Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape

Landscape genetics: where are we now?

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape

Evaluating fine-scale population structure of multiple species in the same landscape increases our ability to identify common patterns as well as discern ecological differences among species' landscape genetic relationships. In the Palouse bioregion of northern Idaho, USA, 99% of the native prairie has been converted to nonirrigated agriculture and exotic grasslands. Columbia spotted frogs (Rana luteiventris) and long-toed salamanders (Ambystoma macrodactylum) in this area breed almost entirely in artificial ponds on private land. We used genetic distances (F(ST) and D(c)) derived from eight microsatellite loci in 783 samples to evaluate the relationships among sympatric breeding populations (N = 20 and 26) of these species in a 213-km(2) landscape. Both species showed a pattern of isolation by distance that was not improved when distance was measured along drainages instead of topographically corrected straight lines (P < 0.01). After testing for autocorrelation among genetic distances, we used an information theoretic approach to model landscape resistance based on slope, soil type, solar insolation, and land cover, and multi-model inference to rank the resistance of landscape surfaces to dispersal (represented by genetic distance). For both species, urban and rural developed land cover provided the highest landscape resistances. Resistance values for long-toed salamanders followed a moisture gradient where forest provided the least resistance, while agriculture and shrub/clearcut provided the least resistance for Columbia spotted frogs. Comparative landscape genetics can be a powerful tool for detecting similarities and differences between codistributed species, and resulting models can be used to predict species-specific responses to landscape change.

Landscape genetics of high mountain frog metapopulations

Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics.

Spurious correlations and inference in landscape genetics

Reliable interpretation of landscape genetic analyses depends on statistical methods that have high power to identify the correct process driving gene flow while rejecting incorrect alternative hypotheses. Little is known about statistical power and inference in individual-based landscape genetics. Our objective was to evaluate the power of causal-modelling with partial Mantel tests in individual-based landscape genetic analysis. We used a spatially explicit simulation model to generate genetic data across a spatially distributed population as functions of several alternative gene flow processes. This allowed us to stipulate the actual process that is in action, enabling formal evaluation of the strength of spurious correlations with incorrect models. We evaluated the degree to which naïve correlational approaches can lead to incorrect attribution of the driver of observed genetic structure. Second, we evaluated the power of causal modelling with partial Mantel tests on resistance gradients to correctly identify the explanatory model and reject incorrect alternative models. Third, we evaluated how rapidly after the landscape genetic process is initiated that we are able to reliably detect the effect of the correct model and reject the incorrect models. Our analyses suggest that simple correlational analyses between genetic data and proposed explanatory models produce strong spurious correlations, which lead to incorrect inferences. We found that causal modelling was extremely effective at rejecting incorrect explanations and correctly identifying the true causal process. We propose a generalized framework for landscape genetics based on analysis of the spatial genetic relationships among individual organisms relative to alternative hypotheses that define functional relationships between landscape features and spatial population processes.

Fat frogs, mobile genes: unexpected phylogeographic patterns for the ornate chorus frog (Pseudacris ornata)

The southeastern coastal plain of the United States is a region marked by extraordinary phylogeographic congruence that is frequently attributed to the changing sea levels that occurred during the glacial-interglacial cycles of the Pleistocene epoch. A phylogeographic break corresponding to the Apalachicola River has been suggested for many species studied to date that are endemic to this region. Here, we used this pattern of phylogeographic congruence to develop and test explicit hypotheses about the genetic structure in the ornate chorus frog (Pseudacris ornata). Using 1299 bp of mtDNA sequence and seven nuclear microsatellite markers in 13 natural populations of P. ornata, we found three clades corresponding to geographically distinct regions; one spans the Apalachicola River (Southern Clade), one encompasses Georgia and South Carolina (Central Clade) and a third comprises more northerly individuals (Northern Clade). However, it does not appear that typical phylogeographic barriers demarcate these clades. Instead, isolation by distance across the range of the entire species explained the pattern of genetic variation that we observed. We propose that P. ornata was historically widespread in the southeastern United States, and that a balance between genetic drift and migration was the root of the genetic divergence among populations. Additionally, we investigated fine-scale patterns of genetic structure and found the spatial scale at which there was significant genetic structure varied among the regions studied. Furthermore, we discuss our results in light of other phylogeographic studies of southeastern coastal plain organisms and in relation to amphibian conservation and management.

Ecological and genetic divergence between two lineages of middle American túngara frogs Physalaemus (= Engystomops) pustulosus

BACKGROUND

Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. Here we combine population genetic methods (microsatellites) with phylogenetic information (mtDNA) to define genetic population clusters of the wide-spread Neotropical túngara frog (Physalaemus pustulosus). We measure gene flow and migration within and between population clusters and compare genetic diversity between population clusters. By applying ecological niche modeling we determine whether the two most divergent genetic groups of the túngara frog (1) inhabit different habitats, and (2) are separated geographically by unsuitable habitat across a gap in the distribution.

RESULTS

Most population structure is captured by dividing all sample localities into two allopatric genetic lineages. The Northern genetic lineage (NW Costa Rica) is genetically homogenous while the Southern lineage (SW Costa Rica and Panama) is sub-divided into three population clusters by both microsatellite and mtDNA analyses. Gene flow is higher within the Northern lineage than within the Southern lineage, perhaps due to increased landscape heterogeneity in the South. Niche modeling reveals differences in suitable habitat between the Northern and Southern lineages: the Northern lineage inhabits dry/pine-oak forests, while the Southern lineage is confined to tropical moist forests. Both lineages seem to have had little movement across the distribution gap, which persisted during the last glacial maximum. The lack of movement was more pronounced for the Southern lineage than for the Northern lineage.

CONCLUSIONS

This study confirms the finding of previous studies that túngara frogs diverged into two allopatric genetic lineages north and south of the gap in the distribution in central Costa Rica several million years ago. The allopatric distribution is attributed to unsuitable habitat and probably other unknown ecological factors present across the distribution gap. Niche conservatism possibly contributes to preventing movements across the gap and gene flow between both groups. Genetic and ecological data indicate that there is the potential for ecological divergence in allopatry between lineages. In this context we discuss whether the Northern and Southern lineages should be recognized as separate species, and we conclude that further studies of pre- and post-zygotic isolation are needed for a final assessment. Identified population clusters should motivate future behavioral and ecological research regarding within-species biodiversity and speciation mechanisms.

Decreased winter severity increases viability of a montane frog population

Many proximate causes of global amphibian declines have been well documented, but the role that climate change has played and will play in this crisis remains ambiguous for many species. Breeding phenology and disease outbreaks have been associated with warming temperatures, but, to date, few studies have evaluated effects of climate change on individual vital rates and subsequent population dynamics of amphibians. We evaluated relationships among local climate variables, annual survival and fecundity, and population growth rates from a 9-year demographic study of Columbia spotted frogs (Rana luteiventris) in the Bitterroot Mountains of Montana. We documented an increase in survival and breeding probability as severity of winter decreased. Therefore, a warming climate with less severe winters is likely to promote population viability in this montane frog population. More generally, amphibians and other ectotherms inhabiting alpine or boreal habitats at or near their thermal ecological limits may benefit from the milder winters provided by a warming climate as long as suitable habitats remain intact. A more thorough understanding of how climate change is expected to benefit or harm amphibian populations at different latitudes and elevations is essential for determining the best strategies to conserve viable populations and allow for gene flow and shifts in geographic range.

Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence

Increasing habitat fragmentation poses an immediate threat to population viability, as gene flow patterns are changed in these altered landscapes. Patterns of genetic divergence can potentially reveal the impact of these shifts in landscape connectivity. However, divergence patterns not only carry the signature of altered contemporary landscapes, but also historical ones. When considered separately, both recent and historical landscape structure appear to significantly affect connectivity among 51 wood frog (Rana sylvatica) populations. However, by controlling for correlations among landscape structure from multiple time periods, we show that patterns of genetic divergence reflect recent landscape structure as opposed to landscape structure prior to European settlement of the region (before 1850s). At the same time, within-population genetic diversities remain high and a genetic signature of population bottlenecks is lacking. Together, these results suggest that metapopulation processes - not drift-induced divergence associated with strong demographic bottlenecks following habitat loss - underlie the strikingly rapid consequences of temporally shifting landscape structure on these amphibians. We discuss the implications of these results in the context of understanding the role of population demography in the adaptive variation observed in wood frog populations.

Population differentiation of temperate amphibians in unpredictable environments

Amphibians are a globally distributed and diverse lineage, but much of our current understanding of their population genetic structure comes from studies in mesic temperate habitats. We characterize the population genetic structure of two sympatric explosive breeding amphibians in the southwestern deserts of the United States: the Great Plains toad (Anaxyrus cognatus) and Couch's spadefoot toad (Scaphiopus couchii). For both species, we find limited genetic differentiation even between populations in adjacent valleys separated by dispersal barriers such as mountainous habitats. To understand how population genetic patterns in these two arid-adapted species compare to taxa in more mesic environments, we computed a standardized measure of population differentiation for A. cognatus, S. couchii, and for pond-breeding amphibians that inhabit mesic temperate environments. Our results indicate that the arid-adapted species have lower population genetic structure at fine and moderate scales than most other amphibian species we surveyed. We hypothesize that stochasticity in the availability of appropriate breeding sites as well as landscape homogeneity may result in increased population connectivity in desert-adapted frogs. Future work examining fine-scale population structure in amphibians from a diversity of habitats will test the generality of our findings. Intraspecific comparisons among localities with varied seasonality and habitats will be particularly useful for investigating the interaction between species-typical population dynamics and environmental characteristics as determinants of population connectivity in pond-breeding amphibians.

Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)

A major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander (Ambystoma californiense), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between-pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least-cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.

Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China

Background

Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow.

Results

Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise F_ST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains.

Conclusion

The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.

Population genetic structure of native versus naturalized sympatric shrub willows (Salix; Salicaceae)

Vegetative propagation of an introduced species can contribute significantly to its ability to spread and become naturalized, potentially in competition with native species. This study focused on the naturalization of a willow shrub, Salix purpurea, which was introduced to the United States from Europe and is commonly sympatric with the native shrub willow, S. eriocephala. Both species are capable of vegetative and sexual reproduction, but little is known about their relative frequency, nor the impact of clonal propagation on population-level genetic diversity. We analyzed genotypes at several microsatellite loci in 993 individuals belonging to 30 subpopulations of S. eriocephala and 28 subpopulations of S. purpurea in areas of sympatry across three watersheds to compare their genetic diversity and genetic structure. Our results revealed six subpopulations of S. purpurea containing plants with identical multilocus genotypes, while clonal individuals were rare among S. eriocephala populations. These species are dioecious with relatively high levels of heterozygosity, but S. eriocephala had much higher allelic diversity and genotypic diversity than did S. purpurea. These results strongly suggest that vegetative propagation has contributed to the naturalization of S. purpurea and has resulted in higher levels of genetic differentiation among S. purpurea populations than among native S. eriocephala populations.

Using genetics to understand the dynamics of wild primate populations

While much can be learned about primates by means of observation, the slow life history of many primates means that even decades of dedicated effort cannot illuminate long-term evolutionary processes. For example, while the size of a contemporary population can be estimated from field censuses, it is often desirable to know whether a population has been constant or changing in size over a time frame of hundreds or thousands of years. Even the nature of "a population" is open to question, and the extent to which individuals successfully disperse among defined populations is also difficult to estimate by using observational methods alone. Researchers have thus turned to genetic methods to examine the size, structure, and evolutionary histories of primate populations. Many results have been gained by study of sequence variation of maternally inherited mitochondrial DNA, but in recent years researchers have been increasingly focusing on analysis of short, highly variable microsatellite segments in the autosomal genome for a high-resolution view of evolutionary processes involving both sexes. In this review we describe some of the insights thus gained, and discuss the likely impact on this field of new technologies such as high-throughput DNA sequencing.

Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation

The iconic and brightly coloured Australian northern corroboree frog, Pseudophryne pengilleyi, and the southern corroboree frog, Pseudophryne corroboree are critically endangered and may be extinct in the wild within 3 years. We have assembled samples that cover the current range of both species and applied hypervariable microsatellite markers and mitochondrial DNA sequences to assess the levels and patterns of genetic variation. The four loci used in the study were highly variable, the total number of alleles observed ranged from 13 to 30 and the average number of alleles per locus was 19. Expected heterozygosity of the four microsatellite loci across all populations was high and varied between 0.830 and 0.935. Bayesian clustering analyses in STRUCTURE strongly supported four genetically distinct populations, which correspond exactly to the four main allopatric geographical regions in which the frogs are currently found. Individual analyses performed on the separate regions showed that breeding sites within these four regions could not be separated into distinct populations. Twelve mtND2 haplotypes were identified from 66 individuals from throughout the four geographical regions. A statistical parsimony network of mtDNA haplotypes shows two distinct groups, which correspond to the two species of corroboree frog, but with most of the haplotype diversity distributed in P. pengilleyi. These results demonstrate an unexpectedly high level of genetic diversity in both species. Our data have important implications for how the genetic diversity is managed in the future. The four evolutionarily significant units must be protected and maintained in captive breeding programmes for as long as it is possible to do.

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.

Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan

Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.

Genetic diversity and structure in Canadian northern leopard frog (Rana pipiens) populations: implications for reintroduction programs

The northern leopard frog ( Rana pipiens Schreber, 1782) underwent a large decline in the western portion of its range and only occurs in 20% of historically occupied sites in Alberta. Its absence may reflect an inability to disperse to these sites because of habitat fragmentation, and human-mediated translocation has been proposed. In this study, we used three criteria to examine the genetic suitability of potential translocation sources: diversity, similarity to area of reintroduction, and evolutionary history. We genotyped 187 samples and sequenced 812 bp of the mitochondrial NADH dehydrogenase 1 gene from 14 Canadian northern leopard frog populations. Nuclear and mitochondrial diversity were highest in Manitoba and western Ontario and declined westward. There was no significant relationship between genetic and geographic distance, suggesting that genetic drift is a driving force affecting the genetic relationships between populations. Regions separated by more than ~50 km were quite differentiated. Therefore, source populations similar to the original inhabitants of an area for reintroduction may be uncommon. Mitochondrial analyses revealed that all populations share a close evolutionary history, belonging to the western haplotype group. While genetic criteria support the use of Manitoba and Ontario as sources, the desirability of environmental similarity to the reintroduction site suggests that ecologically exchangeable Alberta populations should also be considered.

Integrating GIS-based environmental data into evolutionary biology

Many evolutionary processes are influenced by environmental variation over space and time, including genetic divergence among populations, speciation and evolutionary change in morphology, physiology and behaviour. Yet, evolutionary biologists have generally not taken advantage of the extensive environmental data available from geographic information systems (GIS). For example, studies of phylogeography, speciation and character evolution often ignore or use only crude proxies for environmental variation (e.g. latitude and distance between populations). Here, we describe how the integration of GIS-based environmental data, along with new spatial tools, can transform evolutionary studies and reveal new insights into the ecological causes of evolutionary patterns.

Riding the wave: reconciling the roles of disease and climate change in amphibian declines

We review the evidence for the role of climate change in triggering disease outbreaks of chytridiomycosis, an emerging infectious disease of amphibians. Both climatic anomalies and disease-related extirpations are recent phenomena, and effects of both are especially noticeable at high elevations in tropical areas, making it difficult to determine whether they are operating separately or synergistically. We compiled reports of amphibian declines from Lower Central America and Andean South America to create maps and statistical models to test our hypothesis of spatiotemporal spread of the pathogen Batrachochytrium dendrobatidis (Bd), and to update the elevational patterns of decline in frogs belonging to the genus Atelopus. We evaluated claims of climate change influencing the spread of Bd by including error into estimates of the relationship between air temperature and last year observed. Available data support the hypothesis of multiple introductions of this invasive pathogen into South America and subsequent spread along the primary Andean cordilleras. Additional analyses found no evidence to support the hypothesis that climate change has been driving outbreaks of amphibian chytridiomycosis, as has been posited in the climate-linked epidemic hypothesis. Future studies should increase retrospective surveys of museum specimens from throughout the Andes and should study the landscape genetics of Bd to map fine-scale patterns of geographic spread to identify transmission routes and processes.

Once introduced, diseases may spread quickly through new areas, infecting naive host populations, such as has been documented in Ebola virus in African primates or rabies in North American mammals. What drives the spread of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, is of particular concern because it has contributed to the global decline of amphibians. We modeled the spatiotemporal pattern of the loss of upland amphibian populations in Central and South America as a proxy for the arrival of Bd and found that amphibian declines in Central and South America are best explained by Bd spreading through upland populations; we identified four separate introductions of Bd into South America. Climate change seriously threatens biodiversity and influences endemic host–pathogen systems, but we found no evidence that climate change has been driving outbreaks of chytridiomycosis, as has been posited in the climate-linked epidemic hypothesis. Our findings further strengthen the spreading-pathogen hypothesis proposed for Central America, and identify new evidence for similar patterns of decline in South American amphibians. Our results will inform management and research efforts related to Bd and other invasive species, as effective conservation actions depend on correctly identifying essential threats to biodiversity, and possible synergistic interactions.

The spread of chytrid fungus, rather than climate change, best explains amphibian declines in Central and South America, based on an analysis of observed epidemics with predictable spatiotemporal patterns in four of five mountain ranges.

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.