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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    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.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 26 (1987), S. 132-147 
    ISSN: 1432-1432
    Keywords: Branching dates ; Human-ape splitting ; η-Globin pseudogene ; Mitochondrial DNA ; Constancy of molecular evolution ; Bootstrap method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Divergence dates among primates were estimated by molecular clock analysis of DNA sequence data. A molecular clock of η-globin pseudogene was calibrated by setting the date of divergence between Catarrhini and Platyrrhini at 38 million years (Myr) ago. The clock gave dates of 25.3±2.4, 11.9±1.7, 5.9±1.2, and 4.9±1.2 Myr ago (± refers to standard error) for the separation of rhesus monkey, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. In placing confidence intervals of the estimates in a robust way, a bootstrap method was used. The 95% confidence intervals are 20.5–29.5, 9.0–14.8, 4.1–7.8, and 3.1–7.0 Myr ago for the separation of rhesus monkey, orangutan, gorilla, and chimpanzee, respectively. By a molecular clock dating of the Prosimii-Anthropoidea splitting, it was suggested that the evolutionary rate of the η-globin gene was high early in primate evolution and subsequently decreased in the line of Anthropoidea. And, by a relative rate test using bootstrap sampling, the possibility of further decrease of the rate (more than 10%) in the line of Hominoidea compared with that of Cercopithecoidea was suggested. Therefore, the above dating of the splittings within Hominoidea may be biased slightly toward younger dates. On the other hand, mitochondrial DNA (mtDNA) seems to have evolved in mammals with a more uniform rate than the η-globin gene. The ratio of the dates of orangutan splitting to chimpanzee splitting is larger for the mtDNA clock than that for the η-globin clock, suggesting the possibilities of mt-DNA introgression among the early hominids and the early African apes, and/or of mtDNA polymorphism within the common ancestral species of orangutan and the African apes that obscures the date of the true species separation of orangutans.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 32 (1991), S. 443-445 
    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.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 22 (1985), S. 160-174 
    ISSN: 1432-1432
    Keywords: Evolution of hominoids ; Phylogenetic position ofAustralopithecus afarensis ; Interspecies transfer of mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3±11.7, 13.3±1.5, 10.9±1.2, 3.7±0.6, and 2.7±0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 31 (1990), S. 205-210 
    ISSN: 1432-1432
    Keywords: Isozyme ; Intron ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10−3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 34 (1992), S. 3-16 
    ISSN: 1432-1432
    Keywords: Alignment ; Maximum likelihood procedure ; Dynamic programming ; Evolutionary model ; Insertion-deletion model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Our previous evolutionary model is generalized to permit approximate treatment of multiple-base insertions and deletions as well as regional heterogeneity of substitution rates. Parameter estimation and alignment procedures that incorporate these generalizations are developed. Simulations are used to assess the accuracy of the parameter estimation procedure and an example of an inferred alignment is included.
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  • 7
    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.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 33 (1991), S. 114-124 
    ISSN: 1432-1432
    Keywords: DNA sequence alignment ; Maximum likelihood procedure ; Dynamic programming ; Evolutionary model ; Insertion-deletion model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Most algorithms for the alignment of biological sequences are not derived from an evolutionary model. Consequently, these alignment algorithms lack a strong statistical basis. A maximum likelihood method for the alignment of two DNA sequences is presented. This method is based upon a statistical model of DNA sequence evolution for which we have obtained explicit transition probabilities. The evolutionary model can also be used as the basis of procedures that estimate the evolutionary parameters relevant to a pair of unaligned DNA sequences. A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.
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  • 9
    ISSN: 1432-1432
    Keywords: Tuna ; Mitochondrial DNA transfer ; Phylogenetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to infer phylogenetic relationships between tuna species of the genus Thunnus, partial sequences of the mitochondrial cytochrome b and ATPase genes were determined in all eight species. Supplemental restriction analysis on the nuclear rRNA gene was also carried out. Pacific northern bluefin tuna (Thunnus thynnus orientalis) was found to have mtDNA distinct from that of the Atlantic subspecies (T. t. thynnus) but very similar to that from the species albacore (T. alaluga). In contrast, no differentiation in nuclear genome was observed between the Atlantic and Pacific northern bluefin tunas. The Atlantic northern bluefin and southern bluefin tunas possessed mtDNA sequences very similar to species of yellowfin tuna group and not so similar to albacore and bigeye tunas which were morphologically assigned to the bluefin tuna group. The molecular data indicate that (1) mtDNA from albacore has been incorporated into the Pacific population of northern bluefin tuna and has extensively displaced the original mtDNA, and (2) albacore is the earliest offshoot, followed by bigeye tuna in this genus, which is inconsistent with the phylogenetic relationships between these tuna species inferred from morphology.
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  • 10
    ISSN: 1432-1432
    Keywords: Variance of log likelihood ; Confidence limits ; Hominoid tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly. The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.
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