Population genetic structure of Korean pen shell (Atrina pectinata) in Korea inferred from microsatellite marker analysis

The Korean pen shell Atrina pectinata is a commercially valuable species in Korea. The commercial catch of this fish has decreased continuously since 1990. However, its genetic characteristics have never been studied. In order to explore the population genetic structure of this species, 125 pen shells sampled from three major habitats along the western coast of Korea were genotyped at 21 microsatellite loci. Relatively high levels of genetic variability (mean number of allelic richness (A_R) = 14.74; mean hetrerozygosity (He) = 0.849) was found among localities. However, despite the potential of the Korean pen shell to exhibit genetic structure (adults are sedentary), none of the genetic tests applied in this study detected significant genetic differentiation among the samples. The lack of genetic differentiation among samples may be due to high levels of larval dispersal, through passive drift with ocean currents. Alternatively, populations may have diverged too recently for significant genetic differentiation to have become evident. Furthermore, small sample sizes and the limited number of samples may have hampered the detection of genetic structure. The results of this study therefore suggested a lack of genetic structure among the populations of pen shell of Korean waters and should be managed as a single unit. This information on the genetic characteristics of Korean pen shell populations has important implications for the sustainable exploitation of the fishing resources and the preservation of biodiversity.     

Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north‐west Pacific

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life‐history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair‐wise F_ST revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0·53, P < 0·001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration–drift equilibrium.     

Population genetic structure of the tongue sole (Cynoglossus semilaevis) in Korea based on multiplex PCR assays with 12 polymorphic microsatellite markers

The tongue sole, Cynoglossus semilaevis, is an important fishery resource in Korea. About 100 tongue sole sampled from three major habitats along the western coast of Korea were assessed using multiplex assays with 12 highly polymorphic microsatellite loci to explore the population genetic structure of the species; 151 alleles and similar high levels of gene diversity (mean number of alleles (N_A) = 10.42, mean expected heterozygosity (He) = 0.78) were detected. Three populations showed significant Hardy–Weinberg equilibrium deviations at four loci. Although a significant difference in the number of unique alleles was observed among populations, genetic population subdivision was low by F-statistics (overall F _ST = 0.007, p < 0.05). However, this substructure was not supported by analysis of molecular variance or analyses of isolation by distance. The results suggest a lack of genetic structure among the tongue sole populations in Korean waters and that the populations should be managed as a single unit. The lack of genetic differentiation among samples may be due to high levels of larval dispersal in ocean currents. Alternatively, the populations may have diverged too recently for significant genetic differentiation to have become evident. Given the intensity of tongue sole aquaculture activity in China, which adjoins the western coast of Korea, the possibility that aquaculture may have partially contributed to the population genetic characteristics detected cannot be excluded. This study provides the basic information on nature population structure of C. semilaevis that may help to preserve and manage tongue soles in Korea.     

Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north‐western Pacific: effect of past population expansion and contemporary gene flow

Aim Phylogeographical patterns of marine organisms in the north‐western Pacific are shaped by the interaction of past sea‐level fluctuations during glacial maxima and present‐day gene flow. This study examines whether observed population differentiation in the barnacle Chthamalus challengeri, which is endemic to the north‐western Pacific, can be explained by the interactions between historical glacial events and patterns of contemporary gene flow. Location Eleven locations in the north‐western Pacific. Methods Partial sequences of mitochondrial cytochrome c oxidase subunit I (COI), 12S, 16S and nuclear internal transcribed spacer 1 (ITS1) were obtained from 312 individuals. Parsimony haplotype networks and analysis of molecular variance (AMOVA) were used to determine whether the observed genetic structure corresponds to marine provinces (Kuroshio Current and China Sea Coastal Provinces), zoogeographical zones (oriental and Japan warm‐temperate zones) and/or potential refugial areas (Sea of Japan and East China Sea) in the north‐western Pacific. Neutrality tests, mismatch distribution analysis and Bayesian skyline plots were used to infer the demographic history of C. challengeri. Results In total, 312, 117, 182 and 250 sequences were obtained for COI, 12S, 16S and ITS1, respectively. A panmictic population was revealed, which did not conform to the ‘isolation by distance’ model. None of the a priori population groupings based on marine provinces, zoogeographical zones or potential refugial areas was associated with observed genetic patterns. Significant negative values from neutrality tests and the unimodal mismatch distribution and expansion patterns in Bayesian skyline plots for the COI and 16S data sets indicate a population expansion in the mid‐Pleistocene (c. 200 ka). Information from the fossil record suggests that there has been a northward range shift of this species from the East China Sea or the Palaeo‐Pacific coast of Japan to the Sea of Japan since the mid‐Pleistocene. Main conclusions Chthamalus challengeri has experienced a population expansion and range shift since the mid‐Pleistocene. The observed lack of population differentiation can be explained by this past population expansion and present‐day wide‐scale larval dispersal (owing to the long planktonic larval duration) across marine provinces, which have led to the successful establishment of the species in different zoogeographical zones and habitats.     

Historical isolation and hydrodynamically constrained gene flow in declining populations of the South-African abalone, Haliotis midae

Over the past two decades, the South African abalone (Haliotis midae), has been under serious threat mainly due to overexploitation. To assure successful management and conservation of wild stocks, the consideration of species-specific evolutionary and population dynamic aspects is critical. In this study, eight microsatellites and 12 single nucleotide polymorphic loci (SNPs) were applied to determine genetic structure in nine populations sampled throughout the species?? natural distribution range. It spans along three biogeographical regions of the South African coastline: temperate in the West coast, warm temperate in the South coast and subtropical in the East coast. Data analysis applying frequentist and Bayesian-based clustering methods indicated weak genetic differentiation between populations of the West, South and East coast. Spatial Bayesian inference further revealed clinal variation along a longitudinal gradient and a transitional zone in the South coast. Coalescent analysis of long-term migration showed restricted interchange among the sampling locations of the South coast while estimates of effective population size were comparable between coastal regions. Furthermore demographic analysis of microsatellite data suggested population expansion, probably reflecting range expansion that occurred following glacial retreat during the Pleistocene. Overall, population structure analysis suggested contemporary (hydrographical conditions) as well as historical (Pleistocene contraction of habitat) restrictions to gene flow. This study provides the foundation for the establishment of an integrated management policy for preserving the natural diversity and adaptive potential of H. midae.     

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N _ST =0.751> G _ST =0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s F_S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.     

Genetic diversity and population demography of narrow‐ridged finless porpoises from South Korea on the basis of mitochondrial DNA variation: Implications for its conservation in East Asia

The narrow‐ridged finless porpoise, Neophocaena asiaeorientalis, is a small cetacean inhabiting the coastal waters of Taiwan, East China, Korea, and Japan, and is threatened by anthropogenic pressures. We analyzed the mitochondrial control region of N. asiaeorientalis from Korean waters to better understand the genetic diversity, population structure, and demographic history through comparison with previously reported sequences from Japan and China. The network and phylogenetic analyses illustrated that few common haplotypes were centrally located, and that most of the unique haplotypes were on the edges of the branches. Moreover, the estimates of fixation indices and gene flow revealed significant genetic differentiation among the regions in East Asia. The mismatch distribution suggested a population expansion in the late Pleistocene. We propose that the current genetic variation in N. asiaeorientalis in East Asia was shaped by historical demographic expansion during the late Pleistocene. The N. asiaeorientalis of Korean waters has the highest diversity observed with the sampling available at this time. However, the abundance of N. asiaeorientalis in Korean waters has rapidly declined and the species needs protection from bycatch.     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences

Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F_ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation.     

A phylogeographical analysis across three biogeographical provinces of the south-eastern Pacific: the case of the marine gastropod Concholepas concholepas

Aim The present‐day population structure of a species reflects the influence of population history as well as contemporary processes. Little is known about the mechanisms that have shaped the geographical distribution of genetic diversity in marine species present on the south‐eastern Pacific (SEP) coast. Here we provide the first comprehensive phylogeographical study of a species distributed along the SEP coast by analysing the endemic and emblematic muricid gastropod Concholepas concholepas. Location The study localities were distributed along the SEP coast ranging from Matarani (11° S) to Puerto Eden (49° S), crossing three major biogeographical provinces: Peruvian Province, Intermediate Area and Magellanic Province. Methods A total of 337 specimens of C. concholepas were collected from 14 localities in the three biogeographical provinces/areas. Mitochondrial cytochrome oxidase I (COI) gene partial sequences (658 bp) were obtained and analysed using coalescence‐based methods to infer molecular diversity and phylogeographical patterns. Results Across the 337 individuals, we found a large diversity, with a total of 179 haplotypes at the COI gene fragment. Although a slight decrease in gene diversity was observed from north to south, an analysis of molecular variance did not reveal any significant spatial population differentiation from Peru to the tip of Chile, not even across the recognized biogeographical boundaries at 30° S and 42° S. In addition, a star‐like haplotype network suggested the past occurrence of a rapid demographic and geographical expansion over the total range examined. Calculations of the onset of this expansion suggest that it might be due to climatic conditions during the period of the marine isotope stage 11 (MIS 11, 400,000 years ago), the longer and warmer interglacial episode during the Pleistocene epoch. Main conclusions Our phylogeographical analyses indicate that in the recent past C. concholepas mitochondrial DNA lineages underwent a sudden population expansion event. In addition, our data do not support the hypothesis of concordance between biogeographical barriers and phylogeographical breaks along the SEP coast. These two results are in accordance with the paradigm of high larval dispersal ability in marine species with an extended pelagic larval phase.     

Biophysical connectivity explains population genetic structure in a highly dispersive marine species

Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster (Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F _ST of 0.0016 (P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus (P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation (P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

     

Connectivity and Dispersal Patterns of Protected Biogenic Reefs: Implications for the Conservation of Modiolus modiolus (L.) in the Irish Sea

Biogenic reefs created by Modiolus modiolus (Linnaeus, 1758) (horse mussel reefs) are marine habitats which support high levels of species biodiversity and provide valuable ecosystem services. Currently, M. modiolus reefs are listed as a threatened and/or declining species and habitat in all OSPAR regions and thus are highlighted as a conservation priority under the EU Marine Strategy Framework Directive (MSFD). Determining patterns of larval dispersal and genetic connectivity of remaining horse mussel populations can inform management efforts and is a critical component of effective marine spatial planning (MSP). Larval dispersal patterns and genetic structure were determined for several M. modiolus bed populations in the Irish Sea including those in Wales (North Pen Llŷn), Isle of Man (Point of Ayre) and Northern Ireland (Ards Peninsula and Strangford Lough). Simulations of larval dispersal suggested extant connectivity between populations within the Irish Sea. Results from the genetic analysis carried out using newly developed microsatellite DNA markers were consistent with those of the biophysical model. Results indicated moderately significant differentiation between the Northern Ireland populations and those in the Isle of Man and Wales. Simulations of larval dispersal over a 30 day pelagic larval duration (PLD) suggest that connectivity over a spatial scale of 150km is possible between some source and sink populations. However, it appears unlikely that larvae from Northern Ireland will connect directly with sites on the Llŷn or Isle of Man. It also appears unlikely that larvae from the Llŷn connect directly to any of the other sites. Taken together the data establishes a baseline for underpinning management and conservation of these important and threatened marine habitats in the southern part of the known range.     

中国近海银鲳线粒体COⅠ基因序列变异分析

对采自黄海、东海和南海的7个银鲳群体的线粒体COⅠ基因序列变异进行分析,研究银鲳的遗传多样性、遗传结构和群体历史动态。在所分析的111个个体中检测到16个单倍型。7个群体呈现出高的单倍型多样性（h=0.564～0.688） 和低的核苷酸多样性（π=0.001～0.003）。单倍型遗传学关系、两两群体间的F_ST值和分子方差分析均表明中国近海7个银鲳群体间的遗传分化不显著。中性检验和核苷酸不配对分析均表明中国近海银鲳经历了晚更新世的群体扩张事件,扩张时间约为6.0×10⁴～1.04×10⁵ 年前。研究结果表明,银鲳的卵和幼体具有较强的扩散能力、中国近海的海洋环流以及近期的群体扩张可能是造成中国近海银鲳群体在线粒体COⅠ基因序列上存在较高的遗传同质性的原因。     

Low mtDNA variation and shallow population structure of the Chinese pomfret Pampus chinensis along the China coast

In the present study, population genetic structure and genetic diversity of the Chinese pomfret Pampus chinensis, along the China coast were investigated and compared with that from Indonesia using mitochondrial DNA cytochrome b gene sequences. A total of 28 variable sites (including 18 singleton sites and 10 parsimony information sites) were observed and 23 haplotypes were defined in 330 individuals from 11 localities. The haplotype diversity (H_D) of the populations ranged from 0·540 to 0·828, the nucleotide diversity (π) ranged from 0·081 to 0·295%. Pairwise F_ST statistics showed that significant genetic divergence occurred among populations from different geographical regions. The high dispersal capabilities, geographic segregation and ocean currents may be responsible for the present population genetic structure in this species. In addition, a population expansion event during the late Pleistocene period was inferred. The time of population expansion was estimated to occur about 117 000–169 000 years ago.     

Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range

The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps ) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors.     

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.     

Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.Subject terms: Genetic variation, Ecology     

Phylogeography and historical demography of Sicydium salvini in the eastern Pacific

Amphidromy, characterized by freshwater adult and marine larval stages, has been shown to be an important influence on the genetic structure of aquatic populations. Sicydium salvini is a widespread goby species (Teleostei: Gobiidae: Sicydiinae) in the eastern Pacific with a continuous distribution from Mexico to Panama. Here, we use mitochondrial data to infer population genetic and historical demography of this species. Sequences were collected for the mitochondrial gene cytochrome b for 162 specimens sampled across the range of S. salvini with a concentration on rivers in Costa Rica. No genetic structure was detected between regions or rivers in the AMOVA analysis; the phylogeny for this species showed no geographic affinities and very little resolution. Historical demographic analyses indicated a population expansion during the late Pleistocene. These results are consistent with a panmictic population with expansion influenced strongly by Pleistocene glacial cycles and geologic uplift.     

GENETIC DRIFT AND COLLECTIVE DISPERSAL CAN RESULT IN CHAOTIC GENETIC PATCHINESS

Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free‐living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex dispersal patterns to create chaotic genetic patchiness. Here we use a coancestry model and individual‐based simulations to test this idea. We found that chaotic genetic patterns (qualified by global F_ST and spatio‐temporal variation in F_ST's between pairs of samples) arise from the combined effects of (1) genetic drift created by the small local effective population sizes of the sessile phase and variance in contribution among breeding groups and (2) collective dispersal of related individuals in the larval phase. Simulations show that patchiness levels qualitatively comparable to empirical results can be produced by a combination of strong variance in reproductive success and mild collective dispersal. These results call for empirical studies of the effective number of breeders producing larval cohorts, and population genetics at the larval stage.     

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. S. hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa. As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones. Based on microsatellite analyses three groups could be distinguished within the WIO: (1) northern Madagascar, (2) south-west Madagascar together with one site in northern Mozambique (Nacala) and (3) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.Subject terms: Haplotypes, Structural variation, Conservation biology, Population dynamics, Biogeography