DOI: 10.5061/dryad.62hb0
title: Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

description: Understanding how genetic variation is partitioned across genomes within
 and among populations is a fundamental problem in ecological and
 evolutionary genetics. To address this problem, we studied the threespine
 stickleback fish, which has repeatedly undergone parallel phenotypic and
 genetic differentiation when oceanic fish have invaded freshwater
 habitats. While significant evolutionary genetic research has been
 performed using stickleback from geographic regions that have been
 deglaciated in the last 20 000 years, less research has focused on
 freshwater populations that predate the last glacial maximum. We performed
 restriction-site associated DNA-sequencing (RAD-seq) based population
 genomic analyses on stickleback from across Oregon, which was not
 glaciated during the last maximum. We sampled stickleback from coastal,
 Willamette Basin and central Oregon sites, analysed their genetic
 diversity using RAD-seq, performed structure analyses, reconstructed their
 phylogeographic history and tested the hypothesis of recent stickleback
 introduction into central Oregon, where incidence of this species was only
 recently documented. Our results showed a clear phylogeographic break
 between coastal and inland populations, with oceanic populations
 exhibiting the lowest levels of divergence from one another. Willamette
 Basin and central Oregon populations formed a clade of closely related
 populations, a finding consistent with a recent introduction of
 stickleback into central Oregon. Finally, genome-wide analysis of genetic
 diversity (π) and correlations of alleles within individuals in
 subpopulations (FIS) supported a role for introgressive hybridization in
 coastal populations and a recent expansion in central Oregon. Our results
 exhibit the power of next-generation sequencing genomic approaches such as
 RAD-seq to identify both historical population structure and recent
 colonization history.
description: or_stickleback.tarThe contents of or_sticleback.tar.gz relate to the study, "The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq" by Catchen, Julian, Bassham, Susan, Wilson, Taylor, Currey, Mark, O'Brien, Conor, Yeates, Quick, and Cresko, William. The raw data used to create these files are available from the Sequence Read Archive (SRA), accession SRA070979. The Stickleback used for this study were collected from both marine and freshwater sites along the Oregon coast, and from freshwater habitats in the Willamette Basin and central Oregon. Extracted genomic DNA was processed into RAD libraries using the restriction enzyme SbfI-HF to digest the genome. After sequencing, reads were aligned to the stickleback reference genome using GSnap and processed with the Stacks pipeline. File Contents ------------- build_samples.sh - this file contains the commands run to clean and demultiplex the data. This transforms the raw data files into cleaned sample files, one per individual stickleback fish, named according to population. build_tags.sh - this file contains the commands run to align demultiplexed reads to the stickleback reference genome and to execute the Stacks pipeline. batch_2.fst_summary.tsv - a summary of the Fst values for each population. batch_2.structure_1000.tsv - 1000, randomly selected loci take from the batch_2.structure.tsv file for analysis in Structure. batch_2.structure.tsv - all variant sites in the Oregon dataset formatted for analysis in Structure. batch_2.sumstats_summary.tsv - summaries of the summary statistics, Pi, observed/expected heterozygosity, Fis, etc. batch_2.sumstats.tsv - summary statistics for each variable site in the set, Pi, observed/expected heterozygosity, Fis, etc. batch_2.vcf - variant sites in the Oregon dataset formatted in VCF (http://www.1000genomes.org/node/101). popmap - the population map file fed to the populations program. Describes which samples belong to which populations. Here is the population key: Crooked River 1 Cushman Slough 2 Pony Creek Reservoir 3 Paulina Lake 4 South Jetty 5 South Twin Lake 6 Winchester Creek 7 Riverbend 8 Millport Slough 9