Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

Sha Zhu,Bjarki Eldon,James H Degnan,Sharyn J Goldstien

doi:10.1186/s12859-015-0721-y

Abstract

BackgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.Results 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.Conclusions Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Highlights

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously
We introduce the software Hybrid-Lambda for simulating gene trees under two models of -coalescents within rooted species trees and rooted species networks
Hybrid-Lambda outputs simulated gene trees in three different files: one contains gene trees with branch lengths in coalescent units, another uses the number of generations as branch lengths, and the third uses the number of expected mutations as branch lengths

Summary

Results

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. Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the FST statistic. We apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes

Conclusions

Background

Results and discussion