Nov 1, 2017

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

Systematic Biology
Dingqiao Wen, Luay Nakhleh

Abstract

The multispecies network coalescent (MSNC) is a stochastic process that captures how gene trees grow within the branches of a phylogenetic network. Coupling the MSNC with a stochastic mutational process that operates along the branches of the gene trees gives rise to a generative model of how multiple loci from within and across species evolve in the presence of both incomplete lineage sorting (ILS) and reticulation (e.g., hybridization). We report on a Bayesian method for sampling the parameters of this generative model, including the species phylogeny, gene trees, divergence times, and population sizes, from DNA sequences of multiple independent loci. We demonstrate the utility of our method by analyzing simulated data and reanalyzing an empirical data set. Our results demonstrate the significance of not only coestimating species phylogenies and gene trees, but also accounting for reticulation and ILS simultaneously. In particular, we show that when gene flow occurs, our method accurately estimates the evolutionary histories, coalescence times, and divergence times. Tree inference methods, on the other hand, underestimate divergence times and overestimate coalescence times when the evolutionary history is reticulate. While th...Continue Reading

Mentioned in this Paper

Genes
Trees (plant)
Nucleic Acid Hybridization Procedure
Yeasts
Multilocus Sequence Typing
Sorting - Cell Movement
Species
Locus
Integrated Learning System
Acute Biphenotypic Leukemia

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