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  • 1
    Electronic Resource
    Electronic Resource
    Maximum likelihood inference of protein phylogeny and the origin of chloroplasts (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    Details
    ISSN: 1432-1432
    Keywords: Evolutionary tree ; Amino acid sequence ; Insertion/deletion ; Bootstrap probability ; psbA ; Prochlorothrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109483
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  • 2
    Electronic Resource
    Electronic Resource
    Toward a more accurate time scale for the human mitochondrial DNA tree (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 347-354 
    Details
    ISSN: 1432-1432
    Keywords: Third positions of codons ; Control region ; Heterogeneity among sites ; Molecular clock
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several estimates of the time of occurrence of the most recent common mitochondrial DNA (mtDNA) ancestor of modern humans have been made. Estimates derived from noncoding regions based on a model that classifies sites into two categories (variable and invariable) have been consistently older than those derived from the third positions of codons. This discrepancy can be attributed to a violation of the assumption of rate homogeneity among variable sites when analyzing the noncoding regions. Additional data from the partial control region sequences allow us to take into account some of this further heterogeneity. By assigning the sites to three classes (highly variable, moderately variable, and invariable) and by assuming that the last common mtDNA ancestor of humans and chimpanzees lived 4 million years ago, the most recent common mtDNA ancestor of humans is estimated to have occurred 211,000 ±111,000 years ago (±1 SE), consistent with the estimate, 101,000 ± 52,000 years, made from third positions of codons and also with those proposed previously. We used the same technique to estimate when a putative expansion of modern humans out of Africa took place and estimated a time of 89,000 ± 69,000 years ago. Even though the standard errors of these estimates are large, they allow us to reject the multiregional hypothesis of modern human origin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178865
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  • 3
    Electronic Resource
    Electronic Resource
    Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 270-281 
    Details
    ISSN: 1432-1432
    Keywords: Protein phylogeny ; Maximum likelihood ; Dayhoff model ; Change of evolutionary rate ; Relaxation of selective constraint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160483
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  • 4
    Electronic Resource
    Electronic Resource
    Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 380-388 
    Details
    ISSN: 1432-1432
    Keywords: Entamoeba histolytica ; Protozoa lacking mitochondria ; Eukaryotic kingdoms ; Elongation factor-1α ; Maximum likelihood ; Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1α by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182185
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  • 5
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 519-527 
    Details
    ISSN: 1432-1432
    Keywords: Opossum ; Outgroup ; Branching order ; Mammalian evolution ; Maximum likelihood tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173421
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  • 6
    Electronic Resource
    Electronic Resource
    Relationship among coelacanths, lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 602-609 
    Details
    ISSN: 1432-1432
    Keywords: Origin of tetrapods ; Coelacanth Latimeria chalumnae ; Lungfish Lepidosiren paradoxa ; Cytochrome oxidase subunit I (COI) ; Maximum likelihood inference of protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To clarify the relationship among coelacanths, lungfishes, and tetrapods, the amino acid sequences deduced from the nucleotide sequences of mitochondrial cytochrome oxidase subunit I (COI) genes were compared. The phylogenetic tree of these animals, including the coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa, was inferred by several methods. These analyses consistently indicate a coelacanth/lungfish clade, to which little attention has been paid by previous authors with the exception of some morphologists. Overall evidence of other mitochondrial genes reported previously and the results of this study equally support the coelacanth/lungfish and lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175880
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  • 7
    Electronic Resource
    Electronic Resource
    Time of the deepest root for polymorphism in human mitochondrial DNA (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 37-42 
    Details
    ISSN: 1432-1432
    Keywords: Nucleotide sequences ; Major noncoding region ; Evolutionary rates ; Molecular clock ; Rate heterogeneity among sites ; Effective proportion of variable sites ; Maximum likelihood
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A molecular clock analysis was carried out on the nucleotide sequences of parts of the major noncoding region of mitochondrial DNA (mtDNA) from the major geographic populations of humans. Dates of branchings in the mtDNA tree among humans were estimated with an improved maximum likelihood method. Two species of chimpanzees were used as an outgroup, and the mtDNA clock was calibrated by assuming that the chimpanzee/human split occurred 4 million years ago, following our earlier works. A model of homogeneous evolution among sites does not fit well with the data even within hypervariable segments, and hence an additional parameter that represents a proportion of variable sites was introduced. Taking account of this heterogeneity among sites, the date for the deepest root of the mtDNA tree among humans was estimated to be 280,000±50,000 years old (±1 SE), although there remains uncertainty about the constancy of the evolutionary rate among lineages. The evolutionary rate of the most rapidly evolving sites in mtDNA was estimated to be more than 100 times greater than that of a nuclear pseudogene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099927
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  • 8
    Electronic Resource
    Electronic Resource
    On the maximum likelihood method in molecular phylogenetics (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 443-445 
    Details
    ISSN: 1432-1432
    Keywords: Efficiency ; Maximum likelihood method ; Methods for inferring trees ; DNA sequence data
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolutionary rate differs among lineages.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101285
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  • 9
    Electronic Resource
    Electronic Resource
    Mitochondrial DNA evolution in primates: Transition rate has been extremely low in the lemur (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 113-121 
    Details
    ISSN: 1432-1432
    Keywords: Molecular clock with variable rate ; Branching order ; Branching date ; Maximum likelihood ; AIC ; Bootstrap probability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Based on mitochondrial DNA (mt-DNA) sequence data from a wide range of primate species, branching order in the evolution of primates was inferred by the maximum likelihood method of Felsenstein without assuming rate constancy among lineages. Bootstrap probabilities for being the maximum likelihood tree topology among alternatives were estimated without performing a maximum likelihood estimation for each resampled data set. Variation in the evolutionary rate among lineages was examined for the maximum likelihood tree by a method developed by Kishino and Hasegawa. From these analyses it appears that the transition rate of mtDNA evolution in the lemur has been extremely low, only about 1/10 that in other primate lines, whereas the transversion rate does not differ significantly from that of other primates. Furthermore, the transition rate in catarrhines, except the gibbon, is higher than those in the tarsier and in platyrrhines, and the transition rate in the gibbon is lower than those in other catarrhines. Branching dates in primate evolution were estimated by a molecular clock analysis of mtDNA, taking into account the rate of variation among different lines, and the results were compared with those estimated from nuclear DNA. Under the most likely model, where the evolutionary rate of mtDNA has been unifrom within a great apes/human calde, human/chimpanzee clustering is preferred to the alternative branching orders among human, chimpanzee, and gorilla.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109480
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  • 10
    Electronic Resource
    Electronic Resource
    Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 70-78 
    Details
    ISSN: 1432-1432
    Keywords: Phylogenetic tree ; Likelihood method ; RNA polymerase ; Archaebacteria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099931
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