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Title: A stochastic Dollo model for lateral transfer
Author: Kelly, Luke
ISNI:       0000 0004 6499 784X
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2016
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Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data - the signal of the taxa ancestry - as the histories of affected traits are mosaics of the species phylogeny and may conflict with the underlying phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. We infer rooted phylogenetic trees. Our likelihood is highly intractable as its parameters are given by the solution of a sequence of systems of differential equations which represent the expected evolution of traits along a tree and grow exponentially in dimension with the number of taxa under consideration. We construct an accurate parameter approximation framework, and from this we derive an efficient exact-approximate inference scheme. We illustrate our method on data sets of lexical traits in Eastern Polynesian and Indo-European languages and obtain improved fits over the corresponding model without lateral transfer.
Supervisor: Nicholls, Geoff Sponsor: Engineering and Physical Sciences Research Council ; University of Oxford
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available