Molecular Biology and Evolution, Vol 16, 590-601, Copyright © 1999 by Society for Molecular Biology and Evolution
N Takezaki and T Gojobori
Concatenated sequences of all protein-coding genes in mitochondria
recovered a known phylogeny of 11 vertebrate species correctly with
statistical significance. However, when it was rooted by lampreys or sea
urchins, the root of the vertebrate tree was placed between the mammal
cluster and the chicken-frog-fish cluster or between the mammal- chicken
cluster and the frog-fish cluster, depending on the tree-making method
used. Although the frog-fish or chicken-frog-fish cluster was biologically
incorrect, it was again supported with a significantly high bootstrap
value. In this study, we investigated the reasons why this happened. It has
been suggested that an incorrect phylogeny may be constructed due to a
change of amino acid composition in different lineages or due to
homoplasies at sites with hydrophobic amino acids. However, our results
indicated that these were not the causes of the incorrect rooting of the
vertebrate tree. Rather, it was important to take into account an extensive
rate variation across sites and different probabilities of substitution
among different amino acids. The substitution rates for mitochondrial
sequences vary considerably for different vertebrate lineages. In such a
case, it is known to be important to use the model that reflects the actual
substitution probability to obtain a correct tree topology. The correct
rooting of the vertebrate tree was recovered when rate variation across
sites was properly accounted for.
ORIGINAL ARTICLE
Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
National Institute of Genetics, Mishima, Japan. ntakezak@lab.nig.ac.jp
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