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MBE Advance Access published online on August 9, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn172
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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

Subdivision in an ancestral species creates asymmetry in gene trees

Montgomery Slatkin and Joshua L. Pollack

Department of Integrative Biology, University of California at Berkeley

Corresponding author: Montgomery Slatkin, Department of Integrative Biology, 3060 VLSB, University of California, Berkeley, CA 94720-3140, email: slatkin{at}berkeley.edu, telephone: 510-643-6300, fax: 510-643-6264.

Received for publication May 30, 2008. Revision received July 23, 2008. Accepted for publication July 29, 2008.

We consider gene trees in three species for which the species tree is known. We show that population subdivision in ancestral species can lead to asymmetry in the frequencies of the two gene trees not concordant with the species tree and, if subdivision is extreme, cause the one of the non-concordant gene trees to be more probable than the concordant gene tree. Although published data for the human-chimp-gorilla clade and for 3 species of Drosophila show asymmetry consistent with our model, sequencing error could also account for observed patterns. We show that substantial levels of persistent ancestral subdivision are needed to account for the observed levels of asymmetry found in these two studies.

Key Words: gene genealogy • trans-species polymorphism • lineage sorting


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