Abstract
Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose.
Highlights
With the advent of new sequencing technologies, the reconstruction of phylogenetic histories on the genomic scale has become feasible
We summarize fine scale variation in phylogenetic history across the genome of house mice, a recently derived group of subspecies, using a method that combines phylogenetic uncertainty among gene trees
We document substantial variation in phylogenetic history among 14,081 loci and describe a primary history in the face of this variation. These results support the use of genome-scale datasets and methods that accommodate phylogenetic discordance in attempts to reconstruct the history of closely related groups
Summary
With the advent of new sequencing technologies, the reconstruction of phylogenetic histories on the genomic scale has become feasible. Ancestral polymorphisms can segregate, causing some gene trees to disagree with the population tree The effects of this incomplete lineage sorting are greatest when effective population sizes are high and internodes of the population tree are of short duration [11,12,13,14,15,16]. Consistent with these predictions, substantial phylogenetic discordance has been documented on the genomic scale in a few young species groups. The extent of variation on this scale remains poorly understood
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