Genetic evidence for the existence of cryptic species in an endangered clam <Emphasis Type="Italic">Coelomactra antiquata</Emphasis>

Coelomactra antiquata is a commercially important bivalve species, but has been suffering from severe population decline due to over-exploitation and the deterioration of environmental conditions. Previous genetic survey of C. antiquata conducted with allozymes combined with morphology revealed high levels of genetic differentiation between northern and southern populations which suggests a cryptic species might exist in C. antiquata. To test this hypothesis, amplified fragment length polymorphisms (AFLPs) and 16S rRNA gene sequence were used to re-evaluate the spatial genetic structure of six populations of C. antiquata along the coast of China. Both genetic markers display a sharp genetic break between the four northern populations (northern lineage) and two southern population (southern lineage). Large numbers of private alleles (AFLP) were found within the northern or southern populations and a deep divergence of about 6.5% in 16S rRNA gene sequence between the northern and southern lineages suggests the occurrence of potential cryptic or sibling species of C. antiquata. Applying previously published rates of mutation, divergence between the two lineages is estimated to have occurred approximately 3 million years ago and may be due to allopatric isolation during the middle Pliocene times. While no genetic differentiation was found within the northern or southern populations in both AFLP and 16S mtDNA markers, the results indicate that the northern and southern lineage should be managed separately and any translocation between the two areas should be avoided.     

Genetic structure of dictyoceratid sponge populations on the western Coral Sea reefs

Allozyme variation at six polymorphic loci was examined in foliose dictyoceratid sponges from isolated reefs in the western Coral Sea. Four major genetic groups corresponding to the species Phyllospongia lamellosa, P. alcicornis, Carterospongia flabellifera and Collospongia auris were examined. A further two rare morphotypes from individual reefs formed genetic outliers to the P. lamellosa group, and may represent further taxa related to P. lamellosa. Gene frequencies in individual reef populations were largely in Hardy-Weinberg equilibrium, suggesting that random mating occurred in local populations of all four common species. Genetic variability was high and observed heterozygosities within populations ranged from 0.13 to 0.40. All four taxa showed significant genetic differentiation among populations (F _ST=0.05 to 0.36). Genetic distances (Nei's D) among populations within species ranged from 0 to 0.723 and increased with increasing geographical separation. There was evidence that genetic differentiation between populations to the north and to the south of the southern limit of the South Equatorial Current (SEC) divergence was greater than expected on the basis of their geographical separation. The SEC divergence may form a partial barrier to gene flow among populations of these ecologically important sponges on the submerged Queensland Plateau. Levels of migration among populations of three of the species was less than those required to prevent divergence of the populations through genetic drift (Nm<1). Restricted migration among populations may provide a mechanism to explain the occurrence of highly divergent populations of dictyoceratid sponges whose specific identity is not clear, and may allow them additionally to develop partial reproduction isolation from other populations.     

An AFLP-based test of clonality in widespread, putatively asexual populations of Porphyra umbilicalis (Rhodophyta) in the Northwest Atlantic with an in silico analysis for bacterial contamination

Asexual reproduction often predominates in populations of species experiencing range expansion. Locally selected genotypes can lead to the establishment of clonal populations that accumulate genetic diversity through time. Sexual reproduction has never been observed in extensive field and culture studies of the red alga Porphyra umbilicalis from Maine, USA, even though sexual reproduction predominates in this species in the eastern Atlantic (Europe). This suggests that Maine populations are indeed asexual and might consist of one or only a few genetic clones; we have tested this using AFLPs. Individuals were sampled at two sites in Maine (Cobscook Bay [n?=?25], Schoodic Point [n?=?26]) and compared to sexual individuals from England (Sidmouth [n?=?17]). The AFLP analysis determined that individuals at two sites in Maine containing putative asexuals were not strictly clonal; however, two multilocus lineages were sampled more than once. Two genetic clones, one at each Maine site, were comprised of 6 individuals each; the 39 additional Maine individuals had distinctive AFLP genotypes. However, when the individuals from Maine were compared with a known sexual population from Sidmouth, England, much greater genetic diversity was found within the sexual population in England. Finally, we examine how preparation of field-collected material for AFLP investigations can affect the inclusion of non-target DNA and demonstrate an in silico approach for removing some cryptic contaminants from analysis.     

Genetic evidence of population heterogeneity and cryptic speciation in the ommastrephid squid Martialia hyadesi from the Patagonian Shelf and Antarctic Polar Frontal Zone

Horizontal starch gel electrophoresis was used to investigate levels of genetic differentiation between four samples of the nominate squid species Martialia hyadesi Rochbrune and Mabille, 1889, obtained from regions of the Patagonian Shelf and Antarctic Polar Fron-tal Zone over 1000 km apart. M. hyadesi is an ecologically important South Atlantic ommastrephid squid and it is probable that, in the future, fishing effort will be increasingly directed towards this species. Details regarding the population structure of the species are therefore required. In comparison with the other three samples of M. hyadesi, one of the samples from the Patagonian Shelf (PAT 89II) exhibited fixed allelic differences at 16 of the 39 enzyme loci which were resolved (genetic identity, I=0.51). This high level of genetic differentiation contradicts the apparent morphological similarity between samples, indicating the presence of a cryptic or sibling congeneric species. Deviations from Hardy-Weinberg equilibrium and significant differences in allele distribution were also detected within and between the other three putative M. hyadesi samples, suggesting that the species fails to maintain effective panmixia across its geographical range. The occurrence of both temporal (1986 cf. 1989) and geographic structuring within the species complex is consequently indicated, caused possibly by an overlap of reproductively isolated stocks (stock mixing) outside their respective breeding areas. Low levels of genetic variability were detected throughout the samples examined, estimates of average heterozygosity per locus within the two species detected being in the order of 0.01 and 0.002. These values are discussed in relation to levels of genetic variability reported for other squid species, and in comparison with values typically expected for marine invertebrates.     

Systematic status of two oyster populations of the genus Tiostrea from New Zealand and Chile

A systematic examination of Tiostrea chilensis endemic to the Pacific coast of South America and of T. lutaria endemic to new Zealand was conducted using protein-gel electrophoresis. Also, ecological and life-history traits were compared between these two documented species. Our study revealed that although three different ecomorphs could be distinguished from various environmental and ecological conditions, the life-history traits between the two species were remarkably similar. Estimates were made of levels of genetic variation and similary based on 29 structural loci among individuals from each documented species. The percentage of loci polymorphic was estimated at 17.2 and 17.6, while the percentage of loci heterozygous was 2.1 and 6.7 for T. chilensis and T. lutaria, respectively. The genetic similarity between the two species was computed as 0.991, where 1.0 indicates no genetic difference among structural loci. The overwhelming evidence of this study indicates that T. chilensis and T. lutaria are different geographical populations of one species and by priority this species should be T. chilensis.     

Sibling species or poecilogony in the polychaete<Emphasis Type="Italic"> Scoloplos armiger</Emphasis>?

In marine invertebrates multiple modes of development, or poecilogony, may occur in a single species. However, after close examination, many of such putative cases turned out to be sibling species. A case in point may be the cosmopolitan orbiniid polychaete Scoloplos armiger, which inhabits marine shallow sediments. In addition to the well-known direct, holobenthic development from egg cocoons, pelagic larvae have also been described. Our culture experiments revealed a spatially segregated source of the two developmental modes. All females of an intertidal population produced egg cocoons and no pelagic larvae. All but 2 out of 15 females of an adjacent subtidal population produced pelagic larvae and no egg cocoons. Based on these results we performed a molecular genetic analysis (RAPD-PCR) on three intertidal and four subtidal populations in the North Sea. Selected samples from all sites were analysed also by the AFLP method. We found significantly higher genetic diversity within subtidal than within intertidal populations. This is consistent with a wider dispersal by pelagic larvae and a smaller effective population size when development is holobenthic. Total genetic divergence is not related to distance but to the intertidal/subtidal division. We suggest that S. armiger actually represents two sibling species.     

Genetic divergence between east and west Atlantic populations of<Emphasis Type="Italic"> Actinia</Emphasis> spp. sea anemones (Cnidaria: Actiniidae)

The sea anemone Actinia equina was considered a highly variable species with a wide geographical distribution, but molecular systematic studies have shown that this wide distribution may be the result of the lumping of cryptic species. In this work enzyme electrophoresis was used to analyse the genetic variability of A. equina from the Atlantic coasts of Europe and Africa, as well as the relationships between those populations and other species of the genus. Samples of A. equina from the United Kingdom and France were compared with supposedly conspecific populations from South Africa and a recently described species from Madeira, Actinia nigropunctata. The South African and Madeiran populations were genetically very divergent from each other (genetic identity, I=0.15), as well as from the A. equina population from the United Kingdom and from the other species studied (I between 0.23 and 0.78), indicating that the African population of A. equina belongs to a different species. High genetic similarities were found between west Atlantic A. bermudensis and east Atlantic A. sali, in spite of the great geographical distance between them, and between the European A. equina and A. prasina. The results confirm the presence of the new species A. nigropunctata from Madeira and suggest a new species within the A. equina species group, from South Africa.Communicated by O. Kinne, Oldendorf/Luhe     

Lack of mtDNA and morphological differentiation between two acorn barnacles <Emphasis Type="Italic">Tetraclita japonica</Emphasis> and <Emphasis Type="Italic">T. formosana</Emphasis> differing in parietes colours and geographical distribution

Tetraclita japonica and T. formosana are common intertidal barnacles with similar morphology, which leads to uncertainty in their species status. In the present study, we try to elucidate the taxonomic status of the two taxa using morphology and mitochondrial control region and cytochrome c oxidase subunit I (COI) sequences of the barnacles in their distribution range. The two taxa were found to be morphologically similar; a diagnostic difference between them was only observed in the colour of the parietes and opercular plates. Little genetic differentiation was detected in the control region and COI (Φ_CT < 0.025 for both markers) between two taxa, but differentiation was found between the southern (Taiwan and Hong Kong) and northern (Japan) populations of T. japonica/T. formosana, which might be the result of isolation by distance and upwelling in summer. Our data suggest that the two presently recognized species probably represent two colour morphotypes of the same species exhibiting different geographical distribution. T. japonica is abundant in Japan and southeast coast of China, whereas T. formosana is only abundant in Taiwan. The heterogeneous environment might exert a divergent selection pressure leading to asymmetric distribution of the two colour morphotypes. The different colours might be a result of either phenotypic plasticity adaptive to environmental variables or genetic hitchhiking of local adaptive genotypes. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Genetic diversity and relatedness of the mangrove Rhizophora mangle L. (Rhizophoraceae) using amplified fragment polymorphism (AFLP) among locations in Florida, USA and the Caribbean

Rhizophora mangle L. is a widespread mangrove species in the Western Hemisphere. Mangrove habitat loss and their importance to coastal and reef ecosystems make greater understanding of their genetic structure useful for conservation and management. An amplified fragment polymorphism (AFLP) analysis was performed on samples from Florida and the Caribbean to discover the genetic structure present. R. mangle had variable genetic diversity not related to latitude; P ranged 7 %–92 %. Some other factor, perhaps human impact, has caused low genetic diversity in some populations. Across Florida R. mangle populations varied in genetic diversity with less diversity (G_st?=?0.195) and greater gene flow on the Atlantic coast (Nm =2.07) than on the Gulf coast (G_st?=?0.717, Nm?=?0.197). Gene flow between Caribbean islands was low (Nm?=?0.386) compared to continental populations (Nm?=?1.40), indicating that long distance dispersal is not common between islands. Analysis of molecular variance (AMOVA) analysis showed significant deviations from Hardy-Weinberg expectations at the level of region among subpopulations and overall genetic difference among subpopulations for R. mangle. One implication for management is that small continental populations and island populations may be genetically isolated and distinct from each other.     

Calanus marshallae,a new species of calanoid copepod closely allied to the sibling species C. finmarchicus and C. glacialis

Species of the copepod genus Calanus frequently dominate the marine zooplankton in boreal and arctic waters. Up to now there have been no operational means of identifying several species closely related to Calanus finmarchicus. Reanalysis of these taxa, using material from plankton samples collected throughout Northern Hemisphere polar and coreal waters, shows that there are 3 sibling species which have been previously combined under the names C. finmarchicus and C. glacialis. Several new taxonomic characters permit unequivocal identification of C. finmarchicus, C. glacialis, and a new species, C. marshallae. Claims that C. finmarchicus and C. glacialis are subspecies are refuted; there is no evidence that the two species continuously intergrade either where they co-occur or where they are allopatric, nor is there evidence that the two species hybridize. C. finmarchicus is basically restricted to the North Atlantic Ocean and C. marshallae to the North Pacific Ocean and Bering Sea; C. glacialis is primarily an Arctic species, but its geographical distribution slightly overlaps those of the other two species. Taxa closely related to C. finmarchicus and C. helgolandicus probably represent two separate, but closely linked evolutionary lineage; species of these two lineages are placed in one of two species groups, the finmarchicus group and the helgolandicus group.     

Mate choice in the face of both inbreeding and outbreeding depression in the intertidal copepod Tigriopus californicus

 In species vulnerable to both inbreeding and outbreeding depression, individuals might be expected to choose mates at intermediate levels of genetic relatedness. Previous work on the intertidal copepod Tigriopus californicus has repeatedly shown that crosses between populations result in either no effect or hybrid vigor in the first generation, and hybrid breakdown in the second generation. Previous work also shows that mating between full siblings results in inbreeding depression. The present study again found inbreeding depression, with full sibling mating causing significant fitness declines in two of the three populations assayed. In the mate choice assays, a single female was combined with two males. Despite the costs of both inbreeding and outbreeding, mate choice showed clear inbreeding avoidance but no clear pattern of outbreeding avoidance. This lack of outbreeding avoidance may be attributed either to the temporary increase in fitness in the F₁ generation or to the absence of selection for premating isolation in wholly allopatric populations with infrequent migration. If this inability to avoid unwise matings is common to other taxa, it may contribute to the problem of outbreeding depression when allopatric populations are mixed together. Received: 18 May 1999 / Accepted: 25 January 2000     

<Emphasis Type="Italic">Acropora austera</Emphasis> connectivity in the south-western Indian Ocean assessed using nuclear intron sequence data

The hypervariable carbonic anhydrase 3/550 intron marker was sequenced in order to ascertain the levels of genetic variability and connectivity within and between reefal populations of the hard coral, Acropora austera, on the south-east African coastline. Populations were sampled from (north to south) Bazaruto and Inhaca islands (Mozambique), Rabbit Rock, Two-mile and Red Sands Reefs and Leadsman Shoal (Maputaland, South Africa). Populations at Inhaca Island contained two private alleles, part of the only monophyletic clade with fixed differences between populations in this study. Haplotype and nucleotide diversity were higher in the north of the study area. Indices of migration and haplotype sharing supported significant connectivity between populations in South Africa and Mozambique, which may be important in sustaining genetic diversity in the down-current South African A. austera populations. Measures of population subdivision indicated a significant amount of fixation of allele frequencies amongst populations. Although fine, such differentiation in a marker from the nuclear genome of a hard coral is consistent with some demographic isolation between A. austera populations in southern Mozambique and South Africa. Populations at Rabbit Rock and Inhaca Island were found to be significantly isolated from, and thus less connected to, A. austera populations at other reefs.     

Population genetic structure of the prosobranch Nassarius reticulatus (L.) in a ria seascape (NW Iberian Peninsula) as revealed by RAPD analysis

Randomly amplified polymorphic DNA (RAPD) banding patterns were compared between samples of the netted dogwhelk Nassarius reticulatus from 11 locations along the NW Iberian Peninsula coast. To detect if rias (estuaries formed by drowned river valleys) might promote genetic differentiation, five sampling sites were located within a ria (ria of Muros) and the remaining six were scattered along open-coast areas at increasing distances from the ria mouth. Population differentiation statistics (Φ-values) were estimated using a hierarchical analysis of molecular variance (AMOVA) with samples sorted into two groups: open-coast and ria populations. Despite a high potential to disperse, AMOVA demonstrated a modest, statistically significant genetic heterogeneity among N. reticulatus populations. Most of the genetic structure resided in differences among open-coast populations; ria populations were genetically homogeneous. No obvious geographical pattern was detected for the pairwise genetic distances (non-metric multidimensional scaling; UPGMA tree; Mantel test). Unlike previous studies with other species at a variety of estuarine systems other than rias, there was no evidence that the ria of Muros may enhance the genetic divergence of N. reticulatus populations. This discrepancy is discussed in relation to the biological features of the species (high dispersal potential and a preference for mid-low estuarine habitat) and the strong hydrographic connectivity between ria and neighbouring off-shore waters.     

No reproductive character displacement in male advertisement signals of Hyla japonica in relation to the sympatric H. suweonensis

Reproductive interaction between closely related taxa may leave a distinctive signature in which populations of interacting taxa are more dissimilar in sympatry than in allopatry. An ideal condition for such a pattern of reproductive character displacement (RCD) may occur when a population has limited gene flow and experiences strong selection pressure, exerted by an interacting taxon in areas of sympatry. In Korea, there are two closely related treefrog species: Hyla japonica, which is distributed widely throughout the country, and Hyla suweonensis, which occurs sympatrically in a narrow strip of western coastal plains. H. suweonensis is only found within the distribution of H. japonica. These two species have a similar single-note call structure. Here, we tested the possibility of RCD in H. japonica by examining geographic variation in advertisement calls. Although means of temporal and spectral characters were significantly different between the two species, sympatric populations of H. japonica and H. suweonensis overlapped in distributions of most characters. Furthermore, allopatric and sympatric H. japonica populations did not differ in all call characters. Weak genetic differentiation between sympatric and allopatric populations of H. japonica implied either substantial gene flow or recent genetic isolation. Possible explanations for no RCD in male advertisement calls of H. japonica include a difference in fine temporal characteristics between the two species, migration between sympatric and allopatric localities in H. japonica, RCD in female preferences in H. japonica, and weak selection pressure by H. suweonensis.     

Genetic structure and distribution ofPhotololigo spp. in Australia

Four species ofPhotololigo were identified using allozymes from the northern waters of Australia between the North West Shelf (114°00E) and Brisbane (153°00E). Two of these species fitted the gross morphology ofP. edulis documented from Japan and two taxa shared the distinguishing features ofP. chinensis. F-statistic analyses revealed no major population genetic structuring in any of the species over the geographical range sampled and all populations were in Hardy-Weinberg equilibrium. Given that the distributions of the species appear to be correlated with depth, at least during the austral summer, this panmixia is considered to reflect extensive gene flow through longshore movement of these squid. It is suggested that depth constraints, or factors associated with depth, act as effective barriers to gene flow and, therefore, provide mechanisms for allopatric speciation in this genus. The data from northern Australia indicate that the current view thatLoligo species have broad distributions may need revision and that a number of widespread taxa (such asP. edulis andP. chinensis) are likely to comprise a series of hitherto unrecognised allopatric sibling species. Heterozygosity levels were low for all species exceptPhotololigo sp. 1, which had a restricted deep-water distribution. These data are concordant with the habitat specialist-generalist model, which is discussed.Contribution No. 654 from the Australian Institute of Marine Science     

Genetic differentiation in populations of two Palaemon prawn species at the Atlantic east coast: does gene flow prevent local adaptation?

Two Palaemon prawn species, P. adspersus Rathke and P. squilla (L.), occur along the European Atlantic coast. In areas heavily affected by tides (Netherlands and France), one species, P. squilla, inhabits the intertidal zone, and P. adspersus is found subtidally in the Zostera marina meadows. In areas with small tidal ranges (Sweden) both species occur in the Z. marina zone, and here the body size of P. squilla is reduced, something that in turn reduces reproductive output in this species. Is adaptive improvement in non-tidal P. squilla populations prevented by too extensive gene flow from tidal areas? To wanswer this, genetic differentiation was studied by horizontal starch gel electrophoresis. Each of the two species was sampled at five sites along the European Atlantic coast. Twenty-two enzymes representing 25 loci were scored. Significant genetic heterogeneity between sites was found in both species. Thus the extensive gene flow hypothesis was not supported by the results, and non-tidal populations ought to have the possibility to adapt to local conditions.     

Multiscale patterns of genetic structure in a marine snail (Solenosteira macrospira) without pelagic dispersal

The northern Gulf of California (NGC) is one of the most dynamic and productive marine ecosystems in the world, yet knowledge about population connectivity and dispersal patterns is lacking for many of its resident species. Using nuclear and mitochondrial markers, we investigated the effects of open water, geographical distance and suitable habitat on patterns of genetic structure of Solenosteira macrospira, a benthic buccinid whelk with direct development. We collected samples in April 2004, 2005 and May 2007 from the upper NGC (31°34.39″N, 114°44.45″W). Phylogenetic analyses, hierarchical analyses of variance and Bayesian assignment tests substantiated a break between the east and west coasts. Genetic distance between population pairs increased with geographical distance, but only when assuming a U-shaped dispersal pathway over the open water of the NGC. Given S. macrospira’s association with rocky intertidal habitats, and its limited dispersal potential, we assumed that the geographical distribution of rocky habitat would play a significant role in genetic differentiation of S. macrospira. Nevertheless, populations separated by sand were more similar than populations separated by rocks. The influence of open water, geographical distance and suitable habitat (rocks vs. sand) also varied significantly across different genetic markers that presumably evolve at different rates. Specifically, the more rapidly evolving nuclear microsatellites suggested that physical transport processes strongly influence genetic differentiation on contemporary time scales, even in a species with direct benthic development. This underscores the strong, and potentially homogenizing, effect of present-day ocean circulation patterns in the NGC.     

Genetic structure of Patagonian toothfish (Dissostichus eleginoides) populations on the Patagonian Shelf and Atlantic and western Indian Ocean Sectors of the Southern Ocean

The genetic structure of Patagonian toothfish populations in the Atlantic and western Indian Ocean Sectors of the Southern Ocean (SO) were analysed using partial sequences of the mitochondrial 12S rRNA gene and seven microsatellite loci. Both haplotype frequency data (F _ST>0.906, P<0.01) and microsatellite genotype frequency data (F _ST=0.0141–0.0338, P<0.05) indicated that populations of toothfish from around the Falkland Islands were genetically distinct from those at South Georgia (eastern Atlantic Sector SO), around Bouvet Island (western Atlantic Sector SO) and the Ob Seamount (western Indian Ocean Sector of the SO). Genetic differentiation between these populations is thought to result from hydrographic isolation, as the sites are separated by two, full-depth, ocean-fronts and topographic isolation, as samples are separated by deep water. The South Georgia, Bouvet and Ob Seamount samples were characterised by an identical haplotype. However, microsatellite genotype frequencies showed genetic differentiation between South Georgia samples and those obtained from around Bouvet Island and nearby seamounts (F _ST=0.0037, P<0.05). These areas are separated by large geographic distance and water in excess of 3,000 m deep, below the distributional range of toothfish (<2,200 m). No significant genetic differentiation was detected between samples around Bouvet Island and the Ob Seamount although comparisons may have been influenced by low sample size. These localities are linked by topographic features, including both ridges and seamounts, that may act as oceanic “stepping stones” for migration between these populations. As for other species of deep-sea fish, Patagonian toothfish populations are genetically structured at the regional and sub-regional scales.     

Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs

Life-history characteristics exert a profound influence upon the population structure of many marine organisms. However, relatively few genetic studies have compared direct with indirect-developing species in the same ecosystem or geographical region, and none to our knowledge within an Antarctic setting. To address this issue, we have collected novel amplified fragment length polymorphism (AFLP) data from the direct-developing top shell Margarella antarctica to form a comparison with previously published data for the broadcast-spawning Antarctic limpet Nacella concinna. We scored 270 loci in 240 M. antarctica individuals sampled from five populations spanning the full length of the Antarctic Peninsula. Profound differences were identified in the strength and pattern of population structure between the two species, consistent with gene flow being highly restricted in M. antarctica relative to N. concinna.     

Morphological and molecular comparisons of dominant amphioxus populations in the China Seas

The amphioxi Branchiostoma belcheri, Branchiostoma japonicum and Branchiostoma malayanum are recorded from the coast of China Seas. Six amphioxus populations comprising three Branchiostoma species collected from Hong Kong (southern China), Xiamen (south-eastern China) and Qingdao (northern China) were compared at the morphological and molecular levels. Phylogenetic separations among the species and geographic populations were evaluated by the analysis of 12S ribosomal RNA gene sequences and amplified fragment length polymorphism (AFLP) markers. From morphological characters, B. belcheri is more closely related to B. japonicum than to B. malayanum. However, phylogenetic affinities indicated by both 12S rRNA gene sequences and AFLP analysis showed a more recent phylogenetic splitting of B. belcheri and B. malayanum than that of B. belcheri and B. japonicum. In the AFLP similarity tree, geographic populations of B. japonicum were clustered into different clades. The AFLP data also showed that both B. belcheri and B. japonicum populations in Hong Kong have the highest levels of within-population genetic diversity as compared to that in Xiamen and Qingdao, suggesting that genetic diversity of Branchiostoma decreases from low to high latitudes. Results of hierarchical analysis of molecular variance (AMOVA) also revealed a high level of genetic diversity either for the three B. japonicum populations or the two B. belcheri populations in China Seas. However, genetic variation among the three B. japonicum populations was insignificant, indicating that these populations are genetically connected.