Biology subjects

Leache, A.

Publications and source records attributed to Leache, A..

6 recordsLinked to original sources

bioRxiv2026

Gene Flow Creates Fuzzy Species Boundaries in Fence Lizards

Species delimitation is a fundamental challenge in systematic biology, particularly for geographically variable taxa with hierarchical population structure and gene flow. Migration-aware coalescent models provide a powerful framework for investigating lineage divergence and accurately defining species boundaries. In this study, we combine statistical evaluations of gene flow with phylogenetic and population structure analyses to delimit species of fence lizards within the Sceloporus undulatus complex, a group characterized by extensive population subdivision, mitochondrial DNA introgression, and nuclear gene flow. We find that the undulatus complex exhibits uneven variation in genetic, morphological, and bioclimatic traits, resulting in variable distinctiveness among groups. In some cases, species boundaries are recognized by clear genetic discontinuities without gene flow. In others, shallow divergence, paraphyly, and gene flow produce leaky boundaries and fuzzy species limits. Mitochondrial introgression is extensive and concentrated at species boundaries, whereas nuclear gene flow occurs between only a few species and at much lower levels than within species. Neither within-species populations or species are substantially diverged across morphology or bioclimatic space, highlighting the limited utility of these traits for diagnosing species in this group. By integrating estimates of gene flow with phylogenetic and population structure analyses, this study provides a robust and biologically meaningful revised taxonomic framework for the undulatus complex that identifies independently evolving lineages as species.

evolutionary biology↗

bioRxiv2025

Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils"

Herein, we rebut the critique of Patton et al. (2020), entitled, "No evidence that a transmissible cancer has shifted from emergence to endemism", by Stammnitz et al. (2024). First and foremost, the authors do not conduct any phylogenetic or epidemiological analyses to rebut the inferences from the main results of the Patton et al. (2020) article, rendering the title of their rebuttal without evidence or merit. Additionally, Stammnitz et al. (2024) present a phylogenetic tree based on only 32 copy number variants (not typically used in phylogenetic analyses and evolve in a completely different way than DNA sequences) to "rebut" our tree that was inferred from 436.1 kb of sequence data and nearly two orders of magnitude more parsimony-informative sites (2520 SNPs). As such it is not surprising that their phylogeny did not have a similar branching pattern to ours, given that support for each branch of their tree was weak and the essentially formed a polytomy. That is, one could rotate their resulting tree in any direction and by nature, it would not match ours. While the authors are correct that we used suboptimal filtering of our raw whole genome sequencing data, re-analyses of the data with 30X coverage, as suggested, resulted in a mutation rate similar to that reported in Stammnitz et al. (2024). Most importantly, when we re-analyzed our data, as well as Stammnitz et al.s own data, the results of the Patton et al. (2020) article are supported with both datasets. That is, the effective transmission rate of DFTD has transitioned over time to approach one, suggesting endemism; and, the spread of DFTD is rapid and omnidirectional despite the observed east-to-west wave of spread. Overall, Stammnitz et al. (2024) not only fail to provide evidence to contradict the findings of Patton et al. (2020), but rather help support the results with their own data.

evolutionary biology↗

bioRxiv2025

Hybrid zone analysis using coalescent-based estimates of introgression and migration

Hybrid zones can serve as natural experiments allowing us to investigate the evolutionary consequences of introgression between distinct populations with divergent genomic backgrounds. Modeling hybrid zones using a coalescent framework can provide critical insights into the historical demography of populations, including population divergence times, population sizes, introgression proportions, migration rates, and the timing of hybrid zone formation. We used coalescent analyses to test whether a hybrid zone between Plateau Fence Lizard (Sceloporus tristichus) populations in Arizona formed recently because of human-induced landscape alterations or originated during Pleistocene climatic shifts. Introgression analysis places the divergence time between the parental populations at approximately 140 kya and their secondary contact and hybridization at approximately 10 kya at the end of the Pleistocene. Introgression proportions for hybrid populations are correlated with their geographic distance from the parental populations, a pattern that is repeated with admixture proportions and hybrid index values. The multispecies coalescent with migration model supports asymmetric migration rates with a bias for gene flow moving towards the northern end of the hybrid zone. The direction of this asymmetry is consistent with spatial cline analyses that suggest a slow but steady northward shift of the center of the hybrid zone. When analyzing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into the evolutionary history of hybrid zone formation that complement existing spatial and genomic methods.

evolutionary biology↗

bioRxiv2021

Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow.

evolutionary biology↗

bioRxiv2020

A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

High-quality genomic resources facilitate population-level and species-level comparisons to answer questions about behavioral ecology, morphological and physiological adaptations, as well as the evolution of genomic architecture. Squamate reptiles (lizards and snakes) are particularly diverse in characteristics that have intrigued evolutionary biologists, but high-quality genomic resources for squamates are relatively sparse. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, Sceloporus undulatus. We performed synteny analysis with other available squamate chromosome-level assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes in S. undulatus. Using this new S. undulatus genome assembly we conducted reference-based assemblies for 34 other Sceloporus species to improve draft nuclear genomes assemblies from 1% coverage to 43% coverage on average. Across these species, typically >90% of reads mapped for species within 20 million years divergence from S. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

genomics↗

bioRxiv2018

The Spectre of Too Many Species

Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm several of these results and provide their mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of gene trees and sequence data, which explains why no method can use such data to distinguish between population splits and speciation. We suggest that the the protracted speciation model is unrealistic and its mechanism for assigning species status contradicts prevailing taxonomic practice. We confirm the suggestion, based on simulation, that in the case of speciation with gene flow, Bayesian model selection as implemented in BPP tends to detect population splits when the amount of data (the number of loci) increases so over-splitting is a legitimate concern. We discuss the use of a recently proposed empirical genealogical divergence index (gdi) for species delimitation and illustrate that parameter estimates produced by a full likelihood analysis as implemented in BPP provide much more reliable inference under the gdi than the approximate method PHRAPL. We suggest that the Bayesian model-selection approach is useful for identifying sympatric cryptic species while Bayesian parameter estimation under the multispecies coalescent can be used to implement empirical criteria for determining species status among allopatric populations.

evolutionary biology↗