The giant panda is closer to a bear, judged by ?- and ?-hemoglobin sequences

Hashimoto, Takeji; Otaka, Eiko; Adachi, Jun; Mizuta, Keiko; Hasegawa, Masami

doi:10.1007/bf00160484

Cited by 20 publications

(10 citation statements)

References 26 publications

(28 reference statements)

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“…Adachi and Hasegawa (1992a) published the PROTML program for the ML inference of protein phylogeny based on the model. It has been applied to a wide range of problems in molecular phylogenetics (Hasegawa et al 1992Adachi et al 1993;Hashimoto et al 1993Hashimoto et al , 1994Kojima et al 1993), and it turned out that the Dayhoff model is by far more appropriate than the Proportional and Poisson models (Hasegawa et al 1992) in approximating the evolution of the diverse protein data.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

Cao

Adachi

Janke³

et al. 1994

J Mol Evol

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234

117

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The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.

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Section: Methodsmentioning

confidence: 99%

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

Cao

Adachi

Janke³

et al. 1994

J Mol Evol

Self Cite

234

117

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show abstract

“…Adachi and published the PROTML program for the ML inference of protein phylogeny based on the Dayhoff model (Dayhoff et al 1978), and it has been used widely. Subsequently, it has turned out that this model is far more appropriate than the Proportional and Poisson models ) for approximating the evolution of the diverse protein data (Hasegawa et al 1993a;Adachi et al 1993;Hashimoto et al 1993Hashimoto et al , 1994. Recently, Jones et al (1992) updated the amino acid substitution matrix by using about 40 times more abundant substitution data than those of Dayhoff et al (1978).…”

Section: Comparison Between the ML And Nj Methods In Estimating Brancmentioning

confidence: 99%

Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites

Adachi

Hasegawa

1995

J Mol Evol

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The internal branch lengths estimated by distance methods such as neighbor-joining are shown to be biased to be short when the evolutionary rate differs among sites. The variable-invariable model for site heterogeneity fits the amino acid sequence data encoded by the mitochondrial DNA from Hominoidea remarkably well. By assuming the orangutan separation to be 13 or 16 Myr old, a maximum-likelihood analysis estimates a young date of 3.6 +/- 0.6 or 4.4 +/- 0.7 Myr (+/- 1 SE) for the human/chimpanzee separation, and these estimates turn out to be robust against differences in the assumed model for amino acid substitutions. Although some uncertainties still exist in our estimates, this analysis suggests that humans separated from chimpanzees some 4-5 Myr ago.

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“…6 -147.7 +3,137.2 -156.5 liable. The superiority of the Dayhoff model has been demonstrated also for elongation factor Is, DNA-dependent RNA polymerase, and hemoglobins encoded by nuclear DNA (Hasegawa et al 1993;Hashimoto et al 1992Hashimoto et al , 1993.…”

Section: Phylogenetic Relationship Among Eutherian Ordersmentioning

confidence: 98%

“…The following three Markov models for amino acid substitutions were used in the ML analysis of amino acid sequences of mitochondrially encoded proteins (Hasegawa et al , 1993Adachi and Hasegawa 1992b;Hashimoto et al 1993); (1) the "Dayhoff model" was developed by and by Adachi and Hasegawa (1992a) and assumes an empirical transition matrix compiled by Dayhoff et al (1978), (2) the "Proportional model" assumes that, in an infinitesimally short time interval of dt, the probability Pu(dt) of the current amino acid i being replaced by another amino acid j is given by…”

mentioning

confidence: 99%

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

1993

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By using complete sequence data of mitochondrial DNAs, three Markov models (Dayhoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.

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The giant panda is closer to a bear, judged by ?- and ?-hemoglobin sequences

Cited by 20 publications

References 26 publications

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

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