title: Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.
abstract: Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models of sequence evolution, which being highly parametrized and computationally-demanding are not appropriate for large-scale analyses. Here we investigate an alternative methodological option based on probabilistic substitution mapping. The idea is to first reconstruct the substitutional history of each site of an alignment under a homogeneous model of sequence evolution, then to characterize variations in the substitution process across lineages based on substitution counts. Using simulated and published datasets, we demonstrate that probabilistic substitution mapping is robust in that it typically provides accurate reconstruction of sequence ancestry even when the true process is heterogeneous, but a homogeneous model is adopted. Consequently, we show that the new approach is essentially as efficient as and extremely faster than (up to 25 000 times) existing methods, thus paving the way for a systematic survey of substitution process heterogeneity across genes and lineages.
authors.affiliation: Institut des Sciences de l'Evolution de Montpellier, CNRS-Université Montpellier 2, Montpellier, France. jonathan.romiguier@univ-montp2.fr
authors.forename: Jonathan
authors.initials: J
authors.lastname: Romiguier
authors.forename: Emeric
authors.initials: E
authors.lastname: Figuet
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
authors.forename: Emmanuel J P
authors.initials: EJ
authors.lastname: Douzery
authors.forename: Bastien
authors.initials: B
authors.lastname: Boussau
authors.forename: Julien Y
authors.initials: JY
authors.lastname: Dutheil
authors.forename: Vincent
authors.initials: V
authors.lastname: Ranwez
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics*; D000818:Animals; D001482:Base Composition; D003062:Codon; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods; D004272:DNA, Mitochondrial; D019143:Evolution, Molecular; D018740:Genetic Heterogeneity; D006801:Humans; D008957:Models, Genetic; D012337:RNA, Ribosomal, 18S / Q000737:chemistry; D013997:Time Factors
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial; D012337:RNA, Ribosomal, 18S