Data from: Genomic parallelism and lack thereof in contrasting systems of three‐spined sticklebacks ...

• Main Authors: Liu, Shenglin, Ferchaud, Anne-Laure, Grønkjær, Peter, Nygaard, Rasmus, Hansen, Michael M.
• Format: Dataset
• Language: English
• Published: Dryad 2018
• Subjects: divergence time; chromosome inversion; genomic parallelism; Gasterosteus aculeatus; Greenland
• Online Access: https://dx.doi.org/10.5061/dryad.818c434; https://datadryad.org/stash/dataset/doi:10.5061/dryad.818c434

Parallel evolution and the extent to which it involves gene reuse has attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three-spine stickleback (Gasterosteus aculeatus), where freshwater populations have been independently founded by ancestral marine populations, represent prime examples of phenotypic and genomic parallelism, but cases exist where parallelism is low. Based on RAD (Restriction site Associated DNA) sequencing we analyzed SNPs and chromosome inversions in populations in Denmark and Greenland showing low and high parallelism, respectively. We identified parallelism across freshwater populations in Greenland at genomic regions previously identified to be associated with marine-freshwater divergence. These same markers also separated Danish marine and freshwater sticklebacks, albeit to a weaker extent. Hence, parallelism was not absent in ... : VCF file containing the SNPs obtained in this studybatch_1_filtered_auto_adj.vcfR script for finding inverted regions in a genome using population genomic datafindInvert-v2.r ...