Dispersal and genetic structure in the American marten, Martes americana

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.     

Genetic variation of vertebral fusion patterns in coho salmon

The distribution of vertebral fusions along the spinal column differed significantly among crosses from two hatchery stocks of coho salmon, indicating a genetic basis for this character.     

Succession of Beaver Ponds in Colorado 50 Years After Beaver Removal

ABSTRACT In 1954 and 1955, I conducted studies on 4 beaver (Castor canadensis) colonies in Routt County, Colorado, USA, to develop a reliable and practical census method. In fall of 1955, these colonies were trapped to extirpation to obtain accurate counts and colony compositions. I established photo stations and took a series of photographs approximately every 5 years, in late September, from 1955 to 2005 to document beaver-population dynamics and beaver-pond successional changes after complete beaver removal. The number and configuration of dams, ponds, and canals remained remarkably similar, with maintenance conducted by succeeding generations of beaver. Quaking aspen (Populus tremuloides) and autumn willow (Salix serissima) boundaries also remained stable, but conifers slowly encroached. At 3 of 4 colony sites, beaver did not attempt to construct food caches for overwintering. By fall of 2005, the fourth site was also without a cache. Carrying capacity of these areas was likely limited by severe winter weather at 2,620-m to 2,900-m elevations, aspen depletion, pond-depth reduction, and sustained grazing by cattle. Although beaver carefully maintained dams, pond depths were reduced in most cases. This slow transition from an aquatic to a terrestrial system is a natural progression in this region.     

The blood vasculature of the gastrointestinal tract in chinook, Oncorhynchus tshawytscha (Walbaum), and coho, O. kisutch (Walbaum), salmon

The venous and arterial vasculature of the chinook and coho salmon gastrointestinal tract were examined using corrosion casts and India ink injection techniques. Observations derived from 28 individuals of various sizes and of both sexes were used to construct simplified venous and arterial plans. Examination of the blood vasculature revealed the presence of a variety of anastomoses hitherto undescribed in teleosts.     

Population structure of odd-broodline Asian pink salmon and its contrast to the even-broodline structure

Most of the variation (99%) of Asian odd-broodline pink salmon Oncorhynchus gorbuscha , based on data at 32 variable (46 total) allozyme loci from 35 populations, occurred within populations. The remaining interpopulation variation was attributable to: (1) differences between northern (the northern Sea of Okhotsk, eastern Kamchatka Peninsula and western Kamchatka Peninsula) and southern (Hokkaido Island, Kuril Islands and Sakhalin Island) populations; (2) differences between the southern areas; (3) low variation among populations within some areas. The pattern contrasted strongly with that observed for Asian even-broodline populations, which had a strong structure, possibly related to geographic and oceanographic influences. Isolation-by-distance analyses of each of the two broodlines showed a stronger relationship (x 4·8) among even- than odd-broodline populations. Allele frequency differences between even- and odd-broodlines reflected the reproductive isolation of the broodlines. However, there were no fixed frequency differences which, considered with the differing population structures, suggests that migration-drift equilibrium has not yet obtained in one or both broodlines. The structural differences also suggest it is likely that the even- and odd-broodlines are of different ages and that one is derived from the other. Allozyme data do not provide a genealogical basis for identifying the ancestral lineage.     

Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber

We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested.     

Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50–240 years b.p .) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = –0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.     

A comparison of individual‐based genetic distance metrics for landscape genetics

A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population. A variety of methods have been devised to quantify individual genetic distances, but no study has yet compared their relative performance when used for model selection in landscape genetics. In this study, we used population genetic simulations to assess the accuracy of 16 individual‐based genetic distance metrics under varying sample sizes and degree of population genetic structure. We found most metrics performed well when sample size and genetic structure was high. However, it was much more challenging to infer the true model when sample size and genetic structure was low. Under these conditions, we found genetic distance metrics based on principal components analysis were the most accurate (although several other metrics performed similarly), but only when they were derived from multiple principal components axes (the optimal number varied depending on the degree of population genetic structure). Our results provide guidance for which genetic distance metrics maximize model selection accuracy and thereby better inform conservation and management decisions based upon landscape genetic analysis.     

Isolation by environment

The interactions between organisms and their environments can shape distributions of spatial genetic variation, resulting in patterns of isolation by environment (IBE) in which genetic and environmental distances are positively correlated, independent of geographic distance. IBE represents one of the most important patterns that results from the ways in which landscape heterogeneity influences gene flow and population connectivity, but it has only recently been examined in studies of ecological and landscape genetics. Nevertheless, the study of IBE presents valuable opportunities to investigate how spatial heterogeneity in ecological processes, agents of selection and environmental variables contributes to genetic divergence in nature. New and increasingly sophisticated studies of IBE in natural systems are poised to make significant contributions to our understanding of the role of ecology in genetic divergence and of modes of differentiation both within and between species. Here, we describe the underlying ecological processes that can generate patterns of IBE, examine its implications for a wide variety of disciplines and outline several areas of future research that can answer pressing questions about the ecological basis of genetic diversity.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Spatial genetic structuring in a widespread wetland plant on a plateau: Effects of elevation-driven geographic isolation and environmental heterogeneity

1. Highlands are ideal research areas for improving our understanding of the influence of ecological factors on the diversity and spatial patterns of natural species. Elevation-driven physical and environmental isolation greatly affect the evolution of plants. The mechanisms and essential drivers underlying these processes may differ among research scales, habitats and landscapes. Wetlands are important elements of the Qinghai–Tibetan Plateau, which is the highest plateau in the world, and these habitats harbour high aquatic organismal diversity. However, how the environments shape the genetic variation and structure of hydrophilous plants is poorly understood.
2. Using microsatellite markers and a chloroplast fragment, we quantified the genetic diversity and spatial genetic pattern of Stuckenia filiformis, one of the most widespread aquatic plants on the plateau. The relative contributions of geography, climate and local conditions to intra- and interpopulation variation were estimated. The results showed that intrapopulation genetic variation of the plant is moderate to high and not constrained by high-altitude environments. Topographical isolation mainly contributes to the genetic structure of S. filiformis, as inferred by simple sequence repeats and chloroplast DNA data. Significant effects of environmental variables on the spatial genetic patterns of this freshwater species were also suggested by landscape genetic analysis.
3. Infrequent long-distance dispersal, sexual recruitment and annual growth are probably important for the maintenance and distribution of this variation. Our findings imply a combined effect of geography and elevation-driven environmental heterogeneity on the evolution of aquatic organisms in highlands.

     

Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F_ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.     

Abundance and distribution of American beaver, Castor canadensis (Kuhl 1820), in Tierra del Fuego and Navarino islands, Chile

Castor canadensis specimens were imported from Canada and released in the wilderness on the Argentinean part of Tierra del Fuego (TDF) in the year 1946. First studies on the development of the beaver population and subsequent environmental changes were conducted four decades later and indicated a strong expansion of these animals, with negative effects on the forest, especially the dominant Nothofagus sp. Between 1999 and 2001, we investigated the density of the beaver population in the Chilean part of TDF and the southern adjacent island Navarino (NAV). Data were mapped into a geographical information system. The mean colony density was 1.03 (range: 0.15–1.91) and 1.1 per km watercourse for 75% of the area of TDF (mainly south and central region) and the total NAV island, respectively. The average number of individuals estimated per colony was five. Based on these findings, the number of beavers in the Chilean part of TDF and on NAV was estimated at 61,300 individuals. The population is increasing and expanding in the Northern region, with a linear rate of 2.6–6.3 km/year.     

Conservation Genetics of an Endangered Herb, Hanabusaya asiatica (Campanulaceae)

Abstract: Hanabusaya asiatica (Nakai) Nakai (Campanulaceae), a bee- pollinated, perennial herb, is restricted to the mountainous regions of the eastern-central Korean peninsula. Allozyme analyses for 348 individuals assessed the levels of genetic diversity for five populations. Spatial autocorrelation statistics were also used to examine the spatial distribution of allozyme polymorphisms. The species maintains high levels of allozyme diversity ( H _eS = 0.217) and it exhibits low allozyme differentiation among populations ( G _ST = 0.132) compared with other endemics (mean H _e = 0.096, G _ST = 0.248). There is an apparent pattern of isolation by distance among populations. These results suggest that H. asiatica is at a genetic equilibrium. A considerable deficit in numbers of heterozygotes suggests mating among relatives in populations. At least three populations of H. asiatica should be sampled or conserved to capture or maintain > 99 % of the genetic diversity in the species as a whole. Within local populations, individuals are distributed in a structured, isolation by distance, manner. Approximate genetic patch width in the populations of H. asiatica examined is 5 - 8 m. For conservation purposes, it is suggested that, in general, the sampling of H. asiatica should be conducted at intervals in order to efficiently sample the genetic diversity across an entire population.     

Landscape structure and the genetic effects of a population collapse

Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.     

EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION

Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual‐based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real‐world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.     

Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China

Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (F_ST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (F_ST′ = 0.401) than in PN (F_ST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes.     

pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Landscape barriers reduce gene flow in an invasive carnivore: geographical and local genetic structure of American mink in Scotland

To be effective, management programmes geared towards halting or reversing the spread of invasive species must focus on defined and defensible areas. This requires knowledge of the dispersal of non-native species targeted for control to better understand invasion and recolonisation scenarios. We investigated the genetic structure of invasive American mink ( Neovison vison ) in Scotland, and incorporated landscape genetic approaches to examine resultant patterns in relation to geographical features that may influence dispersal. Populations of mink sampled from 10 sites in two regions (Argyll and Northeast Scotland) show a distinct genetic structure. First, the majority of pairwise population comparisons yielded F _ST values that were significantly greater than zero. Second, amova revealed that most of the genetic variance was attributable to differences among regions. Assignment tests placed 89 or more of individuals into their sampled region. Bayesian clustering methods grouped samples into two clusters according to their region of origin. Wombling approach identified the Cairngorms Mountains as a major impediment to gene flow between the regions. Mantel pairwise correlations between genetic and geographical distances estimated as least-cost distance assuming a linear increase in the cost of movement with increasing elevation were higher than Euclidean distances or distance along waterways. Spatial autocorrelation analyses revealed stronger spatial structuring for females than for males. These results suggest that gene flow by American mink is restricted by landscape features (mountain ranges) and that eradication attempt should in the first instance break down the connectivity between management units separated by mountains.     

Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population

Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad‐leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, D_C) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoD_b). Mantel tests between distance matrices highlighted how the Log‐D_C in PEF populations was related to log‐transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log‐EcoD, and particularly by the Log‐EcoD_b, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.