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.

探明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）数据的系统地理学与种群历史分析，以剧毒蝮蛇矛头蝮（Bothrops atrox）为研究对象，评估大型地理屏障亚马逊河对其谱系形成的影响。我们比对了巴西圣塔伦附近横跨亚马逊河、涵盖主要生境类型的4个采样点的遗传分化情况。物种界定分析将每个种群鉴定为独立的演化谱系；而以种群作为分类单元的物种树分析则显示，系统发育树符合从北向南跨亚马逊河扩散的模式。线粒体DNA（mtDNA）变异的系统发育分析验证了这一模式，并表明所有谱系均起源于更新世中晚期。历史种群动态分析支持「大型种群间仅存在极低持续基因流的谱系间隔离所驱动的谱系形成」种群模型，并否决了仅通过距离隔离产生分化的模型。本研究结果提供了一个罕见的系统地理学模式案例，展现了演化时间尺度下跨大型热带河流的扩散事件；同时表明亚马逊河可通过双重机制推动原位分化：一是阻碍（但并非完全阻止）基因流，二是沿生态梯度产生邻域分化。