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Forensic identification of 'wild' versus hatchery-produced (cultured) red drum (Sciaenops ocellatus), an economically important marine fish in the southern United States, was assessed using hypervariable nuclear-encoded microsatellites and sequences of mitochondrial DNA. Both genotype exclusion and likelihood-ratio tests successfully identified 'wild' and 'cultured' individuals within requisite error bounds and within the context of complete parental sampling. Of the two, genotype exclusion was more effective, producing satisfactory results with fewer microsatellites and larger allowable error rates. Assignment tests proved ineffective, most likely because of the low level of genetic divergence between the sampled populations. An optimal, minimum set of ten markers that will reduce potential genotyping costs is identified. Results of the study should allay concerns regarding identification of 'wild'-caught fish sold illegally.

Lane snappers ( Lutjanus synagris), sampled from eight localities in the northern Gulf of Mexico (Gulf) and one locality along the Atlantic coast of Florida, were assayed for allelic variation at 14 nuclear-encoded microsatellites and for sequence variation in a 590 base-pair fragment of the mitochondrially encoded ND-4 gene (mtDNA). Significant heterogeneity among the nine localities in both microsatellite allele and genotype distributions and mtDNA haplotype distributions was indicated by exact tests and by analysis of molecular variance (AMOVA). Exact tests between pairs of localities and spatial analysis of molecular variance (SAMOVA) for both microsatellites and mtDNA revealed two genetically distinct groups: a Western Group that included six localities from the northwestern and northcentral Gulf and an Eastern Group that included three localities, one from the west coast of Florida, one from the Florida Keys, and one from the east (Atlantic) coast of Florida. The between-groups component of molecular variance was significant for both microsatellites ( ΦCT = 0.016, P = 0.009) and mtDNA ( ΦCT = 0.208, P = 0.010). Exact tests between pairs of localities within each group and spatial autocorrelation analysis did not reveal genetic heterogeneity or an isolation-by-distance effect among localities within either group. MtDNA haplotype diversity was significantly less ( P < 0.0001) in the Western Group than in the Eastern Group; microsatellite allelic richness and gene diversity also were significantly less in the Western Group ( P = 0.015 and 0.013, respectively). The difference in genetic variability between the two groups may reflect reduced effective population size in the Western Group and/or asymmetric rates of genetic migration. The relative difference in variability between the two groups was substantially greater in mtDNA and may reflect one or more mtDNA selective sweeps; tests of neutrality of the mtDNA data were consistent with this possibility. Bayesian analysis of genetic demography indicated that both groups have experienced a historical decline in effective population size, with the decline being greater in the Western Group. Maximum-likelihood analysis of microsatellite data indicated significant asymmetry in average, long-term migration rates between the two groups, with roughly twofold greater migration from the Western Group to the Eastern Group. The difference in mtDNA variability and the order-of-magnitude difference in genetic divergence between mtDNA and microsatellites may reflect different demographic events affecting mtDNA disproportionately and/or a sexual and/or spatial bias in gene flow and dispersal. The spatial discontinuity among lane snappers in the region corresponds to a known zone of vicariance in other marine species. The evidence of two genetically distinct groupings (stocks) has implications for management of lane snapper resources in the northern Gulf. [ABSTRACT FROM AUTHOR]

Multiplexed microsatellite markers were evaluated as genetic tags for red drum ( Sciaenops ocellatus) juveniles used in stock enhancement. Offspring were generated from spawns of nine sets of five broodfish (three dams and two sires) in individual brood tanks. Intensive sampling, by trawling, at 2, 7, 8, 10 and 11 days after release of ∼192 500 hatchery-raised fingerlings resulted in recovery of a total of 310 fingerlings. All parents and recovered offspring were genotyped for variation at 30 microsatellites combined for simultaneous assay in six multiplex panels. An optimal combination employing three of the six multiplex panels allowed unambiguous parentage assignment of all recovered offspring. Only 21 of 52 possible dam x sire combinations were represented among recovered offspring. The founder equivalent ( fe) of the recovered offspring was 8.7 vs the expected fe of 36.0 (95% CI = 33.3–38.4) if reproductive success was randomly distributed among breeders. The significantly lower founder equivalent translated into reduced genetic diversity among the recovered offspring and may reflect differing contributions of individual broodfish to spawning events, differing productivity among brood tanks, and/or variable survival of families during early larval and/or juvenile stages. [ABSTRACT FROM AUTHOR]

The stock enhancement program for red drum Sciaenops ocellatus in Texas annually releases from 25 to 30 million fingerlings into Texas bays and estuaries and represents one of the largest such programs for marine fishes worldwide. We used 16 nuclear-encoded microsatellites and a 370-base-pair fragment of the mitochondrial DNA (mtDNA) D-loop to assign red drum sampled from two bays along the Texas coast to either hatchery or wild origin. A total of 30 hatchery-released fish were identified among 321 red drum belonging to three year-classes sampled from Galveston Bay, while a total of 11 hatchery-released fish were identified among 970 red drum belonging to four year-classes sampled from Aransas Bay. Allelic richness (microsatellites) was significantly lower among hatchery-released fish than among hatchery broodfish and wild fish. Similarly, the expected number of mtDNA haplotypes in hatchery-released fish (based on simulation analysis) was significantly lower than that expected in a random sample of both brood and wild fish. The contribution of brood dams, sires, and dam x sire combinations to the hatchery-released fish was nonrandom, as was the distribution of hatchery-released and wild fish with respect to sampling stations (localities) within each bay. The possibility of a Ryman-Laikre effect is discussed. [ABSTRACT FROM AUTHOR]

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11–25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene (∼12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations. [ABSTRACT FROM AUTHOR]

Twenty-five microsatellites from Atlantic bluefin tuna ( Thunnus thynnus thynnus) were characterized. All 25 microsatellites were polymorphic; the number of alleles among up to 56 individuals surveyed ranged from two to 23. Atlantic bluefin tuna are highly exploited and major questions remain as to stock structure and abundance in the eastern and western North Atlantic. The microsatellites will be useful in testing stock-structure hypotheses and in generating estimates of effective population size. The polymerase chain reaction primer sets developed also amplified identifiable alleles in three other species of genus Thunnus: T. albacares (yellowfin tuna), T. alalunga (albacore tuna) and T. obesus (bigeye tuna). [ABSTRACT FROM AUTHOR]

We isolated 11 microsatellites from the Pacific sardine Sardinops sagax sagax. The number of alleles and HE among 30 individuals from a single population ranged from four to 24 and from 0.606 to 0.959, respectively. Pacific sardines are a vital economic resource in the northeastern Pacific Ocean, but insufficiently polymorphic loci have limited inferences about its stock structure and genetic variation. The level of variability of these new markers will prove useful in testing hypotheses on the stock-structure and long-term genetic integrity of the species. [ABSTRACT FROM AUTHOR]

Abstract: Population structure of carite (Serra Spanish mackerel, Scomberomorus brasiliensis) in waters offshore of Trinidad and northern Venezuela was assessed by analysis of allele and genotype distributions at 16 nuclear-encoded microsatellites and mitochondrial (mt)DNA haplotype distribution among individuals from five localities in the southern Caribbean Sea. Tests of homogeneity (microsatellites) revealed a genetically discrete subpopulation (stock) of carite in the Cariaco Basin along the northern coast of Venezuelan mainland. This subpopulation contained a small, highly divergent clade of four mtDNA haplotypes that possibly represent recent admixture of formerly isolated subpopulations. Spatial autocorrelation analysis of the microsatellite data was consistent with the notion that carite from Isla de Margarita (Venezuela) and Trinidad may warrant management as distinct stocks, while spatial autocorrelation analysis and tests of selective neutrality of mtDNA variation suggested that carite off the south coast of Trinidad differ from carite along the west and north coasts. The implication of these findings is that there may be a number of spawning stocks of carite in the southern Caribbean Sea. [Copyright &y& Elsevier]