Are direct developers more locally adapted than planktonic developers?

The hypothesis that populations of direct developers exhibit greater geographic differentiation in life history features than populations of planktonic developers, was tested with two species of grazing snails of the genus Littorina from 1986 to 1987. Littorina sitkana (direct developer) and L. scutulata (planktonic developer) coexist on sun- and wave-sheltered beaches from Alaska to Oregon, USA. Seasonal patterns in growth, survival and reproduction were monitored for samples from four geographically separated populations of each species grown in population cages at a common site, Friday Harbor, Washington, USA. The environmental and population effects on growth in the two species were determined in a four-way reciprocal transplant experiment with the same populations. Both the direct and planktonic developers exhibited geographic differentiation in life history features. Differentiation in the direct developer occurred over distances shorter than 30 km, while differentiation in the planktonic developer occurred over the 500 km distance examined (greater than their larvae would likely travel).     

Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers

Crassostrea ariakensis is an important aquacultured oyster species in Asia, its native region. During the past decade, consideration was given to introducing C. ariakensis into Chesapeake Bay, in the United States, to help revive the declining native oyster industry and bolster the local ecosystem. Little is known about the ecology and biology of this species in Asia due to confusion with nomenclature and difficulty in accurately identifying the species of wild populations in their natural environment. Even less research has been done on the population genetics of native populations of C. ariakensis in Asia. We examined the magnitude and pattern of genetic differentiation among 10 wild populations of C. ariakensis from its confirmed distribution range using eight polymorphic microsatellite markers. Results showed a small but significant global θ _ST (0.018), indicating genetic heterogeneity among populations. Eight genetically distinct populations were further distinguished based on population pairwise θ _ST comparisons, including one in Japan, four in China, and three populations along the coast of South Korea. A significant positive association was detected between genetic and geographic distances among populations, suggesting a genetic pattern of isolation by distance. This research represents a novel observation on wild genetic population structuring in a coastal bivalve species along the coast of the northwest Pacific.     

Evidence for restricted gene flow over small spatial scales in a marine snapping shrimp <Emphasis Type="Italic">Alpheus angulosus</Emphasis>

Despite the apparent absence of geographic barriers, connectivity among marine populations may be restricted by, for example, ecological or behavioral mechanisms. In such cases, populations may show genetic differentiation even over relatively small spatial scales. Here, mitochondrial sequence data from the cytochrome oxidase I (COI) gene and seven polymorphic microsatellite markers were used to investigate fine geographic scale population genetic structure in the snapping shrimp Alpheus angulosus, a member of the A. armillatus species complex, from collections in Florida, Jamaica, and Puerto Rico carried out from 1999 to 2005. The COI data showed a deep divergence that separated these samples into two mitochondrial clades, but this divergence was not supported by the microsatellite data. The COI data reflect past population divergence not reflected in extant population structure on the whole genome level. The microsatellite data also revealed evidence for moderate population structure between populations as close as ∼10 km, and no evidence for isolation by distance, as divergences between near populations were at least as strong as those between more broadly separated populations. Overall, these data suggest a role for restricted gene flow between populations, though the mechanisms that reduce gene flow in this taxon remain unknown.     

Structure and migration corridors in Pacific populations of the Swordfish Xiphius gladius, as inferred through analyses of mitochondrial DNA

 The swordfish Xiphias gladius is a migratory oceanic species distributed in sub-tropical and temperate waters worldwide. Studies utilizing mitochondrial DNA (mtDNA) have demonstrated genetic subdivision between ocean basins, as well as within the Atlantic basin. However, there has been no support of population subdivision within the Pacific. We sequenced 629 base pairs of the control region for 281 swordfish collected in the Pacific. A rate heterogeneity parameter, alpha, was found to be 0.201, indicating substantial variation in mutation rate within the control region of swordfish. Hierarchical analysis of molecular variance supported significant genetic structuring among Pacific populations. Northern and southern populations in the western Pacific were significantly divergent, while populations in the east appeared to be genetically continuous. Regression analysis supported a correlation of genetic differentiation with geographic distance along a U-shaped corridor of gene flow. These results reveal a pelagic biogeographic pattern heretofore unrecognized in the Pacific, and reject the null hypothesis that Pacific populations of swordfish are unstructured and comprise only a single homogeneous stock. Received: 10 November 1998 / Accepted: 4 February 2000     

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.     

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.     

Phylogeography of the diamond turbot (Hypsopsetta guttulata) across the Baja California Peninsula

We compared morphology and sequenced nuclear and mitochondrial genes from 11 populations of a previously genetically unstudied “Baja California disjunct” species, the diamond turbot (Hypsopsetta guttulata). This species exhibits very limited adult movement and restriction to soft-bottom habitats but has a moderately long pelagic larval duration. Therefore, if pelagic larval duration is correlated with gene flow between Gulf of California and Pacific populations, we expect a reduced level of genetic and morphological differentiation. However, if adult habitat and ecology have more effect on gene flow, we expect the populations in the two bodies of water to be more highly differentiated. We used logistic regression to compare morphological features and phylogenetic and population genetic analyses to compare nucleotide sequence data. Gulf of California H. guttulata are different from Pacific populations in morphology and both mitochondrial and nuclear gene sequences. MtDNA shows reciprocal monophyly, and nuclear sequences from the Gulf of California formed a monophyletic group. Population genetic analyses also suggest further population subdivision within the Pacific and within the Gulf of California. We argue that adult ecology has a significant effect on migration rates among populations in the Pacific Ocean and the Gulf of California.     

Comparisons of genetic population structures in four intertidal brachyuran species of contrasting habitat characteristics

Genetic population structures along the Japanese coast, analyzed by sequence data from the mitochondrial DNA COI region, were determined for four intertidal brachyuran species in the superfamily Thoracotremata (Ocypode ceratophthalma, Gaetice depressus, Chiromantes dehaani and Deiratonotus japonicus), which were characterized by different habitat requirements. O. ceratophthalma (seashore; supratidal sand) and C. dehaani (estuarine; supratidal marsh) showed no significant genetic differentiation among Japanese populations. The Japanese populations of O. ceratophthalma, however, were found to genetically differentiated from the Philippine population. G. depressus (seashore; intertidal cobbles) exhibited significant genetic differentiation between the Amami-Ohshima population and other local populations. D. japonicus (estuarine; intertidal cobbles) showed significant genetic differentiation among many local populations separated by about 30–1,200 km. The different patterns of genetic population structure recorded for the four species, thus, do not simply correspond to habitat type. An erratum to this article can be found at     

Comparisons of genetic population structures in four intertidal brachyuran species of contrasting habitat characteristics

Genetic population structures along the Japanese coast, analyzed by sequence data from the mitochondrial DNA COI region, were determined for four intertidal brachyuran species in the superfamily Thoracotremata (Ocypode ceratophthalma, Gaetice depressus, Chiromantes dehaani and Deiratonotus japonicus), which were characterized by different habitat requirements. O. ceratophthalma (seashore; supratidal sand) and C. dehaani (estuarine; supratidal marsh) showed no significant genetic differentiation among Japanese populations. The Japanese populations of O. ceratophthalma, however, were found to genetically differentiated from the Philippine population. G. depressus (seashore; intertidal cobbles) exhibited significant genetic differentiation between the Amami-Ohshima population and other local populations. D. japonicus (estuarine; intertidal cobbles) showed significant genetic differentiation among many local populations separated by about 30–1,200 km. The different patterns of genetic population structure recorded for the four species, thus, do not simply correspond to habitat type.     

Population structure and phylogeography of an acorn barnacle with induced defense and its gastropod predator in the Gulf of California

Using sequence variation in the mitochondrial cytochrome oxidase I locus, we estimated the population structure and phylogeography of the intertidal acorn barnacle, Chthamalus anisopoma, and its gastropod predator, Mexacanthina lugubris angelica. Both are endemic to the Gulf of California, being derived from taxa on the Pacific coast of the Baja peninsula, and both exhibit phenotypic plasticity for traits affecting their coevolutionary interactions. Consistent with expectations based on differences in dispersal, C. anisopoma populations generally lack geographic structure, while those of M. l. angelica are more strongly structured. However, the variable degree of differentiation in both species suggests that the extent of reciprocal selection and local adaptation in the species will vary geographically, a result consistent with the concept of a geographic mosaic of coevolution. The pattern of variation in C. anisopoma shows clear evidence of recent spatial expansion, possibly due to increased habitat availability following the last glacial maximum. Phylogeographic analyses suggest that M. l. angelica diversified into three distinct clades after the colonization of the Gulf. Overall, our results illustrate how dispersal potential, geological and climatic events, and recent population growth have impacted the pattern of sequence variation in the two species.     

Population structure of the black tiger prawn, Penaeus monodon, among western Indian Ocean and western Pacific populations

We examined the population structure of the black tiger prawn, Penaeus monodon Fabricius, 1798, in the Indo-West Pacific by analyzing the geographic distribution of elongation factor 1-alpha intron sequences from specimens collected during the winter and spring of 1997. Both the molecular phylogeny of alleles and F-statistics indicated very strong differentiation between populations from the western Indian Ocean and western Pacific. This pattern is concordant with other recent studies of marine species in this region, implying that the Indo-Australian Archipelago represents a biogeographic break between populations in the Indo-West Pacific. F _ST-values among populations in the western Indian Ocean also indicate structure within this region, whereas no structure was found among western Pacific populations. Nucleotide diversity was significantly lower in the western Indian Ocean populations than in the western Pacific, implying that the populations have regional differences in demographic history. Received: 16 November 1998 / Accepted: 26 May 1999     

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.     

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.     

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.     

Geographic structure in Alaskan Pacific ocean perch (<Emphasis Type="Italic">Sebastes alutus</Emphasis>) indicates limited lifetime dispersal

Prevailing oceanographic processes, pelagic larvae, adult mobility, and large populations of many marine species often leads to the assumption of wide-ranging populations. Applying this assumption to more localized populations can lead to inappropriate conservation measures. The Pacific ocean perch (Sebastes alutus, POP) is economically and ecologically valuable, but little is known about its population structure and life history in Alaskan waters. Fourteen microsatellite loci were used to characterize geographic structure and connectivity of POP collections (1999–2005) sampled along the continental shelf break from Dixon Entrance to the Bering Sea. Despite opportunities for dispersal, there was significant, geographically related genetic structure (F _ST = 0.0123, P < 10⁻⁵). Adults appear to belong to neighborhoods at geographic scales less than 400 km, and possibly as small as 70 km, which indicates limited dispersal throughout their lives. The population structure observed has a finer geographic scale than current management, which suggests that measures for POP fisheries conservation should be revisited.     

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.     

Genetic consequences of long larval life in the starfish Linckia laevigata (Echinodermata: Asteroidea) on the Great Barrier Reef

Gene flow between populations of the asteroid Linckia laevigata (Linnaeus) was investigated by examining over 1000 individuals collected from ten reefs throughout the Great Barrier Reef (GBR), Australia, for genetic variation at seven polymorphic enzyme loci. Despite geographic separations in excess of 1000 km, Nei's unbiased genetic distance (0 to 0.003) and standardised genetic variation between populations (F _ST) values (mean 0.0011) were small and not significant. Genetic homogeneity among L. laevigata populations is consistent with the long-distance dispersal capability of its 28 d planktonic larval phase, and is greater than that observed for other asteroid species, including another high-dispersal species, Acanthaster planci, which has a 14 d larval phase. Variation within populations was also higher than previously recorded for asteroids (mean heterozygosity=0.384; number of alleles per locus ranged from 5.1 to 6.0 in each population). Among asteroids, dispersal ability is positively correlated with gene flow and levels of variation, and negatively correlated with levels of differentiation.     

Extensive gene flow among mytilid (Bathymodiolus thermophilus) populations from hydrothermal vents of the eastern Pacific

Prior studies of the hydrothermal vent mussel Bathymodiolus thermophilus (Bivalvia: Mytilidae), provided conflicting predictions about the dispersal ability and population structure of this highly specialized species. Analyses of morphological features associated with its larval shells revealed a feeding larval stage that might facilitate dispersal between ephemeral vent habitats. In contrast, an allozyme study revealed substantial genetic differentiation between samples taken from populations 2370 km apart on Galápagos Rift (Latitude 0°N) and the East Pacific Rise (13°N). To resolve the discrepancy between these studies, we examined allozyme and mitochondrial (mt) DNA variation in new samples from the same localities plus more recently discovered sites (9° and 11°N) along the East Pacific Rise. Although analysis of 26 enzyme-determining loci revealed relatively low levels of genetic variation within the five populations, no evidence existed for significant barriers to dispersal among populations. We estimated an average effective rate of gege flow (Nm) of 8 migrants per population per generation. Two common mtDNA variants predominated at relatively even frequencies in each population, and similarly provided no evidence for barriers to gene flow or isolation-by-distance across this species' known range. Larvae of this species appear to be capable of dispersing hundreds of kilometers along a continuous ridge system and across gaps separating non-contiguous spreading centers.     

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.     

Isolation by distance in the scleractinian coral <Emphasis Type="Italic">Seriatopora hystrix</Emphasis> from the Red Sea

Pelagic dispersal of larvae in sessile marine invertebrates could in principle lead to a homogeneous gene pool over vast distances, yet there is increasing evidence of surprisingly high levels of genetic differentiation on small spatial scale. To evaluate whether larval dispersal is spatially limited and correlated with distance, we conducted a study on the widely distributed, viviparous reef coral Seriatopora hystrix from the Red Sea where we investigated ten populations separated between ~0.150 km and ~610 km. We addressed these questions with newly developed, highly variable microsatellite markers. We detected moderate genetic differentiation among populations based on both F _ST and R _ST (0.089 vs. 0.136, respectively) as well as considerable heterozygote deficits. Mantel tests revealed isolation by distance effects on a small geographic scale (≤20 km), indicating limited dispersal of larvae. Our data did not reveal any evidence against strictly sexual reproduction among the studied populations.