PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow
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DOI：
10.1093/sysbio/syad030
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发表时间：
2023-07-31
影响因子：
6.5
通讯作者：
Ane，Cecile
中科院分区：
文献类型：
--
作者：
Fogg，John;Allman，Elizabeth S.;Ane，Cecile
根据网络多物种融合过程，考虑系统发育基因树沿着系统发育物种网络的演化，提出了一种新的具有相关遗传基因流的网络融合模型.该模型概括了两种传统的网络合并：独立继承和共同继承。在每个网状结构中，给定基因座的多个谱系从随机选择的亲本群体遗传，或者独立地跨谱系遗传，或者根据狄利克雷过程具有正相关性。例如，这个过程可以考虑基因座特定的遗传概率。我们在Julia软件包PhyloCoalSimulations中实现了这些网络合并模型下的基因树模拟，该软件包依赖于PhyloNetworks及其强大的网络操作工具。输入物种的遗传学可以用扩展的Newick格式来阅读，无论是在世代数还是在聚结单位中。模拟的基因树可以用Newick格式编写，并且可以保留它们在物种网络中嵌入的信息。这种嵌入可用于下游目的，例如模拟物种特定的过程，如物种之间的速率变化，或用于本说明中所示的其他场景。这个软件包应该是有用的仿真研究和基于仿真的推理方法。该软件是开源的，在https://github.com/cecileane/PhyloCoalSimulations.jl上有文档和教程。
We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at https://github.com/cecileane/PhyloCoalSimulations.jl.