HyDe: A Python Package for Genome-Scale Hybridization Detection
HyDe: A Python Package for Genome-Scale Hybridization Detection
复制标题
DOI：
10.1093/sysbio/syy023
复制
发表时间：
2018-09-01
影响因子：
6.5
通讯作者：
Kubatko, Laura S.
中科院分区：
文献类型：
--
作者：
Blischak, Paul D.;Chifman, Julia;Kubatko, Laura S.
分析近缘类群间的杂交和基因流动是物种形成和系统地理学研究人员的共同目标。许多杂交检测方法使用观察到的基因组数据中的简单位点模式频率，并将其与预测基因流缺失的零模型进行比较。利用这些位点模式概率检测杂交的理论利用了种群树内基因树的凝聚过程和基因树分支上的突变过程之间的关系。对于某些模型，预测位点模式以相同的频率出现（即，它们的差异为0），产生一组称为系统发育不变量的函数。在这篇文章中，我们介绍了HyDe，一个软件包，用于检测杂交在聚结模型下产生的系统发育不变量。HyDe是用Python编写的，可以交互式使用，也可以使用预打包的脚本通过命令行使用。我们演示了在模拟数据以及来自文献的两个经验数据集上使用HyDe。我们特别关注在种群样本中识别个体杂交，并区分杂交物种形成和基因流动。
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow.