Data from: Recent lineage diversification in a venomous snake through dispersal across the Amazon River

Identifying the evolutionary and ecological mechanisms that drive lineage diversification in the species-rich tropics is of broad interest to evolutionary biologists. Here, we use phylogeographic and demographic analyses of genomic scale RADseq data to assess the impact of a large geographic feature, the Amazon River, on lineage formation in a venomous pitviper, Bothrops atrox. We compared genetic differentiation in samples from four sites near Santarem, Brazil that spanned the Amazon and represented major habitat types. A species delimitation analysis identified each population as a distinct evolutionary lineage while a species tree analysis with populations as taxa revealed a phylogenetic tree consistent with dispersal across the Amazon from north to south. Phylogenetic analyses of mtDNA variation confirmed this pattern and suggest that all lineages originated during the mid- to late-Pleistocene. Historical demographic analyses support a population model of lineage formation through isolation between lineages with low ongoing migration between large populations and reject a model of differentiation through isolation by distance alone. Our results provide a rare example of a phylogeographic pattern demonstrating dispersal over evolutionary time scales across a large tropical river and suggest a role for the Amazon River as a driver of in-situ divergence by both impeding (but not preventing) gene flow and through parapatric differentiation along an ecological gradient.Batrox6_Part1.txtPartial raw fastq data file (Part 1 of 3). Concatenate with Parts 2 and 3 prior to analysis.Batrox6_Part2.txtPartial raw fastq data file (Part 2 of 3). Concatenate with Parts 1 and 3 prior to analysis.Batrox6_Part3.txtPartial raw fastq data file (Part 3 of 3). Concatenate with Parts 1 and 2 prior to analysis.Batrox13.txt.tarRaw fastq data file.Batrox26.txt.tarRaw fastq data file.Batrox28.txt.tarRaw fastq data file.Batrox50B.txtRaw fastq data file.Batrox51.txtRaw fastq data file.Batrox55.txtRaw fastq data file.Batrox66.txtRaw fastq data file.Batrox69_Part1.txtPartial raw fastq data file (Part 1 of 2). Concatenate with Parts 2 prior to analysis.Batrox69_Part2.txtPartial raw fastq data file (Part 2 of 2). Concatenate with Part 1 prior to analysis.Batrox105.txtRaw fastq data file.Batrox_BarcodeFilesBarcode files (Individual sample names and associated barcode/molecular identifier) associated with AftrRAD runs