History vs. current demography: explaining the genetic population structure of the common frog (Rana temporaria)

The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.     

Conservation of rare species with island-like distributions: A case study of Lasthenia conjugens (Asteraceae) using population genetic structure and the distribution of rare markers

Californian vernal pools, a patchy, island-like habitat, are endangered as a result of habitat destruction. Conservation of the remaining vernal pool habitat is essential for the persistence of several endangered species. We present the first study examining DNA-level genetic diversity within and among populations of a vernal pool plant species. We investigated genetic variation across eight populations of the US federally endangered vernal pool endemic Lasthenia conjugens (Asteraceae) using intersimple sequence repeat (ISSR) markers. Genetic diversity within the species was high (Nei's gene diversity estimate was 0.37), with moderate differentiation among populations (Bayesian F _ST analog of 0.124). Using an amova analysis, we found that the majority of the genetic variation (84%) was distributed within populations. There is a significant relationship between geographical distance and pairwise genetic differentiation as measured by the Bayesian estimate θ^B. The alternative hypotheses of historic geological processes within the Central Valley and contemporary gene flow are discussed as explanations of the data. Because of the vulnerability of the populations, we calculated a probability of loss for rare alleles (fragments) in the populations. Calculations show that sampling only one of the eight populations for ex-situ conservation or restoration will capture approximately 54% of the sampled rare fragments. We believe that one of the sampled populations has become extinct since it was sampled. When removing this population from the above-mentioned calculations, sampling one population will capture only 41.3% of the sampled rare fragments. We recommend sampling strategies for future conservation and restoration efforts of L. conjugens.     

A test of the central–marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

The central–marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core‐to‐edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core‐to‐edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean centre on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core‐to‐edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.     

Using a species distribution model to guide NSW surveys of the long‐footed potoroo (Potorous longipes)

Knowledge of threatened species’ distributions is essential for effective conservation decision‐making. Species distribution models (SDMs) are widely used to map species’ geographic ranges, identify new areas of suitable habitat and guide field surveys. In New South Wales (NSW), Australia, there are grave doubts about whether populations of the critically endangered long‐footed potoroo (Potorous longipes) remain extant, and identification of occupied sites is a high priority for its conservation. We used an SDM (Maxent) to identify regions in NSW that may have suitable habitat for the potoroo. The SDM was built with seven climate layers and had strong predictive performance (cross‐validated AUC = 0.94). We then combined this information on habitat suitability with vegetation and topography, to identify 58 survey sites across NSW. From April 2016 to May 2017, we undertook six field trips deploying six to eight cameras at each site for 52–63 days, resulting in 25 120 camera trap nights. A total of 215 759 images captured 43 native and feral animal species, but no long‐footed potoroos. Following the survey, newly available, independent presence and absence data were used to validate our model. A Kruskal–Wallis H test indicated that habitat suitability values were significantly higher at presence locations than absence locations (H = 58.66, d.f. = 1, P < 0.001). Finally, we refitted the Maxent model with the new data and identified additional regions that future surveys could explore. We conclude, however, that if the long‐footed potoroo remains extant in NSW, it is extremely rare.     

Census (N C) and genetically effective (N e) population size in a lake-resident population of brown trout Salmo trutta

Census (N(C)) and effective population size (N(e)) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (N(e):N(C)) for this population is 0.11 with a range of 0.06-0.26, suggesting that N(e):N(C) ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes.     

Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)

Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models (SDMs). Circuit‐SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fuscaFüller (Noctuidae) across sub‐Saharan Africa. Species abundance was surveyed across its distribution range. SDMs were optimized and selected by cross‐validation. Relationship between observed matrices of genetic differentiation between individuals, and between matrices of resistance distance was assessed through Mantel tests and redundancy discriminant analyses (RDAs). A total of 628 individuals from 130 localities in 17 countries were genotyped at seven microsatellite loci. Six population clusters were found based on a Bayesian analysis. The eastern margin of Dahomey gap between East and West Africa was the main factor of genetic differentiation. The SDM projections at present, last interglacial and last glacial maximum periods were used for the estimation of circuit resistance between locations of genotyped individuals. For all periods of time, when using either all individuals or only East African individuals, partial Mantel r and RDA conditioning on geographic distance were found significant. Under future projections (year 2080), partial r and RDA significance were different. From this study, it is concluded that analytical solutions provided by circuit theory are useful for the evolutionary management of populations and for phylogeographic analysis when coalescence times are not accessible by approximate Bayesian simulations.     

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

The effective population size (N(e) ) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating N(e) from a single sample of genotypes to trace temporal change in N(e) for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both N(e) and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (N(b) ) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to N(e) using the generation interval. The N(e) estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of N(e) > 50 but short of the long-term minimum viable population goal of N(e) > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in N(e) probably in the late 1990s and early 2000s. The new single-sample approaches to the estimation of N(e) provide efficient means for including N(e) in monitoring frameworks and will be of great importance for future management and conservation.     

Isolation and characterization of 19 polymorphic microsatellite DNA markers in the Japanese brown frog (Rana japonica)

We report the isolation and characterization of 19 polymorphic microsatellite DNA markers in the Japanese brown frog (Rana japonica). These markers were tested in 24 individuals each collected from three distinct populations in Ichikai-machi, Tochigi Prefecture. The number of observed alleles per locus ranged from 3 to 24 across all populations, and the values of observed and expected heterozygosities ranged from 0.130 to 1 and from 0.125 to 0.941, respectively. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.     

Evidence of environmental niche differentiation in the striped mouse (Rhabdomys sp.): inference from its current distribution in southern Africa

The aim of this study was to characterize environmental differentiation of lineages within Rhabdomys and provide hypotheses regarding potential areas of contact between them in the Southern African subregion, including the Republic of South Africa, Lesotho, and Namibia. Records of Rhabdomys taxa across the study region were compiled and georeferenced from the literature, museum records, and field expeditions. Presence records were summarized within a 10 × 10 km grid covering the study area. Environmental information regarding climate, topography, land use, and vegetation productivity was gathered at the same resolution. Multivariate statistics were used to characterize the current environmental niche and distribution of the whole genus as well as of three mitochondrial lineages known to occur in southern Africa. Distribution modeling was carried out using MAXENT in order to generate hypotheses regarding current distribution of each taxa and their potential contact zones. Results indicate that the two species within Rhabdomys appear to have differentiated across the precipitation/temperature gradient present in the region from east to west. R. dilectus occupies the wettest areas in eastern southern Africa, while R. pumilio occupies the warmer and drier regions in the west, but also penetrates in the more mesic central part of the region. We provide further evidence of environmental differentiation within two lineages of R. dilectus. Contact zones between lineages appear to occur in areas of strong environmental gradients and topographic complexity, such as the transition zones between major biomes and the escarpment area where a sharp altitudinal gradient separates coastal and plateau areas, but also within more homogeneous areas such as within grassland and savannah biomes. Our results indicate that Rhabdomys may be more specialized than previously thought when considering current knowledge regarding mitochondrial lineages. The genus appears to have differentiated along two major environmental axes in the study region, but results also suggest dispersal limitations and biological interactions having a role in limiting current distribution boundaries. Furthermore, the projection of the potential geographic distribution of the different lineages suggests several contact zones that may be interesting study fields for understanding the interplay between ecological and evolutionary processes during speciation.     

A population genetic study of the endangered plant species Limonium dufourii (Plumbaginaceae) based on amplified fragment length polymorphism (AFLP)

Limonium dufourii ( Plumbaginaceae ) is a triploid species with obligate apomictic reproduction and is endemic to the East Mediterranean coast of Spain, where it is present in only six populations, most of which have a very low number of individuals. Genetic variation and population structure in this species was studied using amplified fragment length polymorphisms (AFLPs) as markers, using the same individuals as in a previous study with random amplified polymorphic DNA (RAPD). Three different primers provided 252 bands of which 51 were polymorphic among the 152 individuals analysed. Those polymorphic bands were able to define 65 different phenotypes, of which all but two were present in only one population. The comparative analyses of data from AFLPs with those from RAPDs show a high degree of concordance. Additionally, and given the nature of these markers, we propose the estimation of nucleotide divergences from AFLP patterns. Relationships among the different AFLP patterns and the estimates of population genetic parameters obtained with this evolutionary distance are in good agreement with previous results. These analyses show that substantial genetic variability and differentiation exist within and among populations of L. dufourii . Their higher reproducibility and the possibility of obtaining estimates of nucleotide divergence make AFLPs a much better DNA fingerprinting technique.     

中国云豹种群分布现状与关键栖息地信息更新

云豹(Neofelis nebulosa)是中国大型猫科动物中对森林生态系统依赖性最高的物种。中国作为云豹的主要分布区, 由于长期以来缺乏深入研究和有效保护, 在盗猎、森林采伐、土地利用变化等威胁因素的共同作用下, 云豹在中国的分布范围和种群数量近数十年来均大幅缩减, 其分布现状亟需全面评估。本研究系统检索和查阅了国内1950年以来的云豹标本、野外调查记录、地方志、新闻报道等直接证据, 整理了中国各省级行政区内云豹记录存在的年代; 基于2010-2020年国内55个地区的红外相机监测数据, 结合同期研究文献中记录的中国云豹确认分布位点, 校准了已发表的云豹栖息地适合度模型, 并在此基础上叠加保护地和行政区划图层, 根据2010-2020年间森林覆盖率的减量评估云豹栖息地适合度的变化, 以识别我国的云豹关键栖息地和保护优先区。结果显示, 1950-2009年, 我国的云南、西藏、四川、陕西、甘肃、重庆、贵州、广西、广东、海南、湖北、湖南、安徽、江西、浙江、福建以及台湾共17个省级行政区有云豹分布, 但其中12个迄今已超过20年无确凿记录, 且目前仅在云南省和西藏自治区仍有云豹记录延续。当前我国大陆地区云豹潜在栖息地总面积64,093 km², 分别位于9个连续的栖息地斑块中, 其中3个为跨境斑块。2010-2020年间, 我国境内共在5个自然保护区的10个样区记录到云豹, 全部位于西藏东南部以及云南西部和南部的2个跨境栖息地斑块(即“喜马拉雅-横断山脉西侧-若开山脉”和“无量山南麓-安南山脉”)的边缘。2010-2020年间, 这两个斑块在中国境内区域的年均森林覆盖率减量(0.84%)小于境外(1.57%)。从本研究的结果推断, 中国目前确认分布的云豹种群极有可能维持在跨境分布的生境中, 面临内部和跨境的双重挑战。相关保护地应有针对性地加强反盗猎执法, 并开展栖息地恢复工作以提升云豹栖息地质量与斑块连通性, 同时与周边分布区国家开展跨境保护合作, 为现有云豹种群的长期生存和发展提供必要基础。     

Testing the utility of species distribution modelling using Random Forests for a species in decline

Habitat suitability estimates derived from species distribution models (SDMs) are increasingly used to guide management of threatened species. Poorly estimating species’ ranges can lead to underestimation of threatened status, undervaluing of remaining habitat and misdirection of conservation funding. We aimed to evaluate the utility of a SDM, similar to the models used to inform government regulation of habitat in our study region, in estimating the contemporary distribution of a threatened and declining species. We developed a presence‐only SDM for the endangered New Holland Mouse (Pseudomys novaehollandiae) across Victoria, Australia. We conducted extensive camera trap surveys across model‐predicted and expert‐selected areas to generate an independent data set for use in evaluating the model, determining confidence in absence data from non‐detection sites with occupancy and detectability modelling. We assessed the predictive capacity of the model at thresholds based on (1) sum of sensitivity and specificity (SSS), and (2) the lowest presence threshold (LPT; i.e. the lowest non‐zero model‐predicted habitat suitability value at which we detected the species). We detected P. novaehollandiae at 40 of 472 surveyed sites, with strong support for the species’ probable absence from non‐detection sites. Based on our post hoc optimised SSS threshold of the SDM, 25% of our detection sites were falsely predicted as non‐suitable habitat and 75% of sites predicted as suitable habitat did not contain the species at the time of our survey. One occupied site had a model‐predicted suitability value of zero, and at the LPT, 88% of sites predicted as suitable habitat did not contain the species at the time of our survey. Our findings demonstrate that application of generic SDMs in both regulatory and investment contexts should be tempered by considering their limitations and currency. Further, we recommend engaging species experts in the extrapolation and application of SDM outputs.     

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east–west split occurred ~13–18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5–11 kya during a period of extreme drought cycles. A range‐wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid‐Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.     

Ecological genomics meets community‐level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, most efforts to model the response of species to climate change ignore intraspecific variation due to local adaptation. Here, we present a new perspective on spatial modelling of organism–environment relationships that combines genomic data and community‐level modelling to develop scenarios regarding the geographic distribution of genomic variation in response to environmental change. Rather than modelling species within communities, we use these techniques to model large numbers of loci across genomes. Using balsam poplar (Populus balsamifera) as a case study, we demonstrate how our framework can accommodate nonlinear responses of loci to environmental gradients. We identify a threshold response to temperature in the circadian clock gene GIGANTEA‐5 (GI5), suggesting that this gene has experienced strong local adaptation to temperature. We also demonstrate how these methods can map ecological adaptation from genomic data, including the identification of predicted differences in the genetic composition of populations under current and future climates. Community‐level modelling of genomic variation represents an important advance in landscape genomics and spatial modelling of biodiversity that moves beyond species‐level assessments of climate change vulnerability.     

The impact of habitat fragmentation on fitness‐related traits in a native prairie plant,Chamaecrista fasciculata (Fabaceae)

Loss and fragmentation of the native prairies in the Midwestern United States have resulted in isolated and smaller habitats and populations. The populations remaining in these prairies are expected to show a decline in the extent of genetic variation and an increase in genetic drift load (accumulation of deleterious recessive alleles due to genetic drift) in fitness‐related traits. Using complementary greenhouse experiments, we tested whether these expected changes have occurred in the native annual prairie plant Chamaecrista fasciculata. In the first experiment, open pollinated C. fasciculata seeds from 12 prairie fragments representing a range in area of habitat were grown in competition with Schizachyrium scoparium to determine if there are changes in plant vigour with changes in fragment size and corresponding changes in population size. Plants from smaller prairie fragments exhibited a slight but significant decline in biomass, suggesting an increase in genetic drift load. In the second experiment, a formal genetic crossing design of four prairie fragment populations was used to estimate quantitative genetic diversity and genetic drift load. We did not find extensive quantitative genetic variation, but we did find a strong effect of genetic drift load on five traits in this experiment. Our overall conclusion is that a decline in relative‐fitness traits in smaller prairie fragments is probably associated with fixation of deleterious alleles due to more isolated and smaller populations, i.e. genetic drift load. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Limited Reintroduction Does Not Always Lead to Rapid Loss of Genetic Diversity: An Example from the American Chestnut (Castanea dentata; Fagaceae)

In restoring species, reasons for introducing limited numbers of individuals at different locations include costs of introduction and maintenance, limited founder supply, and risk “bet hedging.” However, populations initiated from few founders may experience increased genetic drift, inbreeding, and diversity loss. We examined the genetic diversity of an isolated stand of more than 5,000 American chestnut trees relative to that of the 9 surviving stand founders (out of 10 total) planted in the 1880s. We used minisatellite DNA probes to reveal 84 genetic markers (circa 24 loci) among the nine founders, and their genetic diversity was compared with three separate plots of descendant trees, as well as with two natural stands. The descendants were circa 7.3% more heterozygous than the founders (mean estimated H= 0.556 vs. 0.518, respectively; p < 0.0001). Genetic differentiation was not pronounced (F_ST < 0.031), and no markers, including those at low frequency among the founders, were lost in the descendants. The founders and natural transects were not significantly different in H or similarity (mean proportion of bands shared). Special planting or mating protocols for establishment of a vigorous American chestnut population from a low number of founders may not be required to avoid strong effects of genetic drift and inbreeding. These results demonstrate that loss of genetic diversity following reintroduction of a limited number of founders is not always inevitable, such as this case where the species is highly outcrossing, expression of heterozygous advantage may occur, the original founders remain as gene contributors over generations, and the establishing population expands constantly and rapidly.     

Phylogeography and conservation genetics of the Columbia spotted frog (Rana luteiventris; Amphibia, Ranidae)

The Columbia spotted frog (Rana luteiventris) has a widespread distribution in western Canada and the western US, although the southern reach of its range is highly fragmented into several isolated populations. Threats from various factors have raised concerns regarding the long-term survival of many small, isolated populations. Here, we report a study designed to determine the phylogeographic and conservation genetic parameters of R. luteiventris in the western US. Mitochondrial DNA (mtDNA) sequences were examined for phylogeographic structuring using phylogenetic reconstruction methods, coupled with networking and nested clade analyses. These methods permitted a distinction to be made between historic and demographic forces acting to generate geographical patterning of genetic variation. Phylogenetic analysis revealed four geographically correlated monophyletic clades. Three of these clades correspond to well-defined, nonoverlapping geographical locations in the fragmented portion of the range. The other is comprised of all samples collected from the contiguous range and includes one isolate from northern Wyoming. Networking and nested clade analyses confirmed these results and revealed that historical processes, such as range expansion and vicariance, rather than recurrent gene flow are likely responsible for observed patterns of genetic variation. A measure of genetic variation (theta = 4N(e)mu) revealed that R. luteiventris populations in Utah have a relatively low amount of genetic variation compared with populations in the continuous portion of the range.