DOI: 10.5061/dryad.114j8m1
title: Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

description: Effective management of threatened and exploited species requires an
 understanding of both the genetic connectivity among populations and local
 adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from
 Baja California to the central coast of Canada, has a long history of
 population declines due to anthropogenic stressors. For such coastal
 marine species, population structure could follow a continuous
 isolation-by-distance model, contain regional blocks of genetic similarity
 separated by barriers to gene flow, or be consistent with a null model of
 no population structure. To distinguish between these hypotheses in O.
 lurida, 13,424 single-nucleotide polymorphisms (SNPs) were used to
 characterize rangewide population structure, genetic connectivity, and
 adaptive divergence. Samples were collected across the species range on
 the west coast of North America, from southern California to Vancouver
 Island. A conservative approach for detecting putative loci under
 selection identified 235 SNPs across 129 GBS loci, which were functionally
 annotated and analyzed separately from the remaining neutral loci. While
 strong population structure was observed on a regional scale in both
 neutral and outlier markers, neutral markers had greater power to detect
 fine-scale structure. Geographic regions of reduced gene flow aligned with
 known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay,
 and the currents around Cape Flattery. The outlier loci identified as
 under putative selection included genes involved in developmental
 regulation, sensory information processing, energy metabolism, immune
 response, and muscle contraction. These loci are excellent candidates for
 future research and may provide targets for genetic monitoring programs.
 Beyond specific applications for restoration and management of the Olympia
 oyster, this study lends to the growing body of evidence for both
 population structure and adaptive differentiation across a range of marine
 species exhibiting the potential for panmixia. Computational notebooks are
 available to facilitate reproducibility and future open-sourced research
 on the population structure of Ostrea lurida.
description: VCF file of full,
 filtered datasetVCF file of 13,424
 single nucleotide polymorphisms (SNPs) derived from genotype-by-sequencing
 of 117 Olympia oysters (Ostrea lurida) sampled across 19 populations,
 filtered for a minor allele frequency of 2.5% and no more than 75% missing
 data.OL-c85t10-x45m75-maf025.recode.vcfFasta file of outlier GBS lociFasta file of 129 genotype-by-sequencing loci potentially involved in local adaptation, as determined by at least two methods (pcadapt, OutFLANK, or BayeScan). The 18 loci with positive BLASTx hits are annotated.OutlierLoci.fastaVCF file of putative neutral SNPsVCF file of 13,073 putative neutral SNPs derived from genotype-by-sequencing data of 117 Olympia oysters (Ostrea lurida) sampled across 19 populations. Obtained by filtering the full dataset of any SNP found on a locus containing at least one outlier SNP.OL-c85t10-x45m75-maf025-neutI2.recode.vcfVCF file of putative outlier SNPsVCF file of 235 putative adaptive SNPs derived from genotype-by-sequencing data of 117 Olympia oysters (Ostrea lurida) sampled across 19 populations.OL-c85t10-x45m75-maf025-outI2Union.recode.vcfSample MetadataMetadata information for the 117 Olympia oysters (Ostrea lurida) included in the VCF files in this repository. STRATA: population assignment in analyses; LOCATION: sampling location name; REGION: assigned phylogeographic region; LATITUDE and LONGITIDE of sampling site; LIBRARY: the sequencing run of the sampleOL-c85t10-x45.strataOutfiles of ipyrad assemblyOutfiles produced by ipyrad after assembly of genotype-by-sequencing data. .vcf is used as the input for additional, downstream filtering. _stats.txt provides statistics over the course of the ipyrad run.OL-s7filt45-c85-t10_outfiles.zipExample parameter file for EEMSA parameter file for running EEMS (Estimated Effective Migration Surfaces), including parameter values for setting the variance of the proposal distributions.params-nDemes600-SkI-ch3.iniParameters for ipyrad assemblyParameters used in ipyrad for assembling genotype-by-sequencing data.params-OL-s7filt45-c85-t10.txtHabitat file for EEMSThe .outer file required by EEMS(Estimated Effective Migration Surfaces), which outlines the available habitat for the analysis using GPS coordinates.habitat.outer