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PLoS Genet. 2006 May;2(5):e68. Epub 2006 May 26.

Discordance of species trees with their most likely gene trees.

Author information

1
Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. jdegnan@hsph.harvard.edu

Abstract

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.

PMID:
16733550
PMCID:
PMC1464820
DOI:
10.1371/journal.pgen.0020068
[Indexed for MEDLINE]
Free PMC Article

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