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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
doi: https://doi.org/10.1101/023465
Sha Zhu
1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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  • For correspondence: joe.zhu@well.ox.ac.uk
James H. Degnan
2Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico, USA
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Sharyn J. Goldstien
3Department of Biology, University of Canterbury, Christchurch, New Zealand
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Bjarki Eldon
4Institut für Mathematik, Technische Universität Berlin, Berlin, Germany
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Abstract

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 29, 2015.
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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
bioRxiv 023465; doi: https://doi.org/10.1101/023465
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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
bioRxiv 023465; doi: https://doi.org/10.1101/023465

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