Biology subjects

Cobb, K. A.

Publications and source records attributed to Cobb, K. A..

3 recordsLinked to original sources

bioRxiv2024

Genomic Evidence for Hybridization and Introgression in a North American Toad (Anaxyrus) Hybrid Zone

Hybrid zones present an excellent opportunity to study the evolution of reproductive isolation between divergent evolutionary lineages as generations of interbreeding and backcrossing produce many different recombinant genotypes. We can then observe patterns of genetic variation within a hybrid zone to understand how selection is acting on these recombinant genotypes. Using genome-wide sequence data, we characterized patterns of introgression within a putative hybrid zone between two species of North American toads (A. americanus and A. terrestris) to better understand reproductive isolation between these species. Both model based and non-parametric approaches to population structure inference showed that there is likely a substantial level of interbreeding and successful backcrossing at this hybrid zone with admixed individuals located quite far from the center of the hybrid zone. Bayesian genomic cline analysis revealed loci with extreme patterns of introgression relative to other loci which would be expected if these sites were linked to sites under negative selection in a hybrid genomic background. A site-based measure of genetic divergence was found to be weakly correlated with cline parameter estimates. We argue that this weak correlation is consistent with a history of secondary contact following a period of geographic isolation as many highly divergent sites do not have correspondingly high cline parameter estimates consistent with strong selection against introgression. Our findings substantiate previous claims of the existence of a hybrid zone between A. americanus and A. terrestris and highlight the potential for this hybrid zone to further our understanding of the evolution of reproductive incompatibly.

evolutionary biology↗

bioRxiv2019

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these phylogenomic challenges. For evolutionary studies in frogs, we introduce the new publicly available FrogCap suite of genomic resources, which is a large and flexible collection of probes corresponding to [~]15,000 markers that unifies previous frog sequencing work. FrogCap is designed to be modular, such that subsets of markers can be selected based on the phylogenetic scale of the intended study. FrogCap uses a variety of molecular marker types that include newly obtained exons and introns, previously sequenced UCEs, and Sanger-sequencing markers, which span a range of alignment lengths (100-12,000 base pairs). We tested three probe sets from FrogCap using 105 samples across five phylogenetic scales, comparing probes designed using a consensus- or genome-based approach. We also tested the effects of using different bait kit sizes on depth of coverage and missing data. We found that larger bait kits did not result in lowered depth of coverage or increased missing data. We also found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We observed sequence capture success (in terms of missing data, quantity of sequence data, recovered marker length, and number of informative sites) and compared them at all phylogenetic scales. The incorporation of different molecular marker types allowed recovery of the variation required for resolving difficult phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for performing high-throughput sequencing projects across variable timescales.

genomics↗

bioRxiv2019

Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging

Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show previous estimates of co-expansion among five Alaskan populations of threespine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.

evolutionary biology↗