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，是演化生物学界广受关注的研究议题。本研究借助基因组尺度限制性位点关联DNA测序（RADseq）数据的系统地理与种群历史分析，评估了大型地理屏障——亚马孙河对有毒蝮蛇类矛头蝮（Bothrops atrox）谱系形成的影响。我们采集了巴西圣塔伦附近横跨亚马孙河、涵盖主要生境类型的4个采样点的样本，对其遗传分化水平开展比较分析。物种界定分析将每个种群判定为独立的演化谱系；以种群作为类群的物种树分析则显示，其系统发育树与跨亚马孙河的南北向扩散模式一致。线粒体DNA（mtDNA）变异的系统发育分析验证了这一模式，结果显示所有谱系均起源于更新世中晚期。种群历史分析支持“谱系分化形成于大种群间维持低水平基因流的谱系隔离模型”，并否定了“仅通过距离隔离产生分化”的模型。本研究结果为“演化时间尺度下跨大型热带河流的扩散”这一系统地理模式提供了罕见例证，并表明亚马孙河可通过双重途径驱动原地分化：一是阻碍（但未完全阻断）基因流，二是沿生态梯度产生邻域分化。