Abstract
AbstractA 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 often 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 new linked-read genome assemblies for seven murine species with eleven published 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 phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. 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.
Publisher
Cold Spring Harbor Laboratory
Reference132 articles.
1. Pdb (the paleobiology database) [Internet]. 2011 January 21st, 2022]. Available from: http://paleodb.org/
2. Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (rodentia: Muridae);Mol Phylogenet Evol,2018
3. Alda F , Ludt WB , Elias DJ , McMahan CD , Chakrabarty P . 2021. Comparing ultraconserved elements and exons for phylogenomic analyses of middle american cichlids: When data agree to disagree. Genome Biol Evol. 13.
4. Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs;Evolution,2017
5. 3d chromatin remodelling in the germ line modulates genome evolutionary plasticity;Nat Commun,2022