Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences |
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Authors: | Hasegawa M; Adachi J |
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Institution: | Institute of Statistical Mathematics, Tokyo, Japan. hasegawa@ism.ac.jp |
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Abstract: | By a maximum likelihood analysis of mitochondrial DNA sequences, we examine
Graur and Higgins' hypothesis of the Ruminantia/Cetacea clade with
Suiformes as an outgroup. Graur and Higgins analyzed these sequences by the
neighbor-joining and parsimony methods, as well as by the maximum
likelihood method under the assumption that the substitution rate is the
same for all sites. The Ruminantia/Suiformes clade assumed by the
traditional taxonomy was rejected strongly by this analysis and the
Ruminantia/Cetacea clade was supported. Adoption of a more realistic model
distinguishing among rates at different codon positions in the maximum
likelihood analysis of the same data, however, grossly reduces the
significance level on the Graur-Higgins hypothesis. Thus, although the
Ruminantia/Suiformes grouping is indeed least likely from Graur and
Higgins' data set of mitochondrial DNA, this traditional tree cannot be
rejected with statistical significance under the new analysis, and more
data are needed to settle the issue. In the same way, we examine Irwin and
Arnason's suggestion of the Hippopotamus/Cetacea clade by using cytochrome
b and hemoglobins alpha and beta, and it turn out that their suggestion is
also fragile. This analysis demonstrates the importance of selecting an
appropriate model among the alternatives in the maximum likelihood analysis
and of using many different genes from many relevant species in order to
make reliable phylogenetic inferences.
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