DOI: 10.5061/dryad.578qn84
title: Data from: Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group

description: 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.
description: Sample
 barcodesSamples were multiplexed
 for sequencing. This file gives barcodes associated with each sample.
 Note: samples 153148, 26601, and 26601 were dropped from the analysis due
 to low sequencing coverage (153148) and sample mix-up (26601 and
 26606)Barcodes_dryad.txtRAD-sequencing reads in .fastq formatThis file contains RAD-sequencing reads in .fastq format. Raw reads were originally processed by Bejing Genomics Institute, and this file includes only clean reads. This file was used as the initial input to the STACKS pipeline. Note: samples 153148, 26601, and 26601 were dropped from the analysis due to low sequencing coverage (153148) and sample mix-up (26601 and 26606), but reads associated with these samples are present in this file.Abertdata.gz