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Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

Thomas, Gregg1

Published Nov 21, 2023 on Dryad. https://doi.org/10.5061/dryad.866t1g1wq

Data files

Nov 21, 2023 version files 22.89 GB

Abstract

A species tree is a central concept in evolutionary biology whereby a single-branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) – a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that proximate chromosomal regions tended to have more similar phylogenetic histories. While we found no clear relationship between local tree similarity and recombination rates in house mice, we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.