Mitochondrial DNA variation and population structure of the yarkand hareLepus yarkandensis

The yarkand hareLepus yarkandensis Günther, 1875 is one of the endemic mammals in China. We used mitochondrial control region (D-loop) sequences to investigate the genetic variation, population structure and phylogeography of the Yarkand hare from Xinjiang Uighur Autonomous Region. The Yarkand hare holds a high level of haplotype diversity in most populations. In contrast, we found a relatively low level of gene diversity in Niya and Shule populations. The pairwise mismatch distribution suggested a pattern of population expansion. Fu’s test of neutrality was significant for the total population (F _s=−10.458), which also suggested a recent population expansion. The pattern of diversification among populations was not consistent with its geographic distributions. Significant divergence was found among some populations, however, no significant divergence among other populations. The results indicate some degree of dispersal of individuals may exist among populations in recent history. Due to past isolation and habitat fragmentation, genetic variation was reduced within populations and division among populations increased. In order to conserve genetic diversity of the Yarkand hare in isolated populations, in the future, it may be advisable to translocate individuals between isolated populations to maintain current levels of genetic variation.     

塔里木兔种群遗传结构的初步探讨

塔里木兔作为中国特有种, 其种群遗传结构直到现在还未知。我们从采自于新疆维吾尔自治区3 个种群的25 号样品中扩增得到529 bp 线粒体DNA 控制区片段, 共发现存在76 个多态性位点。全部样品中定义了19 个单倍型, 每个种群都显示了很高的单倍型多态性。进一步分析表明, 3 个种群存在明显的遗传分化和较低的基因流。通过错配分布和Fu’s 中性检验分析发现, 阿克苏(AKS) , 若羌(RQ) 和疏勒(SL) 种群相对比较稳定。     

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.     

Linking habitat characteristics with genetic diversity of the European pine marten (Martes martes) in France

Although typically considered as a forest specialist species, the European pine marten (Martes martes) is an example of a number of species that have recently been found to also live in fragmented landscapes. Considering that habitat fragmentation and loss is a major threat to the persistence of mammal species in such landscapes, we investigated the association between habitat characteristics and genetic diversity across four pine marten populations occupying contrasting landscapes in France with different degrees of forest availability and fragmentation. Bayesian and multivariate clustering methods evidenced the presence of three genetic clusters and isolation by distance between populations was found at the national scale. We found an overall moderate level of genetic variability, but no evidence of a bottleneck or deficit in heterozygosity in any of the populations. No pattern of isolation by distance was found within the populations, except in the one located in the Pyrenean Mountains which appeared partly isolated from other continental populations and also showed a lower level of genetic diversity. No obvious association between the pattern of genetic variability and the pattern of forested habitat characteristics was found. We discuss the possibility that pine martens show greater behavioural plasticity than typically expected allowing them to adapt to different habitat types.     

Diversity and structure of fragmented populations of a threatened endemic cyprinodontid (Aphanius sophiae) inferred from genetics and otolith morphology: Implications for conservation and management

The assessment of population structure and genetic diversity is crucial for the management and conservation of threatened species. Natural and artificial barriers to dispersal (i.e., gene flow) increase populations’ differentiation and isolation by reducing genetic exchange and diversity. Freshwater ecosystems are highly fragmented because of human activities. Threatened species with small population sizes are more sensitive to habitat fragmentation effects. Here, we investigate the genetic population structure and gene flow among seven populations of Aphanius sophiae in the Kor Basin by using sequences of the complete Cyt b gene and otolith morphometry. The Cyt b gene showed low level of genetic variation, only 4.12% of the identified sites were variable, and 2.42% were parsimony informative. Overall, haplotype diversity was low to moderate and nucleotide diversity was low to extremely low. Fish populations exhibited high levels of genetic differentiation, suggesting limited gene flow among them. These differences were obtained not only among geographically distant populations, but also among neighboring localities. Genetic population structure was supported by the AMOVA analysis and by the haplotype network (only one of 21 haplotypes were shared by two localities). Otolith morphometric analysis was in agreement with genetic results, the two most distant and isolated populations were clearly separated, and genetically close populations showed less differences in morphometry. A significant pattern of isolation by distance was also detected among A. sophiae populations, with genetic distance more correlated with hydrological distance than with geographic distance. Results suggested that limited gene flow due to habitat fragmentation is an important factor contributing to genetic structuring and to the loss of genetic variation of A. sophiae populations. Aphanius sophiae population structure seems to be the result of habitat fragmentation and water pollution, but other factors such as introduced species should be considered. Given the high degree of genetic structuring, the definition of conservation groups is of particular importance for A. sophiae, which should be considered endangered according to the IUCN criteria. Conservation plans must recognize the genetic independence of populations and manage separately preventing the loss of locally adapted genotypes.     

Strong genetic differentiation on a fragmentation gradient among populations of the heterocarpic annual Catananche lutea L. (Asteraceae)

In landscapes which are predominately characterised by agriculture, natural ecosystems are often reduced to a mosaic of scattered patches of natural vegetation. Species with formerly connected distribution ranges now have restricted gene flow among populations. This has isolating effects upon population structure, because species are often confined by their limited dispersal capabilities. In this study, we test the effects of habitat fragmentation, precipitation, and isolation of populations on the genetic structure (AFLP) and fitness of the Asteraceae Catananche lutea. Our study area is an agro-dominated ecosystem in the desert–Mediterranean transition zone of the Southern Judea Lowlands in Israel. Our analysis revealed an intermediate level of intra-population genetic diversity across the study site with reduced genetic diversity on smaller scale. Although the size of the whole study area was relatively small (20?×?45?km), we found isolation by distance to be effective. We detected a high level of genetic differentiation among populations but genetic structure did not reflect spatial patterns. Population genetic diversity was correlated neither with position along the precipitation gradient nor with different seed types or other plant fitness variables in C. lutea.     

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.     

Genetic evidence of fragmented populations and inbreeding in the Colombian endemic Dahl’s toad-headed turtle (<Emphasis Type="Italic">Mesoclemmys dahli</Emphasis>)

Population fragmentation is one of the most concerning consequences of habitat fragmentation, as small and isolated populations suffer increased genetic drift and inbreeding. However, the extent to which habitat fragmentation leads to population fragmentation depends not only on the landscape structure, but also on the response of organisms to it. This behavioral component makes it difficult to detect population fragmentation even if the habitat is fragmented, unless appropriate tools are used. In this study, we used a molecular approach to evaluate if Dahl’s toad-headed turtle (Mesoclemmys dahli) population was fragmented, given that it occurs in a very restricted area within the most degraded biome of Colombia, the tropical dry forest. We developed a panel of 15 microsatellite loci in order to perform the first genetic assessment of M. dahli across its complete geographic range. We found that M. dahli has significant genetic structure with at least four subpopulations, with surprisingly moderate to high levels of genetic diversity. Despite high levels of genetic diversity, subpopulations are very small (effective population sizes?<?50) and isolated, with little to no contemporary gene flow among them. As a consequence, mating among related individuals has been occurring, and all four populations are showing high degrees of inbreeding. To counteract this threat, we recommend an urgent genetic rescue strategy accompanied by habitat restoration, and advocate for a new conservation status assessment, not based on geographic range, but on adult population size and level of fragmentation.     

A comparison of the population genetic structure of parasitic Viscum album from two landscapes differing in degree of fragmentation

Parasite populations do not necessarily conform to expected patterns of genetic diversity and structure. Parasitic plants may be more vulnerable to the negative consequences of landscape fragmentation because of their specialized life history strategies and dependence on host plants, which are themselves susceptible to genetic erosion and reduced fitness following habitat change. We used AFLP genetic markers to investigate the effects of habitat fragmentation on genetic diversity and structure within and among populations of hemiparasitic Viscum album. Comparing populations from two landscapes differing in the amount of forest fragmentation allowed us to directly quantify habitat fragmentation effects. Populations from both landscapes exhibited significant isolation-by-distance and sex ratios biased towards females. The less severely fragmented landscape had larger and less isolated populations, resulting in lower levels of population genetic structure (F _ST = 0.05 vs. 0.09) and inbreeding (F _IS = 0.13 vs. 0.27). Genetic differentiation between host-tree subpopulations was also higher in the more fragmented landscape. We found no significant differences in within-population gene diversity, percentage of polymorphic loci, or molecular variance between the two regions, nor did we find relationships between genetic diversity measures and germination success. Our results indicate that increasing habitat fragmentation negatively affects population genetic structure and levels of inbreeding in V. album, with the degree of isolation among populations exerting a stronger influence than forest patch size.     

Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi)

Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300‐ km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30‐ km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522‐base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.     

Implications of Anthropogenic Landscape Change on Inter-Population Movements of the Desert Tortoise (Gopherus agassizii)

In the Sonoran Desert of North America, populations of the desert tortoise (Gopherus agassizii) occur in rocky foothills throughout southwestern Arizona and northwestern Mexico. Although tortoise populations appear to be isolated from each other by low desert valleys, individuals occasionally move long distances between populations. Increasingly, these movements are hindered by habitat fragmentation due to anthropogenic landscape changes. We used molecular techniques and radiotelemetry to examine movement patterns of desert tortoises in southern Arizona. We collected blood samples from 170 individuals in nine mountain ranges and analyzed variability in seven microsatellite loci to determine genetic differentiation among populations. Gene flow estimates between populations indicate that populations exchanged individuals historically at a rate greater than one migrant per generation, and positive correlation between genetic and geographic distance of population pairs suggests that the limiting factor for gene flow among populations is isolation by distance. Life history traits of the desert tortoise, a long-lived species with delayed sexual maturity, may severely constrain the ability of small populations to respond to disturbances that increase adult mortality. Historic gene flow estimates among populations suggests that recovery of declining populations may rely heavily on the immigration of new individuals from adjacent mountain ranges. Management strategies compatible with the evolutionary history of gene flow among disjunct populations will help ensure the long-term persistence of Sonoran desert tortoise populations.     

High genetic diversity of the endangered Iberian three‐spined stickleback (Gasterosteus aculeatus) at the Mediterranean edge of its range

1. The three‐spined stickleback (Gasterosteus aculeatus) on the Iberian Peninsula is only distributed in freshwater habitats and has completely disappeared from most of its range, mainly as a consequence of habitat degradation and invasive fish introductions. Genetic investigations have shown that Mediterranean‐Adriatic sticklebacks constitute an evolutionarily significant unit. Here, we present the first genetic data for Iberian populations living on the southern edge of the stickleback’s range. We used microsatellite markers to study gene diversity, population structure and genetic demography of stickleback populations. 2. High genetic differentiation among collections yielded a model of four genetically homogeneous units related to geography. The observed pattern of isolation by distance resulted mainly from the hydrographical pattern and limited gene flow among rivers. Moreover, low levels of gene diversity, high isolation and recent bottleneck events, which have led to small or even critical effective population sizes in several locations, could be explained by additional recent anthropogenic fragmentation. 3. We defined at least four evolutionarily significant units threatened by habitat fragmentation in north‐eastern Iberian sticklebacks. Because they retain long evolutionary histories, these populations should be considered of high conservation priority, and urgent management measures should be implemented.     

Microsatellite variation within and among recently fragmented populations of the golden lion tamarin (Leontopithecus rosalia)

Four variable microsatellite loci were used toexamine the genetic diversity and differentiation of golden lion tamarins (Leontopithecus rosalia) in four populations recently isolated by habitat fragmentation. Using Rst estimates of genetic differentiation, a considerable genetic divergence was detected among these populations, with an averagedifferentiation of 31%. Significant differences in allele number among these populations were found. However, the heterozygosity among these populations was not statistically different. These results suggestthat loss in allele diversity was faster than loss in heterozygosity. Conservation implications, particularly for golden lion tamarins, are then discussed. Loss of allelic diversity might be as serious a concern to endangered species as heterozygosity or inbreeding.     

生境片断化对植物种群遗传结构的影响及植物遗传多样性保护

生境片断化是指大而连续的生境变成空间隔离的小种群的现象。生境片断化对植物种群遗传效应包括生境片断化过程中的取样效应及其后的小种群效应（遗传漂变、近交等）。理论研究表明,生境片断化后,植物种群的遗传变异程度将降低,而残留的小种群间的遗传分化程度将升高。然而对一些植物的研究表明,生境片断化对植物种群的遗传效应要受其他一些因素的影响,如世代长度、片断化时间、片断种群的大小、基因流的改变等。最后,针对生境     

Landscape genetics of a recent population extirpation in a burnet moth species

The intensification of agricultural land use over wide parts of Europe has led to the decline of semi-natural habitats, such as extensively used meadows, with those that remain often being small and isolated. These rapid changes in land use during recent decades have strongly affected populations inhabiting these ecosystems. Increasing habitat deterioration and declining permeability of the surrounding landscape matrix disrupt the gene flow within metapopulations. The burnet moth species Zygaena loti has suffered strongly from recent habitat fragmentation, as reflected by its declining abundance. We have studied its population genetic structure and found a high level of genetic diversity in some of the populations analysed, while others display low genetic diversity and a lack of heterozygosity. Zygaena loti was formerly highly abundant in meadows and along the skirts of forests. However, the species is currently restricted to isolated habitat remnants, which is reflected by the high genetic divergence among populations (F _ST: 0.136). Species distribution modelling as well as the spatial examination of panmictic clusters within the study area strongly support a scattered population structure for this species. We suggest that populations with a high level of genetic diversity still represent the former genetic structure of interconnected populations, while populations with low numbers of alleles, high F _IS values, and a lack of heterozygosity display the negative effects of reduced interconnectivity. A continuous exchange of individuals is necessary to maintain high genetic variability. Based on these results, we draw the general conclusion that more common taxa with originally large population networks and high genetic diversity suffer stronger from sudden habitat fragmentation than highly specialised species with lower genetic diversity which have persisted in isolated patches for long periods of time.     

Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae)

The use of genetic methods to quantify the effects of anthropogenic habitat fragmentation on population structure has become increasingly common. However, in today’s highly fragmented habitats, researchers have sometimes concluded that populations are currently genetically isolated due to habitat fragmentation without testing the possibility that populations were genetically isolated before European settlement. Etheostoma raneyi is a benthic headwater fish restricted to river drainages in northern Mississippi, USA, that has a suite of adaptive traits that correlate with poor dispersal ability. Aquatic habitat within this area has been extensively modified, primarily by flood-control projects, and populations in headwater streams have possibly become genetically isolated from one another. We used microsatellite markers to quantify genetic structure as well as contemporary and historical gene flow across the range of the species. Results indicated that genetically distinct populations exist in each headwater stream analyzed, current gene flow rates are lower than historical rates, most genetic variation is partitioned among populations, and populations in the Yocona River drainage show lower levels of genetic diversity than populations in the Tallahatchie River drainage and other Etheostoma species. All populations have negative F_IS scores, of which roughly half are significant relative to Hardy–Weinberg expectations, perhaps due to small population sizes. We conclude that anthropogenic habitat alteration and fragmentation has had a profoundly negative impact on the species by isolating E. raneyi within headwater stream reaches. Further research is needed to inform conservation strategies, but populations in the Yocona River drainage are in dire need of management action. Carefully planned human-mediated dispersal and habitat restoration should be explored as management options across the range of the species.     

Microsatellite analysis reveals interpopulation differentiation and gene flow in the endangered tree Changiostyrax dolichocarpa (Styracaceae) with fragmented distribution in central China

Polymorphic simple sequence repeat (SSR) markers were used to investigate the impact of habitat fragmentation on the population structure and gene flow of Changiostyrax dolichocarpa, a critically endangered tree in central China. Intrapopulation genetic diversity, population structure and gene flow in the five extant populations of this species were analysed by eight SSR markers. Intrapopulation genetic diversity results suggest that C. dolichocarpa remnants maintained a relatively high degree of genetic diversity despite severe fragmentation. Low genetic differentiation among populations was found based on Wright's F(ST) and amova analysis. Both the F(ST)-based estimate and private allele method revealed high historical gene flow among the remnant populations. Recent immigrants, detected by assignment tests, tend to decrease from the grandparent generation to the current generation. The potentially highly restricted current gene flow among fragments may render the fragmented populations of C. dolichocarpa at a higher risk of local extinction several generations after fragmentation. Both in situ and ex situ conservation management for the remnant populations of C. dolichocarpa are therefore urgently needed to rescue remaining genetic diversity.     

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

ABSTRACT: BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; pi = 0.00314) were almost as high as at PAL (h = 0.836; pi = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.     

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes

We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as theta, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities.     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.