Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

Catchen, Julian, University of Oregon

Bassham, Susan, University of Oregon

Wilson, Taylor, University of Oregon

Currey, Mark, University of Oregon

O'Brien, Conor, University of Oregon

Yeates, Quick, University of Oregon

Cresko, William A., University of Oregon

Published Apr 01, 2013 on Dryad. https://doi.org/10.5061/dryad.62hb0

Cite this dataset

Catchen, Julian et al. (2013). Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing [Dataset]. Dryad. https://doi.org/10.5061/dryad.62hb0

Abstract

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.

Usage notes

or_stickleback.tar

The 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

Location

Oregon

USA