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  • 1
    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
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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.
    Type of Medium: Electronic Resource
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  • 3
    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
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