Biology subjects

Thomson, R. C.

Publications and source records attributed to Thomson, R. C..

3 recordsLinked to original sources

bioRxiv2021

Testing concordance and conflict in spatial replication of landscape genetics inferences

The field of landscape genetics relates habitat features and genetic information to infer dispersal and genetic connectivity between populations or individuals distributed across a landscape. Such studies usually focus on a small portion of a species range, and the degree to which these geographically restricted results can be extrapolated to different areas of a species range remains poorly understood. Studies that have focused on spatial replication in landscape genetics processes either evaluate a small number of sites, are informed by a small set of genetic markers, analyze only a small subset of environmental variables, or implement models that do not fully explore parameter space. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range, using thousands of ddRAD genetic markers distributed across the genome, implemented in the landscape genetics program ResistanceGA. Across study areas, we found a great deal of consistency in the variables impacting genetic connectivity, but also noted site-specific differences in the factors in each study area. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Vegetation type was found to substantially affect gene flow only in the southernmost Sequoia site, likely due to a higher proportion of desert habitat here, thereby fragmenting habitats that have lower costs to dispersal. The effect of roads also varied between sites and may be related to differences in road usage and amount of traffic in each area. Across study areas, canyons were always substantially implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity across landscapes. We emphasize that spatial data layers are complex and multidimensional, and a careful consideration of associations between variables is vital to form sound conclusions about the critical factors affecting dispersal and genetic connectivity across space.

ecology↗

bioRxiv2019

Model-based species delimitation: are coalescent species reproductively isolated?

A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

evolutionary biology↗

bioRxiv2017

Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological?

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of these biological versus methodological factors in explaining gene tree variation is a major unresolved question in phylogenetics. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and that critical evaluation of the fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

evolutionary biology↗