DOI: 10.5061/dryad.1nv6k
title: Data from: Genetic consequences of post-glacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus

description: How does range expansion affect genetic diversity in species with
 different ecologies, and do different types of genetic markers lead to
 different conclusions? We addressed these questions by assessing the
 genetic consequences of post-glacial range expansion using mitochondrial
 DNA (mtDNA) and nuclear restriction site associated DNA (RAD) sequencing
 in two congeneric and co-distributed rodents with different ecological
 characteristics: the desert kangaroo rat (Dipodomys deserti), a sand
 specialist, and the Merriam's kangaroo rat (D. merriami), a substrate
 generalist. For each species, we compared genetic variation between
 populations that retained stable distributions throughout glacial periods
 and those inferred to have expanded since the last glacial maximum. Our
 results suggest that expanded populations of both species experienced a
 loss of private mtDNA haplotypes and differentiation among populations, as
 well as a loss of nuclear SNP private alleles and polymorphism. However,
 only D. deserti experienced a loss of nucleotide diversity (both mtDNA and
 nuclear) and nuclear heterozygosity. For all indices of diversity and
 differentiation that showed reduced values in the expanded areas, D.
 deserti populations experienced a greater degree of loss than did D.
 merriami populations. Additionally, patterns of loss in genetic diversity
 in expanded populations were substantially less extreme (by two orders of
 magnitude in some cases) for nuclear SNPs in both species compared to that
 observed for mitochondrial data. Our results demonstrate that ecological
 characteristics may play a role in determining genetic variation
 associated with range expansions, yet mtDNA diversity loss is not
 necessarily accompanied by a matched magnitude of loss in nuclear
 diversity.
description: Mitochondrial DNA -
 Dipodomys desertiMitochondrial DNA
 control region sequences, 1000 base pairs, Dipodomys deserti,
 fastaD_deserti.fasMitochondrial DNA - Dipodomys merriamiMitochondrial DNA control region sequences, 906 base pairs, Dipodomys merriami, fastaD_merriami.fasDipodomys merriami and deserti Read Mapping Output FilesThis compressed archive directory contains the mapping files for each individual Dipodomys sample used in the RADseq analysis. Each file is in a sorted BAM format, which can easily be converted to SAM or many other desirable formats. These files have been placed into directories that indicate what species (D. deserti or D. merriami) and population (North or South) the individual sample comes from.Jezkova_2014_Dipodomys_Mapped_Reads.tar.bz2Dipodomys merriami and deserti Stacks Catalog FilesThis compressed archive directory contains the complete catalog files for the entire Stacks analysis, including the batch catalog (batch_1...) and the individual sample catalog files (LVT...). All files are tab-delimited and are configured according to the pre-Stacks v. 1.20 formatting. File name extensions also reflect the Stacks naming scheme.Jezkova_2014_Dipodomys_Stacks_Catalog.tar.bz2Dipodomys deserti Raw Sample ReadsThis compressed archive contains individual Illumina read files for each Dipodomys deserti sample. These reads were generated by first excluding PCR clones and then parsing by unique barcodes.Jezkova_2014_Dipodomys_deserti_Raw_Reads.tar.bz2Dipodomys merriami Raw Sample ReadsThis compressed archive contains individual Illumina read files for each Dipodomys merriami sample. These reads were generated by first excluding PCR clones and then parsing by unique barcodes.Jezkova_2014_Dipodomys_merriami_Raw_Reads.tar.bz2README_RADseqReadme to accompany RADseq data.