The population genetics of urban and rural amphibians in North America

Abstract

Human land transformation is one of the leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing animal population sizes in disturbed habitats. With time, this can lead to declines in effective population size and genetic diversity which restrict the ability of wildlife to efficiently cope with environmental change through genetic adaptation. However, it is not well understood whether these effects generally hold across taxa. We address this question by repurposing and synthesizing raw microsatellite data from online repositories for 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban‐rural census designations, and continuous measures of human population density, the Human Footprint Index, and impervious surface cover, we tested for generalizable effects of human land use on amphibian genetic diversity. We found minimal evidence, either positive or negative, for relationships between genetic metrics and urbanization. Together with previous work on focal species that also found varying effects of urbanization on genetic composition, it seems likely that the consequences of urbanization are not easily generalizable within or across amphibian species. Questions about the genetic consequences of urbanization for amphibians should be addressed on a case‐by‐case basis. This contrasts with general negative effects of urbanization in mammals and consistent, but species‐specific, positive and negative effects in birds.

Population demography maintains biogeographic boundaries

“…Further, urbanization is now the primary contemporary driver of land conversion for human use (Liu et al 2020). Urbanization alters the demography, distribution, and genetics of wildlife populations across species in ways that might reshape and reorganize biogeographic regions (Johnson and Munshi-South 2017; Miles et al 2019; Schmidt et al 2020b; Schmidt and Garroway 2021). Finally, translocations and invasive species are a major threat to endemics and homogenize biological communities (Capinha et al 2015; Daru et al 2021; Yang et al 2021).…”

Determinants of genetic diversity and species richness of North American amphibians

“…Macrogenetics approaches mapping multispecies patterns of genetic diversity at broad scales have great potential for incorporation into conservation policies targeting regional conservation of genetic diversity. However, complex ecophysiological requirements, life histories, and population dynamics may render this approach impractical for amphibians because the environmental factors affecting genetic diversity may differ depending on species (Schmidt and Garroway 2021a). Species-specific measures of environmental heterogeneity, resource availability, and habitat suitability may prove to be more reliable predictors of genetic diversity, but may be less relevant for species richness.…”

“…We used raw genotypes (i.e. called allele sizes) of North American amphibians compiled by (Schmidt and Garroway 2021a). This data set was assembled from raw microsatellite datasets publicly archived in Dryad (DataDryad.org).…”

“…We based our conceptual framework on previous findings in mammals (Schmidt et al 2020) and adapted it for amphibians. First, we excluded human presence because previous investigation shows it did not have a clear effect on amphibian genetic diversity (Schmidt and Garroway 2021a). Second, we included a measure of water availability as an additional indicator of resource availability.…”

Editorial 2022

“…The development of next‐generation sequencing now makes it possible to obtain the genomes of non‐model organisms, and to assess coevolution at the genomic level, by co‐analyzing the host and parasite genomes. Märkle et al (2021) focused on three recently developed approaches that simultaneously exploit information from host and parasite whole‐genome data to identify coevolutionary loci and draw conclusions about coevolutionary history: (i) genome‐wide association study (co‐GWAS) methods, (ii) population genomics methods that can detect coevolving genes and infer coevolutionary history, and (iii) correlations between host and parasite population size over time that are indicative of coevolution. Schmidt and Garroway (2021) conducted a meta‐analysis of 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, they estimated genetic diversity, allelic richness, effective population size, and population differentiation.…”