Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression.
Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression.
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DOI：
10.7554/elife.63753
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发表时间：
2020-12-21
期刊：
影响因子：
7.7
通讯作者：
Hahn MW
中科院分区：
文献类型：
--
作者：
Hibbins MS;Gibson MJ;Hahn MW
性状状态与系统发育关系的不一致性常常被解释为趋同进化的证据。然而，性状的进化沿着不一致的基因树也会产生这些不一致--一种被称为偏侧畸形的现象。经典的比较方法不考虑不一致性，导致对性状转变的数量、时间和方向的不正确推断。不一致的生物学来源包括不完全谱系分类（ILS）和基因渗入，但只有ILS在偏侧畸形的背景下得到了理论上的考虑。在这里，我们提出了一个模型，表明基因渗入使偏侧畸形的可能性更大，因此仅考虑ILS的方法将是保守的。我们还提出了一种方法和软件（HeIST），用于在包含ILS和基因渗入的大型数据集中进行有关hemiplasy和homoplasy概率的统计推断。我们将我们的方法应用于两个经验数据集，发现偏瘫可能有助于观察到的特质不一致。
The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for discordance, resulting in incorrect inferences about the number, timing, and direction of trait transitions. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we present a model that shows introgression makes hemiplasy more likely, such that methods that account for ILS alone will be conservative. We also present a method and software (HeIST) for making statistical inferences about the probability of hemiplasy and homoplasy in large datasets that contain both ILS and introgression. We apply our methods to two empirical datasets, finding that hemiplasy is likely to contribute to the observed trait incongruences in both.