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Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks., (© 2014 John Wiley & Sons Ltd.)

Population connectivity studies are a useful tool for species management and conservation planning, particular of highly threatened or endangered species. Here, we evaluated the genetic structure and connectivity pattern of the endangered coral Cladocora caespitosa across its entire distribution range in the Mediterranean Sea. Additionally, we examined the relative importance of sexual and asexual reproduction in the studied populations and their genetic diversity. A total of 541 individuals from 20 localities were sampled and analysed with 19 polymorphic microsatellite markers. Of the genotyped individuals, 482 (89%) had unique multilocus genotypes. Clonality percentages of the populations varied from 0% (in eight populations) to nearly 69% (in one population from Crete). A heterozygosity deficit and a high degree of inbreeding was the general trend in our data set. Population differentiation in C. caespitosa was characterised by significant pairwise FST values with lower ones observed at an intraregional scale and higher ones, between populations from different biogeographic regions. Genetic structure analyses showed that the populations are divided according to the three main sub-basins of the Mediterranean Sea: the Western (Balearic, Ligurian and Tyrrhenian seas), the Central (Adriatic and Ionian seas) and the Eastern (Levantine and Aegean seas), coinciding with previously described gene flow barriers. However, the three easternmost populations were also clearly separated from one another, and a substructure was observed for the other studied areas. An isolation-by-distance pattern was found among, but not within, the three main population groups. This substructure is mediated mainly by dispersal along the coastline and some resistance to larval movement through the open sea. Despite the low dispersal ability and high self-recruitment rate of C. caespitosa, casual dispersive events between regions seem to be enough to maintain the species' considerable genetic diversity. Understanding the population connectivity and structure of this endangered scleractinian coral allows for more informed conservation decision making. [ABSTRACT FROM AUTHOR]

An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava , a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling. [ABSTRACT FROM AUTHOR]

Background: Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods: In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results: Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions: This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region. [ABSTRACT FROM AUTHOR]

Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p <.001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p <.001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (Radj2 = 0.133, p =.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p <.001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (Radj2 = 0.692–0.763; p <.050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource. [ABSTRACT FROM AUTHOR]

Context: Spatially heterogeneous oceanographic properties such as currents, waves, and biogeochemical gradients control the movement of gametes and larvae of marine species. However, it is poorly understood how such spatial dynamics may shape the genetic connectivity, diversity, and structure of marine populations. Objectives: We applied a seascape genetics framework to evaluate the relationships between marine environmental factors and gene flow among populations of the endangered Mediterranean pillow coral (Cladocora caespitosa). Methods: We modelled gene flow among locations in the Adriatic and northern Ionian Seas as a function of sea surface temperature, salinity, currents and geographic distance. Isolation by distance and isolation by resistance hypotheses were then compared using model optimization in a generalized linear mixed effects modelling framework. Results: Overall genetic differentiation among locations was relatively low (FST = 0.028). We identified two genetic groups, with the northernmost location segregating from the rest of the locations, although some admixture was evident. Almost 25% of the individuals analysed were identified as putative migrants and a potential barrier to gene flow was identified between the northern and central-southern basins. The best gene flow models predicted that genetic connectivity in this species is primarily driven by the movement along the coastlines and sea surface currents. Conclusions: A high percentage of self-recruitment and relatively low migration rates has been detected in the studied populations of C. caespitosa. Its fragmented distribution along the coast can be predicted by stepping-stone oceanographic transport by coastal currents among suitable habitat patches. [ABSTRACT FROM AUTHOR]

Abstract: Marine populations are typically characterized by weak genetic differentiation due to the potential for long‐distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (FST = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R2 = .49) than geographic distance (IBD) (R2 = .18), and directional processes played an important role in shaping fine‐scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species. [ABSTRACT FROM AUTHOR]

The silky shark, Carcharhinus falciformis, is a large-bodied, oceanic-coastal, epipelagic species found worldwide in tropical and subtropical waters. Despite its commercial importance, concerns about overexploitation, and likely ecological significance of this shark as an upper trophic-level predator, understanding of its population dynamics remains unclear for large parts of its distribution. We investigated the genetic diversity, population structure and demographic history of the silky shark along the western Atlantic Ocean based on the use of 707 bp of the mitochondrial DNA control region (mtCR). A total of 211 silky sharks were sampled, originating from five areas along the western Atlantic Ocean. The mitochondrial sequences revealed 40 haplotypes, with overall haplotype and nucleotide diversities of 0.88 (± 0.012) and 0.005 (± 0.003), respectively. The overall population structure was significantly different among the five western Atlantic Ocean regions. Phylogenetic analysis of mtCR sequences from globally sourced silky shark samples revealed two lineages, comprising a western Atlantic lineage and western Atlantic—Indo-Pacific lineage that diverged during the Pleistocene Epoch. In general, tests for the demographic history of silky sharks supported a population expansion for both the global sample set and the two lineages. Although our results showed that silky sharks have high genetic diversity, the current high level of overexploitation of this species requires long-term, scientifically informed management efforts. We recommend that fishery management and conservation plans be done separately for the two western Atlantic matrilineal populations revealed here. [ABSTRACT FROM AUTHOR]

Background: Intraspecific variability is seen as a central component of biodiversity. We investigated genetic differentiation, contemporary patterns of demographic connectivity and intraspecific variation of adaptive behavioural traits in two lineages of an intertidal mussel (Perna perna) across a tropical/subtropical biogeographic transition. Results: Microsatellite analyses revealed clear genetic differentiation between western (temperate) and eastern (subtropical/ tropical) populations, confirming divergence previously detected with mitochondrial (COI) and nuclear (ITS) markers. Gene flow between regions was predominantly east-to-west and was only moderate, with higher heterozygote deficiency where the two lineages co-occur. This can be explained by differential selection and/or oceanographic dynamics acting as a barrier to larval dispersal. Common garden experiments showed that gaping (periodic closure and opening of the shell) and attachment to the substratum differed significantly between the two lineages. Western individuals gaped more and attached less strongly to the substratum than eastern ones. Conclusions: These behavioural differences are consistent with the geographic and intertidal distributions of each lineage along sharp environmental clines, indicating their strong adaptive significance. We highlight the functional role of diversity below the species level in evolutionary trends and the need to understand this when predicting biodiversity responses to environmental change. [ABSTRACT FROM AUTHOR]

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster ( Panulirus interruptus) and find slight, but significant global population differentiation in mt DNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites ( FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo- F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance ( P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites ( Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity ( R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. [ABSTRACT FROM AUTHOR]

Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography. [ABSTRACT FROM PUBLISHER]