Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

Genetic and morphological differences between Sebastes vulpes and S. zonatus (Teleostei: Scorpaeniformes: Scorpaenidae)

The taxonomic status of Sebastes vulpes and S. zonatus were clarified by comprehensive genetic (amplif ied fragment length polymorphisms [AFLP] and mitochondrial DNA [mtDNA] variation) and morphological analyses on a total of 65 specimens collected from a single locality. A principal coordinate analysis based on 364 AFLP loci separated the specimens completely into two genetically distinct groups that corresponded to S. vulpes and S. zonatus according to body coloration and that indicated that they are reproductively isolated species. Significant morphological differences were also evident between the two groups; 1) separation by principal component analysis based on 31 measurements, and 2)separation according to differences in counts of gill rakers and dorsal-fin spines without basal scales, and in the frequencies of specimens with small scales on the lower jaw. Restriction of gene flow between the two groups was also indicated by the pairwise ΦST values estimated from variations in partial sequences from the mtDNA control region, although the minimum spanning network did not result in separation into distinct clades. The latter was likely due to incomplete lineage sorting between S. vulpes and S. zonatus owing to their recent speciation.

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 connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Microsatellite multiplex panels for genetic studies of gray snapper (Lutjanus griseus) and lane snapper (Lutjanus synagris)

Microsatellites are codominantly inherited nuclear-DNA markers (Wright and Bentzen, 1994) that are now commonly used to assess both stock structure and the effective population size of exploited fishes (Turner et al., 2002; Chistiakov et al., 2006; Saillant and Gold, 2006). Multiplexing is the combination of polymerase chain reaction (PCR) amplification products from multiple loci into a single lane of an electrophoretic gel (Olsen et al., 1996; Neff et al., 2000) and is accomplished either by coamplification of multiple loci in a single reaction (Chamberlain et al., 1988) or by combination of products from multiple single-locus PCR amplifications (Olsen et al., 1996). The advantage of multiplexing micro-satellites lies in the significant reduction in both personnel time (labor) and consumable supplies generally required for large genotyping projects (Neff et al., 2000; Renshaw et al., 2006).

Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John’s River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998−2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

Baseline biochemical and genetic profiles of four fishes from the River Nile

Six enzyme systems coding for 10 loci and 6 proteins were examined in the blood of Polypterus senegalus, Clarias lazera, Tilapia nilotica and Protopterus annectens, using electrophoresis. Six loci were polymorphic in all the four species, three polymorphic in three species and one polymorphic in T. nilotica. Four protein loci were monomorphic in all the four species with variants in P. senegalus and T. nilotica. Haemoglobin can be used as a species-specific marker. Polymorphism was 53-56 per cent and average heterozygosity was 0.1-0.15.

Genetic variation of rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (S. borealis) inferred from allozymes

Rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (Sebastes borealis) were collected from the Washington coast, the Gulf of Alaska, the southern Bering Sea, and the eastern Kamchatka coast of Russia (areas encompassing most of their geographic distribution) for population genetic analyses. Using starch gel electrophoresis, we analyzed 1027 rougheye rockfish and 615 shortraker rockfish for variation at 29 proteincoding loci. No genetic heterogeneity was found among shortraker rockfish throughout the sampled regions, although shortraker in the Aleutian Islands region, captured at deeper depths, were found to be significantly smaller in size than the shortraker caught in shallower waters from Southeast Alaska. Genetic analysis of the rougheye rockfish revealed two evolutionary lineages that exist in sympatry with little or no gene f low between them. When analyzed as two distinct species, neither lineage exhibited heterogeneity among regions. Sebastes aleutianus seems to inhabit waters throughout the Gulf of Alaska and more southern waters, whereas S. sp. cf. aleutianus inhabits waters throughout the Gulf of Alaska, Aleutian Islands, and Asia. The distribution of the two rougheye rockfish lineages may be related to depth where they are sympatric. The paler color morph, S. aleutianus, is found more abundantly in shallower waters and the darker color morph, Sebastes sp. cf. aleutianus, inhabits deeper waters. Sebastes sp. cf. aleutianus, also exhibited a significantly higher prevalence of two parasites, N. robusta and T. trituba, than did Sebastes aleutianus, in the 2001 samples, indicating a possible difference in habitat and (or) resource use between the two lineages.

Genetic evidence of two sibling species within the Contracoecum ogmorhini Johnson & Mawson 1941 complex (Nematoda; Anisakidae) from otariid seals in boreal and austral regions

Genetic variation of Contracaecum ogmorhini (sensu lato) populations from different otariid seals of the northern and southern hemisphere was studied on the basis of 18 enzyme loci as well as preliminary sequence analysis of the mitochondrial cyt b gene (260 bp). Samples were collected from Zalophus californianus in the boreal region and from Arctocephalus pusillus pusillus, A. pusillus doriferus and A. australis from the austral region. Marked genetic heterogeneity was found between C. ogmorhini (sensu lato) samples from the boreal and austral region, respectively. Two loci (Mdh-2 and NADHdh) showed fixed differences and a further three loci (Iddh, Mdh-1 and 6Pgdh) were highly differentiated between boreal and austral samples. Their average genetic distance was DNei = 0.36 at isozyme level. At mitochondrial DNA level, an average proportion of nucleotide substitution of 3.7% was observed. These findings support the existence of two distinct sibling species, for which the names C. ogmorhini (sensu stricto) and C. margolisi n. sp., respectively, for the austral and boreal taxon, are proposed. A description for C. margolisi n. sp. is provided. No diagnostic morphological characters have so far been detected; on the other hand, two enzyme loci, Mdh-2 and NADHdh, fully diagnostic between the two species, can be used for the routine identification of males, females and larval stages. Mirounga leonina was found to host C. ogmorhini (s.s.) inmixed infections with C. osculatum (s.l.) (of which C. ogmorhini (s.l.) was in the past considered to be a synonym) and C. miroungae; no hybrid genotypes were found,confirming the reproductive isolation of these three anisakid species. The hosts and geographical range so far recorded for C. margolisi n. sp. and C. ogmorhini (s.s.) are given.

Limited genetic structure of Gulf Menhaden (Brevoortia patronus), as revealed by microsatellite markers developed for the genus Brevoortia (Clupeidae)

Long-term sustainable management of wild populations should be based on management actions that account for the genetic structure among populations. Knowledge of genetic structure and of the degree of demographic exchange between discreet [sic] populations allows managers to better define management units. However, adequate gene loci for population assessments are not always available. In this study, variable co-dominant DNA loci in the heavily exploited marine genus Brevoortia were developed with a microsatellite-enriched DNA library for the Gulf Menhaden (Brevoortia patronus). Microsatellite marker discovery was followed by genetic characterization of 4 endemic North American Brevoortia species, by using 14 novel loci as well as 5 previously described loci. Power analysis of these loci for use in species identification and genetic stock structure was used to assess their potential to improve the stock definition in the menhaden fishery of the Gulf of Mexico. These loci could be used to reliably identify menhaden species in the Gulf of Mexico with an estimated error rate of α=0.0001. Similarly, a power analysis completed on the basis of observed allele frequencies in Gulf Menhaden indicated that these markers can be used to detect very small levels of genetic divergence (Fst≈0.004) among simulated populations, with sample sizes as small as n=50 individuals. A cursory analysis of genetic structure among Gulf Menhaden sampled throughout the Gulf of Mexico indicated limited genetic structure among sampling locations, although the available sampling did not reach the target number (n=50) necessary to detect minimal values of significant structure.

Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals

This study examines genetic variation at five microsatellite loci and at the vesicle membrane protein locus, pantophysin, of Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. The Nantucket Shoals sample represents the first time cod south of Georges Bank have been genetically evaluated. Heterogeneity of allelic distribution was not observed (P>0.05) between two temporally separated Georges Bank samples indicating potential genetic stability of Georges Bank cod. When Bonferroni corrections (α=0.05, P<0.017) were applied to pairwise measures of population differentiation and estimates of FST, significance was observed between Nantucket Shoals and Georges Bank cod and also between Nantucket Shoals and Browns Bank cod. However, neither significant differentiation nor significant estimates of FST were observed between Georges Bank and the Browns Bank cod. Our research suggests that the cod spawning on Nantucket Shoals are genetically differentiated from cod spawning on Browns Bank and Georges Bank. Managers may wish to consider Nantucket Shoals cod a separate stock for assessment and management purposes in the future.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data

We used allozyme, microsatellite, and mitochondrial DNA (mtDNA) data to test for spatial and interannual genetic diversity in wall-eye pollock (Theragra chalcogramma) from six spawning aggregations representing three geographic regions: Gulf of Alaska, eastern Bering Sea, and eastern Kamchatka. Interpopulation genetic diversity was evident primarily from the mtDNA and two allozyme loci (SOD-2*, MPI*). Permutation tests ˆindicated that FST values for most allozyme and microsatellite loci were not significantly greater than zero. The microsatellite results suggested that high locus polymorphism may not be a reliable indicator of power for detecting population differentiation in walleye pollock. The fact that mtDNA revealed population structure and most nuclear loci did not suggests that the effective size of most walleye pollock populations is large (genetic drift is weak) and migration is a relatively strong homogenizing force. The allozymes and mtDNA provided mostly concordant estimates of patterns of spatial genetic variation. These data showed significant genetic variation between North American and Asian populations. In addition, two spawning aggregations in the Gulf of Alaska, in Prince William Sound, and off Middleton Island, appeared genetically distinct from walleye pollock spawning in the Shelikof Strait and may merit management as a distinct stock. Finally, we found evidence of interannual genetic variation in two of three North American spawning aggregations, similar in magnitude to the spatial variation among North American walleye pol-lock. We suggest that interannual genetic variation in walleye pollock may be indicative of one or more of the following factors: highly variable reproductive success, adult philopatry, source-sink metapopulation structure, and intraannual variation (days) in spawning timing among genetically distinct but spatially identical spawning aggregates.

Use of allozyme markers to determine the genetic structure of hatchery population of Thai pangas, Pangasius hypophthalmus of Jessore, Bangladesh

Genetic structure of hatchery population of Thai pangas (Pangasius hypophthalmus) of Jessore region, Bangladesh has been investigated from 1 January 2004 to 31 December 2004. Samples for this study were collected from five fish hatcheries viz. Asrom, Banchte Shekha, Chowdhury, Maola and Rezaul Haque. The enzymes were encoded by 15 gene loci: Adh-1*, Est-1*, G3pdh-2*, Gpi-1*, Gpi-2*, Idhp-1*, Idhp-2*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2*, Pgm*, Sdh-1*, Sdh-2* and Sod*. Among them four (Est-1*, G3pdh-2*, Gpi-2*and Pgm*) were found to be polymorphic in different populations but only Gpi-2* was polymorphic in all the sampled populations. The mean proportion of polymorphic loci per population was the highest (26.7%) in Banchte Shekha hatchery while the mean proportion of heterozygous loci was 13.33% per individual in Banchte Shekha and Maola hatcheries. The UPGMA dendrogram of Nei's (1972) genetic distances indicated a relationship between the genetic distance and geographical difference. High genetic variability in stocks of Thai pangas was observed in the Banchte Shekha and Maola hatcheries and less variability was found in the other three hatcheries.

Genetic diversity of Bartail flathead (Platycephalus indicus (Linnaeus,1758)) using AFLP markers in Persian Gulf

Platycephalus indicus is a large benthic fish that inhabits temperate and tropical coastal waters of the Indo-West Pacific and found on sand or mud bottom in vary shallow area of estuary and near shore to depth of 25m. This species is dominant species of platycephalidae family, in Khuzestan, Bushehr and Hormozgan provinces and mainly is captured by bottom trawl, gillnet and moshta in Hormozgan. This study was designed to evaluate population variation and differentiation of bartail flathead (Platycephalus indicus (Linnaeus, 1785))in the Iranian waters of Persian Gulf using the morphometric and meristic characters and by AFLP marker. . A total 180 fish specimens were collected by gill net from six station(khor mosa, bahrekan, shif, motaf, charak and bandar abbas) that was 30 individual related to every station in Iranian shores of Persian Gulf . 28 morphometric factors and 11meristic specialties were measured and morphometric factors was standardized with Beacham formula. Univariate analysis of variance (One-way ANOVA) revealed significant differences with varying degrees between the means for 21 standardized morphometric measurements and 6 meristic counts that showed high significant differences between the six stations sampling. Discriminate function analysis (DFA) or the overall random assignment of individuals into their original groups was for morphometric and meristic characters was 47.9% and 53.9% respectively. The data were subjected to a principle component analysis (PCA) which grouped in eight and four factors for morphometric and meristic charactersrespectively.. Genetic diversity of six populations of bartail flathead (Platycephalus indicus) was investigated using amplified fragment length polymorphism (AFLP). A total of 118 reproducible bands amplified with ten AFLP primer combinations were obtained from 42 fishes that were collected from six different locations in the northern of Persian Gulf. The percentage of polymorphic bands was 57.06%. Average of Nei’s genetic diversity was 0.200±0.008, and Average of Shannon’s index was 0.300±0.011. The results of AMOVA analysis indicated that 66% of the genetic variation contained within populations and 34% occurred among populations and gene flow was 0.6454.The estimated level of population differentiation asmeasured by average Fst value across all loci was 0.327. Plotting discriminant functions 1 and 2 and UPGMA dendrograms based on Euclidian distance and genetic distance also showed at least five separate populations of bartail flathead in the northern Persian Gulf.