Evolution and Phylogenetics
Efficient inference on known phylogenetic trees using Poisson regression
IBM T.J. Watson Research Center, Yorktown Heights NY 10598, USA
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Abstract |
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Motivation: We suggest the use of Poisson regression for time inference and hypothesis testing on a bifurcating Phylogenetic tree with known topology. This method is computationally simple and naturally accommodates variable substitution rates across different sites, without requiring the estimation of these rates. We identify the assumptions under which this is a maximum-likelihood inference approach and show that in some realistic situations—in particular, when the probability of repeated mutation within each branch of the tree is small—these assumptions hold with high probability.
Results: Our motivating domain is human mitochondrial DNA trees, and we illustrate our method on a problem of estimating the time to most recent common ancestor of all non-African mtDNA, using publicly available data. We test for molecular clock violations using multiple comparisons, and conclude that the global molecular clock hypothesis cannot be rejected based on these data.
Contact: srosset{at}us.ibm.com
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  S. Rosset, R. S. Wells, D. F. Soria-Hernanz, C. Tyler-Smith, A. K. Royyuru, D. M. Behar, and and The Genographic Consortium Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA From Partial Phylogenetic Classification Genetics, November 1, 2008; 180(3): 1511 - 1524. [Abstract] [Full Text] [PDF]
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