Open Access
June 2017 Lateral transfer in Stochastic Dollo models
Luke J. Kelly, Geoff K. Nicholls
Ann. Appl. Stat. 11(2): 1146-1168 (June 2017). DOI: 10.1214/17-AOAS1040


Lateral transfer, a process whereby species exchange evolutionary traits through nonancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable, as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages, and obtain an improved fit over the corresponding model without lateral transfer.


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Luke J. Kelly. Geoff K. Nicholls. "Lateral transfer in Stochastic Dollo models." Ann. Appl. Stat. 11 (2) 1146 - 1168, June 2017.


Received: 1 January 2016; Revised: 1 March 2017; Published: June 2017
First available in Project Euclid: 20 July 2017

zbMATH: 06775907
MathSciNet: MR3693561
Digital Object Identifier: 10.1214/17-AOAS1040

Keywords: Bayesian phylogenetics , lateral trait transfer , Stochastic Dollo model

Rights: Copyright © 2017 Institute of Mathematical Statistics

Vol.11 • No. 2 • June 2017
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