Population genetic structure of North American <Emphasis Type="Italic">Ophiactis</Emphasis> spp. brittle stars possessing hemoglobin

With the discovery of previously unreported populations of hemoglobin-possessing Ophiactis from the Texas coast in the Gulf of Mexico, an investigation into its population structure, including populations of O. simplex from the Pacific coast of California and O. rubropoda from the Atlantic coast of Florida, was undertaken using DNA sequence data from the mitochondrial COI gene. The reconstructed haplotype network suggests that California populations contain the ancestral source of mtDNA variation, and there is no evidence of recent introductions into Texas. Population genetic analyses reveal the California, Florida, and Texas Ophiactis populations to each be significantly differentiated from one another. Sequence divergence among the three areas is shallower than would be predicted given biogeographic history. Texas and Florida populations are equally genetically diverged from California populations as they are to one another, despite the greater potential for gene flow between these areas. The genetic distinctiveness of the Texas populations and the concordance of this pattern with phylogeographic patterns in other brittle star systems indicate an isolated and independent evolutionary history and we hypothesize that the three geographic regions included in this study each serve as hypotheses of population-level lineages that remain to be tested with independent sources of data.     

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.     

Sympatry and allopatry in the deeply divergent mitochondrial DNA clades of the estuarine pulmonate gastropod genus <Emphasis Type="Italic">Phallomedusa</Emphasis> (Mollusca,Gastropoda)

DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were collected from estuarine snails in the genus Phallomedusa to examine the effects of estuarine isolation on population structure and gene flow. Three clades were recovered, one corresponding to Phallomedusa austrina and two others with the morphology of Phallomedusa solida. The haplotype diversity in all three clades indicated recent population expansion. Phallomedusa austrina was restricted to the west of a previous land bridge in the Bass Strait between mainland Australia and Tasmania, and P. solida to its east and to northern Tasmania. Phylogeographic analysis of P. austrina and P. solida shows strong geographic separation of species, but no local genetic structure indicative of regional or estuarine isolation. The clades of P. solida exhibit substantial genetic divergence and were sympatric across their entire distribution in eastern Tasmania and mainland Australia. Such a situation, which has not previously been observed in phylogeographic studies of southeast Australia, suggests that P. solida has had a complex refugial history during periods of environmental challenge.     

Genetic structure of natural populations of California red abalone (<Emphasis Type="Italic">Haliotis rufescens</Emphasis>) using multiple genetic markers

Mitochondrial cytochrome oxidase subunit one (COI) sequence, nuclear microsatellites, and amplified fragment length polymorphisms (AFLPs) were used to evaluate connectivity among nine red abalone (Haliotis rufescens) populations sampled between August 1998 and November 2003 along approximately 1,300 km of California coastline from Crescent City (41°46′N, 124°12′W) to San Miguel Island (34°02′N, 120°22′W). COI sequences and microsatellite genotypes did not show significant genetic divergence among nine sampled populations. A subset of five populations spanning the geographic range of the study was scored for 163 polymorphic AFLP markers. Of these, 41 loci showed significant divergence (P < 0.001) among populations. Still, no AFLP markers were diagnostic for any of the study populations, and assignment tests did not consistently assign individuals to the correct population. Although the AFLP data are the first to suggest there is significant genetic differentiation among California red abalone populations, the discordance between the different genetic markers needs further study before unambiguous conclusions can be drawn with respect to connectivity among the populations. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic diversity and population structure of the Chinese mitten crab <Emphasis Type="Italic">Eriocheir sinensis</Emphasis> in its native range

The Chinese mitten crab Eriocheir sinensis is an indigenous and economically important species in China, but can also be found as invasive species in Europe and America. Mitten crabs have been exploited extensively as a food resource since the 1990s. Despite its ecological and economic importance, the genetic structure of native mitten crab populations is not well understood. In this paper, we investigated the genetic structure of mitten crab populations in China by screening samples from ten locations covering six river systems at six microsatellite loci. Our results provide further evidence that mitten crabs from the River Nanliujiang in Southern China are a genetically differentiated population within the native range of Eriocheir, and should be recognized as a separate taxonomic unit. In contrast, extremely low levels of genetic differentiation and no significant geographic population structure were found among the samples located north of the River Nanliujiang. Based on the reproductive biology of mitten crabs and the geography of their habitat we argue that both natural and human-mediated gene flow are unlikely to fully account for the similar allele frequency distributions at microsatellite loci. Large population sizes of mitten crabs suggest instead that a virtual absence of genetic drift and significant homoplasy of microsatellite alleles have contributed to the observed pattern. Furthermore, a coalescent-based maximum likelihood method indicated a more than two-fold lower effective population size of the Southern population compared to the Northern Group and low but significant levels of gene flow between both areas.     

Phylogeography of surfclams,<Emphasis Type="Italic"> Spisula solidissima</Emphasis>, in the western North Atlantic based on mitochondrial and nuclear DNA sequences

The Atlantic surfclam, Spisula solidissima (Dillwyn), is broadly distributed in sandy sediments of the western North Atlantic between the Gulf of St. Lawrence and the Gulf of Mexico. In the United States, a substantial commercial fishery between Long Island and Cape Hatteras harvests offshore populations of one subspecies, S. s. solidissima. A smaller coastal form, S. s. similis Say (also known as S. s. raveneli Conrad), has a partially sympatric geographic distribution, but differs in several life-history characteristics. DNA sequence variation in mitochondrial cytochrome oxidase I (COI) and in introns at two nuclear calmodulin loci was examined to measure genetic divergence between the two subspecies and to test for population structure among populations of S. s. solidissima. Surfclams were collected from seven localities between 1994 and 2001. Based on both mitochondrial and nuclear DNA variation, the two subspecies of S. solidissima are reciprocally monophyletic, with a net COI divergence of 13.9%, indicating long-term reproductive isolation. The only significant differentiation among populations of S. s. solidissima (based on an AMOVA analysis of COI sequences) was between the Gulf of St. Lawrence and more southerly populations. A long internal branch in the S. s. solidissima genealogy coupled with low haplotype diversity in the northern-most population suggests that populations north and south of Nova Scotia have been isolated from each other in the past, with gene exchange more recently. Populations of S. s. similis from Atlantic and Gulf of Mexico coasts had a net COI divergence of 9.2%. Thus, diversification of Spisula spp. clams in the western North Atlantic involved an early adaptive divergence between coastal and offshore forms, with later barriers to dispersal emerging in the offshore form from north to south and in the coastal form between Atlantic and Gulf of Mexico populations.     

Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific

Partial sequences of the mitochondrial DNA (mtDNA) gene cytochrome oxidase subunit 1 (COI) were analysed from individuals of the coralline demosponge Astrosclera willeyana sensu lato out of ten Indo-Pacific populations from the Red Sea to the central Pacific. This taxon is widely distributed in cryptic coral reef habitats of the Indo-Pacific and is regarded as a modern representative of long-extinct, formerly reef-building stromatoporoid-type sponges. The aims were to clarify phylogeographic and taxonomic relationships in this “living fossil” and to explore mitochondrial DNA sequence variation over a wide geographic range. Very low variability was observed across the Indo-Pacific, as only three COI haplotypes were identified, with a maximum p-distance of 0.418% and low nucleotide diversity (π=0.00049). Very low genetic structure was revealed among populations: Haplotype 1 was found in all specimens from nine Pacific populations (N=45), separated by distances of more than 7,000 km; haplotype 2 was restricted to the Red Sea population (N=4); haplotype 3 was only found in the Tuamoto specimens (N=7). COI data presented here do not support the hypothesis of at least two sibling species belonging to genus Astrosclera in the Pacific. Considering the maximum geographic distance of more than 20,000 km between sampled populations, mtDNA COI sequence variation observed here is among the lowest reported to date for a diploblastic taxon and adds to the growing evidence of a general mtDNA conservation in sponges. It is argued that this low mtDNA variation in A. willeyana s.l. is due to a low rate of mtDNA evolution caused by a combination of long generation time and low metabolic rate.     

Song dialects do not restrict gene flow in an urban population of the orange-tufted sunbird, <Emphasis Type="Italic">Nectarinia osea</Emphasis>

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. In this study, we test the hypothesis that song dialect, a culturally transmitted trait, is related to the population genetic structure of the orange-tufted sunbird, Nectarinia osea. To address this, we compared mitochondrial DNA (mtDNA) sequence variation together with allele frequencies at five microsatellite loci from an urban population of sunbirds exhibiting two distinct song dialects on a microgeographic scale. Our findings reveal no association between dialect membership and genetic composition. All genetic measures, from both mitochondrial and nuclear DNA, indicate high levels of gene flow between both dialect populations. The low F _ST values obtained from mtDNA and microsatellite analysis imply that the variation among dialects does not account for more than 2%, at best, of the overall genetic variation found in the entire population. These measures fall well within the range of similar measures obtained in other studies of species exhibiting vocal dialects, most of which fail to detect any dialect-based genetic differentiation. The persistence of dialects in the orange-tufted sunbird may thus best be explained by dispersal of individuals across dialect boundaries and possibly from surrounding areas, followed by postdispersal vocal matching. Because genetic structuring appears weaker than cultural structure in this species, we discuss the behavioral mechanisms underlying dialect maintenance in the presence of apparent gene flow.     

Isolation and population divergence of a widespread Indo-West Pacific marine gastropod at Easter Island

Oceanic islands represent excellent systems for studying the link between geographic isolation and population divergence. Easter Island is the world’s most isolated island and exhibits a high level of endemicity in the nearshore marine environment. Yet few studies have examined the effect of such extreme isolation on the divergence of populations of widespread species that occur at Easter Island. Conus miliaris, a marine gastropod distributed throughout much of the Indo-West Pacific, occurs at Easter Island where the population is ecologically and morphologically distinct from other populations of the species. To determine whether these phenotypic differences are associated with genetic isolation of the Easter Island population, we investigated the phylogeography of this species by examining mitochondrial COI sequences obtained from 141 individuals from eight localities occurring predominantly in the western, central and southeastern Pacific. Results from our analyses show that C. miliaris at Easter Island differs genetically from other populations. We estimate that C. miliaris colonized Easter Island shortly after the origin of the island ≤0.7 million years ago and that since population founding, gene flow has occurred predominantly from Easter Island to the west and that little migration has occurred into Easter Island.     

Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge<Emphasis Type="Italic"> Crambe crambe</Emphasis> (Poecilosclerida)

Crambe crambe is a common encrusting sponge found in the Mediterranean and Atlantic littoral. An analysis of a partial sequence (535 bp) of the mitochondrial DNA (mtDNA) gene cytochrome oxidase subunit I (COI) was conducted in an attempt to determine population structure in this species. This is the first study of population genetics using this kind of marker in the phylum. Samples (N=86) were taken in eight populations separated by distances from 20 to 3,000 km, spanning from the western Mediterranean to the Atlantic. Low variability of this gene was found, as only two haplotypes were identified, along with low nucleotide diversity (=0.0006). However, the different frequencies found among populations revealed genetic structure and low gene flow between close populations, as expected from the dispersal biology of the species. The low variability found in sponges is in agreement with reports on cnidarians and points to a high conservation of mtDNA in diploblastic phyla.     

Genetic evidence of cryptic speciation within hammerhead sharks (Genus Sphyrna)

Surveys of genetic variation within cosmopolitan marine species often uncover deep divergences, indicating historical separation and potentially cryptic speciation. Based on broad geographic (coastal eastern North America, Gulf of Mexico, western Africa, Australia, and Hawaii) and temporal sampling (1991–2003), mitochondrial (control region [CR] and cytochrome oxidase I [COI]) and nuclear gene (lactate dehydrogenase A intron 6 [LDHA6]) variation among 76 individuals was used to test for cryptic speciation in the scalloped hammerhead, Sphyrna lewini (Griffith and Smith). CR and COI gene trees confirmed previous evidence of divergence between Atlantic and Indo-Pacific scalloped hammerhead populations; populations were reciprocally monophyletic. However, the between-basin divergence recorded in the mtDNA genome was not reflected in nuclear gene phylogenies; alleles for LDHA6 were shared between ocean basins, and Atlantic and Indo-Pacific populations were not reciprocally monophyletic. Unexpectedly, CR, COI, and LDHA6 gene trees recovered a deep phylogenetic partition within the Atlantic samples. For mtDNA haplotypes, which segregated by basin, average genetic distances were higher among Atlantic haplotypes (CR: D _HKY=0.036, COI: D _GTR=0.016) than among Indo-Pacific haplotypes (CR: D _HKY=0.010, COI: D _GTR=0.006) and approximated divergences between basins for CR (D _HKY=0.036 within Atlantic; D _HKY=0.042 between basins). Vertebral counts for eight specimens representing divergent lineages from the western north Atlantic were consistent with the genetic data. Coexistence of discrete lineages in the Atlantic, complete disequilibrium between nuclear and mitochondrial alleles within lineages and concordant partitions in genetic and morphological characters indicates reproductive isolation and thus the occurrence of a cryptic species of scalloped hammerhead in the western north Atlantic. Effective management of large coastal shark species should incorporate this important discovery and the inference from sampling that the cryptic scalloped hammerhead is less abundant than S. lewini, making it potentially more susceptible to fishery pressure.     

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 structure and phylogeography of the lined shore crab, Pachygrapsus crassipes, along the northeastern and western Pacific coasts

Marine invertebrates with high larval dispersal capacity typically exhibit low degrees of population differentiation, which reflects both contemporary and historical processes. We sampled 346 individuals from seven populations of the lined shore crab, Pachygrapsus crassipes Randall, along the northeastern Pacific Coast and Korea during summer 2003. DNA sequence analysis of 613 bp of the mitochondrial COI gene showed that overall gene diversity (h) was high (0.92±0.01), whereas overall nucleotide diversity (π) was low (0.009±0.005). A total of 154 mtDNA haplotypes were identified; however, 114 were present in only one individual. Analysis of molecular variance revealed significant genetic structuring at Point Conception, CA, USA, that is likely due to the oceanographic circulation patterns, which result in asymmetrical migration of haplotypes. However, genetic variation among eastern Pacific populations was generally low, probably because of high contemporary gene flow and recent common ancestry of haplotypes. Mismatch analysis and nested clade analysis suggested that the population history of this region is characterized by two contiguous northwards range expansions, which are congruent with Late Pleistocene glacial cycles. Highly significant genetic differentiation was detected between eastern Pacific populations and Korea, indicating transpacific gene flow is restricted. Time of divergence between the two transpacific lineages was estimated between 0.8 and 1.2 Myrs ago. The small, recently founded population of P. crassipes at Bamfield, BC, Canada, did not appear to have undergone a founder effect.     

Intraspecific phylogeographic isolation of Arabian Gulf sailfish<Emphasis Type="Italic"> Istiophorus platypterus</Emphasis> inferred from mitochondrial DNA

The genetic structure of seven sailfish Istiophorus platypterus populations sampled from three locations inside and four locations outside the Arabian Gulf was determined by restriction fragment length polymorphism analysis of mitochondrial DNA of 147 individuals using eight restriction endonucleases. A total of 39 composite haplotypes derived from 27 presumptive restriction sites demonstrated significant differences in frequency between population groups inside and outside the Gulf (analysis of molecular variance 34.80%, P<0.001; F_ST=0.356) and evidence of restricted migration between them (average number of migrants, N_m=0.903). Haplotypes found only inside or outside the Gulf clustered to all major branches of a haplotype phylogeny, as did those found in both areas. The reduced genetic diversity of the Gulf populations and the fact that much of the differentiation between the population groups resulted from differences in haplotype frequency rather than divergence between haplotypes suggest a founder effect and a recent sampling of genotypes from the Indian Ocean. This was probably associated with dispersal into the Gulf after it was flooded by rising sea level after the end of the last glaciation around 8,000 years ago. At some point since then the population has evolved to complete its life cycle within the Gulf and shows a marked disruption to gene flow, consistent with dispersal data, at the Strait of Hormuz. These findings represent the first clear evidence of phylogeographic isolation occurring in a large, highly vagile, predatory istiophorid billfish, within a marginal sea.Communicated by O. Kinne, Oldendorf/Luhe     

Phylogeography of the sub-Antarctic notothenioid fish Eleginops maclovinus: evidence of population expansion

Phylogeography studies add insights into the geographic and evolutionary processes that underline the genetic divergence of populations. This work examines the geographic genetic structure of the Patagonian blennie, Eleginops maclovinus, a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters, using mitochondrial DNA cytochrome b sequences. We found 58 haplotypes in the analysis of 261 individual sequences of 833 base pairs in length. Among-population variance was very low (1.62%) and many haplotypes were shared between several populations across the species geographic range. Genetic differentiation was not consistent with a simple model of isolation by distance, possibly suggesting a lack of equilibrium between gene flow and local genetic drift. The analysis of mismatch distributions, neutrality tests, and the Bayesian Skyline Plot showed a pattern consistent with a recent population expansion event that may have taken place during the Middle Pleistocene.     

Reproductive isolation among morphotypes of the Atlantic seastar species<Emphasis Type="Italic"> Zoroaster fulgens</Emphasis> (Asteroidea: Echinodermata)

Zoroaster fulgens is a slope-dwelling seastar species that is distributed throughout the Atlantic Ocean. Studies into the population structure and systematics of marine animals have increasingly found that species with a reported cosmopolitan distribution are, in fact, collections of closely related cryptic or sibling species. In the Porcupine Seabight, three morphotypes of Z. fulgens can be found that have a distribution that is stratified by depth. This study investigates the genetic divergence between these morphotypes using sections of the cytochrome oxidase 1 (COI) and 16S regions of the mitochondrial genome. Bathymetrically separated morphotypes of Z. fulgens are reproductively isolated over distances of approximately 1 km while gene flow occurs among morphotypes, along isobaths, over distances of approximately 900 km. Reproductive isolation on the continental slope may have occurred as a result of selection exerted by gradients of depth-correlated physical factors, such as pressure and temperature. However, allopatric speciation with subsequent range expansion may also explain the observed patterns of genetic divergence. Further investigation of radiation within this group may provide important information on the evolution of slope species. Taxonomic revision of the genus is required.Communicated by J.P. Thorpe, Port Erin     

Genome-size variation in bivalve molluscs determined by flow cytometry

Six of the nine described species of the mole crab genus Emerita are distributed in the Americas, two [E. analoga (Stimpson, 1857) and E. rathbunae Schmitt, 1935] on the west coast, and four [E. benedicti Schmitt, 1935, E. brasiliensis Schmitt, 1935, E. portoricensis Schmitt, 1935 and E. talpoida (Say, 1817)] on the east. The presence of an extended planktonic larval stage in all Emerita species suggests high dispersal potential and the possibility of extensive gene flow among conspecific populations. Two taxa were sampled to study the extent of gene flow between widely separated conspecific populations: E. analoga (California and Chile) and E. talpoida (Massachusetts, South Carolina, and the west coast of Florida), while all other taxa were characterized from a single location. Portions of two mitochondrial genes, cytochrome oxidase I (COI) and 16S ribosomal RNA (16S rRNA) were sequenced. For data analysis, approximately 500 bp (COI) and 400 bp (16S rRNA) were examined. Estimated genetic divergence of 5.41% in COI between E. talpoida populations sampled from the Gulf of Mexico and the Atlantic coast, and 3.47% between E. analoga sampled in Chile and California, indicates that in both cases there has been no recent gene flow between disjunct populations. Additional molecular and morphological studies are necessary to decide whether disjunct populations should be accorded specific status. We predict that many marine invertebrates with antitropical distributions similar to E. analoga may consist of sibling species. In contrast to relationships inferred earlier from distribution patterns, parsimony analyses of both COI and 16S rRNA data yield similar phylogenetic trees in which E. analoga is separated from a clade composed of other species in the Americas; a bootstrap value (67%) in the COI inferred tree marginally supports the separation, but the same tree topology with a higher bootstrap value (84%) is obtained with 16S rRNA sequence data. Genetic divergence among the taxa indicates that the Emerita species constitute an old group and that distribution of species has been modified by past climatic and geological events.     

Nuclear and mtDNA lineage diversity in wild and cultured Pacific lion-paw scallop, Nodipecten subnodosus (Baja California Peninsula, Mexico)

Pacific lion-paw scallops were collected from natural aggregations in Laguna Ojo de Liebre (Pacific Ocean), the Gulf of California, and from aquaculture facilities for genetic diversity analyses. Mitochondrial DNA sequencing uncovered two highly supported clades separated by 2.5% divergence. Data from ten microsatellite markers suggest individuals from these mitogroups are introgressed, raising questions about the mitotype origin. Some evidence suggests gene flow between La Paz and Ojo de Liebre; otherwise the Gulf of California and Ojo de Liebre are acting as two distinct populations. It is unclear whether translocations between sites have influenced the observed genetic structure or whether gene flow has been facilitated by past geologic events. Finally, scallops spawned for aquaculture are unique from the wild and have significantly less diversity. These results warrant the attention of managers and producers who should work to monitor and conserve genetic diversity in both wild and aquaculture populations.     

Analysis of global and local population stratification of finless porpoises <Emphasis Type="Italic">Neophocaena phocaenoides</Emphasis> in Chinese waters

The existence of three distinct populations is widely accepted for the finless porpoise (Neophocaena phocaenoides) in Chinese waters: the Yellow Sea, Yangtze River, and South China Sea populations. Here, we use nine species-specific microsatellite loci, the complete mitochondrial DNA control region (912 bp), and the complete mitochondrial cytochrome b gene (1,140 bp) to further investigate potential population stratification in the Yellow Sea using 147 finless porpoise samples from the Bohai Sea and adjacent northern Yellow Sea, two regions that were largely underrepresented in previous genetic studies. Our F-statistics analyses confirm the previously described three populations, but further demonstrate significant genetic differentiation between the [Bohai + northern Yellow] Sea and the southern Yellow Sea. On the other hand, median-joining network analyses do not exhibit well-differentiated haplotype groups among different geographic populations, suggesting the existence of shared ancestral haplotypes. Levels of microsatellite diversity are moderate to high (mean H _E = 0.794) among the 147 [Bohai + northern Yellow] Sea finless porpoises and no recent bottleneck was detected, whereas mtDNA control region and cytochrome b gene diversity is low to moderate. The microsatellite genotypic and mtDNA haplotypic data also confirm the presence of mother-calf pairs in single-net bycatch cases. The results presented here highlight the necessity to treat the [Bohai + northern Yellow] Sea population (highly impacted by anthropogenic threats) as a separate Management Unit.     

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.