Data from: Genomic signatures of geographic isolation and natural selection in coral reef fishes

The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.Processed Illumina reads for Acanthurus reversusDemultiplexed and quality filtered Illumina HiSeq2000 reads for all 9 Acanthurus reversus samples used in this study. These samples were used as input files for the Stacks denovo_map.pl pipeline.ARE_rawRAD_ME_2015.tar.gzProcessed Illumina reads for Acanthurus olivaceusDemultiplexed and quality filtered Illumina HiSeq 2000 reads for all 52 Acanthurus olivaceus samples used in this study. These samples were used as the input files for the Stacks denovo_map.pl pipeline.AOL_rawRAD_ME_2015.tar.gzAll Loci Structure FileAll_Loci_StructureFile.txtCytb AlignmentCytbAlignment.txtGpd2 AlignmentGpd2Alignment.txtLoci under balancing selection Structure FileLoci_under_balancing_selection_StructureFile.txtLoci under divergent selection Structure FileLoci_under_divergent_selection_StructureFile.txtNeutral loci Structure FileNeutral_loci _StructureFile .txtS7 AlignmentS7Alignment.txtSample databaseSample_database.xls