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Aim: Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management. Location: European seas of the northeast Atlantic and Mediterranean. Taxa: European clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily fished decapods with extensive dispersal potential. Methods: By RAD‐sequencing 214 H. gammarus from 32 locations and 349 P. elephas from 15 locations, we isolated 6340 and 7681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity. Results: We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region. Main Conclusions: We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographical heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans. [ABSTRACT FROM AUTHOR]

Twelve pairs of sister taxa in the speciose rockfish genus, Sebastes, overlap coastal distributions but are bathymetrically segregated. These pairs are ideal for comparative studies to understand how life-history traits, historical events, and environment interact to produce population genetic structure. Black rockfish, Sebastes melanops, forms one such pair. Its sister species, yellowtail rockfish (Sebastes flavidus), shows a genetic cline likely influenced by a dispersal barrier at Cape Mendocino, CA and northward range expansion. Due to geographic overlap and close systematic relationship, we predicted black rockfish was influenced by similar evolutionary processes and thus would show genetic pattern concordance with yellowtail rockfish. We analyzed ~ 1000 black rockfish from 22 sites spanning the species' range to test the null hypothesis of no structure, using the same markers that characterized yellowtail rockfish (i.e., 812 bp of the mitochondrial cytochrome b gene and six microsatellite loci). We reject the null hypothesis based on existence of at least three populations and microsatellite genetic divergence that separates the Alaskan and Continental U.S. populations (FCT = 0.021, p << 0.001), and a mitochondrial genetic cline near Cape Mendocino (FCT = 0.132, p < 0.01). We also found single collections genetically divergent from neighboring collections. Like yellowtail rockfish, oceanographic dispersal barriers and northern range expansion were inferred to influence black rockfish, however, unlike yellowtail rockfish, Cape Mendocino did not split the range into two stocks and was, therefore, inferred to be a less severe barrier. We hypothesize a higher frequency of extinction/recolonization events in black rockfish populations may have led to more complex genetic structure. [ABSTRACT FROM AUTHOR]

Understanding connectivity over different spatial and temporal scales is fundamental for managing of ecological systems. However, controversy exists for wintertime ecological connectivity between the Yangtze River Estuary (YRE) and inner southwestern Yellow Sea. Here, we investigated ecological connectivity between the YRE and inner southwestern Yellow Sea in wintertime by precisely pinpointing the source of the newly colonized populations of a winter‐spawning rocky intertidal invertebrate, Littorina brevicula (Philippi, 1844), on artificial structures along the coast of the Yangtze River Delta (YRD) using mitochondrial ND6 sequences and microsatellite data. Clear phylogeographic and genetic differentiation were detected between natural rocky populations south and north of the YRE, which resulted from the lack of hard substrate for rocky invertebrates in the large YRD coast. For the newly colonized populations on the coast of YRD, most individuals (98%) to the south of ~33.5°N were from natural rocky populations to the south of the YRE and most of those (94%) to the north of ~33.5°N were from the northern natural rocky populations, which demonstrated strong ecological connectivity between the inner southwestern Yellow Sea and the YRE in winter time. We presented the first genetic evidence that demonstrated a northward wintertime coastal current in the inner southwestern Yellow Sea, and precisely illustrated the boundary of the coastal current recently proposed by numerical experiment. These results indicated that the YRE serves as an important source of materials and energy for the inner southwestern Yellow Sea in winter, which can be crucial for the function of the Yellow Sea ecosystem. [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]

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]

The reef fauna connectivity of the West Indian Ocean ( WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra ( Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio- Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents. [ABSTRACT FROM AUTHOR]

Aim Pleistocene glacial cycles reduced global sea level by up to 130 m below present levels. These changes had profound impacts on coastal marine life, including a reduction of habitable area, changes in ocean currents, and shifts in water column thermal dynamics. We provide a comprehensive review of the impact of glacial sea-level changes during the Pleistocene on tropical coastal marine life and a set of maps showing how coastlines worldwide changed during periods of low sea levels. Location We focused on coastal marine taxa within tropical latitudes, with deeper coverage of the world's major coral reef biogeographical provinces. Methods We examined recent and historical literature that alluded to the effects of Pleistocene sea-level fluctuations in a variety of common marine clades. Data for shelf habitat area and map construction were obtained from the NOAA ETOPO1 database, with final manipulations carried out in Adobe Illustrator CS6. Results Drops in sea level led to a decrease in available coastal habitat and fragmented populations in many taxa, potentially resulting in high population genetic structuring. Habitable shelf area during sea-level lows was reduced as much as 92% from present-day values in some regions. Genetic evidence of population bottlenecks can be seen in many coastal marine taxa worldwide. Main conclusions Pleistocene sea-level fluctuations seem to be linked to population bottlenecks worldwide, and influenced connections among populations separated by barriers that are affected by sea levels. Despite decreased habitat availability, very few species became extinct, and several species may have been formed due to restrictions in water (and consequently larval) flow between regions that are now connected. A variety of interdisciplinary studies have significantly increased our understanding of how Pleistocene sea-level changes have shaped the marine landscape that we see today. [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]

Siphon limpets are an ecologically important component of the intertidal zone of Australia's temperate coast. Using 1/16 of a shotgun pyrosequencing plate, a set of 14 microsatellites was developed for the Van Diemen's siphon limpet ( Siphonaria diemenensis). From 2,744 sequences that contained putative microsatellite motifs, 18 were selected for primer design and tested for amplification. Fourteen microsatellite loci were successfully genotyped in 48 specimens of S. diemenensis from two localities. The number of alleles per locus varied from 5 to 35 (mean = 14.6) and the observed heterozygosity ranged from 0.53 to 0.90 (mean = 0.77). Only one locus showed significant deviation from Hardy-Weinberg equilibrium, probably due to null alleles. No linkage disequilibrium between pairs of loci was detected. Connectivity and seascape genetic studies on siphon limpets using the markers reported here should provide important information for management of temperate Australian marine biodiversity. [ABSTRACT FROM AUTHOR]