DOI: 10.5061/dryad.db6177b
title: Data from: Asymmetric oceanographic processes mediate connectivity and population genetic structure as revealed by RADseq in a highly dispersive marine invertebrate (Parastichopus californicus)

description: Marine populations are typically characterized by weak genetic
 differentiation due to the potential for long-distance dispersal favouring
 high levels of gene flow. However, strong directional advection of water
 masses or retentive hydrodynamic forces can influence the degree of
 genetic exchange among marine populations. To determine the oceanographic
 drivers of genetic structure in a highly dispersive marine invertebrate,
 the giant California sea cucumber (Parastichopus californicus), we first
 tested for the presence of genetic discontinuities along the coast of
 North America in the northeastern Pacific Ocean. Then, we tested two
 hypotheses regarding spatial processes influencing population structure:
 (i) isolation-by-distance (IBD: genetic structure is explained by
 geographic distance), and (ii) isolation-by-resistance (IBR: genetic
 structure is driven by ocean circulation). Using RADseq, we genotyped 717
 individuals from 24 sampling locations across 2,719 neutral SNPs to assess
 the degree of population differentiation, and integrated estimates of
 genetic variation with inferred connectivity probabilities from a
 biophysical model of larval dispersal mediated by ocean currents. We
 identified two clusters separating north and south regions, as well as
 significant, albeit weak, substructure within regions (FST = 0.002, p =
 0.001). After modeling the asymmetric nature of ocean currents, we
 demonstrated that local oceanography (IBR) was a better predictor of
 genetic variation (R2 = 0.48) than geographic distance (IBD) (R2 = 0.17)
 and directional processes played an important role in shaping fine-scale
 structure. Our study contributes to the growing body of literature
 identifying significant population structure in marine systems and has
 important implications for the spatial management of P. californicus and
 other exploited marine species.
description: filtered_3699snps_californicusFiltered dataset consisting of 3,699 SNPs genotyped in 717 giant California sea cucumber individuals2719neutral_snps_noAKAllele frequencies across neutral SNPs (excluding Alaska sites) used for spatial eigenfunction analysis24sites_lat_longGeographic coordinates of the sampling locationsAEM_weight_all_vectorsAEM vectors used as input for RDA; edge weights used to compute AEM vectors are based on connectivity probabilities between sitesdbMEM_straight_all_vectorsdbMEM vectors computed from Euclidean distances between sites used as input for RDAdbMEM_inwater_all_vectorsdbMEM vectors computed from in-water distances between sites used as input for RDAAEM_dbMEM_RDA_scriptscript for computing AEM and dbMEM spatial variables and performing redundancy analysisdapcScript to perform the DAPC analysisfiltered_2719neutral_snps.recodeFiltered .vcf file with 2,719 neutral SNPsstrata.cucumbers.717indstrata file with the population numbers used when converting VCF to other formatsfiltered_2719neutral_snps_genepop2,719 neutral SNPs in genepop format for use in building the population graphpopgraphScript for generating the population graph