Reducing Model Complexity of the General Markov Model of Evolution

Jayaswal, Vivek; Ababneh, Faisal; Jermiin, Lars S.; Robinson, John

doi:10.1093/molbev/msr128

Cited by 32 publications

(24 citation statements)

References 35 publications

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“…Determining how to best depict and model the heterogeneity of the substitution process across branches in large phylogenetic datasets has recently attracted much attention and led to many developments (e.g. Blanquart & Lartillot, 2006;Boussau & Gouy, 2006;Dutheil & Boussau, 2008;Jayaswal et al, 2011;Zhang et al, 2011). In this study, we chose to merge species into clusters based on their body mass because we had strong prior expectations regarding its relationship with dN/dS, and also because we were interested in the first place in the reconstruction of ancestral body mass.…”

Section: Mtdna As a Marker Of Species Life-history Traitsmentioning

confidence: 99%

Mitochondrial DNA as a tool for reconstructing past life‐history traits in mammals

Figuet

Romiguier

Dutheil

et al. 2014

J of Evolutionary Biology

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Reconstructing the ancestral characteristics of species is a major goal in evolutionary and comparative biology. Unfortunately, fossils are not always available and sufficiently informative, and phylogenetic methods based on models of character evolution can be unsatisfactory. Genomic data offer a new opportunity to estimate ancestral character states, through (i) the correlation between DNA evolutionary processes and species life-history traits and (ii) available reliable methods for ancestral sequence inference. Here, we assess the relevance of mitochondrial DNA -the most popular molecular marker in animals -as a predictor of ancestral life-history traits in mammals, using the order of Cetartiodactyla as a benchmark. Using the complete set of 13 mitochondrial protein-coding genes, we show that the lineagespecific nonsynonymous over synonymous substitution rate ratio (dN/dS) is closely correlated with the species body mass, longevity and age of sexual maturity in Cetartiodactyla and can be used as a marker of ancestral traits provided that the noise introduced by short branches is appropriately dealt with. Based on ancestral dN/dS estimates, we predict that the first cetartiodactyls were relatively small animals (around 20 kg). This finding is in accordance with Cope's rule and the fossil record but could not be recovered via continuous character evolution methods.

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Section: Mtdna As a Marker Of Species Life-history Traitsmentioning

confidence: 99%

Mitochondrial DNA as a tool for reconstructing past life‐history traits in mammals

Figuet

Romiguier

Dutheil

et al. 2014

J of Evolutionary Biology

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“…However, standard models are usually designed with the simplifying assumptions that the evolutionary process was globally stationary, reversible, and homogeneous (Yang 2006; Jermiin et al 2008; Jayaswal et al 2011a) (Fig. 1a).…”

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confidence: 99%

“…For instance, some methods do not estimate one matrix per branch, but use groups of branches that share substitution matrices (Yang 1998; Foster 2004; Dutheil and Boussau 2008). These groups can be defined a priori (Dutheil and Boussau 2008), or estimated during the course of the computation (Jayaswal et al 2011a; Dutheil et al 2012). Similarly, Bayesian approaches have been developed that place breakpoints along the branches of the phylogeny: substitution models are shared by all branches between breakpoints, but change at breakpoints (Blanquart and Lartillot 2006, 2008).…”

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confidence: 99%

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

2013

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Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor. [Ancestral sequence reconstruction; nonhomogeneous model; optimal growth temperature; phylogenomics; phylogeny.]

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“…One approach to accommodate data that have evolved under non-SRH conditions is to employ models that relax the SRH assumptions. A number of non-SRH models have been implemented in a variety of software packages (Foster 2004;Lartillot and Philippe 2004;Blanquart and Lartillot 2006;Boussau and Gouy 2006;Jayaswal, et al 2007;Knight, et al 2007;Dutheil and Boussau 2008;Jayaswal, et al 2011;Sumner, et al 2012;Zou, et al 2012;Groussin, et al 2013;Jayaswal, et al 2014;Nguyen, et al 2015;Woodhams, et al 2015).…”

Section: Introductionmentioning

confidence: 99%

The Prevalence and Impact of Model Violations in Phylogenetics Analysis

Naser-Khdour

Minh

Zhang

et al. 2018

Preprint

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In phylogenetic inference we commonly use models of substitution which assume that sequence evolution is stationary, reversible and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic datasets. We show that many partitions (39.5%) reject the SRH assumptions, and that for most datasets, the topologies of trees inferred from all partitions differ significantly from those inferred using the subset of partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. They also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).

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Reducing Model Complexity of the General Markov Model of Evolution

Cited by 32 publications

References 35 publications

Mitochondrial DNA as a tool for reconstructing past life‐history traits in mammals

Mitochondrial DNA as a tool for reconstructing past life‐history traits in mammals

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

The Prevalence and Impact of Model Violations in Phylogenetics Analysis

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