NANUQ: a method for inferring species networks from gene trees under the coalescent model
NANUQ: a method for inferring species networks from gene trees under the coalescent model
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DOI：
10.1186/s13015-019-0159-2
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发表时间：
2019-12-06
影响因子：
1
通讯作者：
Rhodes, John A.
中科院分区：
文献类型：
--
作者：
Allman, Elizabeth S.;Banos, Hector;Rhodes, John A.
物种网络概括了物种树的概念，以允许杂交或其他横向基因转移。在网络多物种聚结模型下，由网络产生的单个基因树可以具有任何拓扑结构，但其产生频率取决于网络结构和数值参数。本文提出了一种基于基因树拓扑结构的1级物种网络统计推断算法，并为该算法提供了理论依据。该算法基于对基因树上显示的四重奏的分析，结合几种统计假设检验和组合思想，如适合网络的基于四重奏的类群间距离、用于圆形分裂系统的NeighborNet算法和用于构造分裂图的圆形网络算法。
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters. We propose a new algorithm for statistical inference of a level-1 species network under this model, from data consisting of gene tree topologies, and provide the theoretical justification for it. The algorithm is based on an analysis of quartets displayed on gene trees, combining several statistical hypothesis tests with combinatorial ideas such as a quartet-based intertaxon distance appropriate to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph.