Lateral trait transfer in phylogenetic inference

Luke Kelly

We are interested in inferring the phylogeny, or shared ancestry, of a set of species descended from a common ancestor. When traits pass vertically through ancestral relationships, the phylogeny is a tree and one can often compute the likelihood efficiently through recursions. Lateral transfer, whereby evolving species exchange traits outside of ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. We propose a novel model of species diversification which explicitly controls for the effect of lateral transfer. Our likelihood is intractable as the parameters are the solution of a sequence of large systems of differential equations over a phylogeny. To address this issue, we exploit symmetries in the differential systems and extrapolation techniques to build an efficient approximation scheme. We illustrate our method on a dataset of lexical traits in Eastern Polynesian languages. (This is joint work with Geoff Nicholls.)

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