Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia

Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F _ST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N _e) ranged from seven to 228 and were significantly correlated with those of historical N _e but not with lake size. A census size (N _C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N _e (i.e. N _e/N _C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.     

Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip

Here we present the first attempt to use the BovineSNP50 Illumina Genotyping BeadChip for genome-wide screening of European bison Bison bonasus bonasus (EB), two subspecies of American bison: the plains bison Bison bison bison (PB), the wood bison Bison bison athabascae (WB) and seven cattle Bos taurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the consequences of bottlenecks on the genetic distances amongst bison subspecies and cattle, and (3) detect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation between plain and wood bison. A linkage disequilibrium based program (LDNE) was used to estimate the effective population size (N _e) for the cattle breeds; N _e was generally low, relative to the census size of the breeds (cattle breeds: mean N _e = 299.5, min N _e = 18.1, max N _e = 755.0). BOTTLENECK 1.2 detected signs of population bottlenecks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have survived severe bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.     

The population-genetic structure of <Emphasis Type="Italic">Corbicula japonica</Emphasis> prime, 1864 (Bivalvia: Cyrenidae) in estuarine water bodies of the Primorsky Region

The population-genetic structure of the bivalve Corbicula japonica from ten estuarine localities in the Primorsky Region was investigated using nine allozyme loci as gene markers. This study revealed spatial genetic heterogeneity between the investigated populations (G _st = 0.05); its degree was dependent on the distance between populations. No linkage disequilibrium was found for any pair of loci. The index of genetic similarity between pairs of populations varied from 0.916 to 0.994. The genetic heterogeneity of the C. japonica populations is probably a result of genetic drift balanced by an irregular gene flow. Such an equilibrium may indicate a relatively recent expansion of C. japonica, which may have occurred during the Holocene climatic optimum (about 7500 years ago).     

Admixture promotes genetic variation in bottlenecked moose populations in eastern Poland

Human activity has led to severe bottlenecks in many wildlife species in the recent past. This usually increases the strength of genetic drift, leading to loss of genetic variation. Gene flow may however counteract the genetic consequences of small population size. Using 11 of 38 tested microsatellite loci and five moose populations in eastern Poland, we investigated the effects of two phenomena: bottlenecks that occurred in the nineteenth century and the first half of twentieth century, and admixture after moose populations expanded demographically and spatially in eastern Poland after the Second World War. The statistical tests indicated a recent bottleneck in all the studied samples with respect to H _E and low Garza–Williamson index values. The Biebrza population, which consists of autochthonous moose representing a branch of the Central Europe mitochondrial DNA (mtDNA) clade and immigrants belonging to the Ural clade, is one of the most variable populations of this species. AMOVA, PCA, and STRUCTURE analyses all revealed significant population structuring, with most probable existence of K?=?2 genetically distinct clusters that exhibited a relatively high level of admixture. Analysis of recent dispersal rates demonstrated that population from the Biebrza Valley may supply individuals to the other four studied moose populations. We also found female-biased sex ratio in nonharvested moose populations inhabiting eastern Poland.     

Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D''Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D''Urville birds among extant LSK. The N_e/N_C ratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size.     

Low population differentiation revealed in the highly threatened elongate loach (Leptobotia elongata,Bleeker), a species endemic to the fragmented upper reaches of the Yangtze River

The elongate loach (Leptobotia elongata) is a typical migratory fish that was formerly found in abundance throughout the upper and middle reaches of the Yangtze River but is now classified as a highly threatened fish on the China Species Red List. Here, a comparative study of microsatellite loci was performed to evaluate the genetic diversity and analyze the population structure in seven locations in the upper reaches of the Yangtze River, China. The results showed that genetic diversity of L. elongata is generally still at a high level. Populations from Xinshi, Panzhihua, Hechuan and Chishui, were found to have lower levels of genetic diversity than those that lived in Leshan, Yibin and Jiangjin. The IAM model indicated that populations from Panzhihua, Xinshi and Hechuan have undergone recent bottlenecks. AMOVA analysis revealed a small amount of differentiation among populations (3.6%), but most of the total variation occurred within populations (96.4%). Pairwise comparisons of populations confirmed a low population differentiation. STRUCTURE analysis showed no obvious genetic structure among populations, indicating that L. elongata living in the main stem of the river and its tributaries should be considered a single management unit.     

Genetic variation in a freshwater prawn species,Palaemon paucidens,in South Korea

The biogeography of freshwater biota in the Korean Peninsula has been affected by recent geological processes and anthropogenic activity. The freshwater prawn, Palaemon paucidens, can serve as a non-fish model organism suitable for assessing these factors, as it is found in all river systems in the Korean Peninsula and may have been introduced by humans in some regions. In this study, we investigated the geographical distribution of genetic variation and the genetic structure of P. paucidens populations using mitochondrial DNA sequences and genotypes identified from four microsatellite loci. Our results showed that populations from westward-flowing river systems that drain into the Yellow Sea have more genetic diversity than those from southward-flowing river systems, and that the highest genetic variance revealed by analysis of molecular variance (AMOVA) using both genetic markers was observed in river systems grouped as HAN + GEUM, NAKDONG + JEJU, YOUNGSAN, and SEOMJIN. These results suggest that HAN and GEUM, in which freshwater prawn populations have higher levels of genetic diversity, were the most recently isolated river systems from Asian continental systems. Therefore, populations from HAN and GEUM experienced less severe bottlenecks than those from YOUNGSAN and SEOMJIN.     

Negligence in the Atlantic forest,northern Brazil: a case study of an endangered orchid

Currently, many Brazilian orchids are threatened with extinction resulting from habitat loss and intense harvesting pressure stemming from their value as ornamental plants. Therefore, the genetic diversity in remaining populations is fundamental to the survival of these species in natural environments. In order to inform conservation strategies, this study evaluated the genetic diversity and structure of Cattleya granulosa populations. The sample consisted of 151 individuals from 12 populations in the Atlantic Forest, northeastern Brazil, evaluated using 91 ISSR markers. Genetic variability was assessed through molecular variance, diversity indexes, clusters of genotypes through Bayesian analysis, and tests for genetic bottlenecks. From all polymorphic loci, genetic diversity (H_E) varied between 0.210 and 0.321 and the Shannon index ranged from 0.323 and 0.472. Significant genetic differentiation between populations (Φ_ST = 0.391; P < 0.0001) resulted in the division of the populations into five groups based on the log-likelihood Bayesian analysis. We found significant positive correlation between geographical and genetic distances between populations (r = 0.794; P = 0.017), indicating isolation by distance. Patterns of allelic diversity within populations suggest the occurrence of bottlenecks in most C. granulosa populations (n = 8). Therefore, in order to maintain the genetic diversity of the species, the conservation of spatially distant groups is necessary.     

Genetic analysis of four wild chum salmon<Emphasis Type="Italic">Oncorhynchus keta</Emphasis> populations in China based on microsatellite markers

Synopsis To assess the genetic variation and population structure of wild chum salmon in China, we analyzed microsatellite loci for populations in the Amur, Wusuli, Suifen Current and the Tumen rivers. We evaluated expected heterozygosity with two estimators of genetic differentiation (F_ST and G_ST) and Nei’s standard genetic distance. The average expected heterozygosity across the 10 loci was 0.65 in the Wusuli River and the Suifen Current River, 0.64 in the Amur River and 0.66 in the Tumen River, The results of this study show that the recent declines in chum salmon have not led to low levels of genetic variability in China. The proportion of inter-population subdivision among chum salmon was between 5.7 and 6.8%. According to the estimator used, the NJ tree based on Nei’s standard genetic distance indicated that there were two different branches (the Sea of Okhotsk branch and the Sea of Japan branch), the Amur River and the Wusuli River populations were closer, while the Suifen Current River and the Tumen River clustered together. The genetic test for population bottlenecks provided no evidence for a significant genetic signature of population decline, which is consistent with the record of the four populations we have in the last few years.     

Patterns of evolution in Graomys griseoflavus (Rodentia,Muridae). IV. A case of rapid speciation

The South American group of rodents known as Graomys griseoflavus comprises two sibling species differing only in diploid chromosomal complement: G. griseoflavus (2n = 36, 37 and 38) and G. centralis (2n=42). Reproductive barriers comprising postzygotic as well as precopulatory mechanisms prevent gene exchange between these species. We have studied genetic polymorphism in two populations of G. centralis and four of G. griseoflavus by means of gel electrophoresis of enzymes and other proteins giving information on a total of 30 loci. Values of interspecific genetic identity were similar to those obtained for conspecific populations, suggesting that fixation of Robertsonian fusions would have occurred without significant bottlenecks. It would also indicate that the cladogenetic process must be relatively recent. F_IS values showed no evidence of inbreeding. Fixation indices (F_ST) for the ancestral species showed a tendency to form demes with very low gene flow among them, while in the derived species such tendency was not shown. However, because of the characteristics of the region they occupy, populations are of moderate size, and genic flow is low. Lack of correlation between gene flow levels and geographical distance between population pairs would indicate a recent and fast colonization of its distribution areas by the derived species. It is possible that fixation of Robertsonian fusions occurred in a marginal deme of the ancestral species, e.g. in a parapatric geographical context.     

Do rivers and human-induced habitat fragmentation affect genetic diversity and population structure of the European ground squirrel at the edge of its Pannonian range?

The European ground squirrel (EGS) (Spermophilus citellus) populations of Vojvodina (Serbia) represent the southernmost part of its distribution in the Pannonian lowland. For species with low dispersal abilities a presence of even weak barriers can have significant influence on genetic structure among adjacent populations. We examined here the effects of habitat fragmentation and river barriers on the genetic structure of the EGS based on 12 microsatellite loci. Bayesian clustering methods were used as additions to classical population genetic approaches. We found that EGS populations in Vojvodina are highly fragmented, but their genetic variation is still higher than in peripheral populations in Central Europe. Populations in Vojvodina consistently grouped into three genetic clusters. The Danube, but not the Tisza River, represents an important barrier to gene flow. EGS populations in the studied area did not show the signs of recent genetic bottlenecks, as would be expected from observations of recent population declines. Conservation strategy should be focused on maintenance of remained suitable habitats and optimal population sizes.     

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise F_ST and exact tests identified weak (global F_ST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects.     

Invasion genetics of <Emphasis Type="Italic">Senecio vulgaris</Emphasis>: loss of genetic diversity characterizes the invasion of a selfing annual,despite multiple introductions

Genetic variation in invasive populations is affected by a variety of processes including stochastic forces, multiple introductions, population dynamics and mating system. Here, we compare genetic diversity between native and invasive populations of the selfing, annual plant Senecio vulgaris to infer the relative importance of genetic bottlenecks, multiple introductions, post-introduction genetic drift and gene flow to genetic diversity in invasive populations. We scored multilocus genotypes at eight microsatellite loci from nine native European and 19 Chinese introduced populations and compared heterozygosity and number of alleles between continents. We inferred possible source populations for introduced populations by performing assignment analyses and evaluated the relative contributions of gene flow and genetic drift to genetic diversity based on correlations of pairwise genetic and geographic distance. Genetic diversity within Chinese populations was significantly reduced compared to European populations indicating genetic bottlenecks accompanying invasion. Assignment tests provided support for multiple introductions with populations from Central China and southwestern China descended from genotypes matching those from Switzerland and the UK, respectively. Genetic differentiation among populations in China and Europe was not correlated with geographic distance. However, European populations exhibited less variation in the relation between G _ST and geographical distance than populations in China. These results suggest that gene flow probably plays a more significant role in structuring genetic diversity in native populations, whereas genetic drift appears to predominate in introduced populations. High rates of selfing in Chinese populations may restrict opportunities for pollen-mediated gene flow. Repeated colonization-extinction cycles associated with ongoing invasion is likely to maintain low genetic diversity in Chinese populations.     

Evidence for genetic differentiation of Octopus vulgaris (Mollusca, Cephalopoda) fishery populations from the southern coast of Brazil as revealed by microsatellites

Octopus vulgaris is a cephalopod species in several oceans and commonly caught by artisanal and industrial fisheries. In Brazil, O. vulgaris populations are mainly distributed along the southern coast and have been subjected to intensive fishing during recent years. Despite the importance of this marine resource, no genetic study has been carried out to examine genetic differences among populations along the coast of Brazil. In this study, 343 individuals collected by commercial vessels were genotyped at six microsatellite loci to investigate the genetic differences in O. vulgaris populations along the southern coast of Brazil. Genetic structure and levels of differentiation among sampling sites were estimated via a genotype assignment test and F-statistics. Our results indicate that the O. vulgaris stock consists of four genetic populations with an overall significant analogous F_ST (Φ_CT = 0.10710, P < 0.05) value. The genetic diversity was high with an observed heterozygosity of Ho = 0.987. The negative values of F_IS found for most of the loci examined suggested a possible bottleneck process. These findings are important for further steps toward more sustainable octopus fisheries, so that this marine resource can be preserved for long-term utilization.     

Effects of founder events on the genetic variation of translocated island populations: implications for conservation management of the northern quoll

Translocation is a strategy commonly used to maximize the persistence of threatened species, but it may sometimes lead to undesirable genetic consequences. The northern quoll (Dasyurus hallucatus) is a carnivorous marsupial that is critically endangered in Australia’s Northern Territory due to rapid population declines in areas recently colonized by the exotic cane toad Chaunus [Bufo] marinus. In 2003, 64 quolls were translocated to two offshore islands to establish insurance populations and reduce the species’ risk of extinction. In this study, we assessed genetic diversity at five microsatellite loci in the translocated populations, two endemic islands and three mainland populations. In the short-term (three generations), the translocated populations showed a slight but non-significant reduction in genetic diversity (A = 4.1–4.2; H _e = 0.56–0.59) compared to the mainland source populations (A = 5.0–8.4; H _e = 0.56–0.71). In comparison, high genetic erosion was observed in the endemic island populations (A = 1.5–2.9; H _e = 0.11–0.34). Genetic bottlenecks were detected on both endemic islands and in one mainland population, indicating recent reductions in population size. Our results are consistent with previous studies describing greater losses of genetic diversity on islands compared to mainland populations. Divergence from ancestral allele frequencies in the translocated populations also suggests effects due to founder events. This study, although short-term, highlights the importance of continued monitoring for detecting changes in genetic diversity over time and makes a significant contribution to our understanding of the effects of founder events on island populations.     

Genetic diversity and population structure of the medicinal orchid Gastrodia elata revealed by microsatellite analysis

The wild resources of Gastrodia elata are currently threatened with extinction due to over-harvesting because of their high medicinal value. Genetic diversity plays a key role in the survival of endangered orchid species. In this study we investigated the genetic pattern in eight microsatellite loci within eight G. elata populations from central China. Compared with the other orchids, G. elata showed a low level of genetic variation within populations (H_E = 0.356–0.622). The main factors responsible for the genetic pattern were the plant's inbreeding system due to mating within clone patches, and the genetic bottlenecks and genetic drift caused by a long-history over-collecting. The significant heterozygote deficit was detected in all the populations. The F statistics calculated by different approaches consistently revealed a clear genetic differentiation among populations, contributing about 20% of the total gene diversity. The results are discussed in relation to both in situ and ex situ conservation efforts of the species. The populations with a high level of genetic diversity or with great genetic distinction were identified, which should be a high priority for conservation managers.     

Genetic Diversity and Population Structure of Indian Golden Silkmoth (Antheraea assama)

Background

The Indian golden saturniid silkmoth (Antheraea assama), popularly known as muga silkmoth, is a semi-domesticated silk producing insect confined to a narrow habitat range of the northeastern region of India. Owing to the prevailing socio-political problems, the muga silkworm habitats in the northeastern region have not been accessible hampering the phylogeography studies of this rare silkmoth. Recently, we have been successful in our attempt to collect muga cocoon samples, although to a limited extent, from their natural habitats. Out of 87 microsatellite markers developed previously for A. assama, 13 informative markers were employed to genotype 97 individuals from six populations and analyzed their population structure and genetic variation.

Methodology/Principal Findings

We observed highly significant genetic diversity in one of the populations (WWS-1, a population derived from West Garo Hills region of Meghalaya state). Further analysis with and without WWS-1 population revealed that dramatic genetic differentiation (global F_ST = 0.301) was due to high genetic diversity contributed by WWS-1 population. Analysis of the remaining five populations (excluding WWS-1) showed a marked reduction in the number of alleles at all the employed loci. Structure analysis showed the presence of only two clusters: one formed by WWS-1 population and the other included the remaining five populations, inferring that there is no significant genetic diversity within and between these five populations, and suggesting that these five populations are probably derived from a single population. Patterns of recent population bottlenecks were not evident in any of the six populations studied.

Conclusions/Significance

A. assama inhabiting the WWS-1 region revealed very high genetic diversity, and was genetically divergent from the five populations studied. The efforts should be continued to identify and study such populations from this region as well as other muga silkworm habitats. The information generated will be very useful in conservation of dwindling muga culture in Northeast India.     

High genetic diversity but limited gene flow among remnant and fragmented natural populations of Liriodendron chinense Sarg

As a relic species, Liriodendron chinense is now recognized as an endangered species. To better understand the genetic structure and differentiation among remnant populations of L. chinense, we determined the genotypes of 14 simple sequence repeats (SSRs) loci across 318 individuals from 12 natural populations and 750 seedlings from five offspring populations. We found that L. chinense maintained high genetic diversity (H_e = 0.7385) within populations but moderate genetic differentiation (F_st = 0.1956) and low gene flow (N_m = 1.0283) between populations. The genetic diversity was slightly lower for offspring populations than for their corresponding natural populations. Moreover, using a two-phased model of mutation (TPM), we demonstrated that significant bottlenecks had occurred in six populations. A Mantel test revealed a statistically significant correlation between the geographic distances and genetic distances between populations (r = 0.5011, P = 0.002). Hence, we presume that geographical isolation and habitat fragmentation might contribute jointly to current population structure of L. chinense. We suggest that populations from southern Yunnan can be regarded as a variety of L. chinense, given their large deviation from other populations. Our findings may be of value for the conservation and use of L. chinense.     

Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks

Evolutionary and conservation biologists often use molecular markers to evaluate whether populations have experienced demographic bottlenecks that resulted in a loss of genetic variation. We evaluated the utility of microsatellites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experimental mesocosms, we established replicate populations by releasing 1, 2, 4 or 8 pairs of the western mosquitofish, Gambusia affinis (Poeciliidae). Using eight polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demographic bottlenecks on populations. We compared indices for the experimentally bottlenecked populations to those for the source population and examined differences between populations established with different numbers of founders. Direct count heterozygosity and the proportion of polymorphic loci were not very sensitive to genetic changes that resulted from the experimental bottlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and temporal variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was slightly more correlated with bottleneck size than was allelic diversity. Based on comparisons to a previous study with allozymes, heterozygosity, temporal variance in allele frequencies and allelic diversity, but not proportion of polymorphic loci, appear to be more sensitive to demographic bottlenecks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottleneck and to obtain an estimate of the magnitude of bottleneck severity.     

Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas

The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC.