Exploring population genetic structure in three species of Lesser Antillean bats

We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe-induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected in Ardops nichollsi (P = 0.718), but could be rejected in B. cavernarum (P < 0.001) and Artibeus jamaicensis (P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using an amova and was rejected in each species [Ardops nichollsi (P = 0.697); B. cavernarum (P = 0.598); Artibeus jamaicensis (P = 0.763)]. In B. cavernarum and Artibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly in Artibeus jamaicensis (PW < 0.01; PSE = 0.04), but cannot be rejected in B. cavernarum (PW = 0.81; PSE = 0.79). A conservative interpretation of the molecular data is that island populations of Artibeus jamaicensis, although isolated geographically, are not isolated genetically.     

Systematics and historical biogeography of Greater Antillean Cichlidae

A molecular phylogenetic analysis recovers a pattern consistent with a drift vicariance scenario for the origin of Greater Antillean cichlids. This phylogeny, based on mitochondrial and nuclear genes, reveals that clades on different geographic regions diverged concurrently with the geological separation of these areas. Middle America was initially colonized by South American cichlids in the Cretaceous, most probably through the Cretaceous Island Arc. The separation of Greater Antillean cichlids and their mainland Middle American relatives was caused by a drift vicariance event that took place when the islands became separated from Yucatan in the Eocene. Greater Antillean cichlids are monophyletic and do not have close South American relatives. Therefore, the alternative hypothesis that these cichlids migrated via an Oligocene landbridge from South America is falsified. A marine dispersal hypothesis is not employed because the drift vicariance hypothesis is better able to explain the biogeographic patterns, both temporal and phylogenetic.     

PACT in practice: comparative historical biogeographic patterns and species–area relationships of the Greater Antillean and Hawaiian Island terrestrial biotas

Aim To compare the evolutionary and ecological patterns of two extensively studied island biotas with differing geological histories (the Hawaiian Islands and the Greater Antilles). We evaluated the results from PACT (phylogenetic analysis for comparing trees), an innovative approach that has been proposed to reveal general patterns of biotic expansion (between regions) and in situ (within a region) diversification, as well as species–area relationships (SAR) and the taxon pulse dynamic. Location The Hawaiian Islands and Greater Antilles. Methods We used the PACT algorithm to construct general area cladograms and identified biotic expansion and in situ nodes. We analysed the power‐law SAR and relative contribution of biotic expansion and in situ diversification events using power‐law and linear regression analyses. Results Both biotic expansion and in situ nodes were prevalent throughout the PACT general area cladograms (Greater Antilles, 55.9% biotic expansion, 44.1% in situ; Hawaiian Islands, 40.6% biotic expansion, 59.4% in situ). Of the biotic expansion events, both forward and backward events occurred in both regions (Greater Antilles, 85.1% forward, 14.9% backward; Hawaiian Islands, 65% forward, 35% backward). Additionally, there is a power‐law SAR for the Greater Antilles but not for the Hawaiian Islands. However, exclusion of Hawai'i (the youngest, largest Hawaiian Island) produced a power‐law SAR for the Hawaiian Islands. Main conclusions The prevalence of in situ events as well as forward and backward biotic expansion events reveals that both Hawaiian and Greater Antillean biotas have evolved through alternating episodes of biotic expansion and in situ diversification. These patterns are characteristic of the taxon pulse dynamic, for which few data have previously been recorded on islands. Additionally, our analysis revealed that historical influences on the power‐law SARs are pronounced in both assemblages: old, small islands are relatively species rich and young, large islands are relatively species poor. Thus, our PACT results are consistent with hypotheses of geological influence on the evolution of island biotas and also provide greater insight into the role of the taxon pulse dynamic in the formation of island equilibria.     

Population genetic structure and demographic history of the fat greenling Hexagrammos otakii

Fat greenling (Hexagrammos otakii) is an important commercial fish in the Northwestern Pacific, being distributed along the coastal waters of the East/Japan Sea and the Yellow Sea. To investigate population genetic structure and demographic history of this species, one hundred and fifty five individuals were collected from five localities in the distribution range of the species and sequence variations in the mitochondrial genes COI, COIII-ND3-ND4L, and cytochrome b were examined. For all the genes in every sampling location, the nucleotide diversities were very low (0.001 ～ 0.005) although the haplotype diversities were relatively high, 0.55 ～ 0.81 for COI, 0.79 ～ 0.84 for COIII-ND3-ND4L, and 0.95 ～ 0.97 for cytochrome b. Hierarchical analysis of molecular variance (AMOVA), the conventional population statistic FST, and exact test of population differentiation revealed no significant genetic structuring among the samples, indicating that fat greening is panmictic throughout the range of its distribution. Neutrality tests such as Tajima’s D and Fu’s FS statistics and mismatch distribution analyses suggested that fat greening has undergone the demographic history of population expansion during the late Pleistocene period approximately 91,000 ～ 327,000 years ago. The star-burst patterns of haplotype networks and low nucleotide diversities also indicated recent population expansion. These results help establish the fisheries management strategy for fat greenling in the Northwestern Pacific.     

An attempt at the historical reconstruction of the genetic demographic structure of the Moscow population at the turn of the 20th century]

The genetic demographic structure of the Moscow population at the turn of the 20th century was studied based on the data from parish books and census records. The main sources of population gene pool replenishment were analyzed, and migration coefficients and the main parameters of the model of isolation by distance were estimated. Data on so-called quasigenetic markers (ethnicity and birthplace) were used to reveal intrapopulation heterogeneity, which facilitates the adaptation of migrants to a new ethnic and cultural environment. The spatial subdivision was analyzed with the use of GST statistics. Muscovites exhibited a considerable positive assortative mating with respect to birthplace. The results of this study provide the necessary historical perspective for predicting the current genetic demographic trends in the Moscow population. It was shown that the co-efficients of marriage migration were almost the same (0.7 < m < 0.8) in the late 19th and mid-20th centuries; however, these values were two times greater than in the late 20th century. This decrease in marriage migration was accompanied by a threefold increase in the radius of centripetal migration and a threefold decrease in the level of isolation by distance. It was determined that the increase in the ethnic and genetic diversity of the Moscow population in the 20th century had started in the 1860s.     

Migration and dispersal patterns of bats and their influence on genetic structure

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Population genetic structure and demographic history of the black fly vector,Simulium nodosum in Thailand

An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600–5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization.     

Ecomorphology of Anolis lizards of the Choco' region in Colombia and comparisons with Greater Antillean ecomorphs

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Characterization of polymorphic microsatellite loci for two species of phyllostomid bats from the Greater Antilles (Erophylla sezekorni and Macrotus waterhousii)

We developed 12 polymorphic microsatellite loci for the buffy flower bat (Erophylla sezekorni) and 10 loci for Waterhouse's big-eared bat (Macrotus waterhousii). In E. sezekorni, we tested 65 individuals from three islands, Cuba, Exuma, and Abaco. Mean number of alleles per locus was 10.7 (range 5-20). In M. waterhousii, we tested 39 individuals from one island, Exuma. Mean number of alleles per locus was 6.9 (range 4-13). We will use these markers to study the phylogeography and mating system of these species.     

Landscape, habitat characteristics and the genetic population structure of two caddisflies

1. In a region of south‐eastern England, we investigated the hierarchical genetic structure of populations of two stream‐dwelling caddisflies (Trichoptera: Polycentropodidae) with contrasting distributions: Plectrocnemia conspersa inhabits numerous small, patchily distributed seeps and streams, while the confamilial Polycentropus flavomaculatus is found in fewer but larger streams and rivers. We also contrasted the genetic structure of P. conspersa in the lowland south‐east with that in an upland region in the north west. 2. Microsatellite genotypes were obtained from samples of both species taken from a ‘core area’ and at sites 15, 40 and 100 km from this core (two regions for P. conspersa, totalling 45 sites and 1405 larvae; one region for P. flavomaculatus, totalling 10 sites and 269 larvae). 3. The genetic structure of P. conspersa differed in the two regions. In the upland north‐west, significant genetic differentiation was observed at a spatial scale of around 40 km from the core, while there was no structure in the lowland south‐east up to around 100 km. Areas of high altitude did not appear directly to reduce gene flow, whereas other potential landscape barriers, including particular geological formations, large urban areas and the sea had a pronounced effect. 4. Weak genetic differentiation in P. conspersa across large distances, particularly in the lowland south‐east, suggests that it disperses strongly, facilitating gene flow within and between catchments. Conversely, for P. flavomaculatus we found strong genetic differentiation between almost all sites, suggesting that dispersal is much more limited. 5. Greater dispersal in the patchily distributed P. conspersa than in P. flavomaculatus, which occupies larger and presumably more persistent habitats, could be a general feature of other similarly distributed aquatic insects. While higher relief is potentially a partial barrier to dispersal, P. conspersamust have effective gene flow through such apparently inhospitable terrain, perhaps attributable to dispersal between neighbouring small and ephemeral populations. Indeed, its exploitation of headwaters and seeps requires the ability to disperse between such sites. Apparently it cannot, however, overcome more continuous barriers, consisting of large tracts of landscape with few habitable larval sites. Such landscapes, including those created by humans, may have a stronger effect on population connectivity and colonization in the longer term.     

AFLP markers resolve intra-specific relationships and infer genetic structure among lineages of the canyon treefrog, Hyla arenicolor

The canyon treefrog, Hyla arenicolor, is a wide-ranging hylid found from southwestern US into southern Mexico. Recent studies have shown this species to have a complex evolutionary history, with several phylogeographically distinct lineages, a probable cryptic species, and multiple episodes of mitochondrial introgression with the sister group, the H. eximia complex. We aimed to use genome wide AFLP markers to better resolve relationships within this group. As in other studies, our inferred phylogeny not only provides evidence for repeated mitochondrial introgression between H. arenicolor lineages and H. eximia/H. wrightorum, but it also affords more resolution within the main H. arenicolor clade than was previously achieved with sequence data. However, as with a previous study, the placement of a lineage of H. arenicolor whose distribution is centered in the Balsas Basin of Mexico remains poorly resolved, perhaps due to past hybridization with the H. eximia complex. Furthermore, the AFLP data set shows no differentiation among lineages from the Grand Canyon and Colorado Plateau despite their large mitochondrial sequence divergence. Finally, our results infer a well-supported sister relationship between this combined Colorado Plateau/Grand Canyon lineage and the Sonoran Desert lineage, a relationship that strongly contradicts conclusions drawn from the mtDNA evidence. Our study provides a basis for further behavioral and ecological speciation studies of this system and highlights the importance of multi-taxon (species) sampling in phylogenetic and phylogeographic studies.     

Spatial genetic structure of European wild boar,with inferences on late-Pleistocene and Holocene demographic history

European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and reassess the genetic consequences of natural and anthropogenic forces. We found that population fragmentation, inbreeding and recent hybridization with domestic pigs have caused the spatial genetic structure to be heterogeneous at the local scale. Underlying local anthropogenic signatures, we found a deep genetic structure in the form of an arch-shaped cline extending from the Dinaric Alps, via Southeastern Europe and the Baltic states, to Western Europe and, finally, to the genetically diverged Iberian peninsula. These findings indicate that, despite considerable anthropogenic influence, the deeper, natural continental structure is still intact. Regarding the glacial refugia, our findings show a weaker signal than generally assumed, but are nevertheless suggestive of two main recolonization routes, with important roles for Southern France and the Balkans. Our results highlight the importance of applying genomic resources and framing genetic results within a species’ demographic history and geographic distribution for a better understanding of the complex mixture of underlying processes.Subject terms: Genomics, Population dynamics, Genetic variation, Evolutionary genetics     

Dynamics of the genetic demographic structure of the Kursk province population: migration processes

Marriage records from parish books of the second half of the 19th century and marriage records of 1967-1970 and 1993-1995 obtained from registry offices were used to analyze the dynamics of genetically significant parameters of migration and marriage structure with respect to spouses' birthplaces in populations of different hierarchical levels in the Kursk oblast. It was found that, among the persons contracting marriage (both males and females), the proportions of those who were born in the same population and those who were born in any population of the Kursk oblast decreased by about one third and one fifth, respectively, for the 130-year period. In rural and small urban populations, the coefficients of marriage migration in the 19th century were an order of magnitude lower than in the 20th century. The immigration to urban populations was maximum in the late 1960s (m = 0.745 in small towns and m = 0.680 in Kursk), and that to rural populations, in the 1990s (m = 0.344). In both urban and rural populations, the mean distance between the spouses' birthplaces has increased by several times for the period studied. The endogamy level has decreased approximately twofold: from 0.797 to 0.380 in Kursk, from 0.897 to 0.419 in small towns, and from 0.958 to 0.440 in rural districts. The marriage assortativeness with respect to birthplace was maximum in the late 19th century (K = 0.393-0.491) and minimum in the 1960s (K = 0.155-0.246). The increase in genetic diversity of the urban population of the Kursk oblast due to migration has been slowing down since the late 20th century, whereas the outbreeding level is still increasing in rural populations.     

Spatial genetic structure and historical demography of East Asian wild boar

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.     

Population genetic structure and the effect of historical human activity on the genetic variability of Cryptomeria japonica core collection,in Japan

Population structure and genome-wide linkage disequilibrium (LD) were investigated in a Cryptomeria japonica core collection consisting of 510 individuals and providing comprehensive coverage of the natural distribution range of the species, using 4,896 SNP markers. Both Bayesian clustering and principal coordinate analyses clearly subdivided the sample into two distinct groups corresponding to the Japan Sea side and the Pacific Ocean side of Japan. The clustering analysis also detected two subgroups located in Northern Tohoku and Yakushima Island, as was also the case in the natural population. This finding is in accord with the ecogeographical origin of the cultivars; however, the spatial distribution of these clusters was slightly different between the natural population and the core collection, especially in the Chugoku district, an effect which might have resulted from historical human activity. The genetic diversity of the core collection is comparable to, or a little higher than, that of natural populations, indicating that the individuals in the core collection have not suffered from diversity losses caused by a domestication bottleneck. LD analysis with mapped markers indicated that the LD decays rapidly, within approximately 5 cM, in both the core collection and natural populations. The results show that the population described here is a valuable resource for both basic and applied research on C. japonica.     

Contemporary genetic structure and postglacial demographic history of the black scorpionfish,Scorpaena porcus,in the Mediterranean and the Black Seas

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.