The Biogeography of Deep Time Phylogenetic Reticulation
The Biogeography of Deep Time Phylogenetic Reticulation
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DOI：
10.1093/sysbio/syy019
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发表时间：
2018-09-01
影响因子：
6.5
通讯作者：
Gehara, Marcelo
中科院分区：
文献类型：
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作者：
Burbrink, Frank T.;Gehara, Marcelo
大多数系统发育通常表现为纯粹的分叉。然而，随着基因组数据在系统发育研究中变得越来越普遍，在末端谱系或内部节点之间发现网状结构（深度时间网状结构；DTR）并不罕见。在这些情况下，基因流动必须发生在相同或相邻的地理区域才能发生这些 DTR，因此生物地理重建应该为亲代节点提供类似的面积估计，前提是灭绝或扩散没有侵蚀这些模式。我们研究了广泛分布的新世界王蛇 (Lampropeltis) 的系统发育，确定该群体中是否存在 DTR，并估计了网纹的祖先区域。重要的是，我们开发了一种新方法，该方法在机器学习框架中使用合并模拟来最终表明，这种系统发育最好地表示为在更深的时间上呈网状。利用来自网状节点的分叉亲代谱系的祖先区域重建的联合概率，我们表明这种网状结构可能发生在墨西哥西北部/美国西南部，随后导致了墨西哥王蛇的多样化。该区域先前已被确定为对于了解蛇和其他有鳞动物的物种形成和基因流的二次接触非常重要的区域。这项研究表明，即使在经过充分研究的群体中，系统发育网状结构也很常见，而且古代杂交的地理范围是可以恢复的。
Most phylogenies are typically represented as purely bifurcating. However, as genomic data have 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 amachine 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.