Regression commonality analyses on hierarchical genetic distances

Landscape genetics is emerging as an important way of supporting decision‐making in landscape management, in response to the deterioration of matrix permeability due to habitat loss and fragmentation. In line with unremitting methodological developments in landscape genetics, a new analytical procedure was recently proposed as a way of evaluating the effects of landscape gradients on genetic structures. This procedure is based on the computation of inter‐individual hierarchical genetic distances (HGD), a metric of genetic differentiation taking into account the hierarchical structure in populations as inferred from clustering algorithms. HGD can be used as dependent variables in multivariate regressions to assess the effects of various landscape predictors on spatial patterns of genetic differentiation. However, multicollinearity may obscure the interpretation of multivariate regressions. We illustrate how regression commonality analyses (CA), a detailed variance partitioning procedure that can be used to deal with multicollinearity issues, can thoroughly improve our understanding of landscape connectivity when HGD are used as a dependent variable, with the red deer Cervus elaphus as an empirical example. Using logistic regression commonality analyses on HGD, we showed that semi‐natural open areas, transportation infrastructures and, to a lesser extent, urban areas and rivers, were associated with an increase in hierarchical genetic differentiation in red deer. Regressions based on HGD provided detailed results that could not have been obtained with regressions based on standard genetic distances, with notably additional insights as to the possible influence of linear features such as roads and highways on landscape connectivity. Furthermore, CA helped identify synergistic associations among variables as well as suppressors, thus resolving inconsistencies among hierarchical levels and revealing spurious correlations that may have gone unnoticed in the course of classical regression analyses. We thus recommend the use of regression commonality analysis on hierarchical genetic distances as a promising statistical tool for landscape geneticists.     

Allozymic variation of the endangered killifishAphanius iberus and its application to conservation

Synopsis Genetic differentiation and patterns of variability in the endangered Iberian endemic,Aphanius iberus, were analyzed by allozyme electrophoresis as a valuable database for conservation purposes. Genetic variability values expressed as heterozygosity (H = 0.015–0.097) were close to the values found in other members of Cyprinodontidae (H = 0.012–0.123). Polymorphism values (P = 0.125–0.542) were higher than reported in the literature (P = 0.036–0.150) for Cyprinodontidae. Significant correlation existed between salinity values and genetic variability expressed as heterozygosity (r = – 0.76, p < 0.01) and polymorphism (r = – 0.60, p = 0.04). Low genetic variability values (H = 0.024–0.055, P = 0.125–0.292) were exhibited by populations which inhabit salty lagoons. The highest values were found in populations occurring in marshes and irrigation channels (H = 0.051–0.097, P = 0.250–0.542). Associations among genetic, geographic and ecological parameters were tested using a Mantel test indicated that most of the genetic distances were explained by geographic distances but not by ecological factors, suggesting that isolation by distance could be the main factor explaining the differentiation between sites. According to the genetic distances obtained, two mainA. iberus groups were discernible: the Atlantic and Mediterranean. Genetic distances between both groups (DRogers = 0.179–0.261) were higher than values between recognized species of other cyprinodontids (DRogers = 0.11–0.27). On the basis of genetic distances we have dated the fragmentation of both populations to the Upper Miocene-Pliocene when most of the Mediterranean sea dried up. Subsequently, gene flow between Mediterranean and Atlantic populations was interrupted. The results of our genetic analyses suggested the existence of five operational conservation units (OCUs) forA. iberus. These units are defined as a continuous area limited by geographical boundaries, and inhabited by one or more populations sharing the same genetic pattern.     

Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (N_e), although N_e is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables. Location Yosemite National Park, California, USA. Methods I estimated F_ST, D_ps and N_e using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between N_e and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation. Results I found substantial variation in genetic distances between populations (F_ST = 0.004–0.396, D_ps = 0.045–0.839) and in effective population sizes (N_e = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with N_e. Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.     

Predators in natural fragments: foraging ecology of wolves in British Columbia's central and north coast archipelago

Aim Predator–prey dynamics in fragmented areas may be influenced by spatial features of the landscape. Although little is known about these processes, an increasingly fragmented planet underscores the urgency to predict its consequences. Accordingly, our aim was to examine foraging behaviour of an apex mammalian predator, the wolf (Canis lupus), in an archipelago environment. Location Mainland and adjacent archipelago of British Columbia, Canada; a largely pristine and naturally fragmented landscape with islands of variable size and isolation. Methods We sampled 30 mainland watersheds and 29 islands for wolf faeces in summers 2000 and 2001 and identified prey remains. We examined broad geographical patterns and detailed biogeographical variables (area and isolation metrics) as they relate to prey consumed. For island data, we used Akaike Information Criteria to guide generalized linear regression model selection to predict probability of black‐tailed deer (main prey; Odocoileus hemionus) in faeces. Results Black‐tailed deer was the most common item in occurrence per faeces (63%) and occurrence per item (53%) indices, representing about 63% of mammalian biomass. Wolves consumed more deer on islands near the mainland (65% occurrence per item) than on the mainland (39%) and outer islands (45%), where other ungulates (mainland only) and small mammals replaced deer. On islands, the probability of detecting deer was influenced primarily by island distance to mainland (not by area or inter‐landmass distance), suggesting limited recolonization by deer from source populations as a causal mechanism. Main conclusions Although sampling was limited in time, consistent patterns among islands suggest that population dynamics in isolated fragments are less stable and can result in depletion of prey. This may have important implications in understanding predator–prey communities in isolation, debate regarding wolf–deer systems and logging in temperate rain forests, and reserve design.     

Association of serum lipid components and obesity with genetic ancestry in an admixed population of elderly women

The prevalence of metabolic disorders varies among ethnic populations and these disorders represent a critical health care issue for elderly women. This study investigated the correlation between genetic ancestry and body composition, metabolic traits and clinical status in a sample of elderly women. Clinical, nutritional and anthropometric data were collected from 176 volunteers. Genetic ancestry was estimated using 23 ancestry-informative markers. Pearsons correlation test was used to examine the relationship between continuous variables and an independent samples t-test was used to compare the means of continuous traits within categorical variables. Overall ancestry was a combination of European (57.49%), Native American (25.78%) and African (16.73%). Significant correlations were found for European ancestry with body mass index (r = 0.165; p = 0.037) and obesity (mean difference (MD) = 5.3%; p = 0.042). African ancestry showed a significant correlation with LDL (r = 0.159, p = 0.035), VLDL (r = −0.185; p = 0.014), hypertriglyceridemia (MD = 6.4%; p = 0.003) and hyperlipidemia (MD = 4.8%; p = 0.026). Amerindian ancestry showed a significant correlation with triglyceride levels (r = 0.150; p = 0.047) and hypertriglyceridemia (MD = 4.5%; p = 0.039). These findings suggest that genetic admixture may influence the etiology of lipid metabolism-related diseases and obesity in elderly women.     

Effects of sample size,number of markers,and allelic richness on the detection of spatial genetic pattern

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially‐explicit, individual‐based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation‐by‐distance, isolation‐by‐barrier, and isolation‐by‐landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non‐equilibrium conditions after introduction of isolation‐by‐landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals.     

Landscape genetics of a specialized grasshopper inhabiting highly fragmented habitats: a role for spatial scale

Aim The study of geographical discontinuities in the distribution of genetic variability in natural populations is a central topic in both evolutionary and conservation research. In this study, we aimed to analyse (1) the factors associated with genetic diversity at the landscape spatial scale in the highly specialized grasshopper Mioscirtus wagneri and (2) to identify the relative contribution of alternative factors to the observed patterns of genetic structure in this species. Location La Mancha region, Central Spain. Methods We sampled 28 populations of the grasshopper M. wagneri and genotyped 648 individuals at seven microsatellite loci. We employed a causal modelling approach to identify the most influential variables associated with genetic differentiation within a multiple hypothesis‐testing framework. Results We found that genetic diversity differs among populations located in different river basins and decreases with population isolation. Causal modelling analyses showed variability in the relative influence of the studied landscape features across different spatial scales. When a highly isolated population is considered, the analyses suggested that geographical distance is the only factor explaining the genetic differentiation between populations. When that population is excluded, the causal modelling analysis revealed that elevation and river basins are also relevant factors contributing to explaining genetic differentiation between the studied populations. Main conclusions These results indicate that the spatial scale considered and the inclusion of outlier populations may have important consequences on the inferred contribution of alternative landscape factors on the patterns of genetic differentiation even when all populations are expected to similarly respond to landscape structure. Thus, a multiscale perspective should also be incorporated into the landscape genetics framework to avoid biased conclusions derived from the spatial scale analysed and/or the geographical distribution of the studied populations.     

Microsatellite variation in China’s Hainan Eld’s deer (<Emphasis Type="Italic">Cervus eldi hainanus</Emphasis>) and implications for their conservation

Hainan Eld’s deer (Cervus eldi hainanus) experienced a dramatic decline in the late 1960s through early 1970s and by 1976 only 26 deer remained in Datian of Hainan Island, China. Since then, conservation efforts have successfully rescued this deer from extinction. We employed 10 microsatellite DNA loci to index genetic variation in the one source (Datian) and two introduced populations (Bangxi and Ganshiling) and suggest implications for the conservation of the species. A total of 40 alleles at 10 loci were examined from 198 deer blood samples. The source population harbored all 40 alleles, while the Bangxi and Ganshiling translocated populations contained 24 and 26 alleles, respectively. The genetic variability was low (H _e ≈ 0.33) for each of the three populations. No significant difference in genetic variability between the three populations was detected (P > 0.05); yet significant differentiation was found among the three populations. Our results suggest that founder effects and genetic drift have affected the two translocated populations. For conservation we recommend the three populations be managed as a meta-population. When establishing future reintroductions, the founder population should have a size larger than the original 26 founders in Datian population or be composed of a cohort of over 20 same-age individuals with 1:1 sex ratio. Genetic monitoring for both the source and translocated populations should be continuously conducted in order to assess the effectiveness of deer conservation in the future.     

Genetic Structure Is Associated with Phenotypic Divergence in Floral Traits and Reproductive Investment in a High-Altitude Orchid from the Iron Quadrangle,Southeastern Brazil

Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.     

Genetic variability in white-tailed deer (Odocoileus virginianus) and its relationship to environmental parameters and herd origin (Cervidae)

Allozyme variation was examined in 1571 white-tailed deer (Odocoileus virginianus) from 29 localities in Tennessee by starch gel electrophoresis. For 11 polymorphic loci, sex-related, age-related and temporal differences were minimal. However, significant spatial hererogeneity was evident in genotypes (contingency table results), allele frequencies (F _ST=0.057) and heterozygosity. Heterozygosity ranged from 16.9% to 26.8% with a mean of 22.9%. The spatial pattern of allele frequencies determined from Rogers' coefficients of genetic similarity indicated associations based on geographic proximity and stocking history. In hierarchial analyses, physiographic regions accounted for more of the total gene diversity than herd origin groups (populations of similar origin) but less than individual populations. For five loci, physiographic regions accounted for more of the gene diversity than populations, suggesting a selection role in the observed genetic variability. Bivariate and canonical correlation analyses revealed significant associations between environmental and genetic variables. Temperature variables and allele frequencies for three loci (alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, sorbitol dehydrogenase) had the prominent roles in the multivariate association between environmental and genetic variables. Herd origin, gene flow and selection appear to be involved in the gene diversity in deer from Tennesee.     

Genetic diversity and environmental associations of wild barley,Hordeum spontaneum,in Turkey

Genetic variability within and between populations of the wild progenitor of barley was studied electrophoretically. Thirty enzyme loci were assayed in 437 individuals representing 11 populations ofH. spontaneum in Turkey. The results indicated that: (a)H. spontaneum in Turkey is genetically rich in allozyme variation, but because of predominant self-pollination the variation is maintained as different homozygotes in the population; (b) genetic differentiation of populations includes clinal, regional, and local patterns, sometimes displaying sharp geographic differentiation over short distances; (c) overall indices of allozymic diversity and some allele frequencies of wild barley are significantly correlated with the environment and are predictable ecologically, chiefly by combinations of temperature and humidity variables; (d) a high percentage of alleles (66%) occur in local areas or are distributed sporadically rather than widespread; (e) Wright Fixation index was very high, F=0.995; (f) genetic distance was high (D=0.11, ranging from 0.031 to 0.288) between populations, and (g) average relative genetic differentiation was high among populations (Gst=0.47, ranging from 0.02 to 0.66). The spatial patterns and environmental correlates and predictors of genetic variation ofH. spontaneum in Turkey, indicated that genetic variation in wild barley populations is not only common, but also at least partly, adaptive. Therefore, a much fuller exploitation of these genetic resources by breeding is warranted.     

Population genetic structure of codling moth (Lepidoptera: Tortricidae) from apple orchards in central Chile

Codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is the main pest of pome fruits worldwide. Despite its economic importance, little is known about the genetic structure and patterns of dispersal at the local and regional scale, which are important aspects for establishing a control strategy for this pest. An analysis of genetic variability using microsatellites was performed for 11 codling moth populations in the two major apple (Malus domestica Borkh) cropping regions in central Chile. Despite the geographical distances between some populations (approximately 185 km), there was low genetic differentiation among populations (F(ST) = 0.002176), with only slight isolation by distance. Only approximately 0.2% of the genetic variability was found among the populations. Geographically structured genetic variation was independent of apple orchard management (production or abandoned). These results suggest a high genetic exchange of codling moth between orchards, possibly mediated by human activities related to fruit production.     

Population genetics of Dioon edule Lindl. (Zamiaceae, Cycadales): biogeographical and evolutionary implications

Dioon edule Lindl. (Zamiaceae) is a cycad endemic to Mexico, that occurs as one species D. edule and the geographical variety D. edule var. angustifolium (Miq.) Miq. Dioon edule has a north to south distribution in eastern Mexico. In this study, we analysed 14 allozymic loci in eight populations of D. edule from its total distribution range by sampling all known populations. Patterns of diversity and genetic variability, within and among populations, were obtained. The mean number of alleles per locus ( A ) was 1.44 and the percentage of polymorphic loci was relatively high ( P  = 54.78). The mean observed ( H _O ) and expected heterozygosity ( H _E ) were 0.27 and 0.24, respectively. F -statistics revealed an excess of heterozygous genotypes, locally and globally ( F  = −0.17 and f  = −0.27, respectively). The genetic variation explained by differences among populations was only 7.5%. We also detected a negative relationship between genetic diversity and latitude. On average, the gene flow between population pairs was relatively high ( Nm  = 2.98); furthermore, gene flow between population pairs was significantly correlated with geographical distances ( r  = −0.38, P  = 0.025). Therefore, patterns of genetic diversity in D. edule appear to be associated with the post-Pleistocene spread of the species, from its southerly (origin) to its northerly range (derived populations, including its central distribution). The biogeographical and evolutionary aspects of the results of this study are discussed. We recognize Dioon angustifolium Miq. for the northernmost disjunct populations.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 457–467     

Landscape Features Fail to Explain Spatial Genetic Structure in White-Tailed Deer Across Ohio,USA

Landscape features influence wildlife movements across spatial scales and have the potential to influence the spread of disease. Chronic wasting disease (CWD) is a fatal prion disease affecting members of the family Cervidae, particularly white-tailed deer (Odocoileus virginianus), and the first positive CWD case in a wild deer in Ohio, USA, was recorded in 2020. Landscape genetics approaches are increasingly used to better understand potential pathways for CWD spread in white-tailed deer, but little is known about genetic structure of white-tailed deer in Ohio. The objectives of our study were to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We collected genetic data from 619 individual deer from 24 counties across Ohio during 2007–2009. We used microsatellite genotypes from 619 individuals genotyped at 11 loci and haplotypes from a 547-base pair fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. Non-spatial genetic clustering tests failed to detect spatial genetic structure, whereas spatial genetic clustering tests indicated subtle spatial genetic structure. The IBD model consistently outperformed IBR models that included land cover, traffic volume, and streams. Our results indicated widespread genetic connectivity of white-tailed deer across Ohio and negligible effects of landscape features. These patterns likely reflect some combination of minimal resistive effects of landscape features on white-tail deer movement in Ohio and the effects of regional recolonization or translocation. We encourage continued CWD surveillance in Ohio, particularly in the proximity of confirmed cases. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.     

A MORPHOLOGIC AND GENETIC STUDY OF THE ISLAND FOX,UROCYON LITTORALIS

The Island Fox, Urocyon littoralis, is a dwarf form found on six of the Channel Islands located 30–98 km off the coast of southern California. The island populations differ in two variables that affect genetic variation: effective population size and duration of isolation. We estimate that the effective population size of foxes on the islands varies from approximately 150 to 1,000 individuals. Archeological and geological evidence suggests that foxes likely arrived on the three northern islands minimally 10,400–16,000 years ago and dispersed to the three southern islands 2,200–4,300 years ago. We use morphometrics, allozyme electrophoresis, mitochondrial DNA (mtDNA) restriction-site analysis, and analysis of hypervariable minisatellite DNA to measure variability within and distances among island fox populations. The amount of within-population variation is lowest for the smallest island populations and highest for the mainland population. However, the larger populations are sometimes less variable, with respect to some genetic measures, than expected. No distinct trends of variability with founding time are observed. Genetic distances among the island populations, as estimated by the four techniques, are not well correlated. The apparent lack of correspondence among techniques may reflect the effects of mutation rate and colonization history on the values of each genetic measure.     

Effects of landscape and history on diversification of a montane, stream-breeding amphibian

Aim The aim of this study was to understand the roles of landscape features in shaping patterns of contemporary and historical genetic diversification among populations of the Andean tree frog (Hypsiboas andinus) across spatial scales. Location Andes mountains, north‐western Argentina, South America. Methods Mitochondrial DNA control region sequences were utilized to assess genetic differentiation among populations and calculate population pair‐wise genetic distances. Three models of movement, namely traditional straight‐line distance and two effective distances based on habitat classification, were examined to determine which of these explained the most variation in pair‐wise population genetic differentiation. The two habitat classifications were based on digital vegetation and hydrology layers that were generated from a 90‐m resolution digital elevation model (DEM) and known relationships between elevation and habitat. Mantel tests were conducted to test for correlations between geographic and genetic distance matrices and to estimate the percentage variation explained by each type of geographic distance. To investigate the location of possible barriers to gene flow, we used Monmonier’s maximum difference algorithm as implemented in barrier 2.2. Results At both geographic scales, effective distances explained more variation in genetic differentiation than did straight‐line distance. The least‐cost distances based on the simple classification performed better than the more detailed habitat classification. We controlled for the effects of historical range fragmentation determined from previous nested clade analyses, and therefore evaluated the effect of different distances on the genetic variation attributable to more recent factors. Effective distances identified populations that were highly divergent as a result of isolation in unsuitable habitats. The proposed locations of barriers to gene flow identified using Monmonier’s maximum difference algorithm corresponded well with earlier analyses and supported findings from our partial Mantel tests. Main conclusions Our results indicate that landscape features have been important in both historical and contemporary genetic structuring of populations of H. andinus at both large and small spatial scales. A landscape genetic perspective offers novel insights not provided by traditional phylogeographic studies: (1) effective distances can better explain patterns of differentiation in populations, especially in heterogeneous landscapes where barriers to dispersal may be common; and (2) least‐cost path analysis can help to identify corridors of movement between populations that are biologically more realistic.     

Mitochondrial DNA and microsatellite analyses of the genetic status of the presumed subspecies Cervus elaphus montanus (Carpathian red deer)

The possibly distinct Carpathian red deer was compared genetically to other European populations. We screened 120 red deer specimens from Serbia, the Romanian lowland and the Romanian Carpathians for genetic variability using 582 bp of the mitochondrial control region and nine polymorphic nuclear microsatellite loci. The study aimed at a population genetic characterization of the Carpathian red deer, which are often treated as a distinct subspecies (Cervus elaphus montanus). The genetic integrity of the Carpathian populations was confirmed through the haplotype distribution, private alleles and genetic distances. The Carpathian red deer are thus identified as one of the few remaining natural populations of this species, deserving special attention among game and conservation biologists. The history of the populations studied, in particular the introduction of Carpathian red deer into Romanian lowland areas in the 20th century, was reflected by the genetic data.     

Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi

White-tailed deer (Odocoileus virginianus) were nearly extirpated from the southeastern USA during the late 19th and early 20th centuries. Recovery programmes, including protection of remnant native stocks and transplants from other parts of the species' range, were initiated in the early 1900's. The recovery programmes were highly successful and deer are presently numerous and continuously distributed throughout the southeastern USA. However, the impact of the recovery programmes on the present genetic structure of white-tailed deer remains to be thoroughly investigated. We used 17 microsatellite DNA loci to assess genetic differentiation and diversity for 543 white-tailed deer representing 16 populations in Mississippi and three extra-state reference populations. There was significant genetic differentiation among all populations and the majority of genetic variation (> or = 93%) was contained within populations. Patterns of genetic structure, genetic similarity and isolation by distance within Mississippi were not concordant with geographical proximity of populations or subspecies delineations. We detected evidence of past genetic bottlenecks in nine of the 19 populations examined. However, despite experiencing genetic bottlenecks or founder events, allelic diversity and heterozygosity were uniformly high in all populations. These exceeded reported values for other cervid species that experienced similar population declines within the past century. The recovery programme was successful in that deer were restored to their former range while maintaining high and uniform genetic variability. Our results seem to confirm the importance of rapid population expansion and habitat continuity in retaining genetic variation in restored populations. However, the use of diverse transplant stocks and the varied demographic histories of populations resulted in fine-scale genetic structuring.     

The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic,Cirsium pitcheri (Asteraceae)

Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north–south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement.     

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within-population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter-patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.