Mammalian Evolution: Timing and Implications from Using the LogDeterminant Transform for Proteins of Differing Amino Acid Composition

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compe...

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Bibliographic Details
Published in:Systematic biology 1999-03, Vol.48 (1), p.76-93
Main Authors: Penny, David, Hasegawa, Masami, Waddell, Peter J., Hendy, Michael D., Olmstead, R.
Format: Article
Language:English
Subjects:
amino acid composition
Amino acids
Amino Acids - analysis
Animals
Biological Evolution
constant site removal LogDeterminant
DNA, Mitochondrial - chemistry
DNA, Mitochondrial - genetics
Evolution
Hedgehogs
Humans
K/T boundary
mammalian evolution
Mammals
Mammals - classification
Mammals - genetics
Mitochondrial DNA
mitochondrial DNA genomes
Primates
Proteins - chemistry
Rabbits
rodent monophyly
Rodents
Software
Steels
Symposium on the Origin of Mammalian Orders
Taxa
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Summary:We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
ISSN:1063-5157
1076-836X
DOI:10.1080/106351599260454