Data from: The biogeography of deep time phylogenetic reticulation

Most phylogenies are typically represented as purely bifurcating. However, as genomic data has become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US and subsequently led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable.

绝大多数系统发育树通常以严格二歧分叉的形式被呈现。然而，随着基因组数据在系统发育研究中的应用愈发普及，在终端支系或内部节点间观测到网状进化（deep time reticulation, DTR）的情况已屡见不鲜。在此类场景中，若要发生深层时间网状进化，基因流必然发生于相同或相邻的地理区域；因此，若灭绝或扩散事件未掩盖此类演化信号，生物地理重建结果应为亲本节点提供相似的区域估计值。

本研究针对广泛分布于新大陆的王蛇属（Lampropeltis）的系统发育关系展开分析，探究该类群是否存在深层时间网状进化，并估算网状进化事件的祖先分布区域。尤为关键的是，本研究开发了一种在机器学习框架下整合溯祖模拟的新方法，确凿证明该系统发育树最适宜以深层时间网状进化的形式进行表征。

通过对网状节点的二歧亲本支系开展祖先区域重建的联合概率分析，本研究发现该网状进化事件大概率发生于墨西哥西北部/美国西南部区域，随后推动了墨西哥王蛇类群的分化。该区域此前已被证实是研究蛇类及其他有鳞类动物物种形成与伴随基因流的二次接触的核心区域。

本研究表明，即便在研究较为充分的类群中，系统发育网状进化现象也普遍存在，且古代杂交事件的地理范围是可以被有效复原的。