PT  - JOURNAL ARTICLE
AU  - Zhu, Sha
AU  - Degnan, James H.
AU  - Goldstien, Sharyn J.
AU  - Eldon, Bjarki
TI  - Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees
AID  - 10.1101/023465
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 023465
4099  - http://biorxiv.org/content/early/2015/07/29/023465.short
4100  - http://biorxiv.org/content/early/2015/07/29/023465.full
AB  - Background There 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 FST 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.