Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus

The taxonomic status of brown bears in the Caucasus remains unclear. Several morphs or subspecies have been identified from the morphological (craniological) data, but the status of each of these subspecies has never been verified by molecular genetic methods. We analysed mitochondrial DNA sequences (control region) to reveal phylogenetic relationships and infer divergence time between brown bear subpopulations in the Caucasus. We estimated migration and gene flow from both mitochondrial DNA and microsatellite allele frequencies, and identified possible barriers to gene flow among the subpopulations. Our suggestion is that all Caucasian bears belong to the nominal subspecies of Ursus arctos. Our results revealed two genetically and geographically distinct maternal haplogroups: one from the Lesser Caucasus and the other one from the Greater Caucasus. The genetic divergence between these haplogroups dates as far back as the beginning of human colonization of the Caucasus. Our analysis of the least‐cost distances between the subpopulations suggests humans as a major barrier to gene flow. The low genetic differentiation inferred from microsatellite allele frequencies indicates that gene flow between the two populations in the Caucasus is maintained through the movements of male brown bears. The Likhi Ridge that connects the Greater and Lesser Caucasus mountains is the most likely corridor for this migration.     

Ecological factors influence population genetic structure of European grey wolves

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.     

Dispersal and population structure of a New World predator, the army ant Eciton burchellii

The army ant Eciton burchellii is probably the most important arthropod predator in the Neotropics, and many animal species depend upon it. Sex-biased dispersal with winged males and permanently wingless queens may render this species especially sensitive to habitat fragmentation and natural barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little differentiation between subpopulations (F(ST) = 0.017), mitochondrial differentiation was maximal in some cases (Phi(ST) = 1). This suggests that, while females are not capable of crossing barriers such as large rivers, flying males are able to promote nuclear gene flow between the studied forest patches. Consistent with this interpretation, we did not find any evidence for inbreeding or genetic deterioration on Barro Colorado Island over the last 90 years since its formation.     

North‐facing slopes and elevation shape asymmetric genetic structure in the range‐restricted salamander Plethodon shenandoah

Species with narrow environmental tolerances are often distributed within fragmented patches of suitable habitat, and dispersal among these subpopulations can be difficult to directly observe. Genetic data can help quantify gene flow between localities, which is especially important for vulnerable species with a disjunct range. The Shenandoah salamander (Plethodon shenandoah) is a federally endangered species known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture from individuals collected across all three mountaintops. Applying population and landscape genetic methods, we found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genomes indicated a deep split between the most southern population and the genetically similar central and northern populations. Although there was some mitochondrial haplotype‐splitting between the central and northern populations, there was admixture in nuclear markers. This is indicative of either a recent split or current male‐biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north‐facing slopes at mid‐elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of incorporating landscape features in understanding and predicting the movement and fragmentation of this range‐restricted salamander species across space.     

Recent divergence,intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi‐Atlantic peatmoss populations

Several lines of evidence suggest that recent long‐distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi‐Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (im and migrate ) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F_ST = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long‐range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000–289 000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi‐Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.     

Genetic structure in the European endemic seabird,Phalacrocorax aristotelis,shaped by a complex interaction of historical and contemporary,physical and nonphysical drivers

Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long‐distance dispersal triggered by extreme environmental conditions (e.g. population crashes).     

利用ITS1和Cyt b位点的DNA单链空间构型多样性研究黑脚硬蜱的种群结构

黑脚硬蜱 (Ixodesscapularis)是莱姆病的主要传毒媒介。本文利用从 12个不同地点采集的 85 3个样本 ,采用DNA单连构型多样性的分子技术 (DNAsinglestrandconformationpolymorphisms)对黑脚硬蜱的种群结构进行了分析。线粒体细胞色素b (Cytb)和核糖体rRNA基因的内部转录空间ITS1被用为种群目标分子标记位点。在Cytb位点上 ,总共发现 7个单倍基因型。在ITS1位点上 ,共发现 13个基因型。基因型频率分析结果显示 ,沿美国东海岸分布的黑脚硬蜱隶属于两个不同的南北种群 ,但是基因流在地理区域间频繁发生。尽管蜱自身的迁徙扩散能力有限 ,但地理区域内个体间的遗传变异程度仍然较大 ,这可能与黑脚硬蜱寄主动物的频繁迁移有关。另外 ,本研究资料显示 ,南方种群的遗传变异程度明显大于北方种群     

REPRODUCTIVE ISOLATION BETWEEN SYMPATRIC RACES OF PEA APHIDS. I. GENE FLOW RESTRICTION AND HABITAT CHOICE

Determining the extent and causes of barriers to gene flow between genetically divergent populations or races of single species is an important complement to post facto analyses of the causes of reproductive isolation between recognized species. Sympatric populations of pea aphids (Acyrthosiphon pisum Harris, Homoptera: Aphididae) on alfalfa and red clover are highly genetically divergent and locally adapted. Here, hierarchical estimates of population structure based on F_st suggest that gene exchange between closely adjacent aphid populations on the two hosts is highly restricted relative to that among fields of the same host plant. Although these host-associated races are presently considered to be the same subspecies, they appear to be significantly reproductively isolated, suggesting incipient speciation. Habitat (host) choice was investigated as the first in a temporal series of factors that could reduce gene exchange between these sympatric populations. Field studies of winged colonists to newly planted fields of each host suggest pronounced habitat fidelity. This result was verified using replicated observations of the host choice behavior of different aphid genotypes for which the relative demographic performance on each host was known. These laboratory observations of behavior revealed a strong genetic correlation between habitat choice (or acceptance) and the relative performance in each habitat. Because mating occurs on the host plant, habitat choice in this system leads to assortative mating and is therefore a major cause of reproductive isolation between the sympatric pea aphid populations on alfalfa and clover. However, the extent of dispersal between hosts estimated from the field study of winged colonists (9–11%) is too great to be consistent with the genetic divergence estimated between the races. This suggests that barriers to gene flow other than host choice also exist, such as selection against migrants or hybrids in the parental environments, hybrid sterility, or hybrid breakdown.     

Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.     

Ecological specialization correlates with genotypic differentiation in sympatric host-populations of the pea aphid

The pea aphid, Acyrthosiphon pisum, encompasses distinct host races specialized on various Fabaceae species, but the extent of genetic divergence associated with ecological specialization varies greatly depending on plant and geographic origins of aphid populations. Here, we studied the genetic structure of French sympatric pea aphid populations collected on perennial (pea and faba bean) and annual (alfalfa and red clover) hosts using 14 microsatellite loci. Classical and Bayesian population genetics analyses consistently identified genetic clusters mostly related to plant origin: the pea/faba bean cluster was highly divergent from the red clover and the alfalfa ones, indicating they represent different stages along the continuum of genetic differentiation. Some genotypes were assigned to a cluster differing from the one expected from their plant origin while others exhibited intermediate genetic characteristics. These results suggest incomplete barriers to gene flow. However, this limited gene flow seems insufficient to prevent ecological specialization and genetic differentiation in sympatry.     

Disturbance of the indigenous gene pool of the threatened brook lamprey Lethenteron sp. S by intraspecific introgression and habitat fragmentation

Artificial introduction and habitat fragmentation affect the indigenous gene pools of fluvial animals. To investigate the effect of human activities on the genetic population structure of vulnerable brook lamprey Lethenteron sp. S in a single river system, samples from 12 tributaries of the Jinzu River, Japan, were analyzed using mitochondrial and microsatellite DNA markers. Exogenous Lake Biwa (Japan) haplotypes and alleles were detected in lampreys from several Jinzu River tributaries. Since Lake Biwa is the source of the commercial ayu fish Plecoglossus altivelis that is introduced in the Jinzu River, the exogenous Lake Biwa lamprey genotypes in the Jinzu River probably originated from the Lake Biwa lampreys that were unintentionally introduced along with the ayu fish. Bayesian admixture and mitochondrial DNA analyses revealed various genetic disturbance phases of the exogenous genotypes in the Jinzu River, such as the six indigenous populations, four admixed populations with low frequencies (average admixture proportion = 0.02–0.04; exogenous haplotype proportion <0.01), one introgressed population (0.71 and 0.57) and one population almost displaced by exogenous genotypes (0.93 and 0.96). Samples from three tributaries with weirs were genetically differentiated from the others by using pairwise F _ST and Bayesian analyses; the results suggested isolation by the weirs. Reduced mitochondrial DNA diversity was observed in 1 of the 3 samples probably due to reduced population size. These findings indicate that the indigenous lamprey populations in the Jinzu River are seriously affected by introgression with exogenous genotypes via unintentional introduction and habitat fragmentation by weirs.     

Phylogeography of the yucca moth Tegeticula maculata: the role of historical biogeography in reconciling high genetic structure with limited speciation

Tegeticula maculata is one of the most ancient and morphologically variable lineages within the yucca moths, yet has apparently undergone little diversification in comparison with much younger yucca moth lineages that have rapidly diversified. A phylogeographic approach was used to determine the number of independent lineages within T. maculata and to examine whether these patterns corresponded with morphological differences between its subspecies maculata and extranea. Phylogenetic analysis of mitochondrial DNA sequence variation indicated that the two subspecies are in separate clades, but there was also an equally deep split within subspecies maculata. There was no evidence for gene flow among regions and there was considerable substructure within clades. The phylogeographic structure of moth populations among and within subspecies can be explained in part by historical biogeographic boundaries and increasingly patchy postglacial distribution of the exclusive host plant, Hesperoyucca whipplei. Local specialization and co-adaptation would be possible in the absence of apparent gene flow, yet gross morphological divergence is limited to the very old split between the subspecies. Sorting of ancient mitochondrial lineages followed by local genetic differentiation may explain the pattern of high genetic structure with limited speciation.     

Re-examination of a proposed case of stasipatric speciation: phylogeography of the Australian morabine grasshoppers (Vandiemenella viatica species group)

Karyotypic differences have been used for delimiting populations or species, although whether these mutations provide strong barriers to gene flow between populations and promote speciation remains contentious. In this study, we assessed whether 11 chromosomal races of Australian morabine grasshoppers ( Vandiemenella viatica species group) represent genetically distinct populations by analyses of cytological and allozyme (35 loci) data and DNA sequences of the elongation factor-1 alpha ( EF -1α), anonymous Mvia11 , and mitochondrial cytochrome c oxidase subunit I ( COI ) loci. While the Vandiemenella chromosomal taxa generally represent genetically distinct units, a substantial portion of the total genetic variation in our samples was not explained by the chromosomal variation. Mantel tests indicated that Vandiemenella populations were spatially structured and have maintained gene flow at a local scale within each of the taxa. The group was subdivided into 13 genetic clusters; four chromosomal taxa comprised single exclusive clusters, while others comprised more than one cluster or clusters shared with other taxa. Boundaries of these cryptic population subdivisions correspond with several biogeographical barriers, such as straits, gulfs, the Murray River, and an ancient mega-lake, Lake Bungunnia. The viatica species group was previously proposed to have diversified without major geographical separation based on the stasipatric speciation model; however, the present study suggests the involvement of allopatric fragmentation. Given extensive nonmonophyly of chromosomal taxa and incomplete barriers to gene flow among taxa, all Vandiemenella chromosomal taxa and genetically distinct populations within chromosomal taxa, except Vandiemenella pichirichi , should be regarded as populations of one species: Vandiemenella viatica .     

Patterns of spatial genetic structuring in the endangered limpet Patella ferruginea: implications for the conservation of a Mediterranean endemic

Patella ferruginea Gmelin, 1791 is an endangered marine gastropod endemic to the Western Mediterranean. Its range is restricted to the Sardinian-Corsican region (SCR), North Africa, a few scattered sites in Southern Spain, and Sicily. Inter-simple sequence repeat (ISSR) markers and three different mitochondrial DNA (mtDNA) regions, Cytochrome c Oxidase subunit I, 12S (small-subunit ribosomal RNA gene) and 16S (large-subunit ribosomal RNA gene), were used to investigate the presence of genetic population structuring. The mtDNA sequences showed very low levels of genetic differentiation. Conversely, ISSRs showed the presence of two main genetic groups, corresponding to Spain, North Africa and Sicily and the SCR. The SCR was further split into two subgroups. The ISSR results suggest that, on a regional scale, the genetic structure of P. ferruginea is mainly determined by the restriction of gene flow by dispersal barriers. On a more local scale human harvesting may play a crucial role in population structuring by increasing the effect of genetic drift.     

Divergent host plant specialization as the critical driving force in speciation between populations of a phytophagous ladybird beetle

Detecting the isolating barrier that arises earliest in speciation is critically important to understanding the mechanism of species formation. We tested isolating barriers between host races of a phytophagous ladybird beetle, Henosepilachna diekei (Coleoptera: Coccinellidae: Epilachnine), that occur sympatrically on distinct host plants. We conducted field surveys for the distribution of the beetles and host plants, rearing experiments to measure six potential isolating factors (adult host preference, adult and larval host performance, sexual isolation, egg hatchability, F(1) hybrid inviability, and sexual selection against F(1) hybrids), and molecular analyses of mitochondrial ND2 and the nuclear ITS2 sequences. We found significant genetic divergence between the host races, and extremely divergent host preference (i.e. habitat isolation) and host performance (i.e. immigrant inviability), but no other isolating barriers. The fidelity to particular host plants arises first and alone can prevent gene flow between differentiating populations of phytophagous specialists.     

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae)

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.     

Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group)

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.     

Spatial distribution of mitochondrial and microsatellite DNA variation in Daubenton's bat within Scotland

Daubenton's bat ( Myotis daubentonii ) is a known reservoir for European bat lyssavirus type 2 (EBLV-2). An appreciation of the potential for epidemiological spread and disease risk requires an understanding of the dispersal of the primary host, and any large-scale geographical barriers that may impede gene flow. The spatial pattern of microsatellite and mitochondrial DNA variation was examined to infer patterns of dispersal of bats among 35 populations across Scotland. DNA sequence variation at the mitochondrial control region and ND1 genes revealed two distinct phylogeographical clades, with generally nonoverlapping geographical distributions except for a small number of populations where both matrilines were found in sympatry. Such discontinuity suggests that Scotland was recolonised twice following the retreat of the Pleistocene ice sheet with little subsequent matrilineal introgression. However, eight microsatellite loci showed low levels of genetic divergence among populations, even between populations from the two distinct mitochondrial DNA clades. An overall, macrogeographical genetic isolation-by-distance pattern was observed, with high levels of gene flow among local populations. Apparently contrasting patterns of mitochondrial and microsatellite divergence at different scales could be explained by sex-specific differences in gene flow at large scales.     

Population subdivision and gene flow among wild orangutans

Genetic variability among populations of orangutans from Borneo and Sumatra was assessed using seven SSR loci. Most SSR loci were highly polymorphic and their allele frequencies exhibited substantial variation across subpopulations. While significant genetic subdivision was observed among the island populations, genetic distance did not increase with geographic distance and sufficient gene flow persists to prevent marked genetic subdivision. Since it is unlikely that the Bornean Orangutans dispersed naturally among locations separated by such formidable geographic barriers, human assistance might already have altered their genetic structure. Our data suggests that there may be at least two subspecific clades of orangutans within Borneo while Central Kalimantan animals may have become more genetically related to animals in Sumatra due to human intervention.