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bioRxiv · 10.1101/023465

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

Sha Zhu·James H Degnan·Sharyn J Goldstien·Bjarki Eldon
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Abstract

BackgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.\n\nResultsHybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingmans 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.\n\nConclusionsHybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

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Sha Zhu, James H Degnan, Sharyn J Goldstien, Bjarki Eldon. 2015-07-29. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. https://doi.org/10.1101/023465

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