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.     

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.     

Comparative phylogeography of marine cladocerans

We examined the population genetics of six species of marine cladocerans, using a ~600 bp fragment of the cytochrome oxidase subunit I gene sequence. Phylogenetic analysis revealed significant intraspecific, semi-allopatric phylogenetic breaks in four out of five species belonging to the Podonidae, supporting an ancient radiation and oceanic expansion for this group. By contrast, Penilia avirostris (Sididae) displayed no phylogeographic structure across a global sampling, suggesting a recent worldwide expansion. Our results also show a transoceanic distribution of identical or very similar haplotypes in several species of marine Cladocera, which may be interpreted as either natural transport or evidence of recent anthropogenic transport. If the latter is the case, marine cladocerans represent one of the first genetically documented cases of exotic or invasive marine zooplankton, likely an underreported group. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. EU675871–EU675924.     

Genetic structure and allozyme variation of sea bass (Dicentrarchus labrax and D. punctatus) in the Mediterranean Sea

This paper reports data on 28 allozyme loci in wild and artificially reared sea bass (Dicentrarchus labrax) samples, originating from either coastal lagoon or marine sites in the Mediterranean Sea. F _ST analysis (θ estimator) indicated strong genetic structuring among populations; around 34% of the overall genetic variation is due to interpopulation variation. Pairwise θ estimates showed that, on average, the degree of genetic structuring was much higher between marine populations than between samples from lagoons. Six polymorphic loci showed differences in allele frequencies between marine and lagoon samples. Multivariate analyses of individual allozymic profiles and of allele frequencies suggested that different arrays of genotypes prevail in lagoons compared to marine samples, particularly at those loci that, on the basis of previous acclimation experiments, had been implicated in adaptation to freshwater. On the other hand, variation at “neutral” allozyme loci reflects to a greater extent the geographic location of populations. Allozyme differentiation was also studied in a D. labrax population from the Portuguese coast. Average genetic distance between this population and the Mediterranean populations was quite high (Nei's D = 0.236) and calls into question the taxonomic status of the Portuguese population. Finally, genetic relationships between D. labrax and D. punctatus were evaluated. Average Nei's D was 0.648, revealing high genetic differentiation between the two species, even for two sympatric populations of these species in Egypt; thus gene flow was not indicated between species. Received: 24 October 1996 / Accepted: 27 November 1996     

Population variation in the mitochondrial cytochrome b gene of the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae

To describe the genetic relationship among regional populations of two commercially valuable species of marine fish, the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae, the mitochondrial (mt) DNA haplotypes of 59 individuals were defined by direct sequencing of the cytochrome b gene. Samples of orange roughy were collected on four fishing grounds around New Zealand, one off the west coast of Tasmania and one near South Africa from 1990–1991. Samples from hoki were collected on three fishing grounds around New Zealand and one off Tasmania during the same period. An average of 252 nucleotides were sequenced from each of 32 orange roughy and an average of 372 nucleotides from each of 27 hoki. Sequence variation allowed the definition of 9 unique orange roughy haplotypes and 5 hoki haplotypes. Genetic variation, as measured by both average sequence divergence and haplotype diversity, was high in the orange roughy (nucleotide diversity=0.590%, haplotype diversity=0.782) and low in the hoki (nucleotide diversity=0.076%, haplotype diversity=0.279) relative to a similar survey of the Atlantic cod, Gadus morhua. Differences in haplotype frequencies of orange roughy from New Zealand, Tasmania and South Africa were not significant, and the most common haplotype was found in similar frequencies in these three geographically distant regions. Differences in haplotype frequencies between the New Zealand and Tasmanian samples of hoki were significant, suggesting restricted gene flow between these two regions. The contrasting patterns of low but regionally subdivided genetic variation in the hoki versus high but geographically undifferentiated genetic variation in the orange roughy may be attributed to the low fecundity, slow maturation and long lifespan of the orange roughy relative to the hoki.     

Genetically isolated stocks of orange roughy (Hoplostethus atlanticus), but not of hoki (Macruronus novaezelandiae), in the Tasman Sea and Southwest Pacific Ocean around New Zealand

Restriction fragment-length polymorphisms of mitochondrial (mt) DNA, generated by six-base restriction enzymes, were used to examine the stock structure of the two major commercial species in New Zealand fisheries, orange roughy (Hoplostethus atlanticus Collett) and hoki (Macruronus novaezelandiae Hector). Samples of orange roughy from six spawning sites around New Zealand and one site off Tasmania show significant genetic heterogeneity. Samples from two sites around the south of New Zealand were genetically similar to each other, but dissimilar to samples from all other sites. The common haplotype observed in northern sites was absent from the two southern sites. Low numbers of unique haplotypes were restricted to the Challenger Plateau in the Tasman Sea. There was no significant genetic heterogeneity in five samples of hoki from two spawning sites off New Zealand and one site off Tasmania.     

Incipient speciation within a subgenus of rockfish (<Emphasis Type="Italic">Sebastosomus</Emphasis>) provides evidence of recent radiations within an ancient species flock

The high frequency of speciation events associated with species flocks (i.e., radiations of closely related species) provides invaluable insight into the speciation process. Investigations of the speciation process in the marine environment are rare, and therefore, the genetic analysis of the rockfish genus Sebastes, considered an ancient marine species flock, provides an opportunity to investigate this process in the sea. Using both mitochondrial and nuclear markers, we analyzed five closely related species within the rockfish subgenus Sebastosomus. Our goal was to understand the evolutionary history and genetic relationships among species within this group and to provide evidence of recent speciation events within the subgenus. In the genetic analysis of the subgenus, we found different stages of the speciation process, with greater genetic divergences among three of the five species, evidence of recent divergence between two of the five species, Sebastes entomelas and S. mystinus, and significant genetic divergence between two lineages within S. mystinus revealing a signature of incipient speciation. We also found frequency differences of the two S. mystinus lineages among sample locations and found no evidence of introgression between the lineages at the location where both coexist. Although Sebastes is an example of an ancient species flock, this study provides evidence of ongoing speciation within the genus and reveals stages of this process from incipient to distinct species.     

Genetic structure of leopard shark (<Emphasis Type="Italic">Triakis semifasciata</Emphasis>) populations in California waters

The leopard shark (Triakis semifasciata) is an important predator in coastal marine ecosystems of California, targeted by recreational and commercial fishermen and of specific interest in fisheries management. From October 2003 to August 2006, 169 leopard sharks were collected from the coast of California (between 40.750°N and 32.678°N) and analyzed for mitochondrial and nuclear genetic structure. Analyses of mtDNA control region sequences revealed relatively low levels of genetic variation (five haplotypes, average pairwise divergence π = 0.0067). In contrast, leopard sharks were highly polymorphic for inter simple sequence repeats (ISSRs), which characterize a broad range of the nuclear genome. The null hypothesis of panmixia in California waters was rejected for both genetic markers, and ISSRs displayed a statistically significant pattern of isolation by distance (IBD) across the species range (P = 0.002). A variety of analyses showed that divergence is most pronounced in the northernmost population of Humboldt Bay. Natal philopatry in T. semifasciata was tested using Siegel-Tukey tests on data partitioned by breeding site status, and sex-specific philopatry was tested by comparing IBD plots between sexes. Although there was some evidence for natal philopatry in leopard sharks (P = 0.038), and population divergence may be related to the proximity of breeding sites (P = 0.064), we found no support for sex-specific philopatry. In addition to identifying a novel set of highly variable genetic markers for use in shark population studies, these results may be used to better inform management decisions for leopard sharks in California.     

Limited population structure in Northern and Spotted Wolffishes (<Emphasis Type="Italic">Anarhichas denticulatus</Emphasis> and <Emphasis Type="Italic">A. minor</Emphasis>) despite low apparent dispersal potential

Northern and Spotted Wolffishes (Anarhichas denticulatus and A. minor) are demersal marine fishes listed as “threatened” in Canadian waters. Both species have unusually large benthic eggs and large size at hatch, which should reduce passive dispersal. We examined population differentiation with microsatellite and AFLP loci across the ranges of both species in the North Atlantic Ocean. Although significant population structure was documented, differentiation was less than expected based on knowledge of life history characteristics. Significant differentiation was found in Northern Wolffish between the Barents Sea and other samples based on both microsatellite and AFLP data. In contrast, population structure in the Spotted Wolffish was notably weaker, particularly with microsatellites. Both species were characterized by low genetic diversity for marine fishes and had significantly lower genetic diversity than the congeneric Atlantic Wolffish. This finding was consistent with the conservation status of these three species and suggests potential vulnerability to over-exploitation in Northern and Spotted Wolffishes.     

Microsatellite DNA markers and morphometrics reveal a complex population structure in a merobenthic octopus species (<Emphasis Type="Italic">Octopus maorum</Emphasis>) in south-east Australia and New Zealand

Five polymorphic microsatellite loci were developed and then used to assess the population genetic structure of a commercially harvested merobenthic octopus species (Octopus maorum) in south-east Australian and New Zealand (NZ) waters. Beak and stylet morphometrics were also used to assess population differentiation in conjunction with the genetic data. Genetic variation across all loci and all sampled populations was very high (mean number alleles = 15, mean expected heterozygosity = 0.85). Microsatellites revealed significant genetic structuring (overall F _ST = 0.024, p < 0.001), which did not fit an isolation-by-distance model of population differentiation. Divergence was observed between Australian and NZ populations, between South Australia and north-east Tasmania, and between two relatively proximate Tasmanian sites. South Australian and southern Tasmanian populations were genetically homogeneous, indicating a level of connectivity on a scale of 1,500 km. Morphometric data also indicated significant differences between Australian and NZ populations. The patterns of population structuring identified can be explained largely in relation to regional oceanographic features.     

High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past?

Historical sea level fluctuations have influenced the genetic structure and evolutionary history of marine species and examining widespread species across their species ranges may elucidate some of these effects. Chlorurus sordidus is a common and widespread parrotfish found on coral reefs throughout the Indo-central Pacific. We used phylogenetic, phylogeographic, and cladistic analyses to examine the genetic composition and population structure of this species across most of its latitudinal range limits. We sequenced 354 bp of the mitochondrial control region I in 185 individuals from nine populations. Populations of C. sordidus displayed high levels of genetic diversity, similar to those recorded for widespread pelagic fish species, but much greater nucleotide diversity values than those previously recorded for other demersal reef fishes. Both phylogenetic and phylogeographic analyses detected strong genetic subdivision at the largest spatial scale (i.e. among oceans). The Pacific Ocean was characterised by weak population genetic structure. Separation of the Hawaiian location from other Pacific and West Indian Ocean sites was evident in phylogenetic analyses, but not from analysis of molecular variance. NCA and isolation-by-distance tests suggested that the genetic structure of this species was the result of multiple contemporary and historical processes, including long-distance colonisation and range expansion arising from fluctuating sea levels, limited current gene flow, and isolation by distance. This pattern is to be expected when historically fragmented populations come into secondary contact. We suggest the patterns of population genetic structure recorded in C. sordidus are caused by large local population sizes, high gene flow, and a recent history of repeated fragmentation and remixing of populations resulting from fluctuating sea levels.Communicated by M.S. Johnson, Crawley     

Global phylogeography of the fissiparous sea-star genus <Emphasis Type="Italic">Coscinasterias</Emphasis>

The fissiparous starfish genus Coscinasterias (Verrill) is represented in shallow waters around many of the world's continents. This wide distribution could be explained by dispersal, vicariance, or translocation associated with shipping, and represents an excellent system for marine biogeographic research. We conducted a global phylogeographic analysis of 42 Coscinasterias mtDNA cytochrome oxidase 1 sequences (15 haplotypes) from 18 sites, including representatives of all four recognised species. Phylogenetic analysis yielded a robust phylogeny, with strong support for the monophyly of the genus (90% bootstrap support) and of each separate species (99-100%). Haplotypes exhibited strong phylogeographic structure, with robust mtDNA clades often associated with distinct land masses. A general lack of genetic differentiation within sites may reflect fissiparity. However, shared haplotypes over larger distances (e.g. across Japan), and the presence of related haplotypes on adjacent land masses (e.g. Tasmania, New Zealand; 1.6-1.8%) suggest that long-distance dispersal is an important biogeographical process for Coscinasterias. The 4.0-4.4% divergence between Japanese and South African sister groups may relate to transequatorial dispersal around the onset of the Pleistocene. Divergent Atlantic and Mediterranean populations of C. tenuispina (maximum 1.5%) may deserve subspecific recognition, and high divergences within Australian C. muricata (maximum 8.0%) suggest a species complex.     

Population structure of the common sole (<Emphasis Type="Italic">Solea solea</Emphasis>) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

Spatial and temporal population genetic structures of the common sole, Solea solea, were studied in Northeastern Atlantic and Mediterranean Sea populations, using three polymorphic exon-primed intron-crossing (EPIC) markers. Results demonstrated significant multilocus differentiation among Eastern Mediterranean and a group composed by Western Mediterranean and Atlantic populations (θ = 0.150, P < 0.001), but also suggested unrecorded genetic differentiation of the Adriatic Sea population. No pattern of isolation-by-distance was recorded across the range covered by sampling, from the Kattegat to the Aegean Sea. Conversely to genetically structured Mediterranean populations, Atlantic populations ranging from Denmark to Portugal could be considered as representative of the same panmictic unit (θ = 0.009, not significant). Results further demonstrated stability of multilocus genetic structure among temporarily replicated cohort samples [0+, 1+, subadults] from several coastal and estuarine locations from Bay of Biscay, excepted for the amylase locus Am2B3-2 at one location (Pertuis d’Antioche). Despite coherence of such observed patterns of multilocus differentiation with previous allozymic surveys in sole, and with patterns generally obtained for other marine fish species, single-locus results from EPICs indicated divergent coalescence schemes supporting a complex response to ecology and history of sole’s populations. Results stress the use of nuclear genes such as EPIC markers to investigate population structure, but also historical, demographic, and possibly selective processes in marine fishes.     

Life style and genetic variation in teleosts: the case of pelagic (<Emphasis Type="Italic">Aphia minuta</Emphasis>) and benthic (<Emphasis Type="Italic">Gobius niger</Emphasis>) gobies (Perciformes: Gobiidae)

The pattern of genetic variability of two species of Mediterranean gobiids was compared, with reference to their different life history traits (Aphia minuta paedomorphic and pelagic; Gobius niger metamorphosed and benthic). The aim was to evaluate how different life histories can affect the genetic structure in these marine teleosts. The study was carried out on populations of both species sampled in the western Mediterranean and in the Adriatic Sea. Seven restriction endonucleases were used for the RFLP analysis of a mitochondrial DNA segment comprising the NADH dehydrogenase subunits 3, 4L and 4. The results highlighted two different patterns of genetic variation, a weak genetic structure in A. minuta and population subdivision in G. niger. These observations may be explained not only in terms of the different dispersal capabilities of these species, but also considering that A. minuta is an abbreviate iteroparous spawner while G. niger is a protracted iteroparous spawner. Because abbreviate iteroparity is a reproductive strategy selected in stable environments with high resource availability, Pliocene and Pleistocene climate oscillations may have represented factors that negatively influenced the reproductive success of A. minuta, producing demographic fluctuations and bottlenecks, as suggested by the mismatch distribution analysis. The weak genetic structure of A. minuta populations seems to be therefore due to a more recent re-colonization of the Mediterranean basin after a severe population decline, rather than to the high vagility of this pelagic goby.     

Population structure of short-beaked common dolphins (<Emphasis Type="Italic">Delphinus delphis</Emphasis>) in the North Atlantic Ocean as revealed by mitochondrial and nuclear genetic markers

The understanding of population structure and gene flow of marine pelagic species is paramount to monitoring, management and conservation studies. Such studies are often hampered by the potentially high dispersal behavior of the species, the lack of obvious geographical barriers in the marine environment and the scarce sample availability. Short-beaked common dolphins (Delphinus delphis) are widespread in coastal and open-ocean habitats of the North Atlantic Ocean, nevertheless population structure and migratory patterns are poorly understood. Furthermore, concern has been raised about the status of the species because large numbers of dolphins have been taken incidentally in several fisheries throughout the North Atlantic in the past decades. In the present study, a large number of individual samples were obtained from seasonal and spatial aggregations of common dolphins from western (wNA) and eastern North Atlantic (eNA) regions, mostly using opportunistic sampling (i.e. from incidental entanglement in fishing gear or beach-cast carcasses). Genetic variability was investigated using nuclear (14 microsatellite loci) and mitochondrial (360 bp of the control region) genetic markers. Levels of genetic diversity were relatively high in all sampled areas and no evidence of recent reduction of effective population size (i.e. bottleneck) was detected at the nuclear loci. Significant population structure was detected between the two main regions (wNA and eNA) where it appeared to be more pronounced at mitochondrial (F _ST = 0.018, P < 0.001) than nuclear markers (F _ST = 0.005, P < 0.05), indicating the presence of at least two genetically distinct populations of common dolphins in the North Atlantic Ocean. In contrast, no significant genetic structure was detected between temporal aggregations of dolphins from within the same region, suggesting possible seasonal movement patterns at a regional scale. The observed levels of genetic differentiation between classes of markers are discussed here as a possible consequence of migratory patterns or recent population subdivision. An erratum to this article can be found at     

Inter-oceanic genetic differentiation among albacore (<Emphasis Type="Italic">Thunnus alalunga</Emphasis>) populations

Albacore (Thunnus alalunga) is a highly migratory pelagic species distributed in all tropical and temperate oceans. Recent analyses using both mitochondrial DNA (mtDNA) and nuclear DNA markers have demonstrated genetic subdivision within and between Atlantic and Pacific populations. However, although numerous biological differences have been reported for Atlantic and Mediterranean albacore, the genetic differentiation for these basins has not been demonstrated. We characterized 373 base pairs of nucleotide sequence from the mitochondrial DNA control region of 134 individuals collected in the Pacific (n=30), the northeast (NE) Atlantic (n=54) and the Mediterranean (n=50). Analysis of molecular variance (AMOVA) revealed a small, but highly significant, proportion of genetic variation separating these three regions (_st =0.041; P=0.009), a pattern also supported by pairwise comparisons. These results demonstrate for the first time the genetic distinctiveness of the Mediterranean albacore from the NE Atlantic population giving support to the current management practices based on separate units. This outcome is concordant with reported migratory movements related to reproductive behavior between the NE Atlantic and the Mediterranean Sea. Additionally, the phylogenetic analyses of DNA sequences revealed the presence of a shallow genetic discontinuity with no geographic association. These two phylogroups are more likely the result of the demographic history of this species (i.e. long demographic stable history) as opposed to historical vicariance as has been proposed for other highly migratory fishes.Communicated by P.W. Sammarco, Chauvin     

Contrasting population structures in two sympatric fishes in the Baltic Sea basin

Detailed multispecies studies on the patterns of genetic variability and differentiation in marine environments are still rare. Using mitochondrial and nuclear genetic markers, we compared genetic variability and population structuring of threespine (Gasterosteus aculeatus) and ninespine (Pungitius pungitius) sticklebacks from the same eleven marine and six freshwater locations within the Baltic Sea basin. Analyses of both marker types revealed a significantly lower degree of genetic structuring in both marine and freshwater populations of threespine than those ninespine sticklebacks. Isolation-by-distance (IBD) was detected across the marine populations in both species, suggesting spatially limited gene flow. However, the levels of genetic diversity and differentiation across the localities were uncorrelated between the two species in both marine and freshwater environments. Accordingly, estimates of effective population sizes were larger and migration rates were higher for three- than for ninespine sticklebacks. Hence, ninespine stickleback populations from the Baltic Sea basin appear to be subject to stronger genetic drift than sympatric threespine sticklebacks, and the proximate reason for this difference is likely to be found from autecological differences between the two species. In accordance with the earlier studies, genetic variability was higher and the degree of genetic differentiation was lower in marine than in freshwater populations in both species.     

Spatiotemporal analysis of population genetic structure in <Emphasis Type="Italic">Geomonhystera disjuncta</Emphasis> (Nematoda,Monhysteridae) reveals high levels of molecular diversity

Species identification in the phylum Nematoda is complicated due to the paucity of easily obtainable diagnostic morphological features. Furthermore, the cosmopolitan distribution of several species despite low dispersal abilities makes cryptic diversity potentially substantial within this phylum. We conducted a population genetic survey in the marine nematode Geomonhystera disjuncta in Belgium and The Netherlands in two seasons. The mitochondrial cytochrome oxidase c subunit 1 (COI) gene was screened with the single-strand conformation polymorphism method in 759 individuals. The 43 haplotypes were grouped into five lineages, with low divergences within (<3%) and high divergences between lineages (>14%). Analysis of the nuclear ITS region yielded concordant tree topologies, indicating the presence of five cryptic taxa within G. disjuncta. Analysis of Molecular Variance (AMOVA) illustrated a significant structuring in all lineages and temporal fluctuations in haplotype frequencies within and between locations. Metapopulation dynamics and/or priority effects best explained this structuring. Finally, our data indicate that the COI gene may be useful for DNA barcoding purposes.     

Mode of reproduction,recruitment, and genetic subdivision in the brooding sponge<Emphasis Type="Italic"> Haliclona</Emphasis> sp.

Sponges display a variety of reproductive strategies that have the potential to influence population genetic structure. Histological examination of ten reproductive individuals of the Western Australian sponge Haliclona sp. showed that this species broods embryonic larvae that are potentially limited in dispersal capabilities. Because sponges have the potential to propagate in a number of modes, allozyme electrophoresis was used to assess the relative importance of asexual and sexual reproduction to recruitment, and to quantify genetic subdivision over different spatial scales. Tissue samples from 227 sponges were collected from reefs within two areas 400 km apart: Hamelin Bay and Rottnest Island. Contrary to expectations for highly clonal populations, genotypic diversity within sites was high, no linkage disequilibrium was found, and there was no evidence of genotypic clustering within reefs. There was no genetic evidence that asexual reproduction is important for the maintenance of populations. Genetic comparisons were consistent with mixing of sexually produced recruits within reefs, on a scale up to a few hundred metres, but significant genetic subdivision between reefs (F_ST=0.069 at Hamelin Bay, 0.130 at Rottnest Island) indicated that water gaps of several hundred metres are effective at preventing dispersal. Subdivision between the two areas, separated by 400 km, was moderately greater (F_ST=0.142) than within, but the same alleles were predominant in the two areas. These genetic patterns are consistent with limited dispersal capabilities of brooded larvae.Communicated by G.F. Humphrey, Sydney