Evidence of recent population bottlenecks and inbreeding in British populations of Bechstein’s bat, Myotis bechsteinii

We investigated the population genetics of seven maternity roosts of Bechstein’s bats widely distributed across the south of England. Across all of the populations sampled, two mitochondrial DNA microsatellite loci were fixed for single haplotypes. Genetic diversity across eight nuclear microsatellite loci was similar in all seven populations, with a mean He of 0.727. However, six of the populations showed substantial homozygote excess, with F _IS estimates greater than zero, indicative of recent inbreeding. Bottleneck tests also implied that six of the populations have experienced recent declines. Genetic differentiation among the populations was low, with a mean intersite F _ST estimate of 0.041. There was no significant isolation by distance using allele frequency-based criteria (F _ST and genetic distances), however, a weak correlation was found using the allele size-based R _ST criterion. Assignment tests were unable to distinguish the seven sampling sites as distinct clusters. Mean intra-roost relatedness (r) was 0.079, indicative of recent inbreeding relative to German populations. All but one of the bats had one or more half or full siblings in its maternity roost. In addition, family relationships of individuals within a colony were significantly commoner than family relationships among four proximal roosts <8 km apart. The results are discussed in the context of conservation requirements for this rare British bat.     

Genetic structure of the northwestern Russian wolf populations and gene flow between Russia and Finland

We examined the genetic diversity and structure of wolf populations in northwestern Russia. Populations in Republic of Karelia and Arkhangelsk Oblast were sampled during 1995–2000, and 43 individuals were genotyped with 10 microsatellite markers. Moreover, 118 previously genotyped wolves from the neighbouring Finnish population were used as a reference population. A relatively large amount of genetic variation was found in the Russian populations, and the Karelian wolf population tended to be slightly more polymorphic than the Arkhangelsk population. We found significant inbreeding (F = 0.094) in the Karelian, but not in the Arkhangelsk population. The effective size estimates of the Karelian wolf population based on the approximate Bayesian computation and linkage disequilibrium methods were 39.9 and 46.7 individuals, respectively. AMOVA-analysis and exact test of population differentiation suggested clear differentiation between the Karelian, Arkhangelsk and Finnish wolf populations. Indirect estimates of gene flow based on the level of population differentiation (ϕ _ST  = 0.152) and frequency of private alleles (0.029) both suggested a low level of gene flow between the populations (Nm = 1.4 and Nm = 3.7, respectively). Assignment analysis of Karelian and Finnish populations suggested an even lower number of recent migrants (less than 0.03) between populations, with a larger amount of migration from Finland to Karelia than vice versa. Our findings emphasise the role of physical obstacles and territorial behaviour in creating barriers to gene flow between populations in relatively limited geographical areas, even in large-bodied mammalian species with long-distance dispersal capabilities and an apparently continuous population structure.     

Effects of population size and forest management on genetic diversity and structure of the tuberous orchid Orchis mascula

Due to societal changes and altered demands for firewood, the traditional forest management of coppicing has been largely abandoned. As a result, many forest herbs that are specifically adapted to regular opening of the canopy, have suffered significant declines in abundance, and the remaining populations of these species often tend to be small and isolated. Reduced population sizes and pronounced spatial isolation may cause loss of within-population genetic diversity and increased between-population differentiation through random genetic drift and inbreeding. In this study, we investigated genetic diversity and genetic structure of 15 populations of the food-deceptive orchid Orchis mascula using AFLP markers. Within-population genetic diversity significantly increased with increasing population size, indicating genetic impoverishment in small populations. Genetic differentiation, on the other hand, was rather low (Φ_ST = 0.083) and there was no significant relationship between genetic and geographic distances, suggesting substantial gene flow within the study area. However, strong differences in levels of within-population diversity and among-population differentiation were found for populations located in forests that have been regularly coppiced and populations found in forests that were neglected for more than 50 years and that were totally overgrown by shrubs. Our data thus indicate that a lack of coppicing leads to decreased genetic diversity and increased differentiation in this orchid species, most likely as a result of genetic drift following demographic bottlenecks. From a conservation point of view, this study combined with previous results on the demography of O. mascula in relation to forest management illustrates the importance of coppicing in maintaining viable populations of forest herbs in the long-term.     

喜马拉雅旱獭种群微卫星变异及遗传多样性

为了解不同地理种群喜马拉雅旱獭(Marmota himalayana)的种群数量变化并探讨其内在的遗传学机制,通过构建部分基因组文库的方法筛选出8个高变异微卫星位点,根据微卫星位点的测序结果设计相应引物,PCR扩增检测了青藏高原4个地理种群(德令哈、乌兰、沱沱河、安多)喜马拉雅旱獭的遗传多态性及其种群结构.研究结果显示:8个位点在喜马拉雅旱獭种群中均为高度多态,观察等位基因数、有效等位基因数、多态信息含量分别为4.75、3.033 2、0.610 2;喜马拉雅旱獭种群总的期望杂合度和观察杂合度分别为0.670、0.699;3个喜马拉雅旱獭种群显著(P＜0.05)或极显著(P＜0.01)偏离H-W平衡状态,且这些偏离平衡的位点均由杂合过度导致(FIS＜0);喜马拉雅旱獭种群的部分位点已经偏离了突变-漂移平衡.结论:筛选出的8个微卫星位点适合于喜马拉雅旱獭种群遗传多样性的研究,所研究的喜马拉雅旱獭种群有较高的遗传多样性,安多地理种群在近期可能经历过瓶颈效应,种群数量曾经下降.     

Mitochondrial DNA variation in the caramote prawn <Emphasis Type="Italic">Penaeus (Melicertus) kerathurus</Emphasis> across a transition zone in the Mediterranean Sea

In this study we analysed mitochondrial DNA variation in Penaeus kerathurus prawns collected from seven locations along a transect across the Siculo–Tunisian region in order to verify if any population structuring exists over a limited geographical scale and to delineate the putative transition zone with sufficient accuracy. Partial DNA sequences of COI and 16S genes were analysed. In contrast to the highly conservative 16S gene, the COI sequences exhibited sufficient diversity for population analysis. The COI gene revealed low levels of haplotype and nucleotide diversities. The size of the annual landings of this commercial species suggests large population sizes. Hence, the low genetic diversity detected in this study could indicate a possible reduction in effective population sizes in the past. We detected significant genetic differentiation between eastern and western populations likely due to restricted gene flow across the Siculo–Tunisian boundary. We discuss the different evolutionary forces that may have shaped the genetic variation and suggest that the genetic divide is probably maintained by present-day dispersal limitation. R. Zitari-Chatti and N. Chatti are contributed equally to the work.     

Population genetic structure of Sorex unguiculatus and Sorex caecutiens (Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

We investigated the genetic structure of Sorex unguiculatus and Sorex caecutiens populations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475 S. unguiculatus individuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240 S. caecutiens individuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations of S. unguiculatus. Allelic richness and island size were positively correlated for S. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations of S. unguiculatus were genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for either S. unguiculatus or S. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non-random spatial genetic structure was approximately 100 km. Isolation by distance was observed in S. unguiculatus, but not in S. caecutiens although there is a positive trend. The lack of correlation for S. caecutiens might have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.     

Rodrigues fruit bats (<Emphasis Type="Italic">Pteropus rodricensis</Emphasis>, Megachiroptera: Pteropodidae) retain genetic diversity despite population declines and founder events

Fruit bats of the genus Pteropus are important contributors to ecosystem maintenance on islands through their roles as pollinators and seed dispersers. However, island faunas are the most prone to extinction and there is a real need to assess the possible genetic implications of population reductions in terms of extinction risk. An effective method of ameliorating extinction risk in endangered species is the establishment of captive populations ex situ. The effectiveness of captive breeding programmes may be assessed by comparing the genetic variability of captive colonies to that of wild counterparts. Here, we use polymorphic microsatellite loci to assess genetic variability in wild, critically endangered Rodrigues fruit bats (Pteropus rodricensis, Dobson 1878) and we compare this variability to that in a captive colony. We document remarkable conservation of genetic variability in both the wild and captive populations, despite population declines and founder events. Our results demonstrate that the wild population has withstood the negative effects of population reductions and that captive breeding programmes can fulfil the goals of retaining genetic diversity and limiting inbreeding.     

The genetic structure of endangered indigenous populations of the amago salmon, <Emphasis Type="Italic">Oncorhynchus</Emphasis><Emphasis Type="Italic">masou</Emphasis><Emphasis Type="Italic">ishikawae</Emphasis>, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise F _ST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.     

Genetic structure of introduced European fallow deer (<Emphasis Type="Italic">Dama dama dama</Emphasis>) in Tasmania,Australia

European fallow deer are an introduced species classified as partly protected wildlife in Tasmania, Australia. Current management practices are primarily governed under the Quality Deer Management regime, in which animals are harvested during designated hunting seasons. Among populations, prominent morphological differences have been reported; however, the genetic relationship of these populations has until now been poorly understood. Representative animals were sampled from three key areas across their range and genotyped at ten polymorphic microsatellite loci to investigate genetic diversity, population structure, and genetic bottlenecks. Allelic richness was low in all three populations and ranged between 2.20 and 2.49 alleles/locus. A genetic bottleneck was detected in two of the three populations (P < 0.001). Population differentiation was evident between Lake Echo and Benham (q = 0.122; P < 0.001) and Benham and Connorville (q = 0.110; P < 0.001), but not between Lake Echo and Connorville (q = 0.0235), with individuals being identified as belonging to two genetic clusters. The pattern of population differentiation from the three study populations suggests that deer from the western region of their range are genetically distinct to those from the eastern region. This correlates with morphological variation within Tasmanian fallow deer, in which differences between the regions maybe attributable to geographical barriers.     

Genetic variability and population structure in Cypriot chukar partridges (Alectoris chukar cypriotes) as determined by microsatellite analysis

For the first time, microsatellite loci were used to study the genetic structure in Alectoris chukar cypriotes. Four of the ten tested microsatellite loci were found to be polymorphic in 33 individuals from four regions of Cyprus. The differentiation test between all the pairs of samples gave non-differentiation exact P values in every case (P>0.05). The posterior probability distribution on the number of source populations indicated only one population (P=0.977); also, a high Bayes factor value (130.020) was obtained. Posterior co-assignment probabilities (measures of similarity) for all pairs of individuals ranged from 0.984 to 1. The global F_IS value was not found to be significant. A recent bottleneck of the Cypriot total partridge population is suggested and this is supported by a significant Wilcoxon test (P=0.031) under the Infinite Alleles Model (IAM) and shifted mode in the alleles frequencies distribution. The results suggest that all the individuals studied belong to only one randomly mating (panmictic) population, with low genetic variation and evidence of recent effective population size reduction (genetic bottleneck). A big hunting pressure exists on the island and about 200,000 captive-bred birds are released every year; these individuals are descendant from a small number of eggs collected in a small area of Cyprus in 1986 and this founder effect could explain the existence of a bottleneck and the low genetic variability.