A review of the population structure of yellowfin tuna, Thunnus albacares, in the Eastern Pacific Ocean

ENGLISH: Since its inception in 1950 by agreement between the Republic of Costa Rica and the United States of America, the Inter-American Tropical Tuna Commission has been engaged in studies of the biology, ecology and population dynamics of yellowfin tuna in the eastern Pacific Ocean. Prime consideration has been given to the evaluation of the effects of fishing pressure on the yellowfin tuna in this area in order to estimate the maximum sustainable yield. A portion of the eastern Pacific has been defined by the Inter-American Tropical Tuna Commission (1963) as a regulatory area for yellowfin tuna (Figure 1). SPANISH: Desde su incepción en 1950, por un acuerdo entre la República de Costa Rica y los Estados Unidos de América, la Comisión Interamericana del Atún Tropical ha estado ocupada en los estudios de la biología, ecología y dinámica de las poblaciones del atún aleta amarilla en el Océano Pacífico Oriental. Se consideró primariamente la evaluación de los efectos de la presión de la pesquería sobre el atún aleta amarilla en esta área, para poder estimar el rendimiento máximo sostenible. Una parte del Pacífico Oriental ha sido definida por la Comisión Interamericana del Atún Tropical (1963), como área de reglamentación del atún aleta amarilla (Figura 1). (PDF contains 60 pages.)

Population structure of Pacific yellowfin tuna

ENGLISH: The population structure and production of Pacific yellowfin tuna, Thunnus albacares, were examined by studying most of the basic data available on stock assessment, as well as other data, for the period 1965 to 1972. The data were obtained mainly from the Japanese longline fishery in the Pacific Ocean east of about 1200E and from the purse-seine fishery in the eastern Pacific east of about 140oW. Data from genetic studies of subpopulations were not used due to their preliminary nature. It was concluded that the concept of "semi-independent" subpopulations proposed by Kamimura and Honma (1963) and Royce (1964) defines the population structure of Pacific yellowfin. At least three stocks (i.e. western, central and eastern), relatively independent of each other, are thought to exist, but the actual number and location of subpopulations is still unclear. Possible north-south separations, indicated to some extent by genetic studies and tagging, could be neither substantiated nor rejected on the basis of this study. Finally, unless some major change in the fishing technology occurs, it is doubtful if any significant sustainable increase in yellowfin production from the Pacific is possible. The greatest potential for increase, if any, appears to be based on changing the size structure of yellowfin in the catch from the central Pacific. SPANISH: Se examino la estructura de la población y la producción del atún aleta amarilla del Pacifico Thunnus albacares para estudiar la mayoría de los datos básicos que se tenían sobre el avalúo de la población, como también otra información correspondiente al periodo de 1965·1972. Los datos fueron obtenidos principalmente de las pescas palangreros japonesas del Océano Pacifico al este de los 1200 E y de las pescas con redes de cerco del Pacifico oriental, al este de los 140oW. No se emplearon los datos de estudios genéticos de las subpoblaciones porque eran mas bien preliminares. Se concluyo que el concepto propuesto por Kamimura y Honma (1963) y Royce (1964) de subpoblaciones "semiindependientes" define la estructura de la población del aleta amarilla en el Pacifico. Se cree que existen por 10 menos tres existencias (e.d. la occidental, central y oriental), relativamente independientes la una de la otra, pero no se conoce con certeza cuantas subpoblaciones hay y donde se encuentran. La posible separación norte-sur, indicada, hasta cierto punto, por los análisis genéticos y del marcado, no puede ni confirmarse ni rechazarse basados en este estudio. Finalmente, a no ser que ocurra algún gran cambio en la tecnología pesquera es dudoso que sea posible obtener un aumento constante e importante en la producción del aleta amarilla del Pacifico. El potencial mayor de aumento, si es que existe alguno, parece que se basa en el cambio de la estructura de talla en la captura del aleta amarilla del Pacifico central. (PDF contains 169 pages.)

A report on the population structure of adult salmon and sea trout in the River Lune using scale samples - with reference to historical data.

During 1993, a comprehensive data set of scale readings, length and weight measurements was established for migratory salmonids on the River Lune. This information was collected using three methods of fish capture: 1. The Lune estuary commercial nets. 2. River Lune Forge weir fish trap. 3. River Lune rod catch scale returns. Additional information was contributed by the Kent, Leven and Duddon rod and commercial fisheries. The data shows that the salmon stock in 1993 was dominated by two year old smolts. This varies from year to year. The sea trout population displays a normal population curve in terms of numbers of fish in each age and weight class. The growth rate of salmon and sea trout is very similar even though salmon have the benefit of high sea feeding.

Population structure of pink salmon (Oncorhynchus gorbuscha) in British Columbia and Washington, determined with microsatellites

Population structure of pink salmon (Oncorhynchus gorbuscha) from British Columbia and Washington was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 16 microsatellite loci was surveyed for approximately 46,500 pink salmon sampled from 146 locations in the odd-year broodline and from 116 locations in the even-year broodline. An index of genetic differentiation, FST, over all populations and loci in the odd-year broodline was 0.005, with individual locus values ranging from 0.002 to 0.025. Population differentiation was less in the even-year broodline, with a FST value of 0.002 over all loci, and with individual locus values ranging from 0.001 to 0.005. Greater genetic diversity was observed in the odd-year broodline. Differentiation in pink salmon allele frequencies between broodlines was approximately 5.5 times greater than regional differentiation within broodlines. A regional structuring of populations was the general pattern observed, and a greater regional structure in the odd-year broodline than in the even-year broodline. The geographic distribution of microsatellite variation in populations of pink salmon likely ref lects a distribution of broodlines from separate refuges after the last glaciation period.

Otolith morphometrics and population structure of Pacific sardine (Sardinops sagax) along the west coast of North America

The broad distribution of Pacific sardine (Sardinops sagax) along the Pacif ic coast of North America makes it difficult for fisheries managers to identify regional stocks of this dominant small pelagic species. An investigation of morphometric characteristics of otoliths of Pacific sardine across most of their range revealed regional differences in populations. In a survey of over 2000 otoliths, all ages (with an emphasis on age-1 recruits) were compared. Principal components analysis, multivariate analysis of variance, and a novel method derived from regression and residuals calculations, termed perimeter-weight profiles (PWPs), revealed otolith similarities and differences. The results of the different approaches to statistical comparisons did not always agree. Sardine otoliths from Mexican waters were generally lighter and more lobate than those from U.S. and Canadian populations. Age-1 otoliths from northern California in 2006–07 tended to be heavier and smoother than those from other areas, including year-class cohorts from southern California. Comparisons of age-groups and year-classes of northern California otoliths with the use of the PWP models indicated signif icant trends in year-to-year patterns. In conjunction with other established indices of population structure, otolith PWPs are a useful tool for identifying local and regional stocks of Pacific sardine and may help distinguish populations of other fish species as well.

Population structure, long-term connectivity, and effective size of mutton snapper (Lutjanus analis) in the Caribbean Sea and Florida Keys

Genetic structure and average long-term connectivity and effective size of mutton snapper (Lutjanus analis) sampled from offshore localities in the U.S. Caribbean and the Florida Keys were assessed by using nuclear-encoded microsatellites and a fragment of mitochondrial DNA. No significant differences in allele, genotype (microsatellites), or haplotype (mtDNA) distributions were detected; tests of selective neutrality (mtDNA) were nonsignificant after Bonferroni correction. Heuristic estimates of average long-term rate of migration (proportion of migrant individuals/generation) between geographically adjacent localities varied from 0.0033 to 0.0054, indicating that local subpopulations could respond independently of environmental perturbations. Estimates of average longterm effective population sizes varied from 341 to 1066 and differed significantly among several of the localities. These results indicate that over time larval drift and interregional adult movement may not be sufficient to maintain population sustainability across the region and that there may be different demographic stocks at some of the localities studied. The estimate of long-term effective population size at the locality offshore of St. Croix was below the minimum threshold size considered necessary to maintain the equilibrium between the loss of adaptive genetic variance from genetic drift and its replacement by mutation. Genetic variability in mutton snapper likely is maintained at the intraregional level by aggregate spawning and random mating of local populations. This feature is perhaps ironic in that aggregate spawning also renders mutton snapper especially vulnerable to overexploitation.

A molecular genetic investigation of the population structure of Atlantic menhaden (Brevoortia tyrannus)

Atlantic menhaden (Brevoortia tyrannus), through landings, support one of the largest commercial fisheries in the United States. Recent consolidation of the once coast-wide reduction fishery to waters within and around Chesapeake Bay has raised concerns over the possibility of the loss of unique genetic variation resulting from concentrated fishing pressure. To address this question, we surveyed variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene region and seven nuclear microsatellite loci to evaluate stock structure of Atlantic menhaden. Samples were collected from up to three cohorts of Atlantic menhaden at four geographic locations along the U.S. Atlantic coast in 2006 and 2007, and from the closely related Gulf menhaden (B. patronus) in the Gulf of Mexico. Genetic divergence between Atlantic menhaden and Gulf menhaden, based on the COI gene region sequences and microsatellite loci, was more characteristic of conspecific populations than separate species. Hierarchical analyses of molecular variance indicated a homogeneous distribution of genetic variation within Atlantic menhaden. No significant variation was found between young-of-the-year menhaden (YOY) collected early and late in the season within Chesapeake Bay, between young-of-the-year and yearling menhaden collected in the Chesapeake Bay during the same year, between YOY and yearling menhaden taken in Chesapeake Bay in successive years, or among combined YOY and yearling Atlantic menhaden collected in both years from the four geographic locations. The genetic connectivity between the regional collections indicates that the concentration of fishing pressure in and around Chesapeake Bay will not result in a significant loss of unique genetic variation.

Population structure of chum salmon (Oncorhynchus keta) across the Pacific Rim, determined from microsatellite analysis

The Pacific Rim population structure of chum salmon (Oncorhynchus keta) was examined with a survey of microsatellite variation to describe the distribution of genetic variation and to evaluate whether chum salmon may have originated from two or more glacial refuges following dispersal to newly available habitat after glacial retreat. Variation at 14 microsatellite loci was surveyed for over 53,000 chum salmon sampled from over 380 localities ranging from Korea through Washington State. An index of genetic differentiation, FST, over all populations and loci was 0.033, with individual locus values ranging from 0.009 to 0.104. The most genetically diverse chum salmon were observed from Asia, particularly Japan, whereas chum salmon from the Skeena River and Queen Charlotte Islands in northern British Columbia and those from Washington State displayed the fewest number of alleles compared with chum salmon in other regions. Differentiation in chum salmon allele frequencies among regions and populations within regions was approximately 18 times greater than that of annual variation within populations. A regional structuring of populations was the general pattern observed, with chum salmon spawning in different tributaries within a major river drainage or spawning in smaller rivers in a geographic area generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of chum salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation, but four possible refuges fit better the observed distribution of genetic variation. The distribution of microsatellite variation of chum salmon on a Pacific Rim basis likely reflects the origins of salmon radiating from refuges after the last glaciation period.

Determination of population structure and stock composition of chum salmon (Oncorhynchus keta) in Russia determined with microsatellites

Variation at 14 microsatellite loci was examined in 34 chum salmon (Oncorhynchus keta) populations from Russia and evaluated for its use in the determination of population structure and stock composition in simulated mixed-stock fishery samples. The genetic differentiation index (Fst) over all populations and loci was 0.017, and individual locus values ranged from 0.003 to 0.054. Regional population structure was observed, and populations from Primorye, Sakhalin Island, and northeast Russia were the most distinct. Microsatellite variation provided evidence of a more fine-scale population structure than those that had previously been demonstrated with other genetic-based markers. Analysis of simulated mixed-stock samples indicated that accurate and precise regional estimates of stock composition were produced when the microsatellites were used to estimate stock compositions. Microsatellites can be used to determine stock composition in geographically separate Russian coastal chum salmon fisheries and provide a greater resolution of stock composition and population structure than that previously provided with other techniques.

A comparison of two fishery-independent survey programs used to define the population structure of American lobster (Homarus americanus) in the Gulf of Maine

The population structure and abundance of the American lobster (Homarus americanus) stock in the Gulf of Maine are defined by data derived from a fishery-independent trawl survey program conducted by the National Marine Fisheries Service (NMFS). Few sampling stations in the survey area are located inshore, in particular along coastal Maine. According to statistics, however, more than two thirds of the lobster landings come from inshore waters within three miles off the coast of Maine. In order to include an inshore survey program, complementary to the NMFS survey, the Maine Department of Marine Resources (DMR) initialized an inshore survey program in 2000. The survey was modeled on the NMFS survey program, making these two survey programs comparable. Using data from both survey programs, we evaluated the population structure of the American lobster in the Gulf of Maine. Our findings indicate that lobsters in the Gulf of Maine tend to have a size-dependent inshore-off-shore distribution; smaller lobsters are more likely to stay inshore and larger lobsters are more likely to stay offshore. The DMR inshore and NMFS survey programs focused on different areas in the Gulf of Maine and likely targeted different segments of the stock. We suggest that data from both survey programs be used to assess the lobster stock and to describe the dynamics of the stock in the Gulf of Maine.

Population structure and variance effective size of red snapper (Lutjanus campechanus) in the northern Gulf of Mexico*

We assayed allelic variation at 19 nuclear-encoded microsatellites among 1622 Gulf red snapper (Lutjanus campechanus) sampled from the 1995 and 1997 cohorts at each of three offshore localities in the northern Gulf of Mexico (Gulf). Localities represented western, central, and eastern subregions within the northern Gulf. Number of alleles per microsatellite per sample ranged from four to 23, and gene diversity ranged from 0.170 to 0.917. Tests of conformity to Hardy-Weinberg equilibrium expectations and of genotypic equilibrium between pairs of micro-satellites were generally nonsignificant following Bonferroni correction. Significant genic or genotypic heterogeneity (or both) among samples was detected at four microsatellites and over all microsatellites. Levels of divergence among samples were low (FST ≤0.001). Pairwise exact tests revealed that six of seven “significant” comparisons involved temporal rather than spatial heterogeneity. Contemporaneous or variance effective size (NeV) was estimated from the temporal variance in allele frequencies by using a maximum-likelihood method. Estimates of NeV ranged between 1098 and >75,000 and differed significantly among localities; the NeV estimate for the sample from the northcentral Gulf was >60 times as large as the estimates for the other two localities. The differences in variance effective size could ref lect differences in number of individuals successfully reproducing, differences in patterns and intensity of immigration, or both, and are consistent with the hypothesis, supported by life-history data, that different “demographic stocks” of red snapper are found in the northern Gulf. Estimates of NeV for red snapper in the northern Gulf were at least three orders of magnitude lower than current estimates of census size (N). The ratio of effective to census size (Ne/N) is far below that expected in an ideal population and may reflect high variance in individual reproductive success, high temporal and spatial variance in productivity among subregions or a combination of the two.