Joint Bayesian Estimation of Alignment and Phylogeny

Abstract

We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are constructed simultaneously, a guide tree is not needed. This sidesteps the problem in which alignments created by progressive alignment are biased toward the guide tree used to generate them. Joint estimation also allows us to model rate variation between sites when estimating the alignment and to use the evidence in shared insertion/deletions (indels) to group sister taxa in the phylogeny. Our indel model makes use of affine gap penalties and considers indels of multiple letters. We make the simplifying assumption that the indel process is identical on all branches. As a result, the probability of a gap is independent of branch length. We use a Markov chain Monte Carlo (MCMC) method to sample from the posterior of the joint model, estimating the most probable alignment and tree and their support simultaneously. We describe a new MCMC transition kernel that improves our algorithm's mixing efficiency, allowing the MCMC chains to converge even when started from arbitrary alignments. Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot.

Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology

“…Alignment and tree building are performed under the same analytical parameters, and both are optimized according to the same optimality criterion. In our analyses, the optimality criterion was parsimony, although optimization in a maximum likelihood or Bayesian frame-work is also possible (Fleissner et al, 2005;Redelings and Suchard, 2005;Wheeler, 2006). POY also allowed us to perform a sensitivity analysis to test the stability of clades under diVerent parameters.…”

Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East

“…All log BF tests of Semitic history incorporated a gamma distribution and relaxed clock since our log BF tests showed support for these models. Marginal likelihoods for each model were estimated using the smoothed harmonic mean of the likelihood distribution ( Newton et al 1994;Redelings & Suchard 2005), and all log BF values were calculated by taking the difference in the log of the marginal likelihoods of each model (Kass & Raftery 1995) with log BF values reported in log units.…”

Absence of positive selection on CenH3 inLuzulasuggests that holokinetic chromosomes may suppress centromere drive

“…The codon alignments and phylogenetic trees were jointly inferred in BAli-Phy 2.3.5 (Redelings and Suchard, 2005;Redelings, 2014) using the M0 substitution model and RS07 model for indels; we ran ten independent chains until they converged and then pooled the results. We masked each codon with a reliability score <80 % as 'NNN' prior to selection analyses, and for selection analyses we used a 50 % consensus tree (Fig.…”