Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments

Abstract

This version is available at https://strathprints.strath.ac.uk/42512/ Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (https://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge.Any correspondence concerning this service should be sent to the AbstractWe address a potential shortcoming of three probabilistic models for detecting interspecific recombination in DNA sequence alignments: the multiple changepoint model (MCP) of Suchard et al. (2003), the dual multiple change-point model (DMCP) of Minin et al. (2005), and the phylogenetic factorial hidden Markov model (PFHMM) of Husmeier (2005). These models are based on the Bayesian paradigm, which requires the solution of an integral over the space of branch lengths. To render this integration analytically tractable, all three models make the same assumption that the vectors of branch lengths of the phylogenetic tree are independent among sites. While this approximation reduces the computational complexity considerably, we show that it leads to the systematic prediction of spurious topology changes in the Felsenstein zone, that is, the area in the branch lengths configuration space where maximum parsimony consistently infers the wrong topology due to long-branch attraction. We apply two Bayesian hypothesis tests, based on an inter-and an intra-model approach to estimating the marginal likelihood. We then propose a revised model that addresses these shortcomings, and compare it with the aforementioned models on a set of synthetic DNA sequence alignments systematically generated around the Felsenstein zone.

Distinguishing Regional from Within-Codon Rate Heterogeneity in DNA Sequence Alignments

“…We simultaneously model recombination and rate heterogeneity with a phylogenetic FHMM, as originally proposed in [9], with the modification discussed in [10]. A hidden variable S t ∈ {τ 1 , .…”

“…We improve the model described in the previous subsection, which was proposed in [10], in two respects. First, we adapt ρ and sample it along with w from the posterior distribution.…”

“…We refer to this as the "old" model. Note that the latter model is equivalent to the one proposed in [10], but with the improvement that ρ is sampled from the posterior distribution, rather than kept fixed.…”

“…However, in the no-common-mechanism model the branch lengths are incidental rather than structural parameters. As we discussed in [10], this implies that maximum likelihood no longer provides a consistent estimator, and that the method systematically infers the wrong tree topology in the Felsenstein zone defined in [3]. The second simplification does not distinguish between two different types of rate heterogeneity: (1) a regional effect, where larger consecutive segments of the DNA sequence alignment might be differently evolved, e.g.…”

“…Our work is based on the model we introduced in [10]. We modify this approach so as to explicitly take the signature of the genetic code into account.…”