Department of Statistics, The Ohio State University, Columbus, OH 43210, USA.
BMC Evol Biol. 2011 Oct 6;11:291. doi: 10.1186/1471-2148-11-291.
A well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility that this arises through incomplete lineage sorting is often incorporated in models for the species-level phylogeny, it is much less common for hybridization to also be formally included in such models.
We have modified the evolutionary model of Meng and Kubatko (2009) to incorporate intraspecific sampling of multiple individuals for estimation of speciation times and times of hybridization events for testing for hybridization in the presence of incomplete lineage sorting. We have also utilized a more efficient algorithm for obtaining our estimates. Using simulations, we demonstrate that our approach performs well under conditions motivated by an empirical data set for Sistrurus rattlesnakes where putative hybridization has occurred. We further demonstrate that the method is able to accurately detect the signature of hybridization in the data, while this signal may be obscured when other species-tree inference methods that ignore hybridization are used.
Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the Sistrurus data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure S. catenatus tergeminus in origin, which has significant conservation implications.
多基因座数据的一个显著特征是，每个基因座都有其自身的进化历史，而这些历史可能与物种的整体进化历史有很大的不同。尽管不完全谱系分选的可能性通常被纳入物种水平系统发育的模型中，但在这些模型中正式纳入杂交的情况要少得多。
我们修改了 Meng 和 Kubatko（2009 年）的进化模型，纳入了多个个体的种内采样，以估计物种形成时间和杂交事件发生的时间，从而在不完全谱系分选的情况下检验杂交。我们还利用了一种更有效的算法来获得我们的估计。通过模拟，我们证明了我们的方法在受 Sistrurus 响尾蛇实证数据集启发的条件下表现良好，其中存在疑似杂交。我们进一步证明，该方法能够准确检测数据中的杂交信号，而当使用忽略杂交的其他种系树推断方法时，该信号可能会被掩盖。
当存在杂交时，我们的方法被证明是强大的。当应用于 Sistrurus 数据时，我们没有发现杂交的证据；相反，密苏里州的所谓杂交蛇似乎最有可能起源于纯 S. catenatus tergeminus，这具有重要的保护意义。
