Population structure of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico, as inferred from variation in nuclear-encoded microsatellites

Allelic variation at eight nuclear-encoded microsatellites was assayed among 967 red drum (Sciaenops ocellatus) sampled from four consecutive cohorts at seven geographic localities (=28 samples total) in the northern Gulf of Mexico (Gulf). Number of alleles per microsatellite ranged from 6 to 21; average direct-count heterozygosity values per sample (-SE) ranged from 0.560ǂ.018 to 0.903ǂ.009. Tests of Hardy-Weinberg equilibrium revealed significant departures from expected genotype proportions at one microsatellite, which was omitted from further analysis. Tests of genotypic equilibrium indicated that genotypes between pairs of microsatellites were randomly associated. Homogeneity tests of allele distributions across cohorts within localities were non-significant following correction for multiple tests executed simultaneously, and results from molecular analysis of variance indicated that the genetic variance component attributable to variation among cohorts did not differ significantly from zero. Homogeneity tests of allele distributions among localities (cohorts pooled) revealed significant differences both before and after correction for multiple tests. Neighbor-joining clustering of a pairwise matrix of Š values (an unbiased estimator of F_ST), spatial autocorrelations, and regression analysis revealed a pattern of isolation by distance, where genetic divergence among geographic samples increases with geographic distance between sample localities. The pattern and degree of temporal and spatial divergence in the nuclear-encoded microsatellites paralleled almost exactly those of mitochondrial (mt) DNA, as determined in a prior study. Stability of both microsatellite and mtDNA allele distributions within localities indicates that the small but significant genetic divergence among geographic samples represents true signal and that overlapping populations of red drum in the northern Gulf may be influenced by independent population dynamics. The degree of genetic divergence in microsatellites and mtDNA is virtually identical, indicating that genetic effective size of microsatellites and mtDNA in red drum are the same. This, in turn, suggests either that gene flow in red drum in the northern Gulf could be biased sexually or that red drum populations may not be in equilibrium between genetic drift and migration. If a sexual bias exists, the observation that divergence in mtDNA is considerably less than 4 times that of microsatellites could suggest female-mediated dispersal and/or male philopatry. The observed isolation-by-distance effect indicates a practical limit to dispersal. Approximate estimates of geographic neighborhood size suggest the limit is in the range 700-900 km. Although the genetic studies of red drum indicate significant genetic divergence across the northern Gulf, the genetic differences do not delimit specific populations or stocks with fixed geographic boundaries.     

Population structure and genetic variation of lane snapper (<Emphasis Type="Italic">Lutjanus synagris</Emphasis>) in the northern Gulf of Mexico

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 (Φ _CT = 0.016, P = 0.009) and mtDNA (Φ _CT = 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.     

Mitochondrial DNA differentiation and population structure in red drum (Sciaenops ocellatus) from the Gulf of Mexico and Atlantic Ocean

Variation in mitochondrial (mt)DNA was examined among 473 red drum (Sciaenops ocellatus) sampled in 1988 and 1989 from nearshore localities in the northern Gulf of Mexico (Gulf) and the Atlantic coast of the southeastern United States (Atlantic). Data were combined with those from a previous study to generate a total of 871 individuals sampled from 11 localities in the Gulf and 5 localities in the Atlantic. Individuals assayed were from the 1986 and 1987 year-classes. A total of 118 composite mtDNA genotypes (haplotypes) was found. The percentage nucleotide sequence divergence among the 118 haplotypes ranged from 0.184 to 1.913, with a mean (±SE) of 0.878±0.004. MtDNA nucleon diversities and intrapopulational nucleotide-sequence divergence values were similar over all Gulf and Atlantic localities, and were high relative to most fish species surveyed to date. These data indicate that the perceived decline in red drum abundance appears not to have affected the genetic variability base of the species. Significant heterogeneity in the frequencies of at least four haplotypes was detected between pooled samples from the Gulf vs pooled samples from the Atlantic. No heterogeneity was found among localities from the Gulf or localities from the Atlantic. High levels of gene flow among all localities were inferred from F _ST values (a measure of the variance in mtDNA haplotype frequencies) and from Slatkin's qualitative and quantitative analyses. Parsimony and phenetic analyses revealed no strong evidence for phylogeographic cohesion of localities, although there was weak support for cohesion of four of five localities from the Atlantic. These data indicate that the red drum population is subdivided, with weakly differentiated subpopulations (stocks) occurring in the northern Gulf and along the Atlantic coast of southeastern USA. Spatial autocor-relation analysis and heterogeneity tests of haplotype frequencies among regions within the Gulf supported the hypothesis of increased gene flow among neighboring localities; i.e., migration of individuals within the Gulf may be inversely related to geographic distance from an estuary or bay of natal origin. Estimates of evolutionary effective female-population size indicate that the red drum subpopulations may be large.     

Temporal stability and spatial divergence of mitochondrial DNA haplotype frequencies in red drum (Sciaenops ocellatus) from coastal regions of the western Atlantic Ocean and Gulf of Mexico

Restriction-site variation in mitochondrial (mt) DNA was assayed among 1675 red drum (Sciaenops ocellatus Linnaeus) sampled from 20 localities along the southeastern coast of the USA (western Atlantic) and the Gulf of Mexico (Gulf). Up to four consecutive year-classes (cohorts) were sampled at most localities. Nucleotide-sequence divergence among 170 mtDNA haplotypes identified ranged (in percentage) from 0.184 to 1.913, with a mean (±SD) of 0.887 ± 0.300. Comparisons of mtDNA haplotype frequencies across year-classes within localities were non-significant, indicating temporal stability of breeding components within localities. Significant heterogeneity in mtDNA haplotype frequencies was found across all localities, between (pooled) samples from the western Atlantic and the Gulf, and among geographically spaced, regional groupings in the Gulf. Genetic divergence between subpopulations of red drum in the western Atlantic and Gulf follows a pattern exhibited in other marine fishes, and probably stems from physical (historical environmental heterogeneity, absence of suitable habitat, and current patterns) and, perhaps, behavioral factors. Genetic differences among red drum in the Gulf appear to be due largely to an isolation-by-distance effect that is attributable to behavioral factors. The latter may include female philopatry to natal bays or estuaries, limited offshore (coastwise) movement of females relative to their natal bay or estuary, or both. Genetic divergence among red drum in the Gulf occurs despite high gene flow (estimated as the number of genetic effective migrants in an island mode). Conservation and management of red drum should be based on the premise that strategies for a given bay or estuary will impact geographically proximal bays or estuaries more than distal ones. Trajectories of correlograms in spatial autocorrelation analysis suggest a geographic neighborhood size, relative to genetic migration of red drum from a bay or estuary, of roughly 500 to 600 km. Received: 22 July 1998 / Accepted: 19 November 1998     

Microsatellite variation, effective population size, and population genetic structure of vermilion snapper, Rhomboplites aurorubens, off the southeastern USA

Vermilion snapper (Rhomboplites aurorubens) were collected from four sites off the Atlantic coast of the USA and one site in the Gulf of Mexico to evaluate effective population size and genetic stock structure. Previous studies had suggested geographic variation in the ratio of males to females, so this population characteristic was explored in conjunction with the genetic analysis. Sex ratio varied greatly among the five sample sites; males comprised 57% of samples in the Gulf of Mexico, while within the South Atlantic Bight they comprised between 36% (Morehead City, North Carolina) and 53% (Carolina Beach, North Carolina) of samples. No clear geographic trends in the sex ratio emerged; instead, it was found to vary with fish length, the percentage of males decreasing with increasing size. Allelic variation assessed at seven dinucleotide microsatellite loci was large; gene diversities ranged from 0.43 to 0.95 and allelic counts from 7 to 39. Estimates of the effective population size ranged from 24 500 (based on the infinite-alleles model) to 150 500 (based on the stepwise-mutation model). There was evidence for excess homozygosity within samples: estimates of F _IS (the correlation of alleles within individuals) ranged from 0.01 to 0.03 among the seven loci, and three estimates were significantly greater than zero. Differentiation among localities was very weak, as estimates of F _ST (the correlation of alleles within populations) were on the order of 0.001 to 0.002 and genetic distance estimates between localities were not related to geographic distances. This suggested that vermilion snapper in the South Atlantic Bight (Cape Hatteras, North Carolina to Cape Canaveral, Florida) and Gulf of Mexico are likely to consist of one genetic stock. Despite the overall homogeneity, there were indications of a temporally dynamic local structure that would bear further examination. Received: 6 July 1998 / Accepted: 9 February 1999     

Geographical subdivision,demographic history and gene flow in two sympatric species of intertidal snails, <Emphasis Type="Italic">Nerita scabricosta</Emphasis> and <Emphasis Type="Italic">Nerita funiculata</Emphasis>, from the tropical eastern Pacific

The patchy distribution of rocky intertidal communities in the tropical eastern Pacific (TEP) may impose severe constraints on the genetic connectivity among populations of marine invertebrates associated with this habitat. In this study, we analyzed a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene in two sympatric species of marine snails, Nerita scabricosta and Nerita funiculata, common inhabitants of the rocky intertidal from the Gulf of California (Sea of Cortez) and outer Pacific coast of the southern Baja California (Baja) peninsula to northern South America, to assess genetic connectivity among populations of each species. One of our aims was to determine whether the morphological, behavioral, and ecological differences observed among populations of both species throughout their range in the TEP corresponded to population genetic differences. In addition, we were interested in elucidating the demographic history of both species. We found no evidence of genetic structure throughout the Gulf of California and outer coast of the Baja peninsula region for either species. Comparisons between Gulf of California/Baja and Panama populations, however, showed significant genetic differentiation for N. scabricosta, but not for N. funiculata. The genetic differences between Mexican and Panamanian populations of N. scabricosta were consistent with previously reported ecological and behavioral differences for this species between these two distant regions. However, previously reported size differences between northern and central/southern Gulf of California individuals of N. scabricosta do not correspond with our findings of genetic connectivity among these populations. Results from neutrality tests (Tajima’s D and Fu’s F _S), the mismatch distribution, and Bayesian skyline analyses suggested that both species have experienced dramatic population expansions dating to the Pleistocene.     

Temporal stability of genetic population structure in the New Zealand snapper, <Emphasis Type="Italic">Pagrus auratus</Emphasis>, and relationship to coastal currents

Genetic diversity and population structure of snapper (Pagrus auratus, Bloch and Schneider), a coastal demersal sparid fish, were determined using six nuclear microsatellite loci and SSCP (single strand conformational polymorphism) analysis of themitochondrial (mt) DNA D-loop in samples collected across the range of the species in New Zealand. Microsatellite data showed similar results to allozyme data collected in the late 1970s that found differentiation between the north-east and southern populations. In addition, an isolated population of snapper in Tasman Bay was identified. The two data sets provide evidence for the temporal stability of the genetic population structure of snapper over 22 years, with differentiation over relatively small spatial scales separated by oceanographic boundaries rather than isolation by distance. In contrast to nuclear markers, mtDNA did not reveal any significant genetic heterogeneity among samples.     

Low-mitochondrial diversity and lack of structure in the velvet swimming crab <Emphasis Type="Italic">Necora puber</Emphasis> along the Galician coast

The velvet swimming crab Necora puber is a common species along the European Atlantic coasts. Due to its increasing commercial importance, many studies have been carried out to characterize its growth and reproduction, but no genetic assessment has ever been attempted at the population level. Here, we describe the genetic diversity and population structure of N. puber in northwestern Spain (Galicia), including additional samples from France, Portugal, and southern Spain. To do so, we analysed two mitochondrial fragments of the COI and 16S genes in 217 individuals collected from ten localities. Our results unveil low-genetic diversity and weak population structure along the studied range. A range expansion after the last glacial maximum, followed by ongoing gene flow, seems to be the most likely explanation for the observed genetic pattern.     

Post-glacial population history and genetic structure of the northern clingfish (Gobbiesox maeandricus), revealed from mtDNA analysis

Mitochondrial d-loop sequences were analyzed to characterize the phylogeographic and population genetic structure of the northern clingfish (Gobbiesox maeandricus Girard). Sequence analysis of 378 bp from 111 individuals sampled in 14 localities along the northeast Pacific coast and within the Strait of Georgia from 1996 to 1999 revealed marked genetic differentiation (Φ_ct=0.247) among regional population groupings. The gene genealogy distinguished two major clades of haplotypes separated by at least 1.1% sequence divergence. One clade with very low haplotype diversity (h=0.2095, n=18) occurred only within the recently unglaciated Strait of Georgia. The other clade had high haplotype diversity (h=0.8808, n=93) and was found in all populations. High haplotype diversity was found in open coastal populations, both north and south of the maximum extant of the Wisconsin ice sheet, suggesting that the clingfish range was not pushed to a southern refugium during the last glacial maximum. A nested clade analysis also did not detect a large northward expansion from a single southern refugium. The level of sequence divergence and coalescent-based analyses suggest that the observed patterns of polymorphism are the result of Pleistocene diversification within multiple refugia, followed by population expansion and asymmetrical lineage introgression. Received: 5 February 2000 / Accepted: 31 August 2000     

Mitochondrial DNA variation and population genetic structure of the blue crab<Emphasis Type="Italic"> Callinectes sapidus</Emphasis> in the eastern United States

The genetic population structure of red grouper, Epinephelus morio (Valenciennes), and scamp, Mycteroperca phenax Jordan and Swain, from the southeastern U.S. Atlantic coast and the Gulf of Mexico was examined using nuclear microsatellite DNA markers in order to test the null hypothesis of panmixia throughout this range. Physical and biological data indicate that relatively isolated populations of these fish exist. Genetic variation was assessed at four microsatellite loci in red grouper and six loci in scamp. The fish were collected on different dates between 1991 and 2001. The microsatellite loci were highly polymorphic, with an average expected heterozygosity of 0.75 in red grouper and 0.68 in scamp. Heterozygote deficiencies (significant deviations from Hardy–Weinberg equilibrium, HWE) were found at two of four loci in all red grouper samples except the eastern Gulf of Mexico, and for all red grouper combined. In contrast, all loci conformed to HWE in the separate scamp samples. Minimal genetic differences distinguished southeastern U.S. Atlantic or Mexican red grouper from other localities, and no indication of genetic differentiation was observed in scamp. This large-scale genetic homogeneity may be attributed to ongoing gene flow and/or historical contact between present-day populations. For management purposes, genetic homogeneity does not necessarily imply a single stock. Because larval dispersal may be sufficient to homogenize gene frequencies but not to replenish depleted stocks, other data must be considered in the management of these species.Electronic Supplementary Material Supplementary material is available in the online version of this article at .Communicated by J.P. Grassle, New Brunswick     

Regional differentiation and post-glacial expansion of the Atlantic silverside, <Emphasis Type="Italic">Menidia menidia,</Emphasis> an annual fish with high dispersal potential

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (F _ST = 0.07; P < 0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species.     

The cockle <Emphasis Type="Italic">Cerastoderma edule</Emphasis> at Northeast Atlantic shores: genetic signatures of glacial refugia

The cockle Cerastoderma (Cardium) edule (L.) ranges from NW Africa to northern Scandinavia. Abundance in shallow coastal sediment is often high, and it attracts commercial harvest. In this study, a complex genetic pattern has been revealed by mitochondrial DNA in 383 individuals from 19 sampling sites. Parsimony network analysis of 79 haplotypes identified two dominant central haplotypes separated by low divergence. One is characteristic for a homogenous southwestern group of populations from Africa to the British Isles. The other is characteristic for a heterogeneous northern group with a deviant Arctic population. At the entrance of the Baltic Sea, a mixture zone of the dominant haplotypes was found. The estimated population expansion time for the northern haplotype group predates that of the southwestern one, suggesting northern glacial refugia and a subsequent southern expansion of C. edule populations.     

Interspecific variation in thermal denaturation of proteins in the congeneric musselsMytilus trossulus andM. galloprovincialis: evidence from the heat-shock response and protein ubiquitination

The genetic population structure of the precominant zooplankter, the copepod Calanus finmarchicus (Gunnerus), was examined to determine whether genetically distinct populations exist in the Gulf of Maine. C. finmarchicus was sampled in three regions of the Gulf of Maine (Great South Channel, spring 1989; northern Gulf of Maine, winter 1990; Great South Channel and Georges Bank, spring 1990). Copepods from seven locations in the Great South Channel, five in the northern Gulf of Maine and four on or near Georges Bank were assayed for allozyme variation and mitochondrial DNA variation of amplified 16S rRNA and cytochrome b genes. Restriction fragment length polymorphism (RFLP) analyses of both mitochondrial DNA genes revealed no variation among any of the individuals assayed. Analysis of five polymorphic allozyme loci revealed that genetic variation among the three geographic regions was low, and genetic identities were high between all locations (I>0.97). Most of the genetic variation was among locations regardless of region. Chi-square tests were used to examine genetic similarity between specific pairs of locations within and between regions. In the northern Gulf of Maine, genetic homogeneity occurred over larger spatial scales (hundreds of km) than in either the Great South Channel or Georges Bank (tens of km). Only copepods from the Bay of Fundy and Nova Scotian Shelf locations were genetically distinct from Wilkinson Basin copepods at two loci. Copepod populations from the northern locations may have been partially isolated or they may represent immigrant populations (e.g., from the Gulf of St. Lawrence). Several pairs of locations were genetically distinct at one or more loci in the two southern regions. Differences between locations in these regions may represent distinct populations advected into the areas at different times or from different sources (e.g., genetic variation may represent a mixture of genetically distinct northern and southern copepod populations). These results suggest extensive gene flow among populations of C. finmarchicus in the Gulf of Maine with some evidence of genetic population subdivision near the Gulf's northeastern and southern boundaries.     

Mitochondrial DNA variation in king mackerel (Scomberomorus cavalla) from the western Atlantic Ocean and Gulf of Mexico

King mackerel (Scomberomorus cavalla Cuvier) collected in 1992 and 1993 from 13 localities along the Atlantic coast of the southeastern USA and in the northern Gulf of Mexico were surveyed for variation in mitochondrial (mt)DNA and a nuclear-encoded dipeptidase locus (PEPA-2). Both polymorphic and fixed mtDNA restriction sites were identified and mapped using conventional and polymerase chain-reaction (PCR)-based methods. Heterogeneity in mtDNA haplotype frequencies was found only in comparisons of pooled haplotypes from Atlantic localities versus pooled haplotypes from Gulf localities. This finding indicates weak genetic divergence between king mackerel from the Atlantic and those from the Gulf. Frequencies of two PEPA-2 alleles essentially paralleled previous findings: one allele (PEPA-2a) was common among samples from western Gulf localities, whereas the other allele (PEPA-2b) was common among samples from Atlantic and eastern Gulf localities. There was considerable variation in PEPA-2 allele frequencies within broadly-defined regions. Variation in mtDNA haplotypes and PEPA-2 genotypes was independent, as was variation in mtDNA haplotypes with sex or age of individuals. Variation in PEPA-2 genotypes was not independent of sex or age of individuals. The latter result suggests that frequencies of PEPA-2 alleles in samples of king mackerel may stem, in part, from sex and age distributions of individuals within samples, and indicates that caution should be exercised in using allelic variation at PEPA-2 as a measure of population (stock) structure in king mackerel. The discordance in spatial patterning of mtDNA haplotypes versus PEPA-2 alleles across the Gulf (i.e. homogeneity in mtDNA haplotype frequencies versus heterogeneity in PEPA-2 allele frequencies) may be due to either female excess at several localities, sex-biased migration, or both. Observed patterns of genetic variation also are consistent with the hypothesis that king mackerel in the western Atlantic may have been subdivided during Pleistocene glaciation, and that the current distribution of PEPA-2 alleles may be a historical artefact. Received: 17 December 1996 / Accepted: 2 April 1997     

Genetic heterogeneity among <Emphasis Type="Italic">Eurytemora affinis</Emphasis> populations in Western Europe

Evolutionary diversification of the broadly distributed copepod sibling species complex Eurytemora affinis has been documented in the northern hemisphere. However, the fine scale geographic distribution, levels of genetic subdivision, evolutionary, and demographic histories of European populations have been less explored. To gain information on genetic subdivision and to evaluate heterogeneity among European populations, we analyzed samples from 8 locations from 58° to 45°N and 0° to 23°E, using 549 base pairs of the mitochondrial cytochrome oxidase subunit I (COI) gene. We discovered three distinct lineages of E. affinis in Western Europe, namely the East Atlantic lineage, the North Sea/English Channel (NSEC) lineage, and the Baltic lineage. These geographically separated lineages showed sequences divergence of 1.7–2.1%, dating back 1.9 million years (CI: 0.9–3.0 My) with no indication of isolation by distance. Genetic divergence in Europe was much lower than among North American lineages. Interestingly, genetic structure varied distinctively among the three lineages: the East Atlantic lineage was divided between the Gironde and the Loire populations, the NSEC lineage comprised one single population unit spanning the Seine, Scheldt and Elbe rivers and the third lineage was restricted to the Baltic Proper (Sweden). We revealed high haplotype diversity in the East Atlantic and the Baltic lineages, whereas in the NSEC lineage haplotype diversity was comparatively low. All three lineages showed signs of at least one demographic expansion event during Pleistocene glaciations that marked their genetic structure. These results provide a preliminary overview of the genetic structure of E. affinis in Europe.     

Molecular population structure of the kuruma shrimp <Emphasis Type="Italic">Penaeus</Emphasis><Emphasis Type="Italic"> japonicus</Emphasis> species complex in western Pacific

In a previous study on the kuruma shrimp Penaeus japonicus from the South China Sea, we detected high genetic divergence between two morphologically similar varieties (I and II) with distinct color banding patterns on the carapace, indicating the occurrence of cryptic species. In the present study, we clarify the geographical distribution of the two varieties in the western Pacific by investigating the genetic differentiation of the shrimp from ten localities. Two Mediterranean populations are also included for comparison. Based on the mitochondrial DNA sequence data, the shrimps are separated into two distinct clades representing the two varieties. Variety I comprises populations from Japan and China (including Taiwan), while variety II consists of populations from Southeast Asia (Vietnam, Singapore and the Philippines), Australia and the Mediterranean. Population differentiation is evident in variety II, as supported by restriction profiles of two mitochondrial markers and analysis of two microsatellite loci. The Australian population is genetically diverged from the others, whereas the Southeast Asian and Mediterranean populations show a close genetic relationship. Variety I does not occur in these three localities, while a small proportion of variety II is found along the northern coast of the South China Sea and Taiwan, which constitute the sympatric zone of the two varieties. The present study reveals high genetic diversity of P. japonicus. Further studies on the genetic structure of this species complex, particularly the populations in the Indian Ocean and Mediterranean, are needed not only to understand the evolutionary history of the shrimp, but also to improve the knowledge-based fishery management and aquaculture development programs of this important biological resource.     

Genetic studies in marine fishes

Nine polymorphic loci were found among 42 presumptive protein-coding gene loci surveyed among 474 red drum (Sciaenops ocellatus) sampled in 1987 from 13 nearshore and 1 offshore localities from the Atlantic coast of the southeastern USA and the northern Gulf of Mexico. The mean number of alleles over the polymorphic loci was 3.8, and the average heterozygosity over all loci examined was estimated as 0.047. These data indicate that red drum have normal levels of genetic variability. Wright'sF1 _ST values (the standardized variance of allele frequencies between samples) over all polymorphic loci ranged from 0.009 to 0.027 (meanF1 _ST =0.019), and estimates of the effective number of migrants (N _e m) per generation using Wright's island model ranged from 9.0 to 27.5. High levels of gene flow among the red drum samples were also indicated by Slatkin's qualitative analysis using conditional average allele frequencies. Nei's estimates of genetic distance between pairs of samples ranged from 0.000 to 0.009, indicating a high degree of nuclear gene similarity among all samples. Highly significant heterogeneity in allele frequencies at the locus for adenosine deaminase was detected between red drum sampled from the Atlantic and those sampled from the Gulf and among red drum sampled from the Gulf.     

RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) populations from the eastern Pacific

White shrimp (Litopenaeus vannamei) population genetic structure from the eastern Pacific was determined by restriction fragment length polymorphism analysis of the mitochondrial DNA control region. Four localities were surveyed with four endonucleases (Alu I, Taq I, Spe I, Ssp I) yielding 48 composite haplotypes. White shrimp showed high average within-locality haplotype (0.823) and nucleotide (5.41%) diversities and also high average nucleotide divergence between all pairs of localities (0.73%). A mismatch analysis of pairwise differences between haplotypes indicated that white shrimp does not fit the sudden population expansion model. An analysis of molecular variance showed significant geographic variation in the frequencies of haplotypes (Φ_ST=0.1382, P<0.0001). Population differentiation may be maintained by a combination of physical, oceanographic, and biological factors acting as barriers to gene flow among localities. Because of its high polymorphism, the control region might be useful as a genetic marker for monitoring genetic diversity in aquaculture stocks.     

Mitochondrial DNA Variability of the Gray Wolf: Genetic Consequences of Population Decline and Habitat Fragmentation

The gray wolf is a large, highly mobile predator whose original geographic range included most of the Northern Hemisphere. High rates of genetic exchange probably characterized even distantly-separated populations in the past, but recent population declines and habitat fragmentation have isolated previously contiguous populations, especially in the Old World. We examine mitochondrial DNA (mtDNA) variability among twenty-six populations of wolves from throughout their geographic range. We find eighteen mtDNA genotypes in gray wolves, seven of these are derived from hybridization with coyotes, four are confined to the New World, six are confined to the Old World and one is shared by both areas. Genetic differentiation among wolf populations is significant but small in magnitude. In the Old World, most localities have a single unique genotype, whereas in the New World several genotypes occur at most localities and three of the five genotypes are nearly ubiquitous. The pattern of genetic differentiation in the gray wolf contrasts with that of another large, highly vagile canid, the coyote, in which genetic differentiation among populations is not significant even among widely separated localities. We suggest that the difference between these two species reflects the rapid, recent increase in coyote numbers and expansion of their geographic range, and the coincident decline in gray wolf populations. Apparent genetic differences among extant wolf populations may be a recent phenomenon reflecting population declines and habitat fragmentation rather than a long history of genetic isolation.     

Population genetic structure of the stalked barnacle <Emphasis Type="Italic">Pollicipes pollicipes</Emphasis> (Gmelin, 1789) in the northeastern Atlantic: influence of coastal currents and mesoscale hydrographic structures

Within its distribution range in the northeastern Atlantic, the stalked barnacle Pollicipes pollicipes shows a well-defined pattern of genetic variation, comprising (a) a subtropical/temperate northern assemblage, made up of populations distributed between 47°N and 28°N along the French, Iberian, North African and Canary Islands coastlines, and (b) a single isolated and highly divergent tropical population in the Cape Verde Islands (16°N), at the southernmost limit of the species’ distribution. However, within the northern assemblage several populations show a level of genetic differentiation that allows rejection of the hypothesis of genetic homogeneity. The congruence observed between genetic and hydrographic patterns suggests a crucial role of hydrodynamics, and of the dispersal of the planktonic larvae, in the determination of population structure. Along the southern European Atlantic coast, the Iberian Poleward Current and mesoscale hydrographic structures are, respectively, facilitating gene flow at the regional level and genetic differentiation at the local level. On the Atlantic coast of North Africa, the homogenizing equatorward flow of the Canary Current does not extend as far as the Cape Verde Islands. A demographic expansion is dated to the late Pleistocene, preceding the Eemian interglacial, and is oldest in the case of the long-standing Cape Verde population, sustained by a stable tropical habitat. The divergence between the Cape Verde population and the remaining populations is thus ancient, and suggests that oceanic current patterns may constitute a generalized physical barrier to the dispersal of marine organisms between Cape Verde and the rest of Macaronesia.