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Molecular Biology and Evolution 18:1976-1978 (2001)
© 2001 Society for Molecular Biology and Evolution

Unveiling the Molecular Clock in the Presence of Recombination

David Posada

Department of Zoology, Brigham Young University

In a recent letter in Molecular Biology and Evolution, Schierup and Hein (2000a)Citation showed that the likelihood ratio test (LRT) of the molecular clock (Felsenstein 1981Citation ) "wrongly" rejects the clock hypothesis when recombination has occurred. However, this result should not be taken as a failure of the LRT. Because in the presence of recombination often there is not one single tree describing the history of the sequences, but several, the LRT is correctly rejecting the actual null hypothesis tested, that is, that the data are evolving under a clock on one single tree.

To appropriately test the clock hypothesis in the presence of recombination, we need to use a test independent of tree topology. Muse and Weir (1992)Citation proposed a triplet likelihood ratio test to test for equality of evolutionary of rates for two species at a time using a third species as an outgroup (to avoid . . . [Full Text of this Article]

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