DOI: 10.5061/dryad.jh2fp
title: Data from: Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

description: Identifying the genetic structure of a species and the factors that drive
 it is an important first step in modern population management, in part
 because populations evolving from separate ancestral sources may possess
 potentially different characteristics. This is especially true for
 climate-sensitive species such as pikas, where the delimitation of
 distinct genetic units and the characterization of population responses to
 contemporary and historical environmental pressures are of particular
 interest. We combined a restriction site-associated DNA sequencing
 (RADSeq) data set containing 4156 single nucleotide polymorphisms with
 ecological niche models (ENMs) of present and past habitat suitability to
 characterize population composition and evaluate the effects of historical
 range shifts, contemporary climates and landscape factors on gene flow in
 Collared Pikas, which are found in Alaska and adjacent regions of
 northwestern Canada and are the lesser-studied of North America's two
 pika species. The results suggest that contemporary environmental factors
 contribute little to current population connectivity. Instead, genetic
 diversity is strongly shaped by the presence of three ancestral lineages
 isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and
 genetic data, populations originating from a northern refugium experienced
 longer-term stability, whereas both southern lineages underwent population
 expansion – contradicting the southern stability and northern expansion
 patterns seen in many other taxa. Current populations are comparable with
 respect to generally low diversity within populations and little-to-no
 recent admixture. The predominance of divergent histories structuring
 populations implies that if we are to understand and manage pika
 populations, we must specifically assess and accurately account for the
 forces underlying genetic similarity.
description: Structure and PCA
 datasetDataset used in
 STRUCTURE and PCA analyses.structure_and_pca_dataset.struPopulation tree datasetConcatenated SNP data in phylip format used in population tree analysespopulation_tree.txtPriors and rules for FastSimCoal2 analysesPriors and rules input file for analyses in FastSimCoal2hl80.estParameters for FastSimCoal2Parameter input file for the coalescence simulation program FastSimCoal2.hl80.tplObserved site frequency spectrum dataObserved site frequency spectrum data used in FastSimCoal2 analyseshl80_DSFS.obsFastSimCoal2 resultsSummary of results from fifty independent parameter estimations in FASTSIMCOAL2 to achieve the maximum composite likelihood of the joint SFS.50run_hl80_bestlhoods.summaryCollared pika locationCoordinate data used in Maxent simulationsochotona_locations.csvClimate data used in ENM (0 kya)Trimmed climate data (current climates) used to generate niche models in Maxent.0K_AK_bio_vars_cut.zipClimate data used in ENM (21 kya)Trimmed climate data from the Last Glacial Maximum (21 kya) used to generate niche models in Maxent.21K_AK_bio_vars.zipMantel testDistance data used in mantel testsmantel_test_data.xlsxRaw genomic data (Allie's Valley)Raw genomic RadSeq data from individuals in the Allie's Valley population. This zip archive contains 8 gzip compressed fastq files.AlliesValley.zipRaw genomic data (Anchorage)Raw genomic RadSeq data from individuals in the Anchorage population. This zip archive contains 6 gzip compressed fastq files.Anchorage.zipRaw genomic data (Crescent Creek)Raw genomic RadSeq data from individuals in the Crescent Creek population. This zip archive contains 7 gzip compressed fastq files.CrescentCreek.zipRaw genomic data (Denali Hwy)Raw genomic RadSeq data from individuals in the Denali Highway population. This zip archive contains 6 gzip compressed fastq files.DenaliHwy.zipRaw genomic data (Eagle Summit)Raw genomic RadSeq data from individuals in the Eagle Summit population. This zip archive contains 6 gzip compressed fastq files.EagleSummit.zipRaw genomic data (Jawbone Lake)Raw genomic RadSeq data from individuals in the Jawbone Lake population. This zip archive contains 2 gzip compressed fastq files.JawboneLake.zipRaw genomic data (Lake Kenibuna)Raw genomic RadSeq data from individuals in the Lake Kenibuna population. This zip archive contains 8 gzip compressed fastq files.LakeKenibuna.zipRaw genomic data (Pika Camp)Raw genomic RadSeq data from individuals in the Pika Camp population. This zip archive contains 8 gzip compressed fastq files.PikaCamp.zipRaw genomic data (Rock Lake)Raw genomic RadSeq data from individuals in the Rock Lake population. This zip archive contains 7 gzip compressed fastq files.RockLake.zip