Intraspecific Genetic Structure Research Articles

Phylogeography of ants from the Brazilian Atlantic Forest

Known for its remarkable biodiversity and high levels of endemism, the Brazilian Atlantic Rainforest has been characterized as one of the most threatened biomes on the planet. Despite strong interest in recent years, we still lack a comprehensive scenario to explain the origin and maintenance of diversity in this region, partially given the relatively low power of analyses involving few independent genetic loci. In this study, we examine a phylogenomic dataset of five ant species to investigate phylogeographical patterns across the Brazilian Atlantic Forest. We sequenced ultraconserved elements to generate hundreds of loci using a bait set developed specifically for hymenopterans. We analyzed the data using Bayesian and maximum likelihood approaches of phylogenetic inference. Results were then integrated with environmental niche modeling of current and past climates, including the Last Glacial Maximum and the last interglacial period. The studied species showed differentiation patterns that were consistent with the north/south division of the Atlantic Rainforest indicated in previous studies for other taxa. However, there were differences among species, both in the location of phylogeographic breaks and in the pattern of genetic variation within these areas. Samples from southern localities tended to show recent genetic structure, although a site in Tapirai (state of Sao Paulo) repeatedly showed an intriguing older history of differentiation. All species experienced shifts in areas of suitability through the time. Our study suggests that distinct groups may have responded idiosyncratically to the climatic changes that took place in the Brazilian Atlantic Forest. The amount of intraspecific genetic structure was related to the inferred geographical distribution of habitat suitability according to current and past times. Also, a parallel between the amount of Quaternary climatic suitability and the level of interspecific differentiation was detected for four species. Finally, despite strong contractions at the northeastern region of the forest, the remaining areas appear to have been able to act as refugia.

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana).

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species.

BackgroundThe rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy.MethodsWe reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato.ResultsThe molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov.DiscussionElaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.

A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts.

Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Both factors reflect the joint effect of ecoevolutionary processes on the geographical heterogeneity of populations. We used a collection of 301 georeferenced accessions of the annual plant Arabidopsis thaliana in its Iberian Peninsula range, where the species shows strong geographical genetic structure. We developed spatial and nonspatial hierarchical Bayesian models (HBMs) to depict current and future distribution ranges for the four genetic clusters detected. We also compared the performance of HBMs with Maxent (a presence-only model). Maxent and nonspatial HBMs presented some shortcomings, such as the loss of accessions with high genetic admixture in the case of Maxent and the presence of residual SAC for both. As spatial HBMs removed residual SAC, these models showed higher accuracy than nonspatial HBMs and handled the spatial effect on model outcomes. The ease of modelling and the consistency among model outputs for each genetic cluster was conditioned by the sparseness of the populations across the distribution range. Our HBMs enrich the toolbox of software available to evaluate GCC-induced distribution range shifts by considering both genetic heterogeneity and SAC, two inherent properties of any organism that should not be overlooked.

On the importance of accounting for intraspecific genomic relatedness in multi‐species studies

Abstract Analyses in many fields of ecology are increasingly considering multiple species and multiple individuals per species. Premises of statistical tests are often violated with such datasets because of the non‐independence of residuals due to phylogenetic relationships or intraspecific population structure. If comparative approaches that account for the phylogenetic relationships of species are well developed and their benefits demonstrated, the importance of considering the intraspecific genetic structure, especially in combination with the phylogenetic structure, has rarely been addressed. We investigated whether it is beneficial to account for intraspecific genomic relatedness in multi‐species studies. For this, we used a phylogenetic mixed model to analyse first a suite of simulated data and then results from one example ecological study—a budburst experiment where clippings of 10 tree and shrub species were subjected to different temperatures and photoperiods. We found that accounting for intraspecific genetic structure yields more accurate and precise fixed effects as well as increased statistical power, but more so when the relative importance of the intraspecific to the phylogenetic genetic structure is greater. Analysis of the budburst experiment further showed that accounting for intraspecific and phylogenetic structures yields improved estimates of warming and photoperiod effects and their interaction in explaining the time to budburst. Our results show that statistical gains can be made by incorporating information on the intraspecific genomic relatedness of individuals in multi‐species studies. This is relevant to investigations that are interested in intraspecific variation and that plan to include such observations in statistical tests.

Environmental effects on gene flow in a species complex of vagile, hilltopping butterflies

Butterflies have played a pivotal role in our understanding of animal movement, but little is known about landscape-scale movement in highly vagile species with large ranges and open population structure. We investigate the effect of environment and landscape on both inter- and intraspecific genetic differentiation and population structure in the Papilio machaon group of swallowtail butterflies in Alberta, Canada. These butterflies exhibit strong hilltopping behaviour, where individuals congregate on topographical prominences to mate, and thus we expect topography to influence population connectivity. We use redundancy analysis to explore the relationship between two genetic datasets (mitochondrial DNA and microsatellites) and topographic, climatic and habitat-related environmental variables at multiple spatial scales. Shared variation across these environmental variables explained a large portion of both mitochondrial (≤ 75%) and microsatellite genetic variation (≤ 40%). Individual variables, such as elevation, terrain profile, solar radiation and precipitation, had moderate explanatory power; however, the water component of land cover had the greatest explanatory power of the individual variables and acted as a surrogate variable for the larval habitat of P. machaon. Despite high levels of retained ancestral polymorphism in the mitochondrial dataset, we found similar relationships between environmental characteristics and genetic variation. Finally, the spatial scale of our analyses greatly influenced our results, and without exploring the effect of scale we would have missed or discounted the effects of several environmental characteristics. This point emphasizes the importance of exploratory analysis in systems where there is little prior knowledge of movement dynamics and the influence of the environment.

Neither Diplectanum nor specific: a dramatic twist to the taxonomic framework of Diplectanum (Monogenea: Diplectanidae)

The taxonomy of the genus Diplectanum has been exclusively based on morphological features, with 28 nominal species parasitic on perciform fishes recognised. We used molecular data, to our knowledge for the first time, to evaluate the taxonomic framework of Diplectanum, infer the relationships amongst species attributed to this genus, re-assess the degree of host specificity and explore the population genetic structure of Diplectanum spp. parasitising Mediterranean sciaenids, which are potential target fish species for aquaculture diversification in the region. A minimum of 10 specimens of Diplectanum spp. were sequenced per host species (Argyrosomus regius, Sciaena umbra, Umbrina canariensis and Umbrina cirrosa) and locality (Burriana, Sant Carles de la Ràpita and Santa Pola (Spain)) together with five individuals of the type species Diplectanum aequans. Sequences of partial 28S rDNA and internal transcribed spacer region of Diplectanum spp. were analysed together with those from other Diplectanidae spp. in GenBank using Bayesian inference and maximum likelihood phylogenetic methods. Population genetic analyses were performed using cytochrome c oxidase subunit I gene sequences for a diplectanid species with a wide distribution across host species and localities. Results showed that Diplectanum was not monophyletic, nor were the specimens infecting sciaenids. Instead they formed two separate clades, 26.1–28.6% divergent for the internal transcribed spacer and 13.2–16.9% for the 28S region from D. aequans. Altogether, our results suggest that these specimens represent two distinct new genera from Diplectanum and five putative species with low host specificity. It is likely that morphological variability has led to the description of more species than were detected by molecular methods. In contrast to other monogeneans, Diplectaninae gen. spp. are chiefly generalists. Nonetheless, intraspecific genetic divergence in the internal transcribed spacer region of Diplectaninae gen. spp., and population genetic analyses of one presumed generalist species, Diplectaninae gen. sp. 1.2, showed significant variation between subpopulations living on different hosts. The intraspecific genetic structure by host also suggests different cross-infection potential amongst sciaenid species.

Thermal selection as a driver of marine ecological speciation.

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic regions based on selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine species, and biogeographic disjunctions in species assemblages. Our results indicate that temperature-mediated selection represents an early stage of marine ecological speciation in coastal regions that lack physical dispersal barriers.

Genetic diversity of eight wild populations of Pampus argenteus along the coast of China inferred from fifteen polymorphic microsatellite markers

Pampus argenteus (Perciformes: Stromateidae) is widely distributed along the coast of China, Indian Ocean, Arabian Gulf and North Sea. Due to overfishing and environmental degradation, its resources reduced year after year. Thus, new management strategies are urgently needed for the sustainable growth and utilization of this species. Characterization of the genetic variation of this fish species is essential for conserving the genetic resource and restraining the population decline. Therefore, it is necessary to have a clear understanding of the intraspecific genetic diversity and population structure of the species. In this study, we assess the genetic diversity and population structure of P. argenteus by using microsatellites. We genotyped 240 P. argenteus individuals from eight wild populations collected from Shidao (SD), Lianyungang (LYG), Lvsi (LS), Zhoushan (ZS), Dongtou (DT), Xiapu (XP), Haikou (HK), and Beibuwan (BBW) along the coast of China using fifteen polymorphic microsatellites. A total of 139 alleles were determined at 15 loci across the eight populations, and a relatively high level of genetic diversity was observed, with observed heterozygosity (Ho) and expected heterozygosity (He) ranging from 0.100 to 1.000, and from 0.669 to 0.934 per locus-location combination, respectively. LS had the highest average allele (number of alleles, A=15.200), and HK the lowest (A=13.000). Hos of P. argenteus are less than Hes, indicating lack of heterozygote within populations. Analysis of molecular variance (AMOVA) showed that most variation (95.66%) occurred within populations, suggesting that this is the main source of total variance. This study will provide useful information for conservation and sustainable exploitation of this important fishery resource.

Genetic structure in parasitic Rhinanthus angustifolius is determined by geographical distance rather than habitat – implications for taxonomy and conservation

Analyses of intraspecific genetic structure can promote the conservation of genetic diversity of rare or declining plant species by enabling identification of proper management units. Here we investigate the genetic structure of the annual hemiparasitic herb Rhinanthus angustifolius to evaluate the genetic distinctness of two currently described subspecies and three habitat‐related groups of populations inferred from recent common‐garden data. Data from 11 nuclear microsatellite loci, obtained from 17 southern Swedish populations of R. angustifolius, were analyzed with a variety of population genetic techniques to examine how intraspecific genetic structure relates to taxonomy, habitat and geography. Neither the two subspecies nor the three recently identified population groups formed genetically coherent lineages. Rather, there was a clear isolation‐by‐distance pattern, pointing to a major role of geographically restricted gene flow in structuring the diversity at the putatively neutral microsatellite loci. Although uncertainties remain regarding the influence of homoplasy and possible introgression from the closely related R. minor, our microsatellite data argue against the recognition of previously identified subspecies or population groups as management units for conservation purposes. As currently described entities do not contain much unique genetic variation, we recommend conserving populations from a large geographical range, rather than populations from specific habitats, to preserve the long‐term evolutionary potential of the species.

Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species.

Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long‐eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co‐occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long‐eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter‐ and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species‐specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.

Ancient east-west divergence, recent admixture, and multiple marginal refugia shape genetic structure of a widespread oak species (Quercus acutissima) in China

The interactions of major topographic features with climate fluctuations over time are key factors that influence the spatial genetic structure of trees species. As an important characteristic of China’s terrain, the boundary between the mountainous West China and the lowland East China has been found to contribute to the divergence of many species. In this study, we examined whether the stepped geomorphology of China has shaped the genetic structure of Quercus acutissima, a widespread oak species native to East Asia, at a much larger geographic scale. Thirty natural populations of the species were sampled across the entire distribution in China and genotyped using ten nuclear microsatellite markers. To determine the genetic structure and demographic history, we conducted Bayesian cluster analysis and approximate Bayesian computation. A significant east-west divergence was detected at the species level, with western populations presenting much stronger differentiation and lower genetic diversity than eastern populations. The divergence between the groups of Southwest China and East China was estimated to have occurred 3.55–2.37 million years ago (Ma), closely associated with the recent uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes during the late Pliocene to the early Pleistocene. The Central China group may arise from the admixture of these two groups, which was dated to 0.83–0.55 Ma, a period covering several interglacial intervals with unusually warm and wet climate in Central China. The spatial genetic structure of Q. acutissima indicates the possibility of central-marginal dispersal dynamics along latitude and existence of multiple refugia at distribution edges. Our findings highlight that the stepped geomorphology in China and climatic changes since the Pliocene play an important role in shaping the intraspecific genetic structure of widespread species in East Asia.

Combining Bayesian genetic clustering and ecological niche modeling: Insights into wolf intraspecific genetic structure.

The distribution of intraspecific genetic variation and how it relates to environmental factors is of increasing interest to researchers in macroecology and biogeography. Recent studies investigated the relationships between the environment and patterns of intraspecific genetic variation across species ranges but only few rigorously tested the relation between genetic groups and their ecological niches. We quantified the relationship of genetic differentiation (F ST) and the overlap of ecological niches (as measured by n‐dimensional hypervolumes) among genetic groups resulting from spatial Bayesian genetic clustering in the wolf (Canis lupus) in the Italian peninsula. Within the Italian wolf population, four genetic clusters were detected, and these clusters showed different ecological niches. Moreover, different wolf clusters were significantly related to differences in land cover and human disturbance features. Such differences in the ecological niches of genetic clusters should be interpreted in light of neutral processes that hinder movement, dispersal, and gene flow among the genetic clusters, in order to not prematurely assume any selective or adaptive processes. In the present study, we found that both the plasticity of wolves—a habitat generalist—to cope with different environmental conditions and the occurrence of barriers that limit gene flow lead to the formation of genetic intraspecific genetic clusters and their distinct ecological niches.

Evolution of the Grey-bellied pygmy mouse group: Highly structured molecular diversity with predictable geographic ranges but morphological crypsis

The grey-bellied pygmy mouse (Mus triton) from the endemic African subgenus Nannomys is a widespread rodent species inhabiting the highlands of eastern and central Africa. Although it has long been considered as a single species, recent data has suggested the existence of a species complex. In order to evaluate the geographical structure and current taxonomy of M. triton, we analysed one mitochondrial and six nuclear genes from individuals covering most of its distribution range. Our analysis revealed the existence of at least five distinct genetic lineages with only marginal overlaps among their distributional ranges. Morphological comparisons, however, showed large overlaps in external body measurements and only a weak differentiation in skull form. Therefore, we suggest maintaining M. triton as a single taxon with pronounced intraspecific genetic structure. Divergence dating analysis placed the most recent common ancestor of the extant lineages of M. triton to the early Pleistocene (about 2.0 Ma). The phylogeographic structure of the species was likely shaped by Pleistocene climatic oscillations and the highly diverse topography of eastern Africa.

Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis.

Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time.

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.

Population genetic structure of Patagonian toothfish (Dissostichus eleginoides) in the Southeast Pacific and Southwest Atlantic Ocean.

Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf.

Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations

BackgroundSex-biased dispersal is widespread among mammals, including the brown bear (Ursus arctos). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow.ResultsWe analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins.ConclusionsBrown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels.