Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 27, Issue 3, Pages 570-580Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msp274
Keywords
multispecies coalescent; species trees; gene trees; molecular systematics; Bayesian inference; censored coalescent
Funding
- Marsden [UOA0502]
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For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.
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