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

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.