Efficient inference on known phylogenetic trees using Poisson regression.
BACKGROUND
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.
Rosset
Saharon
S
IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA. srosset@us.ibm.com
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010802:Phylogeny; D016012:Poisson Distribution; D012044:Regression Analysis; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004272:DNA, Mitochondrial