Distance Methods for Inferring Phylogenies: A Justification

Felsenstein, Joseph

doi:10.1111/j.1558-5646.1984.tb00255.x

Cited by 340 publications

(125 citation statements)

References 28 publications

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“…We calculated the genetic distance between each pair of samples using both Nei (1978) clustering algorithm; the other used the optimality criteria of Fitch and Margoliash (1967), first with (MTscH), and then without (FITcH) the tree constrained to have contemporary tips (Felsenstein, 1984).…”

Section: Discussionmentioning

confidence: 99%

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Allozyme divergence and phylogenetic relationships among species of tephritid flies

et al. 1996

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Multilocus enzyme electrophoresis data from 24 orthologous loci (212 alleles) were used to infer the genetic similarities between 11 Tephritidae pest species from the Ceratitis, Trirhithrum, Capparimyia, Bactrocera, Anastrepha and Rhagoletis genera. Within some of the considered species, different degrees of genetic variability were demonstrated, which appear to be related to zoogeography and to the biological traits peculiar to each species. Nei (1978) and Cavalli-Sforza & Edwards (1967) genetic distances were used to express the genetic divergence and to infer phylogenetic relationships among the species. The UPGMA clustering algorithm and the optimality criteria of Fitch & Margoliash (1967), with (KIT5cH) and without (FITCH) the tree constrained to have contemporary tips, were used. All the methods indicate the same clusters of species. One cluster is composed of Ceratitis capitata, Trirhithrum coffeae and Capparimyia savastanoi, another is composed of Rhagoletis cerasi, Bactrocera dorsalis and Bactrocera oleae. A further loose cluster is comprised of Ceratitis rosa and Anastrepha spp. The congruence between electrophoretic phylogeny and morphological classification is discussed. Our analysis also elucidated cases, within the Ceratitis and Bactrocera genera, of interest from the evolutionary point of view, where allozyme dendrograms do not correlate well with morphological taxonomic relationships.

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Section: Discussionmentioning

confidence: 99%

“…2 Tephritid relationships inferred from KITSCH (ultrametric) tree derived from Fitch-Margoliash optimality criteria with the assumption of equal rates of evolution (Felsenstein, 1984). The numbers represent the length of the branches (only those greater than 0.04).…”

Section: Genetic Distancesmentioning

confidence: 99%

Allozyme divergence and phylogenetic relationships among species of tephritid flies

et al. 1996

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“…Based on convergence of likelihood scores, the first 500 trees were discarded and a consensus tree was generated using the remaining trees, including posterior probability of clades and branch lengths. Maximum-parsimony (MP) trees were reconstructed and their robustness was evaluated by using bootstrap methods with DNAPARS of the PHYLIP package (Felsenstein, 1984). The phylogenies generated based on the four methods and the two types of alignments were congruent.…”

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confidence: 99%

Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'

Jumas‐Bilak

Roudière

Marchandin

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

182

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“…Minimum evolution analysis with the parameter model suggested by Felsenstein (1984) with neighbor joining (Saitou & Nei 1987) was performed by PHYLIP (Felsenstein 2005). Maximum likelihood analysis was also done by PAUP* with settings from the best-fit model (Felsenstein 1981).…”

Section: Visualization In Form Of Treesmentioning

confidence: 99%

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

Jakó¹,

Ari²,

Ittzés³

et al. 2009

Molecular Phylogenetics and Evolution

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Distance Methods for Inferring Phylogenies: A Justification

Cited by 340 publications

References 28 publications

Allozyme divergence and phylogenetic relationships among species of tephritid flies

Allozyme divergence and phylogenetic relationships among species of tephritid flies

Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

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