Marjorie D. Matocq

Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum)

The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (FST). We then compared five hypothetical dispersal routes with a straight‐line distance model using two approaches: (i) partial Mantel tests using Akaikes information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global FST of 0.24. While there is a significant isolation‐by‐distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight‐line topographic route, with river crossings and open shrub habitat correlated with lower FST and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.

Phylogeographical structure and regional history of the dusky-footed woodrat, Neotoma fuscipes.

The dusky‐footed woodrat, Neotoma fuscipes, is a medium‐sized rodent that inhabits low elevation woodland habitats along the Pacific coast of North America from Oregon, throughout California and into Baja California. Analyses of mitochondrial sequence variation throughout the distribution reveal substantial phylogeographical structure within N. fuscipes. The major mitochondrial lineages are largely concordant with previously identified morphological subdivisions within the taxon. The geographical distribution of distinct clades suggests that a combination of topographic barriers and the expansion and contraction of suitable habitat during the past 2 million years, especially along particular mountain ranges, have played a major role in the diversification of N. fuscipes. Furthermore, relatively low levels of genetic variation across the northern half of the distribution suggest that dusky‐footed woodrats may have only recently expanded into this region.

Low genetic diversity in an endangered species: recent or historic pattern?

Abstract Examining patterns of genetic diversity has become an integral component of many management plans concerning endangered species, yet interpreting the processes underlying such patterns remains challenging. We demonstrate low genetic diversity in a critically endangered small mammal population. A common interpretation of this pattern would be that it is the result of a known, recent decline in this population. We test this interpretation and find it to be incorrect. Instead, by using museum voucher specimens, we show that the pattern of low genetic diversity is historical. This study demonstrates the importance of choosing appropriate reference groups by which to interpret modern levels of genetic diversity in endangered species. We conclude that analysis of archival specimens may be essential in cases where genetic diversity is driving conservation management decisions because it may allow us to distinguish the effects of low genetic diversity from the process of losing diversity. We recognize that this approach can be limited due to several sampling issues: archival material may not be available, statistical power needs to be evaluated, sample sizes and sequence lengths may be suboptimal due to intrinsic difficulties associated with amplification of degraded DNA. These issues are discussed and possible solutions identified.

POPULATION GENETIC STRUCTURE OF TWO ECOLOGICALLY DISTINCT AMAZONIAN SPINY RATS: SEPARATING HISTORY AND CURRENT ECOLOGY

Abstract. Population history and current demographic and ecological factors determine the amount of genetic variation within and the degree of differentiation among populations. Differences in the life history and ecology of codistributed species may lead to differences in hierarchical population genetic structure. Here, we compare patterns of genetic diversity and structure of two species of spiny rats in the genus Proechimys from the Rio Jurua of western Amazonian Brazil. Based on the ecological and life‐history differences between the two species, we make predictions as to how they might differ in patterns of genetic diversity and structure. We use mitochondrial sequence data from the cytochrome b gene to test these predictions. Although both species maintain nearly the same number of mitochondrial haplotypes across the sampled range, they differ in levels of genetic diversity and geographic structure. Patterns of gene flow are also different between the two species with average M‐values of nearly three in P. steerei and less than one in P. simonsi. Our initial predictions are largely upheld by the genetic data and where conflicting hypotheses arise, we suggest further studies that may allow us to distinguish among evolutionary scenarios. Separating the effects of history and ongoing demography on patterns of genetic diversity is challenging. Combining genetic analyses with field studies remains essential to disentangling these complex processes.

Molecular evidence for historical and recent population size reductions of tiger salamanders (Ambystoma tigrinum) in Yellowstone National Park

Population declines caused by natural and anthropogenic factors can quickly erode genetic diversity in natural populations. In this study, we examined genetic variation within 10 tiger salamander populations across northern Yellowstone National Park in Wyoming and Montana, USA using eight microsatellite loci. We tested for the genetic signature of population decline using heterozygosity excess, shifts in allele frequencies, and low ratios of allelic number to allelic size range (M-ratios). We found different results among the three tests. All 10 populations had low M-ratios, five had shifts in allele frequencies and only two had significant heterozygosity excesses. These results support theoretical expectations of different temporal signatures among bottleneck tests and suggest that both historical fish stocking, recent, sustained drought, and possibly an emerging amphibian disease have contributed to declines in effective population size.

Morphological and Molecular Analysis of a Contact Zone in the Neotoma Fuscipes Species Complex

Abstract Neotoma fuscipes, the dusky-footed wood rat, is a morphologically diverse taxon with recognized intraspecific subdivisions that are based on both quantitative and qualitative morphology. Although there is substantial morphological variation within this taxon, intergradation among the various forms has been observed by previous workers. A recent survey of mitochondrial DNA revealed a high degree of molecular divergence within the taxon. Here, morphological, mitochondrial sequence, and nuclear microsatellite data are examined in a contact zone between 2 reciprocally monophyletic mitochondrial clades. On the basis of concordance of qualitative cranial, glans penes, and molecular characters, the 2 units appear to be genetically isolated from one another, leading to the elevation of N. macrotis to a species separate from N. fuscipes.

Historic hybridization and persistence of a novel mito-nuclear combination in red-backed voles (genus Myodes)

BackgroundThe role of hybridization in generating diversity in animals is an active area of discovery and debate. We assess hybridization across a contact zone of northern (Myodes rutilus) and southern (M. gapperi) red-backed voles using variation in skeletal features and both mitochondrial and nuclear loci. This transect extends approximately 550 km along the North Pacific Coast of North America and encompasses 26 populations (n = 485). We establish the history, geographic extent and directionality of hybridization, determine whether hybridization is ongoing, and assess the evolutionary stability of novel genomic combinations.ResultsIdentification of M. rutilus and M. gapperi based on the degree of closure of the post-palatal bridge was concordant with the distribution of diagnostic nuclear MYH6 alleles; however, an 80 km zone of introgressed populations was identified. The introgressant form is characterized by having mitochondrial haplotypes closely related to the northern M. rutilus on a nuclear background and morphological characteristics of southern M. gapperi.ConclusionIntrogression appears to have been historic as pure populations of M. rutilus are now isolated to the north from introgressants or pure M. gapperi by the LeConte Glacier. As we do not find pure M. rutilus or M. gapperi individuals throughout the distribution of the introgressant form, it appears that the introgressants are a self-sustaining entity not requiring continued hybridization between pure parental forms to generate this novel combination of characters.

Reproductive success and effective population size in woodrats (Neotoma macrotis).

Discrepancies between the census size and the genetically effective size of populations (Ne) can be caused by a number of behavioural and demographic factors operating within populations. Specifically, strong skew in male reproductive success, as would be expected in a polygynous mating system, could cause a substantial decrease in Ne relative to census size. Because the mating system of Neotoma macrotis had previously been described as one nearing harem polygyny, I examined the distribution of reproductive success and genetic variation within a population of this species. Combining genetic data and three years of field observations, I show that variance in reproductive success does not deviate from poisson expectations within either sex and variance in success is similar between the sexes. Furthermore, both males and females had multiple partners across litters in addition to some evidence of multiple paternity within litters. Despite a lack of strong skew in reproductive success, an estimate of Ne based on a number of demographic parameters suggests that the ratio of Ne/N in this population is 0.48. Although the ratio of Ne/N suggests that the population is experiencing higher rates of genetic drift than would be expected based on census size alone, the population maintains high levels of genetic diversity. Estimates of neighbourhood size and patterns of recruitment to the study site suggest that immigration plays an important role in this population and may contribute to the maintenance of high levels of genetic diversity.

Biodiversity and Topographic Complexity: Modern and Geohistorical Perspectives

Topographically complex regions on land and in the oceans feature hotspots of biodiversity that reflect geological influences on ecological and evolutionary processes. Over geologic time, topographic diversity gradients wax and wane over millions of years, tracking tectonic or climatic history. Topographic diversity gradients from the present day and the past can result from the generation of species by vicariance or from the accumulation of species from dispersal into a region with strong environmental gradients. Biological and geological approaches must be integrated to test alternative models of diversification along topographic gradients. Reciprocal illumination among phylogenetic, phylogeographic, ecological, paleontological, tectonic, and climatic perspectives is an emerging frontier of biogeographic research.

Multiscale connectivity and graph theory highlight critical areas for conservation under climate change

Conservation planning and biodiversity management require information on landscape connectivity across a range of spatial scales from individual home ranges to large regions. Reduction in landscape connectivity due changes in land use or development is expected to act synergistically with alterations to habitat mosaic configuration arising from climate change. We illustrate a multiscale connectivity framework to aid habitat conservation prioritization in the context of changing land use and climate. Our approach, which builds upon the strengths of multiple landscape connectivity methods, including graph theory, circuit theory, and least-cost path analysis, is here applied to the conservation planning requirements of the Mohave ground squirrel. The distribution of this threatened Californian species, as for numerous other desert species, overlaps with the proposed placement of several utility-scale renewable energy developments in the American southwest. Our approach uses information derived at three spatial scales to forecast potential changes in habitat connectivity under various scenarios of energy development and climate change. By disentangling the potential effects of habitat loss and fragmentation across multiple scales, we identify priority conservation areas for both core habitat and critical corridor or stepping stone habitats. This approach is a first step toward applying graph theory to analyze habitat connectivity for species with continuously distributed habitat and should be applicable across a broad range of taxa.