Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain.
J Math Biol. 2022 May 3;84(6):47. doi: 10.1007/s00285-022-01746-y.
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately represented by a phylogenetic tree, and rooted phylogenetic networks that describe such complex processes have been introduced as a generalization of rooted phylogenetic trees. In fact, estimating rooted phylogenetic networks from genomic sequence data and analyzing their structural properties is one of the most important tasks in contemporary phylogenetics. Over the last two decades, several subclasses of rooted phylogenetic networks (characterized by certain structural constraints) have been introduced in the literature, either to model specific biological phenomena or to enable tractable mathematical and computational analyses. In the present manuscript, we provide a thorough review of these network classes, as well as provide a biological interpretation of the structural constraints underlying these networks where possible. In addition, we discuss how imposing structural constraints on the network topology can be used to address the scalability and identifiability challenges faced in the estimation of phylogenetic networks from empirical data.
生物体之间的进化关系传统上使用有根系统发生树来表示。然而，由于杂交或横向基因转移等网状过程，进化并不能总是通过系统发生树充分表示，因此已经引入了描述这种复杂过程的有根系统发生网络作为有根系统发生树的推广。事实上，从基因组序列数据估计有根系统发生网络并分析其结构特性是当代系统发生学中最重要的任务之一。在过去的二十年中，文献中已经引入了几种有根系统发生网络的子类（以特定的结构约束为特征），要么是为了模拟特定的生物学现象，要么是为了实现可处理的数学和计算分析。在本手稿中，我们对这些网络类进行了全面的回顾，并尽可能为这些网络的结构约束提供生物学解释。此外，我们还讨论了如何在网络拓扑结构上施加结构约束，以解决从经验数据估计系统发生网络时面临的可扩展性和可识别性挑战。
