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Background  Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert’s squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested.    Results  We used RAD-seq to unravel the complex evolutionary history of the Abert’s squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that  S. aberti kaibabensis , found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of  S. aberti kaibabensis  DNA into other  S. aberti  populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon.    Conclusions  Overall, the evolutionary history of Abert’s squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1248-4) contains supplementary material, which is available to authorized users.

bmc evolutionary biology

Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert’s squirrel (Sciurus aberti) species group