Identifiability and inference of non-parametric rates-across-sites models on large-scale phylo\-genies

DOI10.1007/S00285-012-0571-4zbMATH Open1276.92082arXiv1108.0129OpenAlexW2963738166WikidataQ51335274 ScholiaQ51335274MaRDI QIDQ376326FDOQ376326

Authors: Elchanan Mossel, Sebastien Roch 

Publication date: 4 November 2013

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general rates-across-sites models. Our results imply, in particular, that large phylogenies are typically identifiable under rate variation. We also derive sequence-length requirements for high-probability reconstruction. Our main contribution is a novel algorithm that clusters sites according to their mutation rate. Following this site clustering step, standard reconstruction techniques can be used to recover the phylogeny. Our results rely on a basic insight: that, for large trees, certain site statistics experience concentration-of-measure phenomena.

Full work available at URL: https://arxiv.org/abs/1108.0129

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zbMATH Keywords

phylogenetic reconstructionconcentration of measures

Mathematics Subject Classification ID

Problems related to evolution (92D15) Special processes (60K99) Computational methods for problems pertaining to biology (92-08)

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Cited In (10)

• Analytic solutions for three taxon ML trees with variable rates across sites
• Phylogenetic mixtures: concentration of measure in the large-tree limit
• Reversible polymorphism-aware phylogenetic models and their application to tree inference
• Counting mutations by parsimony and estimation of mutation rate variation across nucleotide sites -- a simulation study
• Identifiability and inference of phylogenetic birth-death models
• Consistency and identifiability of the polymorphism-aware phylogenetic models
• Phase transition in the sample complexity of likelihood-based phylogeny inference
• Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies
• Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
• Continuous and tractable models for the variation of evolutionary rates

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