Poster Presentation Society for Molecular Biology and Evolution Conference 2016

Time-reversible vs. Lie-Markov phylogenetic models in the presence of inhomogeneous substitution processes. (#329)

Michael Woodhams 1 , Jeremy Sumner 1 , Barbara Holland 1 , Michael Charleston 1
  1. University of Tasmania, Hobart, TAS, Australia

We present simulation results showing that Lie-Markov DNA evolution models outperform time-reversible models when inferring phylogenetic trees for sequence data that has been generated under a inhomogeneous process.

The Lie-Markov models form a hierarchy of DNA models which are ``multiplicatively closed'', meaning if we take any two Markov matrices generated by a Lie-Markov model, their matrix product is also generated by the same model.

This property is useful for analysing non-homogeneous DNA evolution, where model parameters can vary between branches.

Without this closure property, non-homogeneous analysis, where the fitted model is allowed to vary parameters across the tree, is mathematically inconsistent.

Many time-reversible (TR) DNA models currently in use fail to be multiplicatively closed (e.g. HKY, GTR), and are hence not Lie-Markov.

Our conclusions are obtained by comparing our hierarchy of 37 Lie-Markov models which enable differing transition/transversion rates, to a comparable hierarchy of 28 time-reversible models.