Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
- M. Hasegawa, H. Kishino, T. Yano
- BiologyJournal of Molecular Evolution
- 2005
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed, and this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago, was ancestral to man and evolved after the human-ape splitting.
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
- Hidetoshi Shimodaira, M. Hasegawa
- BiologyMolecular biology and evolution
- 1 August 1999
A modiļ¬cation of the KH test to take into account a multiplicity of testings is presented, which shows how the test was designed for comparing two topologies but is often used for comparing many topologies.
CONSEL: for assessing the confidence of phylogenetic tree selection
- Hidetoshi Shimodaira, M. Hasegawa
- Computer ScienceBioinform.
- 1 December 2001
UNLABELLED CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees using the multi-scale bootstrap technique, which is less biased than the other conventional p- values.
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
- H. Kishino, M. Hasegawa
- BiologyJournal of Molecular Evolution
- 1 August 1989
A new method for estimating the variance of the difference between log likelihood of different tree topologies is developed by expressing it explicitly in order to evaluate the maximum likelihood branching order among Hominoidea.
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
- W. Martin, T. Rujan, D. Penny
- Biology, Environmental ScienceProceedings of the National Academy of Sciencesā¦
- 6 September 2002
A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloropleft proteins strongly affects plastid genome phylogeny.
Model of amino acid substitution in proteins encoded by mitochondrial DNA
- J. Adachi, M. Hasegawa
- BiologyJournal of Molecular Evolution
- 1 April 1996
A transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins is presented and shows some differences from the matrix estimated from the nuclear-encoding proteins.
Models of amino acid substitution and applications to mitochondrial protein evolution.
- Z. Yang, R. Nielsen, M. Hasegawa
- BiologyMolecular biology and evolution
- 1 December 1998
The mechanistic models were found to fit the data better than empirical models derived from large databases, and the mutational distance between amino acids and the physicochemical distance are found to have strong effects on amino acid substitution rates.
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions.
- Hidenori Nishihara, M. Hasegawa, N. Okada
- BiologyProceedings of the National Academy of Sciencesā¦
- 27 June 2006
The interordinal mammalian relationships presented here provide a cornerstone for future studies in the reconstruction of mammalian classifications, including extinct species, on evolution of large genomic sequences and structure, and in developmental analysis of morphological diversification.
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
- N. Iwabe, K. Kuma, M. Hasegawa, S. Osawa, T. Miyata
- BiologyProceedings of the National Academy of Sciencesā¦
- 1 December 1989
A composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely is proposed, revealing that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases.
Gene transfer to the nucleus and the evolution of chloroplasts
- W. Martin, B. Stoebe, V. Goremykin, S. Hansmann, M. Hasegawa, K. Kowallik
- BiologyNature
- 14 May 1998
The process of gene loss from chloroplast genomes across the inferred tree is mapped and it is found that independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more than 4:1.
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