Ocean circulation model predicts high genetic structure observed in a long‐lived pelagic developer

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.     

Self‐recruitment and sweepstakes reproduction amid extensive gene flow in a coral‐reef fish

Identifying patterns of larval dispersal within marine metapopulations is vital for effective fisheries management, appropriate marine reserve design, and conservation efforts. We employed genetic markers (microsatellites) to determine dispersal patterns in bicolour damselfish (Pomacentridae: Stegastes partitus). Tissue samples of 751 fish were collected in 2004 and 2005 from 11 sites encompassing the Exuma Sound, Bahamas. Bayesian parentage analysis identified two parent–offspring pairs, which is remarkable given the large population sizes and 28 day pelagic larval duration of bicolour damselfish. The two parent–offspring pairs directly documented self‐recruitment at the two northern‐most sites, one of which is a long‐established marine reserve. Principal coordinates analyses of pair‐wise relatedness values further indicated that self‐recruitment was common in all sampled populations. Nevertheless, measures of genetic differentiation (F_ST) and results from assignment methods suggested high levels of gene flow among populations. Comparisons of heterozygosity and relatedness among samples of adults and recruits indicated spatially and temporally independent sweepstakes events, whereby only a subset of adults successfully contribute to subsequent generations. These results indicate that self‐recruitment and sweepstakes reproduction are the predominant, ecologically‐relevant processes that shape patterns of larval dispersal in this system.     

Mitochondrial DNA and nuclear microsatellites reveal high diversity and genetic structure in an avian top predator,the white‐tailed sea eagle,in central Europe

We analysed 123 white‐tailed sea eagles (Haliaeetus albicilla) from (primarily central) Europe with respect to variability and differentiation based on 499 bp of the mitochondrial control region and genotypes at seven unlinked nuclear microsatellites. Variability was high (overall expected heterozygosity, haplotype and nucleotide diversity being 0.70, 0.764 and 0.00698, respectively) and both marker systems showed a subdivision into two main genetic clusters (microsatellites) or haplogroups (mtDNA). In line with earlier analyses focusing on populations from northern and eastern Europe, as well as from Asia, we found a high level of admixture in Europe and no signs of a bottleneck – despite a severe decline of white‐tailed sea eagle populations during the 20^th century. Europe is thus a global stronghold for this species not only with respect to the number of breeding pairs but also regarding the proportion of species‐wide genetic diversity. Our dense sampling revealed a possibly clinal variation within central Europe from north‐west to south‐east that was reflected by the distribution of mtDNA haplotypes as well as the two microsatellite‐based clusters. This population differentiation in central Europe probably originated from a geographically structured postglacial colonization and was later enhanced by recent demographic fluctuations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 727–737.     

Widespread gene flow and high genetic variability in populations of water voles Arvicola terrestris in patchy habitats

Theory predicts that the impact of gene flow on the genetic structure of populations in patchy habitats depends on its scale and the demographic attributes of demes (e.g. local colony sizes and timing of reproduction), but empirical evidence is scarce. We inferred the impact of gene flow on genetic structure among populations of water voles Arvicola terrestris that differed in average colony sizes, population turnover and degree of patchiness. Colonies typically consisted of few reproducing adults and several juveniles. Twelve polymorphic microsatellite DNA loci were examined. Levels of individual genetic variability in all areas were high ( H _O= 0.69–0.78). Assignments of juveniles to parents revealed frequent dispersal over long distances. The populations showed negative F _IS values among juveniles, F _IS values around zero among adults, high F _ST values among colonies for juveniles, and moderate, often insignificant, F _ST values for parents. We inferred that excess heterozygosity within colonies reflected the few individuals dispersing from a large area to form discrete breeding colonies. Thus pre-breeding dispersal followed by rapid reproduction results in a seasonal increase in differentiation due to local family groups. Genetic variation was as high in low-density populations in patchy habitats as in populations in continuous habitats used for comparison. In contrast to most theoretical predictions, we found that populations living in patchy habitats can maintain high levels of genetic variability when only a few adults contribute to breeding in each colony, when the variance of reproductive success among colonies is likely to be low, and when dispersal between colonies exceeds nearest-neighbour distances.     

Fine‐scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific

Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine‐scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine‐scale genetic patterns among localities.     

Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios

The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish ( Amphiprion polymnus ) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2–6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population ( F _ST = 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.     

Genetic evidence for high propagule pressure and long‐distance dispersal in monk parakeet (Myiopsitta monachus) invasive populations

The monk parakeet (Myiopsitta monachus) is a successful invasive species that does not exhibit life history traits typically associated with colonizing species (e.g., high reproductive rate or long‐distance dispersal capacity). To investigate this apparent paradox, we examined individual and population genetic patterns of microsatellite loci at one native and two invasive sites. More specifically, we aimed at evaluating the role of propagule pressure, sexual monogamy and long‐distance dispersal in monk parakeet invasion success. Our results indicate little loss of genetic variation at invasive sites relative to the native site. We also found strong evidence for sexual monogamy from patterns of relatedness within sites, and no definite cases of extra‐pair paternity in either the native site sample or the examined invasive site. Taken together, these patterns directly and indirectly suggest that high propagule pressure has contributed to monk parakeet invasion success. In addition, we found evidence for frequent long‐distance dispersal at an invasive site (～100 km) that sharply contrasted with previous estimates of smaller dispersal distance made in the native range (～2 km), suggesting long‐range dispersal also contributes to the species’ spread within the United States. Overall, these results add to a growing body of literature pointing to the important role of propagule pressure in determining, and thus predicting, invasion success, especially for species whose life history traits are not typically associated with invasiveness.     

Divergence,gene flow,and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison‐dart frogs

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here, we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighbouring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between ‘leapfroging’ taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome‐averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.     

Congruent phylogeographic patterns in a young radiation of live‐bearing marine snakes: Pleistocene vicariance and the conservation implications of cryptic genetic diversity

Aim

To investigate phylogeographic patterns among and within co‐occurring sea snake species from Australia's endemic viviparous Aipysurus lineage, which includes critically endangered species, and evaluate the conservation implications of geographically structured patterns of genetic divergence and diversity.

Location

Australia's tropical shallow water marine environments spanning four regions: Great Barrier Reef (GBR), Gulf of Carpentaria (GoC), Timor Sea (TS) and coastal WA (WAC).

Methods

Samples from >550 snakes representing all nine nominal Aipysurus group species were obtained from throughout their known Australian ranges. Coalescent phylogenetic analyses and Bayesian molecular dating of mitochondrial DNA, combined with Bayesian and traditional population genetic analyses of 11 microsatellite loci, were used to evaluate genetic divergence and diversity.

Results

Mitochondrial DNA revealed highly congruent phylogeographic breaks among co‐occurring species, largely supported by nuclear microsatellites. For each species, each region was characterized by a unique suite of haplotypes (phylogroups). Divergences between the TS, GoC and/or GBR were invariably shallow and dated as occurring 50,000–130,000 years ago, coinciding with the cyclic Pleistocene emergence of the Torres Strait land bridge. By contrast, sea snakes from coastal WA were consistently highly divergent from other regions and dated as diverging 178,000–526,000 years ago, which was not associated with any known vicariant events.

Main Conclusions

Previously unappreciated highly divergent sea snake lineages in coastal WA potentially represent cryptic species, highlighting this region as a high‐priority area for conservation. The cyclic emergence of the Torres Strait land bridge is consisted with observed divergences between the TS, GoC and/or GBR; however, processes involved in the earlier divergences involving the WAC remain to be determined. The observed strong population genetic structures (as surrogates for dispersal) indicate that sea snakes have limited potential to reverse population declines via replenishment from other sources over time frames relevant to conservation.

     

Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific

The sea cucumber, Holothuria nobilis, has a long-lived planktotrophic larvae, and previous allozyme surveys have suggested that high dispersal is realized. In contrast, recent ecological studies indicate that dispersal is low. To reconcile these data, and to investigate the evolution of this Indo-Pacific species, we screened geographical variation in 559 bp of a mitochondrial gene (COI) in 360 samples from the Australasian region and La Réunion. Sequences from La Réunion differed by > 7% from others and may constitute another species. Haplotype diversity in other samples was high (0.942, SD = 0.007), but haplotypes were closely related (mean nucleotide diversity: 0.0075, SD = 0.0041). AMOVA, pairwise FST values and exact tests did not detect significant population structure. Nested clade analysis showed that one of two main clades was over-represented in west Australia, whereas the other was more common in the northern Great Barrier Reef. Isolation-by-distance was identified as the main determinant of population structure at several clade levels. Contiguous range expansion was inferred for evolutionary older clade levels and this may correspond to a late Pleistocene (88 000-193 000 years ago) population expansion inferred from haplotype mismatch distributions. Thus, the population genetic structures detected are likely to be formed prior to the last ice age, with some indications for high dispersal on shorter time scales.     

Intraspecific genetic structure,divergence and high rates of clonality in an amphi‐Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species’ distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria–Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo‐Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations’ genetic divergence could be observed between some populations.     

Intra‐ and interpopulation genetic differentiation and gene flow in a group of isolated populations of Bradybaena fruticum (O. F. Müller, 1774) in South Poland

Intra‐ and interpopulation variation was studied, by means of cellulose acetate allozyme electrophoresis, on 16 populations of helicoid snail Bradybaena fruticum (O. F. Müller, 1774) in South Poland. Four enzyme systems, coded by seven loci, were analysed. Calculated with Fisher's technique and Ohta's D‐statistics, four cases of linkage disequilibrium were detected, reflecting population subdivision. The mean number of alleles per locus equalled 2.16 and the mean expected heterozygosity was 0.287. Exact multipopulation and multilocus tests for Hardy–Weinberg equilibrium indicated a statistically significant homozygote excess in all the loci and all populations but three. Each population, however, was at Hardy–Weinberg equilibrium for most loci, though the values of f (F_IS) were usually high. Homozygote excess was ascribed partly to inbreeding and partly to Wahlund's effect (spatial subdivision of population; at least two cohorts of adult, reproducing snails), disrupting selection in this polymorphic species not excluded. F‐statistics showed relatively low values of θ (F_ST ; mean for all loci = 0.224) and those of Nm usually below 1 (mean 0.866). Pairwise values of either θ or Cavalli‐Sforza and Edwards arc distance were statistically significantly associated with geographic distances. Contrary to this, no geographic pattern of interpopulation differences was detected by correspondence analysis on allele frequencies, non‐linear multidimensional scaling, UPGMA clustering or neighbour‐joining trees constructed on θ and Cavalli‐Sforza and Edwards arc distance. Accordingly, some most distant populations were more similar to one another than the close ones.     

A synthesis of genetic connectivity in deep‐sea fauna and implications for marine reserve design

With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep‐sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep‐sea taxa are hypothesized to disperse greater distances than shallow‐water taxa, which implies that reserves would need to be larger in size and networks could be more widely spaced; however, this paradigm has not been tested. We compiled population genetic studies of deep‐sea fauna and estimated dispersal distances for 51 studies using a method based on isolation‐by‐distance slopes. Estimates of dispersal distance ranged from 0.24 km to 2028 km with a geometric mean of 33.2 km and differed in relation to taxonomic and life‐history factors as well as several study parameters. Dispersal distances were generally greater for fishes than invertebrates with the Mollusca being the least dispersive sampled phylum. Species that are pelagic as adults were more dispersive than those with sessile or sedentary lifestyles. Benthic species from soft‐substrate habitats were generally less dispersive than species from hard substrate, demersal or pelagic habitats. As expected, species with pelagic and/or feeding (planktotrophic) larvae were more dispersive than other larval types. Many of these comparisons were confounded by taxonomic or other life‐history differences (e.g. fishes being more dispersive than invertebrates) making any simple interpretation difficult. Our results provide the first rough estimate of the range of dispersal distances in the deep sea and allow comparisons to shallow‐water assemblages. Overall, dispersal distances were greater for deeper taxa, although the differences were not large (0.3–0.6 orders of magnitude between means), and imbalanced sampling of shallow and deep taxa complicates any simple interpretation. Our analyses suggest the scales of dispersal and connectivity for reserve design in the deep sea might be comparable to or slightly larger than those in shallow water. Deep‐sea reserve design will need to consider the enormous variety of taxa, life histories, hydrodynamics, spatial configuration of habitats and patterns of species distributions. The many caveats of our analyses provide a strong impetus for substantial future efforts to assess connectivity of deep‐sea species from a variety of habitats, taxonomic groups and depth zones.     

Spatiotemporal analyses suggest the role of glacial history and the ice‐free corridor in shaping American badger population genetic variation

Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star‐like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice‐free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range‐wide patterns and identifies unique genetic units that can likely be used to inform conservation of at‐risk populations at the northern periphery.     

Genetic assignment of recruits reveals short‐ and long‐distance larval dispersal in Pocillopora damicornis on the Great Barrier Reef

Understanding connectivity of coral populations among and within reefs over ecologically significant timescales is essential for developing evidence‐based management strategies, including the design of marineprotected areas. Here, we present the first assessment of contemporary connectivity among populations of two Molecular Operational Taxonomic Units (MOTUs) of the brooding coral Pocillopora damicornis. We used individual‐based genetic assignment methods to identify the proportions of philopatric and migrant larval recruits, settling over 12 months at sites around Lizard Island (northern Great Barrier Reef [GBR]) and over 24 months at sites around the Palms Islands (central GBR). Overall, we found spatially and temporally variable rates of self‐recruitment and dispersal, demonstrating the importance of variation in local physical characteristics in driving dispersal processes. Recruitment patterns and inferred dispersal distances differed between the two P. damicornis MOTUs, with type α recruits exhibiting predominantly philopatric recruitment, while the majority of type β recruits were either migrants from identified putative source populations or assumed migrants based on genetic exclusion from all known populations. While P. damicornis invests much energy into brooding clonal larvae, we found that only 15% and 7% of type α and type β recruits, respectively, were clones of sampled adult colonies or other recruits, challenging the hypothesis that reproduction is predominantly asexual in this species on the GBR. We explain high rates of self‐recruitment and low rates of clonality in these MOTUs by suggesting that locally retained larvae originate predominantly from spawned gametes, while brooded larvae are mainly vagabonds.