DOI: 10.5061/dryad.kp11q
title: Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments

description: Heterogeneous genomic divergence between populations may reflect
 selection, but should also be seen in conjunction with gene flow and
 drift, particularly population bottlenecks. Marine and freshwater
 threespine stickleback (Gasterosteus aculeatus) populations often exhibit
 different lateral armor plate morphs. Moreover, strikingly parallel
 genomic footprints across different marine-freshwater population pairs are
 interpreted as parallel evolution and gene reuse. Nevertheless, in some
 geographic regions like the North Sea and Baltic Sea different patterns
 are observed. Freshwater populations in coastal regions are often
 dominated by marine morphs, suggesting that gene flow overwhelms
 selection, and genomic parallelism may also be less pronounced. We used
 RAD sequencing for analyzing 28,888 SNPs in two marine and seven
 freshwater populations in Denmark, Europe. Freshwater populations
 represented a variety of environments: river populations accessible to
 gene flow from marine sticklebacks and large and small isolated lakes with
 and without fish predators. Sticklebacks in an accessible river
 environment showed minimal morphological and genome-wide divergence from
 marine populations, supporting the hypothesis of gene flow overriding
 selection. Allele frequency spectra suggested bottlenecks in all
 freshwater populations, and particularly two small lake populations.
 However, genomic footprints ascribed to selection could nevertheless be
 identified. No genomic regions were consistent freshwater-marine outliers,
 and parallelism was much lower than in other comparable studies. Two
 genomic regions previously described to be under divergent selection in
 freshwater and marine populations were outliers between different
 freshwater populations. We ascribe these patterns to stronger
 environmental heterogeneity among freshwater populations in our study as
 compared to most other studies, although the demographic history involving
 bottlenecks should also be considered in the interpretation of results.
description: Danish_sticklebackssticklebacks_DKsticklebacks_DK.bed, Plink input file for running Faststructure on the nine threespine stickleback populationssticklebacks_DKsticklebacks_DK.bim, Plink input file for running Faststructure on the nine threespine stickleback populationssticklebacks_DKsticklebacks_DK.fam, Plink input file for running Faststructure on the nine threespine stickleback populationssticklebacks_DKsticklebacks_DK.log, Plink input file for running Faststructure on the nine threespine stickleback populationssticklebacks_DKsticklebacks_DK.nosex, Plink input file for running Faststructure on the nine threespine stickleback populationsDanish_sticklebacks_genepopinput file for running Genepop on the nine danish threespine stickleback populationssticklebacks_Danishvcf from Stacks version 1.13 for the nine danish threespine stickleback populationsamova_Fst_outlier_test_sorted_by_chromosome_used_for_Fig_5Results of the FST-based outlier test by Beaumont & Nichols (1996) as implemented in Arlequin 3.5 (Excoffier & Lischer 2010) sorted by chromosome. The analysis encompasses all samples and p-values are plotted for each SNP across all 21 chromosomes.This file was used to make the figure 5 in the manuscript. SNPs that show significantly high FST (p ≤ 0.001) are candidates for marking genomic regions under diversifying selection, whereas SNPs showing significantly low FST (p ≤ 0.001), potentially reflecte balancing selection.phenotypic_data_newDescription of the lateral plate morphology in danish threespine populations. The morph is determined by the number of lateral plates : low plated (10 or fewer plates), partially plated (between 10 and 21 plates) and full plated (more than 21 plates) (Le Rouzic et al. 2011). See the manuscript for more details. Note: For HAL population, the HAL phenotypes are from individuals from the locality HAL reported in the manuscript but not those that were sequenced (due to technical issues)