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

Sha Zhu, James H Degnan, Sharyn J Goldstien, Bjarki Eldon
2015 biorxiv/medrxiv   pre-print
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
more » ... alescent 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. Keywords: hybridization; multiple merger; gene tree; coalescent; FST ; infinite sites model; hybrid-lambda; skewed offspring distribution
doi:10.1101/023465 fatcat:eozb6viq4zalverymnp2oym6pu