Format

Send to:

Choose Destination
See comment in PubMed Commons below
PLoS One. 2012;7(3):e33852. doi: 10.1371/journal.pone.0033852. Epub 2012 Mar 27.

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Author information

  • 1Institut des Sciences de l'Evolution de Montpellier, CNRS-Universit√© Montpellier 2, Montpellier, France. jonathan.romiguier@univ-montp2.fr

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.

PMID:
22479459
[PubMed - indexed for MEDLINE]
PMCID:
PMC3313935
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Public Library of Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk