School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne 3010, Australia.
Institut des Sciences de l'Evolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier, 34095, France.
Syst Biol. 2021 Jun 16;70(4):822-837. doi: 10.1093/sysbio/syaa084.
Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T), and loss (L). These processes are usually modeled independently, but in reality, ILS can affect gene copy number polymorphism, that is, interfere with DTL. This has been previously recognized, but not treated in a satisfactory way, mainly because DTL events are naturally modeled forward-in-time, while ILS is naturally modeled backward-in-time with the coalescent. Here, we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realized rate of D, T, and L becomes nonhomogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent, which also accounts for any level of linkage between loci, generalizes the multispecies coalescent (MSC) model and offers a versatile, powerful framework for proper simulation, and inference of gene family evolution. [Gene duplication; gene loss; horizontal gene transfer; incomplete lineage sorting; multispecies coalescent; hemiplasy; recombination.].
不完全谱系分选（ILS）是合并和物种形成之间的相互作用，会导致基因树和物种树之间的不一致，基因复制（D）、转移（T）和丢失（L）也是如此。这些过程通常是独立建模的，但实际上，ILS 会影响基因拷贝数多态性，即干扰 DTL。这以前已经被认识到，但没有得到令人满意的处理，主要是因为 DTL 事件通常是正向时间建模的，而 ILS 是与合并一起向后时间建模的。在这里，我们考虑了 ILS 和 DTL 对基因树/物种树问题的联合作用，包括其所有的复杂性。特别是，我们表明 ILS 和复制/转移（没有丢失）之间的相互作用可能导致通常被解释为基因丢失的模式，并且当考虑到 ILS 时，D、T 和 L 的实现率在时间上变得不均匀。我们为这些问题引入了算法解决方案。我们的新模型，多基因座多物种合并，也考虑了基因座之间的任何水平的连锁，推广了多物种合并（MSC）模型，并提供了一个通用的、强大的框架，用于正确模拟和推断基因家族进化。[基因复制；基因丢失；水平基因转移；不完全谱系分选；多物种合并；半同型；重组。]。
