Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.
复制标题
DOI：
10.1186/s12859-015-0721-y
复制
发表时间：
2015-09-15
影响因子：
3
通讯作者：
Eldon B
中科院分区：
文献类型：
--
作者：
Zhu S;Degnan JH;Goldstien SJ;Eldon B
人们对承认祖先谱系多重合并的聚结模型越来越感兴趣；同时模拟杂化和聚结。Hybrid-Lambda是一个在物种网络或物种树中模拟多重合并和Kingman合并过程下的基因谱系的软件包。Hybrid-Lambda允许为不同的种群指定不同的聚结过程，并允许在代和聚结单位之间转换时间，通过指定每个种群的种群大小。此外，Hybrid-Lambda可以生成模拟数据集，假设无限多位点突变模型，并计算fst统计量。作为一个例子，我们应用Hybrid-Lambda来推断某些海洋无脊椎动物在不同聚结过程下的细分时间。Hybrid-Lambda使得研究高繁殖力、后代分布偏态的物种间的生物地理一致性成为可能。
There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman’s coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.