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THE LOCAL‐CLOCK PERMUTATION TEST: A SIMPLE TEST TO COMPARE RATES OF MOLECULAR EVOLUTION ON PHYLOGENETIC TREES
Author(s) -
Lanfear Robert
Publication year - 2011
Publication title -
evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.84
H-Index - 199
eISSN - 1558-5646
pISSN - 0014-3820
DOI - 10.1111/j.1558-5646.2010.01160.x
Subject(s) - macroevolution , biology , molecular clock , phylogenetic tree , macroecology , test (biology) , evolutionary biology , simple (philosophy) , genealogy , genetics , ecology , epistemology , history , biogeography , gene , philosophy
Rates of molecular evolution vary substantially between lineages, and a growing effort is directed at uncovering the causes and consequences of this variation. Comparing local‐clocks (rates of molecular evolution estimated from different sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local‐clocks in most cases. Instead, I propose the local‐clock permutation test (LCPT), a simple test that can be used to test the significance of differences between local‐clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local‐clocks.