Fine scale population genetic structure of pumas in the Intermountain West

In this study, I examined the population genetic structure of subpopulations of pumas (Puma concolor) in Idaho and surrounding states. Patterns of genetic diversity, population structure, levels of inbreeding, and the relationship between genetic differentiation and dispersal distance within and between 15 subpopulations of pumas were compared. Spatial analyses revealed that the Snake River plain was an important barrier to movement between northern and southern regions of Idaho. In addition, subpopulations south of the Snake River plain exhibited lower levels of genetic diversity, higher levels of inbreeding, and a stronger pattern of isolation by distance relative to subpopulations north of the Snake River plain. Lower levels of diversity and restricted gene flow are likely the result of historically lower population sizes in conjunction with more recent changes in habitat use and available dispersal corridors for movement. The subdivision of puma populations north and south of the Snake River plain, along with the patterns of genetic diversity within regions, indicate that landscape features are affecting the population genetic structure of pumas in Idaho. These results indicate that information about the effects of landscape features on the distribution of genetic diversity should be considered when designing plans for the management and conservation of pumas.     

Population genetic structure of Vitex negundo (Verbenaceae) in Three-Gorge Area of the Yangtze River: The riverine barrier to seed dispersal in plants

Previous studies have demonstrated that large rivers can influence inter- and intra-specific gene flow for many animals. The effects of large rivers on the genetics of plant populations have focused on either hydrochoric impacts of water current on gene flow or genetic differentiation among populations from different watersheds. Few studies have explicitly tested the barrier effects on plant gene flow across banks of large rivers, especially their relative effects on pollen and seed dispersals. The Yangtze River (Changjiang River), one of the major rivers of the world, provides an excellent model to evaluate the impacts of rivers on gene flow in plants. Using RAPD (random amplified polymorphic DNA) and cpDNA (chloroplast DNA) markers, we investigated the genetic structure of 10 populations of Vitex negundo in two regions of Three-Gorge Area along the Yangtze River. Each region contained two populations on the north bank, two on the south bank and one island population along the river. The analyses indicated low RAPD between banks, and similar or a little higher differentiation between populations within the same bank. In contrast, a large proportion of chloroplast polymorphism was ascribed to among-bank variation but much lower cpDNA differentiation was among populations within the same bank. These results indicate that the Yangtze River represents a general barrier to the dispersal of seeds but not to the movement of pollen in V. negundo. The cpDNA genetic distances or differentiations between the island populations and those on either bank of the river are intermediate to those between the banks across the river, implying that the islands in the Yangtze River may serve as a stepping-stone for seed dispersal. Our results suggest that large rivers may serve as a general barrier, not only for the movement of animals, but also for the dispersal of plants, which should be of great significance for the conservation of biodiversity around the rivers.     

Population genetics and phylogeography of freshwater mussels in North America, Elliptio dilatata and Actinonaias ligamentina (Bivalvia: Unionidae)

Extrinsic and intrinsic forces combined shape the population structure of every species differently. Freshwater mussels are obligate parasites to a host fish during a juvenile stage (glochidia). Elliptio dilatata (ED) and Actinonaias ligamentina (AL) are co-occurring freshwater mussel taxa with similar North American distribution and share some potential host fish. Using mitochondrial DNA, we determined the genotypes of 190 + individuals from collection sites in at least two tributaries in the Lake Erie and Ohio River watersheds, along with the Ouachita and Strawberry rivers in the southeast. Both species had followed a stepping-stone model of dispersal, with greater pairwise genetic structure among collection sites of ED. Also, phylogeographical analysis for ED found significant geographical structuring of haplotype diversity. Overall, within-population variation increased significantly from north to south, with low genetic diversity in the Strawberry River. We calculated significant among-population structure for both species (ED: Phi(ST) = 0.62, P < 0.001; AL: Phi(ST) = 0.16, P < 0.001). Genetic analysis identified the Ouachita River as an area of significant reproductive isolation for both species. Results for AL indicated dispersal into northern areas from two genetically distinct glacial refugia, where results for ED indicated dispersal followed by low gene flow in northern areas. The conservation strategies for mussels that co-occur in the same 'bed' could be species specific. Species such as ED have management units on the population scale, where AL has a more homogeneous genetic structure across its range.     

Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halli

Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli , a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure.     

Assessing natural and disturbed population structure in European grayling Thymallus thymallus: melding phylogeographic,population genetic and jurisdictional perspectives for conservation planning

Natural and human‐mediated population structure of European grayling Thymallus thymallus was assessed in primarily Austrian reaches of the Danube River catchment. Data on phylogeographic structure based on mitochondrial DNA (mtDNA) were combined with variation found across 13 microsatellite loci to assess introgression stemming from stocking activities. Populations north of the Alps generally showed no signs of long‐term introgression from allochthonous stocks, although one population comprised two distinct genotypic groups, one of which may stem from recently stocked material. South of the Alps, levels of introgression with stocks from the north were extensive and only one of six populations is believed to represent a reference state. Allelic diversity and expected heterozygosity were positively correlated with mtDNA admixture supporting more recent introgression and that there is little or no reproductive barrier between these two major lineages north and south of the Alps. A third unrelated mtDNA lineage is described from the Lafnitz, a tributary of the Raab drainage. The high lineage diversity in the upper Austrian Danube is not concordant with an existing model of T. thymallus evolutionarily significant units in Europe. Caveats in naming such units or following a strict hierarchical conservation unit structure for broadly distributed species with complex phylogeographic distributions stretching over various jurisdictions are discussed. The necessity of using both phylogeographic and population genetic approaches in evaluating the history and conservation value of populations in a conservation context is additionally highlighted.     

Genetic differentiation among migrant and resident populations of the threatened Asian houbara bustard

The Asian houbara bustard Chlamydotis macqueenii is a partial migrant of conservation concern found in deserts of central Asia and the Middle East. In the southern part of the species range, resident populations have been greatly fragmented and reduced by sustained human pressure. In the north, birds migrate from breeding grounds between West Kazakhstan and Mongolia to wintering areas in the Middle East and south central Asia. Extensive satellite tracking has shown substantial partitioning in migration routes and wintering grounds, suggesting a longitudinal barrier to present-day gene flow among migrants. In this context, we explored genetic population structure using 17 microsatellite loci and sampling 108 individuals across the range. We identified limited but significant overall differentiation (F(CT) = 0.045), which was overwhelmingly due to the differentiation of resident Arabian populations, particularly the one from Yemen, relative to the central Asian populations. Population structure within the central Asian group was not detectable with the exception of subtle differentiation of West Kazakh birds on the western flyway, relative to eastern populations. We interpret these patterns as evidence of recent common ancestry in Asia, coupled with a longitudinal barrier to present-day gene flow along the migratory divide, which has yet to translate into genetic divergence. These results provide key parameters for a coherent conservation strategy aimed at preserving genetic diversity and migration routes.     

Sampling affects the detection of genetic subdivision and conservation implications for fisher in the Sierra Nevada

The small population of fisher (Pekania pennanti) in the southern Sierra Nevada is completely geographically and genetically isolated putting it at increased risk of extinction. Previous research using a clustered sampling scheme found a high amount of genetic subdivision within the southern Sierra Nevada population hypothesized to be caused by the Kings River Canyon. In this study, we use a larger and more geographically continuous set of genetic samples (n = 127) than was previously available to test this hypothesis and evaluate the genetic structure of the population. Both spatial and non-spatial population assignment models found three primary genetic clusters with moderate divergence between the clusters (F _ST = 0.05–0.13) at 10 microsatellite loci. These clusters appear to be associated with areas around the Kings River and Mountain Home State Demonstration Forest. One model also detected additional fine scale subdivision north of the Kings River that may be evidence of founder effects from a recent population expansion. The amount of population subdivision detected in this study is lower than previously found and indicates that while certain landscape features may reduce gene flow, these landscape features may be less of a barrier than initially thought. In the previous work, samples were collected in clusters which can inflate estimates of population structure by increasing the likelihood of oversampling related individuals. This study demonstrates how clustered sampling from a continuously distributed population can affect the assessment of population subdivision and influence conservation implications.     

Analyses of gene flow among populations of deer mice (Peromyscus maniculatus) at sites near hantavirus pulmonary syndrome case-patient residences

Gene flow and potential for Sin Nombre virus (SNV) trafficking of the deer mouse (Peromyscus maniculatus) was studied in Delta and Mesa counties of western Colorado (USA). The study areas included Grand Mesa and surrounding grazing and agricultural areas. This area has several natural potential barriers to rodent gene flow, including rivers, cliffs, and mountains. Ten study sites were utilized in a spatially nested design ranging from 0.65-81 km apart; four of these sites were at or near human hantavirus pulmonary syndrome (HPS) case-patient residences. One HPS case occurred on the north side of Grand Mesa in 1993; the other three (two confirmed, one presumptive) occurred on the south side of Grand Mesa between 1999-2000. Blood and tissue samples were collected from each of 221 deer mice captured from 1999-2000. Blood samples were tested for IgG antibody to SNV. At least one deer mouse had antibody to SNV at nine of 10 sites. Genomic DNA was isolated from tissue samples and alleles at six microsatellite loci were amplified by polymerase chain reaction (PCR). Polymorphisms were resolved on denaturing polyacrylamide gels and visualized by silver staining. Traditional population genetic analyses of this study indicated moderate population subdivision among the populations surveyed, slight evidence of isolation by distance, and that the Gunnison River system may hinder gene flow in this area. Application of assignment tests indicated that approximately 73-85% of mice were assigned to their population of capture. Many of the misclassifications occurred among sites less than 1 km apart; however, some long-distance misclassifications were noted. Additionally, some misclassifications were noted among study sites on different sides of the Gunnison River system, indicating that the riparian corridor of this system may facilitate some gene flow. Overall, these data indicate that SNV trafficking is more likely at the local level, but some long-distance trafficking may be possible, especially where select habitat variables favor long-distance movements.     

Foundations for conservation of intraspecific genetic diversity revealed by analysis of phylogeographical structure in the endangered endemic lizard Podarcis lilfordi

Aim  To describe and analyse phylogeographical patterns in the endangered endemic lizard Podarcis lilfordi from across its remaining range and thereby establish baseline information on genetic diversity that will help determine conservation priorities and assist future reintroduction programs.
Location  Balearic Islands, Spain.
Methods  We analysed mitochondrial DNA (2382 bp sequence from eight genes) from 118 individuals and characterized the relationships among haplotypes using parsimony networks, as well as phylogenetic inference. Analyses of historical gene flow and population growth were used to provide further insights into population histories.
Results  Four unconnected parsimony networks were obtained that mirrored the main clades in the phylogenetic tree: (I) all Menorcan populations, (II) Dragonera, Malgrats and Toro islands (Western Mallorca) (III and IV) and the remaining populations from Cabrera and Mallorca. Two major haplotype groups were detected in Menorca (I) and these provided signatures of a demographic expansion and asymmetrical historical gene flow, respectively, concordant with the expected direction of colonization from south to north of the island. Populations from western Mallorca (II) showed evidence of historical allopatric fragmentation events following isolation around the start of the Pleistocene. In networks III and IV, Cabreran populations appear to have become isolated from north and south Mallorca quite recently, with asymmetric gene flow indicating a northwards dispersal direction.
Main conclusions  P. lilfordi is a genetically diverse species that shows substantial mtDNA structuring both between regions and, at a finer scale, between some islet populations within regions. The precarious state of some islet populations shown here to be quite divergent (e.g. Toro island in western Mallorca) means that conservation of this intraspecific biodiversity requires urgent action.     

Species‐level view of population structure and gene flow for a critically endangered primate (Varecia variegata)

Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining V. variegata range. We used 10 polymorphic microsatellite loci and ~550 bp of mtDNA sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the Mangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNA haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average F_ST (0.247) and Φ_ST (0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.     

Rivers influence the population genetic structure of bonobos (Pan paniscus)

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.     

High levels of population structure caused by habitat islands in the malarial vector Anopheles scanloni

The genetic structure of four populations of the malarial vector Anopheles scanloni in Thailand was studied using mitochondrial DNA sequences. Four highly divergent lineages were observed, all with signals of population expansion. Since An. scanloni is restricted to 'islands' of limestone karst habitat, this suggests there is a metapopulation-type dynamic in this species, with restricted gene flow, extinctions and drift all contributing to lineage divergence. Historical environmental change and marine transgressions may also have contributed to population extinction, expansion and divergence. Although there is some current gene flow inferred between nearby populations, it is extremely restricted between the northern and southern populations, which also differed by one fixed polymorphism at the ITS2 rDNA locus. Crossing experiments showed no post-mating barriers existing between the north and the south, but the lack of gene flow between these populations could ultimately result in speciation and has implications for malaria control strategies.     

Perpendicular axes of differentiation generated by mitochondrial introgression

Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north–south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north–south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial‐nuclear combinations. This likely generated an axis of coastal‐inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north–south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).     

Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east-west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour-joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.     

The Neovolcanic Axis Is a Barrier to Gene Flow among Aedes aegypti Populations in Mexico That Differ in Vector Competence for Dengue 2 Virus

Background

Aedes aegypti is the main mosquito vector of the four serotypes of dengue virus (DENV). Previous population genetic and vector competence studies have demonstrated substantial genetic structure and major differences in the ability to transmit dengue viruses in Ae. aegypti populations in Mexico.

Methodology/Principal Findings

Population genetic studies revealed that the intersection of the Neovolcanic axis (NVA) with the Gulf of Mexico coast in the state of Veracruz acts as a discrete barrier to gene flow among Ae. aegypti populations north and south of the NVA. The mosquito populations north and south of the NVA also differed in their vector competence (VC) for dengue serotype 2 virus (DENV2). The average VC rate for Ae. aegypti mosquitoes from populations from north of the NVA was 0.55; in contrast the average VC rate for mosquitoes from populations from south of the NVA was 0.20. Most of this variation was attributable to a midgut infection and escape barriers. In Ae. aegypti north of the NVA 21.5% failed to develop midgut infections and 30.3% of those with an infected midgut failed to develop a disseminated infection. In contrast, south of the NVA 45.2% failed to develop midgut infections and 62.8% of those with an infected midgut failed to develop a disseminated infection.

Conclusions

Barriers to gene flow in vector populations may also impact the frequency of genes that condition continuous and epidemiologically relevant traits such as vector competence. Further studies are warranted to determine why the NVA is a barrier to gene flow and to determine whether the differences in vector competence seen north and south of the NVA are stable and epidemiologically significant.     

Origin and phylogeography of African savannah elephants (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in Kruger and nearby parks in southern Africa

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger and nearby regions.     

极度濒危植物五针白皮松的保护遗传学研究

用随机扩增多态(RAPD)方法对极度濒危植物五针白皮松(Pinus squamata X.W.Li)的遗传多样性和居群遗传结构进行了研究。14个随机引物共获得93条RAPD谱带,其中6条为多态带,多态位点百分率仅为6．45％,遗传多样性极低。Shannon指数I和Nei指数h在种内也只有0．020和0．030,两个亚居群间(半阴坡亚居群与半阳坡亚居群)遗传分化程度不高,遗传分化系数Gst只有0．110,与大多数松科植物近似,居群每代迁移数为4．032。五针白皮松极低的遗传多样性可能是由于它在演化过程中遭受过严重的灾害,造成严重的瓶颈效应,丧失其大部分遗传变异。在随后的演化过程中由于遗传漂变、自交衰退等小种群现象,导致遗传多样性的进一步丧失。另外,阔叶树种对其生存的挤压和人类的干扰也是导致五针白皮松遗传多样性降低的因素之一。本文最后对该结果的保护生物学意义进行了评价。     

Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time

The isolation of phylogenetically distinct primate immunodeficiency viruses from at least seven wild-born, captive chimpanzees indicates that viruses closely related to HIV-1 may be endemic in some wild chimpanzee populations. The search for the chimpanzee population or populations harbouring these viruses is therefore on. This paper attempts to answer the question of whether or not such populations of chimpanzees are likely to exist at all, and, if so, where they are likely to be found. We summarize what is known about gene flow in wild populations of chimpanzees, both between major phylogeographical subdivisions of the species, and within these subdivisions. Our analysis indicates that hitherto undocumented reproductively isolated chimpanzee populations may in fact exist. This conclusion is based on the observation that, despite limited geographical sampling and limited numbers of genetic loci, conventional notions of the nature and extent of chimpanzee gene flow have recently been substantially revised. Molecular genetic studies using mitochondrial DNA sequences and hypervariable nuclear microsatellite markers have indicated the existence of heretofore undocumented barriers to chimpanzee gene flow. These studies have identified at least one population of chimpanzees genetically distinct enough to be classified into a new subspecies (Pan troglodytes vellerosus). At the same time, they have called into question the long-accepted genetic distinction between eastern chimpanzees (Pan troglodytes schweinfurthii) and western equatorial chimpanzees (Pan troglodytes troglodytes). The same studies have further indicated that gene flow between local populations is more extensive than was previously thought, and follows patterns sometimes inconsistent with those documented through direct behavioural observation. Given the apparently incomplete nature of the current understanding of chimpanzee gene flow in equatorial Africa, it seems reasonable to speculate that a chimpanzee population or populations may exist which both harbour the putative HIV-1 ancestor, and which have remained reproductively isolated from other chimpanzee populations over the time-scale relevant to the evolution of the SIVcpz-HIV-1 complex of viruses. Continued extensive sampling of wild chimpanzee populations, both for their genes and their viruses, should be performed quickly considering the high probability of extinction that many wild chimpanzee populations face today. The history of human-chimpanzee contacts is discussed.     

Genetic structure in the marbled rockfish (Sebastiscus marmoratus) across most of the distribution in the northwestern Pacific

The marbled rockfish (Sebastiscus marmoratus) is an important species that is widely distributed across the marginal seas of the northwestern Pacific. Several kinds of DNA markers, such as amplified fragment length polymorphisms (AFLP), mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs), have been used to assess the population genetic characteristics of this species in previous studies. However, there have been no genetic profiling studies to cover the entire distribution. Here, six highly polymorphic microsatellite markers were applied to 18 populations across a spatially large area (from the Sea of Japan in the north to the South China Sea in the south). The results showed that the whole population exhibits high, stable genetic diversity, low relatedness and large effective population size. There was very weak genetic differentiation overall and no isolation by distance occurred among the populations, which may be attributed to significant contemporary gene flow, each generation. The above results may lead us to infer that the recent S. marmoratus population structure could be considered as one large integrated population. The present study will be beneficial to population conservation and fisheries management of S. marmoratus and will lead to better insights into the genetic characteristics of other species that belong to the Sebastidae family.     

Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits

The Atlantic Iberian brown trout is at the southwestern limit of its distribution. At this ecological edge, which was once a glacial refugia, anadromy becomes less common as increased water temperatures restricted populations closer to the headwaters. We examined 847 individuals from 20 populations from throughout this region and assessed spatial genetic structure using 11 protein and four microsatellite loci. The higher levels of heterozygosity and allelic diversity north of the southernmost limit of anadromy (SLA), as well as an isolation-by-distance model of population structure, likely influenced by the anadromous forms, suggest that more stable demographic conditions existed over time in this region. Populations south of the SLA were highly differentiated given the restricted size of the area (protein F(ST) = 0.16 in the north and 0.63 in the south of the SLA; microsatellite F(ST) = 0.18 in the north and 0.70 in the south of the SLA). The low levels of heterozygosity and the pattern of southward allele depletion in resident populations is indicative of fragmentation, caused by stressful ecological conditions that reduced the anadromy (restricting gene flow) and the effective population sizes (higher genetic drift), which, in combination, dramatically decreased within-population genetic variation and increased among-population genetic variation. The higher gene diversity north of the SLA does not reflect ancestry but rather the signature of a population size expansion, as evidence suggest the persistence of older populations (with several private alleles) south of the SLA. These data support a scenario that demonstrates how contemporary events (critical ecological conditions) can moderate historical influences, suggesting that careful interpretation of the evolutionary history of glacial refugia is necessary, especially where populations persisted for a long time but not always with optimal ecological conditions. These peripheral populations are of high conservation value and should be preserved to help conserve the future potential of the species.