1989
DOI: 10.1007/bf02100115
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Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

Abstract: 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 … Show more

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Cited by 3,141 publications
(1,958 citation statements)
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References 52 publications
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“…Five independent analyses were run for one million generations, with sampling every 100 simulations (30% burn‐in). Statistically supported topological incongruence between alternate mitochondrial and nuclear phylogenies was evaluated using Kishino–Hasegawa (KH) (Kishino & Hasegawa 1989) and Shimodaira–Hasegawa (SH) (Shimodaira & Hasegawa 1999) likelihood tests in paml v.4 (Yang 2007). Haplotype diversity ( H d ) was calculated using dnasp v5.10.1 (Librado & Rozas 2009).…”
Section: Methodsmentioning
confidence: 99%
“…Five independent analyses were run for one million generations, with sampling every 100 simulations (30% burn‐in). Statistically supported topological incongruence between alternate mitochondrial and nuclear phylogenies was evaluated using Kishino–Hasegawa (KH) (Kishino & Hasegawa 1989) and Shimodaira–Hasegawa (SH) (Shimodaira & Hasegawa 1999) likelihood tests in paml v.4 (Yang 2007). Haplotype diversity ( H d ) was calculated using dnasp v5.10.1 (Librado & Rozas 2009).…”
Section: Methodsmentioning
confidence: 99%
“…The comparison of competing topologies (MP, ME, ML, Bayesian analysis, and constraint) was carried out using two-tailed Wilcoxon signed-ranks tests (Templeton, 1983) and Kishino-Hasegawa (KH) test (Kishino and Hasegawa, 1989), using 1000 bootstrap replicates with …”
Section: Sequence Analysismentioning
confidence: 99%
“…When possible branchand-bound searches were conducted on taxonomically reduced data sets to compare to the heuristic results. The shortest observed cladograms were compared, using the KH test (Kishino and Hasegawa, 1989) and most parsimonious tree (MP) indices, to trees based on earlier, morphological-based hypotheses of belonid phylogenetic relationship.…”
Section: Phylogenetic Analysismentioning
confidence: 99%
“…We also used the KH test (Kishino and Hasegawa, 1989) to determine that the likelihood score (18927.76) for a tree constraining Strongylura to be monophyletic was significantly worse than the MP tree (18874.93) (p ¼ 0:0020). We also forced Belone to its hypothetical basal position within the Belonidae (Collette and Berry, 1965) and maintained the monophyly of Strongylura.…”
Section: Phylogenetic Analysismentioning
confidence: 99%