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

作者：Zhu Sha^*; Degnan James H; Goldstien Sharyn J; Eldon Bjarki

来源：BMC Bioinformatics, 2015, 16(1): 292.

DOI：10.1186/s12859-015-0721-y

• Hybridization
• Multiple merger
• Gene tree
• Coalescent
• F-ST
• Infinite sites model
• Hybrid-lambda
• Skewed offspring distribution

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.

• 出版日期2015-9-15