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（phylogeny）通常以纯二歧分枝的形式呈现。然而，随着基因组数据（genomic data）在系统发育研究中的应用愈发普遍，在末端支系间或内部节点间发现网状进化（reticulation）的情况已屡见不鲜，这类现象被称为深时网状进化（deep time reticulation，简称DTR）。在此类情形下，若要形成深时网状进化，基因流（gene flow）必然发生于相同或相邻的地理区域；因此，倘若未因灭绝或扩散事件破坏该信号，生物地理重建（biogeographic reconstruction）应当能为亲本节点（parental nodes）提供一致的分布区估计结果。本研究以分布广泛的新世界王蛇属（Lampropeltis）的系统发育树为研究对象，旨在判断该类群中是否存在深时网状进化，并估算网状进化事件的祖先分布区。尤为重要的是，我们开发了一种全新方法：在机器学习框架（machine learning framework）中结合溯祖模拟（coalescent simulation），最终确凿证明该系统发育树的最优呈现形式为深时网状进化。通过对网状进化节点的二歧分枝亲本支系开展联合祖先分布区重建概率分析，我们发现此次网状进化大概率发生于墨西哥西北部/美国西南部地区，且该事件后续推动了墨西哥王蛇类群的分化。此前已有研究指出，该区域是理解蛇类及其他有鳞类（squamates）物种形成与具基因流的次生接触的关键区域。本研究表明，即便在被充分研究的类群中，系统发育网状进化也颇为常见，且古杂交事件的地理范围是可被还原的。