Biology subjects

Oaks, J. R.

Publications and source records attributed to Oaks, J. R..

6 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↗

bioRxiv2021

Generalizing Bayesian phylogenetics to infer shared evolutionary events

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a "super-spreading" event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes, because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find the new method accurately infers shared and multifurcating divergence events when they occur, and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our new approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands landscape caused bursts of speciation. Unlike our previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences. Significance statementPhylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution, violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a new way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the new approach to genomic data from geckos distributed across the Philippines, and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level.

evolutionary biology↗

bioRxiv2020

Neglected Quaternary legacy of biodiversity for the Mountains of Southwest China

Mountains of Southwest China (MSWC) is a biodiversity hotspot with a very unique and highly complex terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, with temporally clustered divergence events during severe glacial cycles, indicating the importance of riverine barriers in the phylogeographic history of the vertebrate community. We conclude that the repeated glacial cycles are associated with temporal synchrony of divergence patterns that are themselves structured by the heterogeneity of the montane landscape has of the MSWC. This orderly process of diversifications has profound implications for conservation by highlighting the relative independence of different geographic areas in which communities have responded similarly to climate changes and calls for further comparative phylogeographic investigations to reveal the extent to which these findings might apply more broadly to other taxa in this biodiversity hotspot.

evolutionary biology↗

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↗

bioRxiv2018

The comparative biogeography of geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification One often-invoked but seldom tested process is the \"species-pump\" model, in which repeated bouts of co-speciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation has not been an important mechanism of speciation for gekkonid lizards on the Philippine Islands.

evolutionary biology↗

bioRxiv2018

Full Bayesian comparative phylogeography from genomic data

A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions.

evolutionary biology↗