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.

解析物种丰富的热带地区中驱动谱系分化的演化与生态机制，是演化生物学家广泛关注的核心议题。本研究借助基因组尺度限制性位点关联DNA测序（RADseq，Restriction-site Associated DNA sequencing）数据的系统地理学（phylogeography）与种群统计分析，探究大型地理屏障亚马孙河对有毒蝮蛇矛头蝮（Bothrops atrox）谱系形成的影响。我们比对了巴西圣塔伦附近横跨亚马孙河、涵盖主要生境类型的4个采样点的遗传分化情况。物种界定（species delimitation）分析将每个种群鉴定为独立的演化谱系；以种群作为分类单元的物种树（species tree）分析结果显示，系统发育树符合从北向南跨亚马孙河扩散的模式。线粒体DNA（mtDNA，mitochondrial DNA）变异的系统发育分析验证了上述模式，结果表明所有谱系均起源于更新世中晚期。种群历史分析支持“大型种群间持续低水平基因流的谱系间隔离”驱动谱系形成的种群模型，并排除了仅通过距离隔离（isolation by distance）产生分化的模型。本研究结果罕见地展示了演化时间尺度下跨大型热带河流扩散的系统地理学模式，同时表明亚马孙河可通过双重机制驱动原位分化（in-situ divergence）：一是阻碍（但未完全阻断）基因流，二是沿生态梯度形成邻域分化（parapatric differentiation）。