The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree
The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree
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DOI：
10.1089/cmb.2021.0647
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发表时间：
2022-05-11
影响因子：
1.7
通讯作者：
Rosenberg, Noah A.
中科院分区：
文献类型：
--
作者：
Mehta, Rohan S.;Steel, Mike;Rosenberg, Noah A.
单系性是一组遗传谱系的特征，其中每个谱系与该集合中的所有其他成员的关系比与该集合外的任何谱系的关系更密切。分别为单系的多组世系称为互系单系或联合单系。互惠单系或联合单系（JM）的普遍性已被用于评估系统发育和系统地理假说，以及划分物种。这些应用通常利用基因谱系进化模型下的JM概率。聚结理论的研究已经计算了任意种树中小数目的分离群和平凡种树中任意数目的分离群的JM概率。在此基础上，我们推广了已有的关于多物种合并下的单系概率的结果，得到了任意物种树中任意数量的独立群的JM概率。我们说明了我们的结果如何与先前研究的案例相对应。我们还研究了树高、样本量和种数对JM发生概率的影响。我们得到了相对简单的JM概率的下界和上界。我们的结果扩大了JM计算的范围，超出了少数物种，包括过去在更简单的情况下使用的公式。
Monophyly is a feature of a set of genetic lineages in which every lineage in the set is more closely related to all other members of the set than it is to any lineage outside the set. Multiple sets of lineages that are separately monophyletic are said to be reciprocally monophyletic, or jointly monophyletic. The prevalence of reciprocal monophyly, or joint monophyly (JM), has been used to evaluate phylogenetic and phylogeographic hypotheses, as well as to delimit species. These applications often make use of a probability of JM under models of gene lineage evolution. Studies in coalescent theory have computed this JM probability for small numbers of separate groups in arbitrary species trees and for arbitrary numbers of separate groups in trivial species trees. In this study, generalizing existing results on monophyly probabilities under the multispecies coalescent, we derive the probability of JM for arbitrary numbers of separate groups in arbitrary species trees. We illustrate how our result collapses to previously examined cases. We also study the effect of tree height, sample size, and number of species on the probability of JM. We obtain relatively simple lower and upper bounds on the JM probability. Our results expand the scope of JM calculations beyond small numbers of species, subsuming past formulas that have been used in simpler cases.