comparison, the Fabens growth equation was also fitted separately to observed size-at-age data, and the fits to the data were found to be similar. The oldest aged specimens were 8.0 and 8.1 yr, and theoretical longevity estimates were 14.4 and 8.5 yr for females and males, respectively. Median length at maturity was 1187 and 1230 mm TL, equivalent to 3.9 and 4.3 yr for males and females, respectively. Two scenarios, based on the results of the two equations used to describe growth, were considered for population modeling and the results were similar. Annual rates of survivorship estimated through five methods ranged from 0.850/yr to 0.607/yr for scenario 1 and from 0.840/yr to 0.590/yr for scenario 2. Productivities were 0.041/yr for scenario 1 and 0.038/yr for scenario 2 when the population level that produces maximum sustain-able yield is assumed to occur at an instantaneous total mortality rate (Z) equaling 1.5 M, and were 0.071/yr and 0.067/yr, when Z=2 M for scenario 1 and 2, respectively. Mean generation time was 6.96 yr and 6.34 yr for scenarios 1 and 2, respectively. Elasticities calculated through simulation of Leslie matrices averaged 12.6% (12.1% for scenario 2) for fertility, 47.7% (46.2% for scenario 2) for juvenile survival, and 39.7% (41.6% for scenario 2) for adult survival. In all, the finetooth shark exhibits life-history and population characteristics intermediate to those of sharks in the small coastal complex and those from some large coastal species, such as the blacktip shark (Carcharhinus limbatus).

Modeling the effect of striped bass (Morone saxatilis) on the population viability of Sacramento River winter-run chinook salmon (Onchorhynchus tshawytscha)

We estimated the impact of striped bass (Morone saxatilis) predation on winter-run chinook salmon (Oncorhynchus tshawytscha) with a Bayesian population dynamics model using striped bass and winter-run chinook salmon population abundance data. Winter-run chinook salmon extinction and recovery probabilities under different future striped bass abundance levels were estimated by simulating from the posterior distribution of model parameters. The model predicts that if the striped bass population declines to 512,000 adults as expected in the absence of stocking, winter-run chinook salmon will have about a 28% chance of quasi-extinction (defined as three consecutive spawning runs of fewer than 200 adults) within 50 years. If stocking stabilizes the striped bass population at 700,000 adults, the predicted quasi-extinction probability is 30%. A more ambitious stocking program that maintains a population of 3 million adult striped bass would increase the predicted quasi-extinction probability to 55%. Extinction probability, but not recovery probability, was fairly insensitive to assumptions about density dependence. We conclude that winter-run chinook salmon face a serious extinction risk without augmentation of the striped bass population and that substantial increases in striped bass abundance could significantly increase the threat to winter-run chi-nook salmon if not mitigated by increasing winter chinook salmon survival in some other way.

Population status, seasonal variation in abundance, and long-term population trends of Steller sea lions (Eumetopias jubatus) at the South Farallon Islands, California

We examined seasonal and annual variation in numbers of Steller (northern) sea lions (Eumetopias jubatus) at the South Farallon Islands from counts conducted weekly from 1974 to 1996. Numbers of adult and subadult males peaked during the breeding season (May–July), whereas numbers of adult females and immature individuals peaked during the breeding season and from late fall through early winter (September–December). The seasonal pattern varied significantly among years for all sexes and age classes. From 1977 to 1996, numbers present during the breeding season decreased by 5.9% per year for adult females and increased by 1.9% per year for subadult males. No trend in numbers of adult males was detected. Numbers of immature individuals also declined by 4.5% per year during the breeding season but increased by 5.0% per year from late fall through early winter. Maximum number of pups counted declined significantly through time, although few pups were produced at the South Farallon Islands. The ratio of adult females to adult males averaged 5.2:1 and declined significantly with each year, whereas no trend in the ratio of pups to adult females was discernible. Further studies are needed to determine if reduced numbers of adult females in recent years have resulted from reduced survival of juvenile or adult females or from changes in the geographic distribution of females.

Population structure of king mackerel (Scomberomorus cavalla) around peninsular Florida, as revealed by microsatellite DNA

A total of 1006 king mackerel (Scomberomorus cavalla) representing 20 discrete samples collected between 1996 and 1998 along the east (Atlantic) and west (Gulf) coasts of Florida and the Florida Keys were assayed for allelic variation at seven nuclear-encoded microsatellites. No significant deviations from Hardy-Weinberg equilibrium expectations were found for six of the microsatellites, and genotypes at all microsatellites were independent. Allele distributions at each microsatellite were independent of sex and age of individuals. Homogeneity tests of spatial distributions of alleles at the microsatellites revealed two weakly divergent “genetic” subpopulations or stocks of king mackerel in Florida waters—one along the Atlantic coast and one along the Gulf coast. Homogeneity tests of allele distributions when samples were pooled along seasonal (temporal) boundaries, consistent with the temporal boundaries used currently for stock assessment and allocation of the king mackerel resource, were nonsignificant. The degree of genetic divergence between the two “genetic” stocks was small: on average, only 0.19% of the total genetic variance across all samples assayed occurred between the two regions. Cluster analysis, assignment tests, and spatial autocorrelation analysis did not generate patterns that were consistent with either geographic or spatial-temporal boundaries. King mackerel sampled from the Florida Keys could not be assigned unequivocally to either “genetic” stock. The genetic data were not consistent with current spatial-temporal boundaries employed in stock assessment and allocation of the king mackerel resource. The genetic differences between king mackerel in the Atlantic versus those in the Gulf most likely stem from reduced gene flow (migration) between the Atlantic and Gulf in relation to gene flow (migration) along the Atlantic and Gulf coasts of peninsular Florida. This difference is consistent with findings for other marine fishes where data indicate that the southern Florida peninsula serves (or has served) as a biogeographic boundary.

Chronic and catastrophic influences of the environment on the population dynamics of the common fishes [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Seasonal, interannual, decadal and centennial influences on population dynamics have been described for several species. It now seems possible to interpret environmental changes that initiate population change ...