Biology subjects

Leache, A. D.

Publications and source records attributed to Leache, A. D..

6 recordsLinked to original sources

bioRxiv2025

Comparative phylogeography of lizards (Squamata: Phrynosomatidae) in Baja California and expansion of Callisaurus draconoides within the North American deserts

We examined the comparative phylogeography of five co-distributed lizard complexes (representing four genera within Phrynosomatidae) along the Baja California Peninsula (BCP) in the context of the regions complex geological history. Double-digest restriction-associated-DNA (ddRAD) sequencing was used to collect genome-wide sequence data for 228 peninsular lizards. Using phylogenetic analyses of concatenated loci and population admixture analysis of unlinked SNPs, we identified 24 potential lineages within the five co-distributed complexes. Four of the five complexes exhibited contact zones between lineages at the Isthmus of La Paz, and all five did in the Vizcaino Desert. To generate data for a species tree model, we subsampled two lizards from each of these 24 lineages for use with a target sequence capture (TSC) protocol. The resulting time-calibrated species tree shows that within each genus, the La Paz divergences are older than those across the Vizcaino Desert. A full-likelihood Bayesian comparative phylogeographic approach was also used to test the simultaneous divergence hypothesis for the Isthmus of La Paz and Vizcaino Desert, providing strong support for at least three independent divergence events at each contact zone, thereby rejecting the simultaneous divergence hypothesis. Finally, we demonstrate through expanded geographic sampling (n=142) and ddRAD that zebra-tailed lizards (Callisaurus), in which the most divergent lineages are endemic to the southern BCP, exhibit a clear pattern of Pleistocene range expansion from the northern BCP into the deserts of the western United States and mainland Mexico. The most deeply nested individuals in our tree occur at the northern, eastern, and southeastern range limits in temperate, subtropical, and tropical biomes, respectively. These results collectively highlight the importance of the BCPs tectonic isolation as a driver not only of local or peninsular endemism, but potentially also as a contributing factor to lineage diversification more broadly in the region.

evolutionary biology↗

bioRxiv2025

Demographic history explains mitochondrial genome capture and mitonuclear discordance among South American collared Tropidurus lizards

Mitonuclear discordance--evolutionary discrepancies between mitochondrial and nuclear DNA phylogenies--can arise from various factors, including introgression, incomplete lineage sorting, recent or ancient demographic fluctuations, sex-biased dispersal asymmetries, among others. Understanding this phenomenon is crucial for accurately reconstructing evolutionary histories, as failing to account for discordance can lead to misinterpretations of species boundaries, phylogenetic relationships, and historical biogeographic patterns. We investigate the evolutionary drivers of mitonuclear discordance in the Tropidurus spinulosus species group, which contains nine species of lizards inhabiting open tropical and subtropical environments in South America. Using a combination of population genetic and phylogenomic approaches applied to mitochondrial and nuclear data, we identified different instances of gene flow that occurred in ancestral lineages of extant species. Our results point to a complex evolutionary history marked by prolonged isolation between species, demographic fluctuations, and potential episodes of secondary contact with genetic admixture. These conditions likely facilitated mitochondrial genome capture while diluting signals of nuclear introgression. Furthermore, we found no strong evidence supporting incomplete lineage sorting or natural selection as primary drivers of the observed mitonuclear discordance. Therefore, the unveiled patterns are most consistent with neutral demographic processes, coupled with ancient mitochondrial introgression, as the main factors underlying the mismatch between nuclear and mitochondrial phylogenies in this system. Future research could further explore the role of other demographic processes, such as asymmetric sex-biased dispersal, in shaping these complex evolutionary patterns.

genomics↗

bioRxiv2021

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

AO_SCPLOWBSTRACTC_SCPLOWGenome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multi-locus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real datasets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative.

evolutionary biology↗

bioRxiv2020

Andean uplift, drainage basin formation, and the evolution of riverweeds (Marathrum, Podostemaceae) in northern South America

O_LINorthern South America is a geologically dynamic and species-rich region. While fossil and stratigraphic data show that reconfiguration of river drainages resulted from mountain uplift in the tropical Andes, investigations of the impact of landscape change on the evolution of the flora in the region have been restricted to terrestrial taxa. C_LIO_LIWe explore the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenomic, phylogenetic networks, and divergence-dating analyses for populations of riverweeds (Marathrum, Podostemaceae). C_LIO_LIWe show that mountain uplift and drainage basin formation isolated populations of Marathrum and created barriers to gene flow across rivers drainages. Sympatric species hybridize and the hybrids show the phenotype of one parental line. We propose that the pattern of divergence of populations reflect the formation of river drainages, which was not complete until <4 Ma C_LIO_LIOur study provides a clear picture of the role of landscape change in shaping the evolution of riverweeds in northern South America, advances our understanding of the reproductive biology of this remarkable group of plants, and spotlights the impact of hybridization in phylogenetic inference. C_LI

evolutionary biology↗

bioRxiv2019

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

AO_SCPLOWBSTRACTC_SCPLOWBirth-death processes have given biologists a model-based framework to answer questions about changes in the birth and death rates of lineages in a phylogenetic tree. Therefore birth-death models are central to macroevolutionary as well as phylodynamic analyses. Early approaches to studying temporal variation in birth and death rates using birth-death models faced difficulties due to the restrictive choices of birth and death rate curves through time. Sufficiently flexible time-varying birth-death models are still lacking. We use a piecewise-constant birth-death model, combined with both Gaussian Markov random field (GMRF) and horseshoe Markov random field (HSMRF) prior distributions, to approximate arbitrary changes in birth rate through time. We implement these models in the widely used statistical phylogenetic software platform RevBayes, allowing us to jointly estimate birth-death process parameters, phylogeny, and nuisance parameters in a Bayesian framework. We test both GMRF-based and HSMRF-based models on a variety of simulated diversification scenarios, and then apply them to both a macroevolutionary and an epidemiological dataset. We find that both models are capable of inferring variable birth rates and correctly rejecting variable models in favor of effectively constant models. In general the HSMRF-based model has higher precision than its GMRF counterpart, with little to no loss of accuracy. Applied to a macroevolutionary dataset of the Australian gecko family Pygopodidae (where birth rates are interpretable as speciation rates), the GMRF-based model detects a slow decrease whereas the HSMRF-based model detects a rapid speciation-rate decrease in the last 12 million years. Applied to an infectious disease phylodynamic dataset of sequences from HIV subtype A in Russia and Ukraine (where birth rates are interpretable as the rate of accumulation of new infections), our models detect a strongly elevated rate of infection in the 1990s. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWBoth the growth of groups of species and the spread of infectious diseases through populations can be modeled as birth-death processes. Birth events correspond either to speciation or infection, and death events to extinction or becoming noninfectious. The rates of birth and death may vary over time, and by examining this variation researchers can pinpoint important events in the history of life on Earth or in the course of an outbreak. Time-calibrated phylogenies track the relationships between a set of species (or infections) and the times of all speciation (or infection) events, and can thus be used to infer birth and death rates. We develop two phylogenetic birth-death models with the goal of discerning signal of rate variation from noise due to the stochastic nature of birth-death models. Using a variety of simulated datasets, we show that one of these models can accurately infer slow and rapid rate shifts without sacrificing precision. Using real data, we demonstrate that our new methodology can be used for simultaneous inference of phylogeny and rates through time.

evolutionary biology↗

bioRxiv2018

Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across both micro- and macroevolutionary timescales.

evolutionary biology↗