Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect

Fernando Alvarez-Valin, Oliver Clay, Stéphane Cruveiller, Giorgio Bernardi

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

It has recently been proposed, based on an analysis of orthologous gene sequences from closely related species, that GC-rich regions of primate and cetartiodactyl genomes are becoming GC-poorer, i.e., that GC-rich isochores are now vanishing in these lineages. We review an artefact of parsimony-based ancestor reconstruction in GC-rich DNA, and show that its magnitude explains the apparent vanishing of the GC-richest regions in cetartiodactyls, even if they are in fact at compositional equilibrium. The presently available data do not allow the disequilibrium hypothesis to be entirely ruled out in primates, yet, as we argue here, second-order artefacts can accumulate. They are therefore likely to explain many if not all of the observations, rendering unnecessary the general hypothesis of vanishing GC-rich isochores in mammals.

Original languageEnglish (US)
Pages (from-to)788-793
Number of pages6
JournalMolecular Phylogenetics and Evolution
Volume31
Issue number2
DOIs
StatePublished - May 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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