Abstract
One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM—a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.
Highlights
Hybridization is the mating between species that can result in the transient or permanent transfer of genetic variants from one species to another
Genealogies can be taken as a signal of introgression [4]. (Here, we focus on topological incongruence; see [5] for a related discussion on local variation of coalescence times.) in reality, the analysis is more involved than this, owing to potentially confounding signal produced by several factors, a major one of which is incomplete lineage sorting (ILS)
Of great relevance to our work here is an array of hidden Markov model (HMM) based techniques that were introduced recently for analyzing genomic data in the presence of recombination and ILS [12,13,14]; these methods do not account for introgression
Summary
Hybridization is the mating between species that can result in the transient or permanent transfer of genetic variants from one species to another. The latter outcome is referred to as introgression. In a comparative framework, detecting introgressed regions can be achieved by evolutionary analysis of genomes from the parental species, as well as genomes from introgressed individuals. In such an analysis, a walk across the genomes is taken, and local genealogies are inspected; incongruence between two local
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