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MBE Advance Access published online on January 29, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn024
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Divergence times in Caenorhabditis and Drosophila, inferred from direct estimates of the neutral mutation rate

Asher D. Cutter

Department of Ecology and Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Harbord St., Toronto M5S 3G5, Canada, Tel: 416-978-4602 Fax: 416-978-5878 E-mail: asher.cutter{at}utoronto.ca

Received for publication December 6, 2007. Revision received January 18, 2008. Accepted for publication January 21, 2008.

Accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. Molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. This underlies the notion of a molecular clock. Most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa with poor fossil records must rely on external, potentially inappropriate, calibration with distantly related species. The classic biological models Caenorhabditis and Drosophila are examples of such problem taxa. Here, I illustrate internal-calibration in these groups with direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection on the assumption of neutrality of substitutions. Divergence times are inferred among six species each of Caenorhabditis and Drosophila based on thousands of orthologous groups of genes. I propose that the two closest known species of Caenorhabditis shared a common ancestor <24 Mya (C. briggsae and C. sp. 5) and that C. elegans diverged from its closest known relatives <30 Mya, assuming that these species pass through at least 6 generations per year; these estimates are much more recent than reported previously with molecular clock calibrations from non-nematode phyla. Dates inferred for the common ancestor of D. melanogaster and D. simulans are roughly concordant with previous studies. These revised dates have important implications for rates of genome evolution and the origin of self-fertilization in Caenorhabditis.


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