Molecular Biology and Evolution, Vol 12, 451-458, Copyright © 1995 by Society for Molecular Biology and Evolution
Z Yang and D Roberts
Simplifying assumptions made in various tree reconstruction methods--
notably rate constancy among nucleotide sites, homogeneity, and
stationarity of the substitutional processes--are clearly violated when
nucleotide sequences are used to infer distant relationships. Use of tree
reconstruction methods based on such oversimplified assumptions can lead to
misleading results, as pointed out by previous authors. In this paper, we
made use of a (discretized) gamma distribution to account for variable
rates of substitution among sites and built models that allowed for unequal
base frequencies in different sequences. The models were nonhomogeneous
Markov-process models, assuming different patterns of substitution in
different parts of the tree. Data of the small-subunit rRNAs from four
species were analyzed, where base frequencies were quite different among
sequences and rates of substitution were highly variable at sites.
Parameters in the models were estimated by maximum likelihood, and models
were compared by the likelihood-ratio test. The nonhomogeneous models
provided significantly better fit to the data than homogeneous models
despite their involvement of many parameters. They also appeared to produce
reasonable estimation of the phylogenetic tree; in particular, they seemed
able to identify the root of the tree.
ORIGINAL ARTICLE
On the use of nucleic acid sequences to infer early branchings in the tree of life
Department of Zoology, Natural History Museum, United Kingdom.
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