Origin and radiation of the house mouse: mitochondrial DNA phylogeny

On the basis of patterns of allele frequency variation in nuclear genes (Din et al., in press) it has been proposed that the house mouse M. musculus originated in the northern Indian subcontinent, from where it radiated in several directions to form the well-described peripheral subspecies (M. m. domesticus, M. m. musculus and M. m. castaneus). Here we use a mitochondrial DNA (mtDNA) phylogeny to test this hypothesis and to analyse the historical and demographic events that have accompanied this differentiation. This marker also provides a powerful means to check for genetic continuity between the central and peripheral populations. We studied restriction site polymorphism of samples from India and the Middle East as well as samples from the rest of Eurasia and northern Africa. M. m. domesticus and M. m. musculus are both monophyletic for mtDNA and belong to the subspecies-specific mtDNA lineages that have been described previously. Average nucleotide diversity is low in M. m. musculus (0.2–5%). It is not only higher in M. m. domesticus (0.7–0.9%) but the distribution of pairwise divergence is wider, and the rate of evolution in this branch appears to be higher than in M. m. musculus. The nucleotide diversity found in M. m. castaneus (0.4%) is due to the existence of two rather divergent linages with little intralineage variation. These two lineages are part of a diversified bush of the phylogenetic tree that also comprises several previously undescribed branches and includes all samples from the northern Indian subcontinent and Iran. The degree of diversity found in each of the samples from this region is high (1.2–2.4%) although they come from small geographic areas. This agrees well with the idea that the origin of the radiation was in the northern Indian subcontinent. However, as neither haplotypes on the M. m. domesticus nor on the M. m. musculus branches were found in this region, there appear to be important phylogeographic discontinuities between this central region and these peripherial subspecies. On the basis of the present result and the nuclear data (Din et al., in press), we propose that M. musculus originated in the north of the indian subcontinent. Our calibration of the evolutionary rate of mtDNA in mice suggests that the mouse settlement in this region could be as old as 900 000 years. Possibly from there, a first radiation could have reach the Middle East and the Caspian Sea, where the M. m. domesticus and M. m. musculus lineages, respectively, would have started to differentiate a few hundred thousand years ago, and from where they could have colonised the peripheral part of their ranges only recently.M. m. castaneus appears from its mtDNA to be recent offshoot of the northern Indian population. This multiple and gradual radiation ultimately led to recent peripheral secondary contacts, such as the well-known European hybrid zone.     

Small edge populations at risk: genetic diversity of the green lizard (<Emphasis Type="Italic">Lacerta viridis viridis</Emphasis>) in Germany and implications for conservation management

Edge and central populations can show great differences regarding their genetic variation and thereby also in their probability of extinction. This fact might be of great importance for the conservation strategies of endangered species. In this study we examine the level of microsatellite variability within three threatened edge populations of the green lizard subspecies Lacerta viridis viridis (Laur.) in Brandenburg (Germany) and compare the observed variation to other edge and central populations within the northern species range. We demonstrate that the northernmost edge populations contain less genetic variation in comparison to the central population. However, there were no observable significant differences to the other edge population included in this study. Surprisingly, we observed a high genetic differentiation in a small geographical range between the three endangered populations in Brandenburg, which can be explained by processes like fragmentation, isolation, genetic drift and small individual numbers within these populations. We also detected unique genetic variants (alleles), which only occurred in these populations, despite a low overall genetic variation. This study demonstrates the potential of fast evolving markers assessing the genetic status of endangered populations with a high resolution. It also illustrates the need for a comparative analysis of different regions within the species range, achieving a more exact interpretation of the genetic variation in endangered populations. This will aid future management decisions in the conservation of genetic diversity in threatened species.     

Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated?>?20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.

     

Do seed transfer zones for ecological restoration reflect the spatial genetic variation of the common grassland species Lathyrus pratensis?

A common ecological restoration approach is the reestablishment of vegetation using seed mixtures. To preserve the natural genetic pattern of plant species local seed material should be used. Consequently, seed transfer zones (seed production areas and seed provenance regions) have been delineated for ecological restoration in Germany. Although it is assumed that these transfer zones represent genetic variation, there remains a lack of empirical data. In this study, we analyzed whether seed transfer zones reflect the genetic variation of the common grassland species Lathyrus pratensis. We sampled 706 individuals from 37 populations in Bavaria, Germany and analyzed genetic variation using amplified fragment length polymorphisms. In our study, we observed higher levels of genetic variation and fragment rarity in the southern Bavarian populations compared to northern populations. Our analyses revealed a strong genetic differentiation between southern and northern Bavarian populations delineated along the Danube River. However, seed production areas and seed provenance regions reflected genetic variation of L. pratensis only to a limited degree. Our study illustrates that the level of genetic variation within populations strongly depends on population history. Furthermore, the geomorphological and climatic attributes, which have been used to delineate seed provenance regions, do not reduce gene flow among populations. Seed collections for gene banks and seed production should comprise seeds from populations in southern and northern Bavaria representing the strong genetic variation between both regions, but prioritize southern populations due to higher levels of variation.     

Glacial refugia and postglacial expansion of the alpine–prealpine plant species Polygala chamaebuxus

The shrubby milkwort (Polygala chamaebuxus L.) is widely distributed in the Alps, but occurs also in the lower mountain ranges of Central Europe such as the Franconian Jura or the Bohemian uplands. Populations in these regions may either originate from glacial survival or from postglacial recolonization. In this study, we analyzed 30 populations of P. chamaebuxus from the whole distribution range using AFLP (Amplified Fragment Length Polymorphism) analysis to identify glacial refugia and to illuminate the origin of P. chamaebuxus in the lower mountain ranges of Central Europe. Genetic variation and the number of rare fragments within populations were highest in populations from the central part of the distribution range, especially in the Southern Alps (from the Tessin Alps and the Prealps of Lugano to the Triglav Massiv) and in the middle part of the northern Alps. These regions may have served, in accordance with previous studies, as long‐term refugia for the glacial survival of the species. The geographic pattern of genetic variation, as revealed by analysis of molecular variance, Bayesian cluster analysis and a PopGraph genetic network was, however, only weak. Instead of postglacial recolonization from only few long‐term refugia, which would have resulted in deeper genetic splits within the data set, broad waves of postglacial expansion from several short‐term isolated populations in the center to the actual periphery of the distribution range seem to be the scenario explaining the observed pattern of genetic variation most likely. The populations from the lower mountain ranges in Central Europe were more closely related to the populations from the southwestern and northern than from the nearby eastern Alps. Although glacial survival in the Bohemian uplands cannot fully be excluded, P. chamaebuxus seems to have immigrated postglacially from the southwestern or central‐northern parts of the Alps into these regions during the expansion of the pine forests in the early Holocene.     

Population size,center–periphery,and seed dispersers’ effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species’ distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation (H_E: 0.04–0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long‐distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates (F_IS = 0.155–0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among‐population differentiation highlight the conservation value of large populations throughout the species’ range, particularly in light of climate change and direct human threats.     

Microsatellite genetic variation of Asian populations of Dolly Varden char

Genetic variation at eight microsatellite loci was examined in 21 populations of Dolly Varden charrs, Salvelinus malma, representing five geographical regions (Kamchatka Peninsula, Sea of Okhotsk coast, Sea of Japan coast, Sakhalin Island, and Kuril islands). Hierarchical analysis of molecular variance showed that 11% (58% in terms of R-statistics) of the variation was distributed among of northern subspecies of Dolly Varden, Salvelinus malma malma and southern Asian Dolly Varden, S. m. krascheninnikovi while similar values were attributed to the among-regional level within northern Dolly Varden 9% (7%) and southern Asian Dolly Varden 11% (14%). Permutation-based tests indicated a mutational component to genetic differentiation based on allelic size variance and suggested that divergence of the two subspecies had occurred at least 3,000 generations ago. On large spatial scales (within the Asian range of the species), populations clustered according to their geographical location. On smaller scales (within regions and subregions) correlation between genetic and geographic distances was not significant. Northern Dolly Varden has higher allelic diversity and more private alleles than southern subspecies, this probably indicating differences in demographic history.     

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.     

Near panmixia at the distribution‐wide scale but evidence of genetic differentiation in a geographically isolated population of the Terek Sandpiper Xenus cinereus

Populations from different parts of a species range may vary in their genetic structure, variation and dynamics. Geographically isolated populations or those located at the periphery of the range may differ from those located in the core of the range. Such peripheral populations may harbour genetic variation important for the adaptive potential of the species. We studied the distribution‐wide population genetic structure of the Terek Sandpiper Xenus cinereus using 13 microsatellite loci and the mitochondrial DNA (mtDNA) control region. In addition, we estimated whether genetic variation changes from the core towards the edge of the breeding range. We used the results to evaluate the management needs of the sampled populations. Distribution‐wide genetic structure was negligible; the only population that showed significant genetic differentiation was the geographically isolated Dnieper River basin population in Eastern Europe. The genetic variation of microsatellites decreased towards the edge of the distribution, supporting the abundant‐centre hypotheses in which the core area of the distribution preserves the most genetic variation; however, no such trend could be seen with mtDNA. Overall genetic variation was low and there were signs of past population contractions followed by expansion; this pattern is found in most northern waders. The current effective population size (N_e) is large, and therefore global conservation measures are not necessary. However, the marginal Dnieper River population needs to be considered its own management unit. In addition, the Finnish population warrants conservation actions due to its extremely small size and degree of isolation from the main range, which makes it vulnerable to genetic depletion.     

Joint effects of natural selection and recombination on gene flow between Drosophila ananassae populations

We estimated DNA sequence variation in a 5.7-kb fragment of the furrowed (fw) gene region within and between four populations of Drosophila ananassae; fw is located in a chromosomal region of very low recombination. We analyzed gene flow between these four populations along a latitudinal transect on the Indian subcontinent: two populations from southern, subtropical areas (Hyderabad, India, and Sri Lanka) and two from more temperate zones in the north (Nepal and Burma). Furthermore, we compared the pattern of differentiation at fw with published data from Om(1D), a gene located in a region of normal recombination. While differentiation at Om(1D) shows an isolation-by-distance effect, at fw the pattern of differentiation is quite different such that the frequencies of single nucleotide polymorphisms are homogenized over extended geographic regions (i.e., among the two populations of the northern species range from Burma and Nepal as well as among the two southern populations from India and Sri Lanka), but strongly differentiated between the northern and southern populations. To examine these differences in the patterns of variation and differentiation between the Om(1D) and fw gene regions, we determine the critical values of our previously proposed test of the background selection hypothesis (henceforth called F(ST) test). Using these results, we show that the pattern of differentiation at fw may be inconsistent with the background selection model. The data depart from this model in a direction that is compatible with the occurrence of recent selective sweeps in the northern as well as southern populations.     

Cold adaptation in the Asian tiger mosquito's native range precedes its invasion success in temperate regions

Adaptation to environmental conditions within the native range of exotic species can condition the invasion success of these species outside their range. The striking success of the Asian tiger mosquito, Aedes albopictus, to invade temperate regions has been attributed to the winter survival of diapause eggs in cold environments. In this study, we evaluate genetic polymorphisms (SNPs) and wing morphometric variation among three biogeographical regions of the native range of A. albopictus. Reconstructed demographic histories of populations show an initial expansion in Southeast Asia and suggest that marine regression during late Pleistocene and climate warming after the last glacial period favored expansion of populations in southern and northern regions, respectively. Searching for genomic signatures of selection, we identified significantly differentiated SNPs among which several are located in or within 20 kb distance from candidate genes for cold adaptation. These genes involve cellular and metabolic processes and several of them have been shown to be differentially expressed under diapausing conditions. The three biogeographical regions also differ for wing size and shape, and wing size increases with latitude supporting Bergmann's rule. Adaptive genetic and morphometric variation observed along the climatic gradient of A. albopictus native range suggests that colonization of northern latitudes promoted adaptation to cold environments prior to its worldwide invasion.     

Patterns of morphological evolution in the mandible of the house mouse Mus musculus (Rodentia: Muridae)

The worldwide distributed house mouse, Mus musculus, is subdivided into at least three lineages, Mus musculus musculus, Mus musculus domesticus, and Mus musculus castaneus. The subspecies occur parapatrically in a region considered to be the cradle of the species in Southern Asia (‘central region’), as well as in the rest of the world (‘peripheral region’). The morphological evolution of this species in a phylogeographical context is studied using a landmark‐based approach on mandible morphology of different populations of the three lineages. The morphological variation increases from central to peripheral regions at the population and subspecific levels, confirming a centrifugal sub‐speciation within this species. Furthermore, the outgroup comparison with sister species suggests that M. musculus musculus and populations of all subspecies inhabiting the Iranian plateau have retained a more ancestral mandible morphology, suggesting that this region may represent one of the relevant places of the origin of the species. Mus musculus castaneus, both from central and peripheral regions, is morphologically the most variable and divergent subspecies. Finally, the results obtained in the present study suggest that the independent evolution to commensalism in the three lineages is not accompanied by a convergence detectable on jaw morphology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 635–647.     

Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L

Fossil evidence shows that populations of species that currently inhabit arctic and boreal regions were not isolated in refugia during glacial periods, but instead maintained populations across large areas of central Europe. These species commonly display little reduction in genetic diversity in northern areas of their range, in contrast to many temperate species. The mountain hare currently inhabits both temperate and arctic-boreal regions. We used nuclear microsatellite and mtDNA sequence data to examine population structure and alternate phylogeographic hypotheses for the mountain hare, that is, temperate type (lower genetic diversity in northern areas) and arctic-boreal type (high northern genetic diversity). Both data sets revealed concordant patterns. Highest allelic richness, expected heterozygosity and mtDNA haplotype diversity were identified in the most northerly subspecies, indicating that this species more closely maps to phylogeographic patterns observed in arctic-boreal rather than temperate species. With regard to population structure, the Alpine and Fennoscandian subspecies were most genetically similar (F(ST) approximately 0.1). These subspecies also clustered together on the mtDNA tree and were assigned with highest likelihood to a common Bayesian cluster. This is consistent with fossil evidence for intermediate populations in the central European plain, persisting well into the postglacial period. In contrast, the geographically close Scottish and Irish populations occupied separate Bayesian clusters, distinct clades on the mtDNA maximum likelihood tree and were genetically divergent from each other (F(ST) > 0.4) indicating the influence of genetic drift, long isolation (possibly dating from the late glacial era) and/or separate postglacial colonisation routes.     

Phylogeny and genetic structure of the goitered gazelle (Artiodactyla,Bovidae) in north-western China indicated by the hypervariable mitochondrial control region

The goitered gazelle, Gazella subgutturosa, is a medium-sized ungulate inhabiting arid and semi-arid regions in the Middle East and central Asia. The intraspecific classification of the species remains unclear. We analysed the genetic diversity in mitochondrial DNA control region (CR) sequences (976?bp) from 104 wild samples from the Xinjiang Uyghur Autonomous Region (XUAR) in north-west China, and reconstructed phylogeny with additional sequences from across the species’ range. We detected 58 haplotypes in XUAR populations, all but three of which were specific to single sampling sites. The phylogenetic analysis displayed two obvious clades of mtDNA haplotypes and the other haplotypes differed from the two clades. A median-joining network showed three groups of haplotypes were to a high extent concordant with the phylogenetic tree. The haplotype clustering was consistent with their geographic distribution. Nei’s net sequence divergences amongst the three groups ranged from 0.010 to 0.018 and indicated three subspecies, two of which inhabit XUAR. We detected strong differentiation between northern (NX) and southern (SX) XUAR populations overall (F_ST?=?0.4448, P?相似文献   

Photoperiod and variation in life history traits in core and peripheral populations in the damselfly Lestes sponsa

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Phylogeography and genetic structure of the orchid Himantoglossum hircinum (L.) Spreng. across its European central–marginal gradient

Aim This study aims to link demographic traits and post‐glacial recolonization processes with genetic traits in Himantoglossum hircinum (L.) Spreng (Orchidaceae), and to test the implications of the central–marginal concept (CMC) in Europe. Location Twenty sites covering the entire European distribution range of this species. Methods We employed amplified fragment length polymorphism (AFLP) markers and performed a plastid microsatellite survey to assess genetic variation in 20 populations of H. hircinum located along central–marginal gradients. We measured demographic traits to assess population fitness along geographical gradients and to test for correlations between demographic traits and genetic diversity. We used genetic diversity indices and analyses of molecular variance (AMOVA) to test hypotheses of reduced genetic diversity and increased genetic differentiation and isolation from central to peripheral sites. We used Bayesian simulations to analyse genetic relationships among populations. Results Genetic diversity decreased significantly with increasing latitudinal and longitudinal distance from the distribution centre when excluding outlying populations. The AMOVA revealed significant genetic differentiation among populations (F_ST = 0.146) and an increase in genetic differentiation from the centre of the geographical range to the margins (except for the Atlantic group). Population fitness, expressed as the ratio N_R/N, decreased significantly with increasing latitudinal distance from the distribution centre. Flower production was lower in most eastern peripheral sites. The geographical distribution of microsatellite haplotypes suggests post‐glacial range expansion along three major migratory pathways, as also supported by individual membership fractions in six ancestral genetic clusters (C1–C6). No correlations between genetic diversity (e.g. diversity indices, haplotype frequency) and population demographic traits were detected. Main conclusions Reduced genetic diversity and haplotype frequency in H. hircinum at marginal sites reflect historical range expansions. Spatial variation in demographic traits could not explain genetic diversity patterns. For those sites that did not fit into the CMC, the genetic pattern is probably masked by other factors directly affecting either demography or population genetic structure. These include post‐glacial recolonization patterns and changes in habitat suitability due to climate change at the northern periphery. Our findings emphasize the importance of distinguishing historical effects from those caused by geographical variation in population demography of species when studying evolutionary and ecological processes at the range margins under global change.     

Chloroplast population genetics reveals low levels of genetic variation and conformation to the central–marginal hypothesis in Taxus wallichiana var. mairei,an endangered conifer endemic to China

The central–marginal hypothesis predicts that geographically peripheral populations should exhibit reduced genetic diversity and increased genetic differentiation than central populations due to smaller effective population size and stronger geographical isolation. We evaluated these predictions in the endangered conifer Taxus wallichiana var. mairei. Eight plastid simple sequence repeats (cpSSRs) were used to investigate plastid genetic variation in 22 populations of Taxus wallichiana var. mairei, encompassing nearly its entire distribution range. Low levels of plastid genetic variation and differentiation were detected in the populations, and the findings were attributed to low mutation rates, small population sizes, habitat fragmentation and isolation, and effective pollen or seed dispersal. Hunan and Hubei were identified as major refugia based on the number of private haplotypes and species distribution modeling. Trends in plastid genetic diversity and genetic differentiation from central to peripheral populations supported the predictions of the central–marginal hypothesis. In scenarios wherein the future climate becomes warmer, we predict that some peripheral populations will disappear and southern and southeastern regions will become significantly less habitable. Factors that include the levels of precipitation during the driest month, annual precipitation level, and annual temperature range will be decisive in shaping the future distribution of these populations. This study provides a theoretical basis for the conservation of T. wallichiana var. mairei.     

Ancient onset of geographical divergence,interpopulation genetic exchange,and natural selection on the Mc1r coat‐colour gene in the house mouse (Mus musculus)

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single‐gene networks revealed not only gene‐specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variation. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 778–794.     

Genetic differentiation of the Thorn‐tailed Rayadito Aphrastura spinicauda (Furnariidae: Passeriformes) revealed by ISSR profiles suggests multiple palaeorefugia and high recurrent gene flow

Nucleotide sequence data (cytochrome b) and ISSR genomic fingerprints were used to analyse the genetic variation and population differentiation in Thorn‐tailed Rayadito, a widespread Patagonian forest bird. We included samples from eight populations of Thorn‐tailed Rayadito covering most of the distribution range of the species: from fragmented patches of Olivillo forest in northern Chile to Isla Navarino forests in the extreme south of South America. Low levels of genetic diversity were found among populations, with a large within‐population molecular variance indicating high levels of gene flow. The multivariate and cluster analyses based on ISSR markers show that the subspecies bullocki (from Mocha Island) differs significantly from all other populations. The subspecies fulva (Chiloé Island) shows less differentiation than bullocki, sharing several alleles with continental populations. Bayesian analyses suggest that the Mocha Island population contributes most to the total genetic diversity observed in the species. Mantel tests revealed no significant correlation between geographical distance and pairwise genetic distance and cytochrome b sequence analyses failed to detect differentiation among subspecies. Mocha Island might have been a palaeorefuge and this population may have diversified by genetic drift after the last glacial maximum. There is also the possibility of a postglacial colonization of the Thorn‐tailed Rayadito from an austral palaeorefugium, supporting a multiple refugia hypothesis. This study illustrates the usefulness of the rarely used ISSR genomic fingerprint method in avian phylogeography.     

Colour polymorphism and genetic variation in Idotea baltica populations from the Adriatic Sea and Baltic Sea

Phenotypic and genetic variation was studied in two of the four European subspecies of the marine isopod Idotea baltica; the Mediterranean I. b. basteri and the Baltic I. b. baltica. Spatial and temporal patterns of colour polymorphism were analysed in northern Adriatic and western Baltic Sea populations. Pronounced differences in phenotype composition were observed between populations of both subspecies as seen in the distribution of various colour variants bilineata, lineata, flavafusca and several combined forms). Compared with Adriatic samples, western Baltic Sea populations show higher phenotypic diversity. To obtain an estimate of the degree of genetic divergence between the subspecies, 12 gene-enzyme systems were investigated electrophoretically. The results obtained indicate a relatively high level of genetic variation; I. b. basteri from the nothern Adriatic tends to be more polymorphic and more heterozygous than I. b. baltica from the western Baltic. Both subspecies share identical electrophoretic mobilities of the homologous enzyme proteins examined; however, in allelic composition they exhibit significant differences at approximately half the number of loci scored. The genetic distance (Nei's D) measured at the subspecific level was 0.04. Amounts and geographical patterns of variation, observed both in colour phenotype and electrophoretic variation, are considered.