How evolution of genomes is reflected in exact DNA sequence match statistics.
Genome evolution is shaped by a multitude of mutational processes, including point mutations, insertions, and deletions of DNA sequences, as well as segmental duplications. These mutational processes can leave distinctive qualitative marks in the statistical features of genomic DNA sequences. One such feature is the match length distribution (MLD) of exactly matching sequence segments within an individual genome or between the genomes of related species. These have been observed to exhibit characteristic power law decays in many species. Here, we show that simple dynamical models consisting solely of duplication and mutation processes can already explain the characteristic features of MLDs observed in genomic sequences. Surprisingly, we find that these features are largely insensitive to details of the underlying mutational processes and do not necessarily rely on the action of natural selection. Our results demonstrate how analyzing statistical features of DNA sequences can help us reveal and quantify the different mutational processes that underlie genome evolution.
Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany UR1077, Unite Mathematiques Informatique et Genome, INRA, domaine de Vilvert, Jouy-en-Josas, France florian.massip@jouy.inra.fr.
Florian
F
Massip
Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
Michael
M
Sheinman
UR1077, Unite Mathematiques Informatique et Genome, INRA, domaine de Vilvert, Jouy-en-Josas, France.
Sophie
S
Schbath
Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
Peter F
PF
Arndt
D000818:Animals; D005075:Biological Evolution; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D056916:Segmental Duplications, Genomic / Q000235:genetics; D012641:Selection, Genetic
comparative genomics; genome evolution; segmental duplication; sequence similarities