Silene rothmaleri P. Silva (Caryophyllaceae), a rare, fragmented but genetically diverse species

Silene rothmaleri is an endemic Portuguese species considered extinct until 1992, when it was rediscovered in the wild with a highly fragmented distribution. These rare plants occur along the southwestern Portuguese coast in small populations, which in addition to phenological differences that occur along the north–south gradient could create a pattern of genetic isolation. To evaluate the degree of genetic diversity and estimate the relationship between population fragmentation and genetic variability, we analysed the five known populations of S. rothmaleri using random amplified polymorphic DNA. Degree of polymorphism and Shannon Index of phenotypic diversity revealed high levels of diversity, found mainly within populations. PCo and cluster analysis revealed a distinct north–south cline, which was confirmed by spatial autocorrelation (Mantel) analysis. This indicates the existence of gene flow between small nearby populations and its insufficiency between widely separated populations. Levels of gene flow (Nm) estimated from the Shannon Index reveal a pattern consistent with a larger past distribution that went through a period of contraction and lack of gene flow followed by population differentiation. The central and largest population probably acts as a core of genetic variability inherited as a relict from a larger and more diverse ancestral population.     

Strong genetic impoverishment from the centre of distribution in southern Europe to peripheral Baltic and isolated Scandinavian populations of the pearly heath butterfly

Aim Climatic changes and fluctuations in the past have strongly influenced the distribution of animal and plant species. Such fluctuations are also reflected in the patterns of genetic diversity on both local and global scales. The genetic pattern of the pearly heath butterfly, Coenonympha arcania, was used to evaluate the genetic differentiation of isolated (in north‐western Europe), peripheral (in north‐eastern Europe) and central (in southern Europe) populations in the context of post‐glacial distributional changes of the species. Location Europe (Sweden, Germany, the Baltic states, Italy, Slovenia, Hungary, Romania, Bulgaria). Thus, samples were collected from large parts of the species’ distribution representing the three categories mentioned above. Methods We analysed 18 loci of 569 individuals from 28 populations by allozyme electrophoresis. We used both individual‐based and population‐based analyses, including F‐statistics, various clustering methods and Markov chain Monte Carlo simulations. Results All loci, except Fum, were polymorphic. The mean F_ST for all samples was 0.18. The mean genetic distance among populations was 0.046. Two major genetic lineages were distinguished. Populations from the centre of the distributional range in southern Europe and the northern periphery of the distributional range differed significantly in their level of genetic variability. The central populations of south‐eastern Europe showed high levels of genetic diversity and no differentiation among populations. Main conclusions Most probably the two major genetic lineages evolved during glacial isolation in two disjunct Mediterranean refugia. The lack of genetic differentiation across south‐eastern Europe implies a continuous Würm ice age distribution in this area, thus supporting the functional existence of steppe forests throughout this region. The peripheral‐isolated populations in Sweden seem to have suffered from one or more severe bottlenecks, resulting in substantial genetic impoverishment. The peripheral‐connected eastern Baltic populations, on the other hand, are affected by post‐glacial and possibly recurrent gene flow from more central parts of the distribution.     

Population structure of the Atlantic sand fiddler crab Uca pugilator along the eastern coast of US revealed by molecular data

The Atlantic sand fiddler crab Uca pugilator is an extremely abundant crab found along the eastern coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30-90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However, a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U.pugilator and to determine whether these differences may have a genetic basis. The population structure of the fiddler crab was analyzed using 472 individuals collected from 12 sites along the eastern coast. PCR-based single stand conformation polymorphism (SSCP) was used to investigate between-site variation in the mitochondrial 16S rRNA gene of these individuals. Analysis of genetic variation indicated frequent gene flow between nearby localities, but much reduced levels between populations separated by larger geographic distances. Thus, despite the potential for high dispersal by planktonic larvae, population differentiation and isolation by distance is evident between northern and southern populations of U.pugilator. A high amount of genetic differentiation (FST=0.3468) was found between northern and southern regions suggesting that the morphological and behavioral differences between these two regions have a genetic basis and may represent subspecies [Current Zoology 55(2):150-157,2009].     

Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction‐site‐associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome‐wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype–environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.     

Functional significance of phylogeographic structure in a toxic benthic marine microbial eukaryote over a latitudinal gradient along the East Australian Current

Genetic diversity in marine microbial eukaryotic populations (protists) drives their ecological success by enabling diverse phenotypes to respond rapidly to changing environmental conditions. Despite enormous population sizes and lack of barriers to gene flow, genetic differentiation that is associated with geographic distance, currents, and environmental gradients has been reported from planktonic protists. However, for benthic protists, which have reduced dispersal opportunities, phylogeography and its phenotypic significance are little known. In recent years, the East Australian Current (EAC) has intensified its southward flow, associated with the tropicalization of temperate waters. Benthic harmful algal species have been increasingly found in south‐eastern Australia. Yet little is known about the potential of these species to adapt or extend their range in relation to changing conditions. Here, we examine genetic diversity and functional niche divergence in a toxic benthic dinoflagellate, Ostreopsis cf. siamensis, along a 1,500 km north–south gradient in southeastern Australia. Sixty‐eight strains were established from eight sampling sites. The study revealed long‐standing genetic diversity among strains established from the northern‐most sites, along with large phenotypic variation in observed physiological traits such as growth rates, cell volume, production of palytoxin‐like compounds, and photophysiological parameters. Strains from the southern populations were more uniform in both genetic and functional traits, and have possibly colonized their habitats more recently. Our study reports significant genetic and functional trait variability in a benthic harmful algal species, indicative of high adaptability, and a possible climate‐driven range extension. The observed high trait variation may facilitate development of harmful algal blooms under dynamic coastal environmental conditions.     

Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour‐joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within‐prairie genetic diversity (92%). Using Bayenv 2, 14 top‐ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScan F_ST outliers were in common with Bayenv 2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.     

Population structure of Squatina guggenheim (Squatiniformes,Squatinidae) from the south‐western Atlantic Ocean

Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most‐widespread endemic species inhabiting coastal ecosystems in the south‐western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south‐west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its‐2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent‐based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long‐term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south‐west Atlantic Ocean shark, given its longevity and low reproductive potential.     

Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced‐representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex‐specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north–south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.     

The distribution of the ectoparasite fauna of Sebastes capensis from the southern hemisphere does not correspond with zoogeographical provinces of free-living marine animals

Aim We examined the ectoparasite fauna of Sebastes capensis over almost all its geographical distribution range (Chilean, Argentinean and South African coasts) to determine (1) whether the ectoparasites of this host show a zoogeographical pattern and, if so, (2) how this pattern is related to known zoogeographical patterns for free‐living organisms. Location Fish were captured from 20, 24, 30, 33, 36, 40, 45 and 52° S along the Chilean coast; 11° S on the Peruvian coast; 43° S on the Argentina coast; and 34° S on the South African coast. Methods From April to September 2003 and from April to August 2004, 626 fish were captured. The parasites were collected using standard parasitological techniques. At the component community level, zoogeographical distribution patterns were evaluated using cluster analysis. At the infra‐community level, patterns of similarity in parasite composition among localities were investigated with multivariate discriminant analyses. Results The ectoparasite fauna of S. capensis consists of six species distributed along the whole of the Chilean coast. Four other species are distributed only within the transitional zone between the northern warm temperate region (Peruvian faunistic province), extending from Peru to the northern Chilean coast up to c. 30° S, and the cold temperate region (Magellanic faunistic province). The component communities from latitudes 30 to 40° S showed higher ectoparasite species richness, while localities on the margins of the geographical range showed lower species richness. Cluster analysis indicated a grouping of localities consistent with the transitional zone. Argentina and South Africa always emerged as separate localities. Main conclusions The ectoparasite communities of S. capensis do not follow a distributional pattern concordant with the known biogeographical zones for invertebrates and/or fish along the south‐eastern Pacific. Therefore their ectoparasite fauna is not useful as a zoogeographical indicator, although it does allow us to distinguish the transitional zone of the south‐eastern Pacific. On a more extended geographical scale, it is possible to distinguish the ectoparasite communities of S. capensis in the south‐eastern Pacific (as a whole) from those of Argentina and South Africa.     

Tracing geographical patterns of population differentiation in a widespread mangrove gastropod: genetic and geometric morphometrics surveys along the eastern African coast

In the present study, we assessed the inter‐ and intrapopulation genetic and morphological variation of Cerithidea decollata along the eastern coast of Africa. The population structure of C. decollata along the latitudinal gradient was examined by sequencing 420 bp of the mitochondrial cytochrome c oxidase I (COI) gene in 172 snails from 29 sites, in a combined analysis with geometric morphometrics in 1799 snails from 32 sites. Analysis of molecular variance and spatial analysis of molecular variance showed a moderate spatial population differentiation from Kenya to the Republic of South Africa, suggesting genetic divergence between the northern, central, and southern regions. This structure appears to be the result of life‐history traits combined with oceanographic features. Haplotype network and mismatch analysis suggest a recent population expansion during the Holsteinian interglacial period in the northern region and several colonization events in the central and southern regions. The morphometric approach suggests that morphological variation in shell shape is somewhat independent of the genetic divergence, revealing an overlap of shape across the latitudinal gradient but significant differences among‐population at a local level. This may indicate that similar ecological pressures are acting along the coast, leading to the occurrence of similar morphological characters. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 647–663.     

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.     

The role of altitude and associated habitat stability in determining patterns of population genetic structure in two species of Atalophlebia (Ephemeroptera: Leptophlebiidae)

1. Previous studies have identified lowland areas as barriers to gene flow (dispersal) between distinct mountain ranges in montane species of aquatic insects. In this study, we investigated the population genetic structure of two closely related Atalophlebia (mayfly) species inhabiting lowland areas of south‐east Queensland, Australia, with the expectation of widespread gene flow throughout the low‐altitude environment and associated homogeneous genetic structure. 2. In particular, we asked whether species with lower‐altitude distributions demonstrate greater spatial distribution of mtDNA (COI) alleles than the upland species studied previously. This pattern would be expected if good dispersal ability is associated with population persistence in these drought‐prone habitats. 3. The two species demonstrated contrasting genetic population structure. Atalophlebia sp. AV13 D revealed strong population structure, with populations on each side of the low‐altitude area isolated from each other for a long time (c.350 kya), and the presence of an isolation‐by‐distance pattern over relatively small geographical distances (<40 km). In contrast, Atalophlebia sp. AV13 A was panmictic at the scale investigated (≤160 km), with no history of past population fragmentation. 4. Examination of sample distribution along the altitudinal gradient reveals that Atalophlebia sp. AV13 D may have a more upland distribution (associated with greater habitat stability) than previously supposed, while Atalophlebia sp. AV13 A inhabits more xeric lowland areas, where freshwater habitats are less stable. We consequently hypothesise that these contrasting genetic population structures result from differences in habitat stability along the altitudinal gradient, only species with good dispersal ability being able to persist in unstable habitats. These findings may be applicable to other regions of the globe where habitat instability is associated with altitudinal gradients.     

Spatio‐temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south‐eastern Pacific Ocean and potential implications for its fishery management

The genetic population structure and genetic diversity of yellowtail kingfish Seriola lalandi from the coastal south‐eastern Pacific Ocean (SEP) were evaluated at spatiotemporal scale in order to understand the ecology of this species. Between 2012 and 2015, temporal and spatial population genetic structure and a low genetic diversity were detected in S. lalandi from SEP. These results suggest that S. lalandi specimens arriving annually from offshore to the SEP coast could come from at least two genetically distinct populations, revealing a particular life strategy (i.e. reproductive or habitat segregation) for this fish species. Therefore, the SEP coast might constitute a point of population mixing for this species. Additionally, the low genetic diversity of S. lalandi in the SEP could be a result of a founder effect or overfishing. Regardless of the process explaining the genetic diversity and structure of S. lalandi in this geographical area, this new information should be considered in order to implement successful fishery management of this resource in the South Pacific.     

Could specialization to cold‐water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue‐footed booby,Sula nebouxii

Aim We assessed population differentiation and gene flow across the range of the blue‐footed booby (Sula nebouxii) (1) to test the generality of the hypothesis that tropical seabirds exhibit higher levels of population genetic differentiation than their northern temperate counterparts, and (2) to determine if specialization to cold‐water upwelling systems increases dispersal, and thus gene flow, in blue‐footed boobies compared with other tropical sulids. Location Work was carried out on islands in the eastern tropical Pacific Ocean from Mexico to northern Peru. Methods We collected samples from 173 juvenile blue‐footed boobies from nine colonies spanning their breeding distribution and used molecular markers (540 base pairs of the mitochondrial control region and seven microsatellite loci) to estimate population genetic differentiation and gene flow. Our analyses included classic population genetic estimation of pairwise population differentiation, population growth, isolation by distance, associations between haplotypes and geographic locations, and analysis of molecular variance, as well as Bayesian analyses of gene flow and population differentiation. We compared our results with those for other tropical seabirds that are not specialized to cold‐water upwellings, including brown (Sula leucogaster), red‐footed (S. sula) and masked (S. dactylatra) boobies. Results Blue‐footed boobies exhibited weak global population differentiation at both mitochondrial and nuclear loci compared with all other tropical sulids. We found evidence of high levels of gene flow between colonies within Mexico and between colonies within the southern portion of the range, but reduced gene flow between these regions. We also found evidence for population growth, isolation by distance and weak phylogeographic structure. Main conclusions Tropical seabirds can exhibit weak genetic differentiation across large geographic distances, and blue‐footed boobies exhibit the weakest population differentiation of any tropical sulid studied thus far. The weak population genetic structure that we detected in blue‐footed boobies may be caused by increased dispersal, and subsequently increased gene flow, compared with other sulids. Increased dispersal by blue‐footed boobies may be the result of the selective pressures associated with cold‐water upwelling systems, to which blue‐footed boobies appear specialized. Consideration of foraging environment may be particularly important in future studies of marine biogeography.     

Gene flow connects coastal populations of a habitat specialist,the Clapper Rail Rallus crepitans

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographical range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of the USA, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks and a weak pattern of genetic differentiation that increased with geographical distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the Atlantic coast of the USA, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioural factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.     

Significant population structure and asymmetric gene flow patterns amidst expanding populations of Clinus cottoides (Perciformes,Clinidae): application of molecular data to marine conservation planning in South Africa

Clinus cottoides is a fish endemic to the coast of South Africa, predominantly inhabiting rock pools. All South African clinids are viviparous, but probably breed throughout the year; as such, their dispersal may be limited, unlike species with pelagic larval stages. We analysed 343 fish from 14 localities on the west, south and east coasts using two mitochondrial genes and the second intron of the S7 ribosomal gene. Mitochondrial DNA analyses recovered significant genetic differentiation between fish populations from the east coast and other sampling locations, with a second break found between Gansbaai and Cape Agulhas on the south coast. Nuclear DNA recovered shallower, but significant, levels of population structure. Coalescent analyses suggested remarkably asymmetrical gene flow between sampling locations, suggesting that the cold Atlantic Benguela Current and Indian Ocean Agulhas counter‐current play important roles in facilitating dispersal. There was no gene flow between the east coast and the other sites, suggesting that these populations are effectively isolated. Divergence times between them were estimated to at least 68 000 years. Neutrality tests and mismatch distributions suggest recent population expansions, with the exception of peripheral western and eastern populations (possibly a consequence of environmental extremes at the edge of the species distribution). Analyses of the current South African marine protected areas network show that it is not connected and that De Hoop, one of South Africa's largest marine reserves, appears to be an important source population of recruits to both the south and southwest coasts.     

Genetic patchiness of the shore crab Pachygrapsus marmoratus along the Portuguese coast

The population genetic structure of the shore crab Pachygrapsus marmoratus was studied along the Portuguese coast based on six variable microsatellite loci. Genetic differentiation among populations according to a geographic gradient was not detected. This lack of genetic structure reflects the continuous distribution of the species along the Portuguese coast and suggests that gene flow occurs within the studied distribution range. Gene flow is probably maintained by the planktonic larvae of P. marmoratus that can last up to 31 days in the plankton. Tests for population differentiation demonstrated that the Praia das Avencas population is genetically more separated from all other populations, and Bayesian methodologies tend to form 4 groups that clustered together populations that are several hundred kilometres apart. This grouping pattern could be due to coastal hydrological events that are apparently influencing larval flux. Other hypotheses to explain the significant genetic heterogeneity among populations on a local scale and the absence of geographic variation are pre- and post-settlement natural selection events. Results suggest that the forces causing genetic differentiation may be acting on a local scale and that the larval pool is possibly not always mixed homogeneously.     

Phylogeography of Emerita analoga (Crustacea,Decapoda, Hippidae), an eastern Pacific Ocean sand crab with long‐lived pelagic larvae

Aim Phylogeographic analyses have confirmed high dispersal in many marine taxa but have also revealed many cryptic lineages and species, raising the question of how population and regional genetic diversity arise and persist in dynamic oceanographic settings. Here we explore the geographic evolution of Emerita analoga, an inter‐tidal sandy beach crab with an exceptionally long pelagic larval phase and wide latitudinal, amphitropical, distribution. We test the hypothesis that eastern Pacific E. analoga constitute a single panmictic population and examine the location(s), timing and cause(s) of phylogeographic differentiation. Location Principally the eastern Pacific Ocean. Methods We sequenced cytochrome c oxidase subunit I (COI) from 742 E. analoga specimens collected between 1997 and 2000 and downloaded homologous sequences of congeners from GenBank. We reconstructed a phylogeny for Emerita species using maximum likelihood and Bayesian methods and estimated times to most recent common ancestors (TMRCAs), using a COI divergence rate of 1% Myr^?1 and timing of closure of the Central American Seaway. We constructed the COI haplotype network of E. analoga using statistical parsimony, calculated population genetic and spatial structure statistics in Arlequin , and estimated the demographic history of E. analoga using Bayesian skyline analysis. Results Population subdivision and allele frequency differences were insignificant among north‐eastern Pacific locations over 2000 km apart (Φ_ST = 0.00, P = 0.70), yet two distinct phylogroups were recovered from the north‐eastern and south‐eastern Pacific (Φ_CT = 0.87, P < 0.001). Amphitropical differentiation of these temperate clades occurred after TMRCA 1.9 ± 0.02 (mean ± SE) Ma and E. analoga has expanded into its present‐day north‐eastern Pacific range since c. 250 ka. Main conclusions Emerita analoga is not panmictic but is very widely dispersed and approaching genetic homogeneity, i.e. ‘eurymixis’, in the north‐eastern Pacific. North‐eastern and south‐eastern Pacific populations of E. analoga probably became isolated c. 1.5 Ma as the tropical eastern Pacific Ocean warmed and expanded, intensifying barriers to gene flow. The fragmentation of a widespread ancestral species previously connected by long‐distance gene flow (‘soft vicariance’) coincident with changing oceanographic conditions may be a common theme in the evolution of Emerita species and in other highly dispersive taxa. Highly dispersive species may differentiate because of, not despite, the dynamic oceanographic setting.     

Genetic population structure in prickly sculpin (Cottus asper) reflects isolation‐by‐environment between two life‐history ecotypes

Life‐history transitions have evolved repeatedly in numerous taxa, although the ecological and evolutionary conditions favouring such transitions in the presence of gene flow remain poorly understood. The present study aimed to disentangle the effects of isolation‐by‐distance and isolation‐by‐environment on genetic differentiation between two sympatric life‐history ecotypes. Using 14 microsatellite loci, we first characterized amphidromous and freshwater groups of Cottus asper in a high gene flow setting in the Lower Fraser River system (south‐western British Columbia, Canada) to test for the effects of habitat and geographical distance on the distribution of life‐history ecotypes. Within the main river channel, no genetic differentiation was found, whereas tributaries even close to the estuary were genetically differentiated. Partial mantel tests confirmed that genetic differentiation between river tributaries and the main channel was independent from geographical distance, with distance‐scaled migration rates indicating reduced gene flow from the main channel into the tributaries. Our results suggest that isolation‐by‐environment can play an important role for the early stage of life‐history transitions, and may promote differentiation among life‐history ecotypes despite the presence of gene flow. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 943–957.     

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ_ST values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ_ST (0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ_ST = 0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.