Microhabitat Types Promote the Genetic Structure of a Micro-Endemic and Critically Endangered Mole Salamander (Ambystoma leorae) of Central Mexico

The reduced immigration and emigration rates resulting from the lack of landscape connectivity of patches and the hospitality of the intervening matrix could favor the loss of alleles through genetic drift and an increased chance of inbreeding. In order for isolated populations to maintain sufficient levels of genetic diversity and adapt to environmental changes, one important conservation goal must be to preserve or reestablish connectivity among patches in a fragmented landscape. We studied the last known population of Ambystoma leorae, an endemic and critically threatened species. The aims of this study were: (1) to assess the demographic parameters of A. leorae and to distinguish and characterize the microhabitats in the river, (2) to determine the number of existing genetic groups or demes of A. leorae and to describe possible relationships between microhabitats types and demes, (3) to determine gene flow between demes, and (4) to search for geographic locations of genetic discontinuities that limit gene flow between demes. We found three types of microhabitats and three genetically differentiated subpopulations with a significant level of genetic structure. In addition, we found slight genetic barriers. Our results suggest that mole salamander’s species are very sensitive to microhabitat features and relatively narrow obstacles in their path. The estimates of bidirectional gene flow are consistent with the pattern of a stepping stone model between demes, where migration occurs between adjacent demes, but there is low gene flow between distant demes. We can also conclude that there is a positive correlation between microhabitats and genetic structure in this population.     

Microsatellite Analyses of Blacktip Reef Sharks (Carcharhinus melanopterus) in a Fragmented Environment Show Structured Clusters

The population dynamics of shark species are generally poorly described because highly mobile marine life is challenging to investigate. Here we investigate the genetic population structure of the blacktip reef shark (Carcharhinus melanopterus) in French Polynesia. Five demes were sampled from five islands with different inter-island distances (50–1500 km). Whether dispersal occurs between islands frequently enough to prevent moderate genetic structure is unknown. We used 11 microsatellites loci from 165 individuals and a strong genetic structure was found among demes with both F-statistics and Bayesian approaches. This differentiation is correlated with the geographic distance between islands. It is likely that the genetic structure seen is the result of all or some combination of the following: low gene flow, time since divergence, small effective population sizes, and the standard issues with the extent to which mutation models actually fit reality. We suggest low levels of gene flow as at least a partial explanation of the level of genetic structure seen among the sampled blacktip demes. This explanation is consistent with the ecological traits of blacktip reef sharks, and that the suitable habitat for blacktips in French Polynesia is highly fragmented. Evidence for spatial genetic structure of the blacktip demes we studied highlights that similar species may have populations with as yet undetected or underestimated structure. Shark biology and the market for their fins make them highly vulnerable and many species are in rapid decline. Our results add weight to the case that total bans on shark fishing are a better conservation approach for sharks than marine protected area networks.     

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (<Emphasis Type="Italic">Rallus obsoletus obsoletus</Emphasis>)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.     

Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management

The chamois is a habitat specialist ungulate occupying “continental archipelagos” of fragmented rocky habitats which are frequently restricted to high altitudes. It is not clear whether forest habitats separating such population fragments act as barriers to gene flow. We studied the genetic makeup of the chamois in a topographically diverse landscape at the contact zone of two mountain ranges in Slovenia. Based on sequences of mitochondrial DNA, all Slovenian populations belong to a Northern chamois (Rupicapra r. rupicapra) subspecies. The range of chamois in Slovenia encompasses three different regions, each with unique topography, habitat connectivity and abundance of chamois: the Alps, the Dinaric Mts., and the Pohorje Mts. The habitat of the chamois is extensive and more or less continuous in the Alps, but suboptimal and fragmented in the remaining regions. In agreement with neutral genetic theory, large Northern chamois populations tended to have higher allelic richness and observed heterozygosity. Spatial clustering bears the differentiation into four geographically associated clusters within Slovenia and also revealed a strong substructure within all mountain ranges with suboptimal chamois habitat. Surprisingly, some small Dinaric populations have stayed genetically isolated in restricted habitat patches, even if they are geographically very close to each other. The four clusters, each having a unique demographic history, should be regarded as independent units for management purposes.     

Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific

Background

Coral reefs in the Tropical Eastern Pacific (TEP) are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis from across its Indo-Pacific range indicate that gene flow (i.e. larval dispersal) is generally limited over hundreds of kilometers or less. Little is known about the population genetic structure and the dispersal potential of P. damicornis in the TEP.

Methodology

Using multilocus microsatellite data, we analyzed the population structure of TEP P. damicornis among and within nine reefs and test for significant genetic structure across three geographically and ecologically distinct regions in Panama.

Principal Findings/Conclusions

We detected significant levels of population genetic structure (global R_ST = 0.162), indicating restricted gene flow (i.e. larvae dispersal), both among the three regions (R_RT = 0.081) as well as within regions (R_SR = 0.089). Limited gene flow across a distinct environmental cline, like the regional upwelling gradient in Panama, indicates a significant potential for differential adaptation and population differentiation. Individual reefs were characterized by unexpectedly high genet diversity (avg. 94%), relatively high inbreeding coefficients (global F_IS = 0.183), and localized spatial genetic structure among individuals (i.e. unique genets) over 10 m intervals. These findings suggest that gene flow is limited in TEP P. damicornis populations, particularly among regions, but even over meter scales within populations.     

Low genetic diversity and limited gene flow in a dominant mangrove tree species (Rhizophora stylosa) at its northern biogeographical limit across the chain of three Sakishima islands of the Japanese archipelago as revealed by chloroplast and nuclear SSR analysis

We examined the genetic diversity, population structure and gene flow in a dominant mangrove tree (Rhizophora stylosa) at its northern biogeographical limit in Sakishima islands of the Japanese archipelago. Simple sequence repeat (SSR) markers from chloroplast (cpSSR) and nuclear DNA were used to analyze 16 populations recovered from various river basins across the chain of three Sakishima islands—Iriomote, Ishigaki and Miyako. The average number of alleles (1.7–2.7) and observed heterozygosities (0.031–0.216) at nuclear SSR and haploid diversity (0.000–0.489) at cpSSR across the populations suggested low genetic diversity in R. stylosa in Sakishima islands. cpSSR analysis identified two haplotypes, and Bayesian clustering analysis (nuclear SSR) revealed two genetic clusters. Analysis of molecular variance (nuclear SSR) showed significant population differentiations. Pairwise tests consistently revealed significant differentiation between most of the population pairs; however, the degrees of differentiations are generally correspondent to the relative geographical distances as suggested from pairwise F _ST and cpSSR genetic distances. Moreover, Mantel tests showed some signals of correlations between genetic distances (nuclear and chloroplast) and geographical distances. These results suggest that combined contribution of gene flow via pollen and propagule dispersal in R. stylosa mostly occurred between neighboring river basins. The appearances of two cpSSR haplotypes (maternal lineages) as well as two nuclear genetic clusters (putative ancestral lineages) at various river basins support the hypothesis that present-day R. stylosa populations across the Sakishima islands were established from few identical founders; however, significant differentiations among various river basins most likely resulted from the limited gene flow and high inbreeding.     

Geographic variation in relict populations: genetics and phenotype of bush-cricket Pholidoptera frivaldskyi (Orthoptera) in Carpathians

A decreasing population size is often causing species extinction, however, relict species persisting in small-sized populations counter this. We analysed spatial genetic variation and past changes in population size at the maternally-inherited mitochondrial DNA level to clarify the origin of all recently known isolated populations of Pholidoptera frivaldskyi occurring in the range of Carpathian Mountains. Along with that we analysed also morphological variation as some phenotypic traits can retain useful information on population genetic structure. We found a relatively low genetic diversity within isolated populations as 778 bp COI gene sequences revealed only 13 unique haplotypes (n = 173 individuals from 10 populations). The spatial analysis of molecular variance identified three geographically homogenous genetic clusters (one in Slovakia and two in Romania) with a high level of differentiation among them, suggesting restricted gene flow, whilst Bayesian skyline simulation reconstructed a negative demographic change through evolutionary time. Inferred genetic pattern clearly coincides with differences in males’ colour phenotype as the extent of pigmentation on the lateral pronotum varied significantly among genetic lineages. We suggest that geographical variation in the species populations has relict-like character and their isolated occurrence is not a result of recent introduction events. Identification of ‘evolutionary units’ may help in the conservation and management of this rare insect species.     

Effect of the landscape matrix on gene flow in a coastal amphibian metapopulation

Functional connectivity is crucial for the persistence of a metapopulation, because migration among subpopulations enables recolonization and counteracts genetic drift, which is especially important in small subpopulations. We studied the degree and drivers of connectivity among occupied patches of a coastal dune metapopulation of the Natterjack Toad (Epidalea calamita Laurenti), on the basis of microsatellite variation. As spatial landscape heterogeneity is expected to influence dispersal and genetic structure, we analyzed which landscape features affect functional connectivity and to what extent. Sixty different landscape resistance scenarios as well as the isolation-by-distance model were compared using two landscape genetics approaches. We identified three subpopulations with unidirectional levels of gene flow among the two most geographically separated subpopulations, while inferred gene flow into the geographically intermediate subpopulation was limited. Urbanization and vegetation height negatively affected connectivity. Low estimates of genetic diversity and effective population size indicate that conservation measures in the smallest and most isolated subpopulation are required.     

生境片段化对千岛湖岛屿上黄足厚结猛蚁遗传多样性的影响

利用相关序列扩增多态性(SRAP)分子标记法,对千岛湖片段化生境中14个岛屿上的黄足厚结猛蚁(Pachycondyla luteipes)种群遗传结构和多样性进行研究。利用5对SRAP引物对42份材料的基因组进行扩增,共得到大小在50-800 bp之间的71个可重复位点,其中63个为多态性位点,多态性比率达88.73%。AMOVA分析结果显示,65.03%的遗传变异存在于种群间,34.97%的遗传变异来自种群内(P < 0.001)。利用PopGene Version 1.32软件对SRAP多态性数据进行分析,不同岛屿种群的多态位点比例和Nei's基因多样性指数变化范围分别介于35.21%-91.55%和0.2662-0.4905之间,平均值分别为58.25%和0.3729,其中多态位点比率最高的岛屿为面积最大的JSE岛。多态位点比例和Nei's基因多样性指数与岛屿面积、海拔均无显著相关性,但与隔离度呈显著正相关关系。种群间遗传分化指数介于0.0777-0.9328之间,平均值为0.4419,基因流值介于0.0360-5.9350之间,平均值为1.0451,种群间遗传分化程度较高,基因流较低。利用UPGMA聚类分析法对14岛屿上的42个个体进行遗传聚类分析,表明地理距离较近的个体和岛屿具有优先聚在一起的趋势。Mantel 检验表明黄足厚结猛蚁各种群间地理距离与遗传距离间存在显著相关性(r=0.7757,P < 0.01)。以上结果表明地理隔离是影响千岛湖黄足厚结猛蚁种群遗传结构和多样性的主要因素。     

Discordant patterns of population structure for two co‐distributed snake species across a fragmented Ontario landscape

Aim The goal of our study was to investigate the effects of a fragmented landscape on the genetic population structure of two sympatric snake species that differ in habitat preference. The eastern garter snake (Thamnophis sirtalis sirtalis) is a common, habitat generalist, whereas the endangered eastern foxsnake (Mintonius [Elaphe] gloydi) is rarer, geographically restricted, and a marsh‐specialist. We were most interested in comparing the genetic population structure of both species and identifying any natural and human‐created features of the landscape that overlap with genetic disjunctions. Location Southwestern Ontario, Canada, surveying over half of the remaining range of the eastern foxsnake. Methods We utilized DNA microsatellite markers to examine genetic population structure of both species. The number of genetically distinct clusters for each species was determined using both Bayesian spatial assignment and spatial principal component analyses (sPCA). Genetic clusters were overlaid onto a habitat map to deduce possible physiognomic barriers to gene flow. Results Spatial assignment revealed three genetic clusters for garter snakes and five for foxsnakes. Each individual garter snake had a near equal probability of membership to two or more clusters with no cluster mapping onto a discrete geographic region, indicating that garter snakes comprise a single genetic population. The identified foxsnake clusters correspond to geographically circumscribed locations on the landscape, roughly coincident with isolated patches of suitable habitat. sPCAs revealed significant global allelic structure for foxsnakes, but not for garter snakes. No significant local structure was found for either species. Main Conclusions Our results imply that foxsnakes and garter snakes are differentially impacted by the same landscape or have dramatically different effective population sizes. Unsuitable intervening habitat such as agricultural tracts and roads between existing populations of foxsnakes appears to act as barriers to gene flow, while garter snake movement appears unrestricted by these features. Our findings have important implications for the management of eastern foxsnakes.     

Population genetic structure and diversity of the endangered Cantabrian capercaillie

The Cantabrian capercaillie (Tetrao urogallus cantabricus) occupies the southwestern edge of the grouse family distribution range in Eurasia. It is endemic to the Cantabrian Mountains in northwestern Spain and is geographically isolated and separated from the neighboring population in the Pyrenees by a distance of 300 km. Over the last decades, the population has undergone a dramatic decline and is now threatened with extinction. This study presents the genetic analysis of the Cantabrian capercaillie population using non-invasive samples. We performed genotyping of 45 individuals using 20 microsatellites and a sex marker. The data highlight the need for using a large number of markers when considering fragmented small populations. Genetic diversity (H_E = 0.50) and average number of alleles (3.40) in the population were low. The population is fragmented into 2 clusters (F_ST = 0.113) that fit with areas on both sides of the transportation ways that divide its range. Both clusters exhibited additional heterozygote deficits. Geographical distance was negatively correlated with genetic relatedness (r = −0.44, P ≤ 0.001). The data show a recent decline in effective population size that can be related to an ongoing process of population reduction and fragmentation. Conservation actions should focus on the protection of local demes by maintaining a dense network of suitable patches to maximize reproductive output and the number of potential dispersers to reconnect the 2 subpopulations. © 2012 The Wildlife Society.     

Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

We propose a two‐step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192 : 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade‐off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC‐type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.     

A Global Population Genetic Study of Pantala flavescens

Among terrestrial arthropods, the dragonfly species Pantala flavescens is remarkable due to their nearly global distribution and extensive migratory ranges; the largest of any known insect. Capable of migrating across oceans, the potential for high rates of gene flow among geographically distant populations is significant. It has been hypothesized that P. flavescens may be a global panmictic population but no sufficient genetic evidence has been collected thus far. Through a population genetic analysis of P. flavescens samples from North America, South America, and Asia, the current study aimed to examine the extent at which gene flow is occurring on a global scale and discusses the implications of the genetic patterns we uncovered on population structure and genetic diversity of the species. This was accomplished using PCR-amplified cytochrome oxidase one (CO1) mitochondrial DNA data to reconstruct phylogenetic trees, a haplotype network, and perform molecular variance analyses. Our results suggested high rates of gene flow are occurring among all included geographic regions; providing the first significant evidence that Pantala flavescens should be considered a global panmictic population.     

Restricted gene flow in fragmented populations of a wind-pollinated tree

Fragmentation of natural populations can have negative effects at the genetic level, thus threatening their evolutionary potential. Many of the negative genetic impacts of population fragmentation can be ameliorated by gene flow and it has been suggested that in wind-pollinated tree species, high or even increased levels of gene flow are a feature of fragmented populations, although several studies have disputed this. We have used a combination of nuclear microsatellites and allele-specific PCR (AS-PCR) analysis of chloroplast single nucleotide polymorphisms (SNPs) to examine the levels and patterns of genetic diversity and population differentiation in fragmented populations of juniper (Juniperus communis) in Ireland and inform conservation programs for the species. Significant population differentiation was found for both chloroplast and nuclear markers, indicating restricted gene flow, particularly over larger geographic scales. For conservation purposes, the existence of genetically distinct clusters and geographically localised chloroplast haplotypes suggests that the concept of provenance should be taken into account when formulating augmentation or reintroduction strategies. Furthermore, the potential lack of seed dispersal and seedling establishment means that ex-situ approaches to seed and seedling management may have to be considered.     

Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin)

The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were N_A = 6.54 and H_E = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.     

Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.     

Crossing barriers in an extremely fragmented system: two case studies in the afro-alpine sky island flora

The flora on the afro-alpine sky islands is renowned for extreme fragmentation, representing a unique natural experiment in biogeography. Here we address the roles of isolation and gene flow, in particular across the narrow Rift Valley (the RV barrier) that cuts through the Ethiopian Highlands (EH), and across the vast low-lying landscape that separates EH from the East African mountains (the EH–EA barrier). We inferred the history of two species with different dispersal mechanisms, but with similar geographic ranges and habitats based on Amplified fragment length polymorphisms (AFLPs). Contrary to our predictions, we found that the populations from opposite sides of the RV barrier were less similar than those from opposite sides of the EH–EA barrier, and that only the supposedly short distance-dispersed species (Trifolium cryptopodium) showed a strong signal of secondary gene flow across the RV barrier. In the wind-dispersed Carduus schimperi, we rather found an evidence for the gene flow between differentiated populations inhabiting different EA mountains. Both species harbored little genetic diversity but considerable genetic rarity in several individual mountains, suggesting long-term isolation and bottlenecks during climatically unfavorable periods. Our genetic data corroborate a division of C. schimperi into three subspecies, but with new delimitation of their ranges, and of T. cryptopodium into two intraspecific taxa. Our findings support the idea that stochasticity may play a major role in shaping extremely fragmented ecosystems such as the afro-alpine. After initial colonization of different mountains, periods of isolation may alternate with unpredictable episodes of intermountain gene flow.     

Reproductive Isolation with Little Genetic Divergence in Sympatric Populations of Brown Trout (SALMO TRUTTA)

Two reproductively isolated demes of brown trout coexist in a small Swedish mountain lake, Lake Bunnersj?rna. We electrophoretically examined 102 specimens from that lake for 27 enzymes encoded by 54 loci. The two demes are fixed for different alleles at a lactate dehydrogenase locus (LDH-1); statistically significant allele frequency differences at five other loci further support the complete lack of gene flow between these demes. There are significant differences in growth rates between fish in the two demes, but no further morphological differentiation h-s been detected.--In light of these findings, the genetic distance between these populations is surprisingly small (Nei's I = 0.975). These demes represent one of the least genetically divergent, reproductively isolated sympatric pair of vertebrate populations that have been identified. The results are discussed from both an evolutionary and ecological perspective.     

Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae) in China: two gene pools inferred by microsatellites

Background

Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet.

Methodology/Principal Findings

This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy–Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F _ST = 0.156). Pairwise differentiation between populations were lower within clusters (F _ST = 0.008–0.028 in cluster I and F _ST = 0.004–0.048 in cluster II) than between clusters (F _ST = 0.120–0.201). A reduced gene flow (Nm = 1–1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations.

Conclusions/Significance

Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The structured populations may limit the migration of genes under pressures/selections, such as insecticides and immune genes against malaria.     

Population structure of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia: the role of contemporary and historical processes

Rivers of Western Queensland, Australia, represent a discontinuous and variable aquatic habitat for the freshwater fauna of the region. Rivers periodically fluctuate between being highly fragmented, with numerous disconnected waterholes and ephemeral channels, and being highly connected by a dominant system of anastomosing channels. We used mitochondrial sequences to investigate the genetic structure and inferred patterns of dispersal associated with this flow regime for the freshwater prawn, Macrobrachium australiense (Decapoda: Palaemonidae), sampling 28 localities throughout eight catchments. Based on a 505 base pair fragment of mitochondrial cytochrome c oxidase subunit I, we identified 98 haplotypes in a sample of 402 individuals. The haplotypes clustered into two main clades corresponding geographically to the major drainages: the Lake Eyre and Murray-Darling basins. Populations of M. australiense inhabiting the two basins appear to have diverged around 800,000 years ago (estimated sequence divergence of 1.6%). Analysis of population differentiation indicated contemporary high levels of genetic subdivision and restricted gene flow among populations within and among catchments. Phylogenetic analysis detected a series of historical range expansions in the region and we suggest that climate fluctuations during the Pleistocene have resulted in extensive floods that have promoted historical movements of aquatic organisms across catchment boundaries.