Phylogenetic Relationships of Fungi, Plantae, and Animalia Inferred from Homologous Comparison of Ribosomal Proteins

Veuthey, Anne‐Lise; Bittar, Gabriel

doi:10.1007/pl00006365

Cited by 28 publications

(18 citation statements)

References 65 publications

(61 reference statements)

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“…When the orthologous proteins in the recently sequenced genome of the ␣-purple bacterium Rickettsia prowazekii, supposedly more closely related to mitochondria than P. denitrificans (Andersson et al 1998;Gray, Burger, and Lang 1999), were used as outgroup, the same topology was found again (not shown). The relationship found between animals and fungi is in agreement with other molecular studies (Baldauf and Palmer 1993;Wainright et al 1993;Kumar and Rzhetsky 1996;Borchiellini et al 1998;Gray, Burger, and Lang 1999)-although not all had adequate support (Rodrigo, Bergquist, and Bergquist 1994)-and in contrast with other works that support a closer relationship of animals and plants (Gouy and Li 1989;Veuthey and Bittar 1998). The positions of other eukaryotic groups are, however, not easy to define, because 24 different trees-with different positions for the amoeboid A. castellanii, the red alga C. crispus, and the jacobid flagellate R. americana-had log-likelihood values not significantly different from the one in the maximum-likelihood tree (table 4).…”

Section: Phylogenetic Reconstruction By Maximum Likelihood and Eukarysupporting

confidence: 90%

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Castresana¹

2000

Molecular Biology and Evolution

8,943

6,134

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The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

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Section: Phylogenetic Reconstruction By Maximum Likelihood and Eukarysupporting

confidence: 90%

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Castresana¹

2000

Molecular Biology and Evolution

8,943

6,134

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“…Surprisingly, r-proteins from A. thaliana and not from S. cerevisiae show on average higher similarity with metazoan rproteins, although it is widely accepted that Metazoa and Fungi are closer relatives. Similar findings based on r-protein comparison were already reported several years ago (Veuthey and Bittar, 1998). C. elegans r-proteins are generally most diverged metazoan r-proteins.…”

Section: Concatenated R-proteinssupporting

confidence: 89%

The complete set of ribosomal proteins from the marine sponge Suberites domuncula

Perina

Ćetković

Harcet

et al. 2006

Gene

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“…Nikoh et al (1994) concluded that, from a phylogenetic analysis of trees inferred from 23 different protein species from the three kingdoms by three different methods, i.e., the maximum likelihood (ML) method, the neighbor-joining (N J) method, and the maximum parsimony (MP) method, the kingdom Animalia is closely related to the kingdom Fungi and is distantly related to the kingdom Plantae. In contrast, on the basis of the ribosomal protein peptide and nucleotide sequences, Plantae and Animalia are sister clades and Fungi form a more distinct clade to them (Veuthey and Bittar, 1998). In conclusion, the full evidence from both molecules and morphology is lacking concerning the boundaries between the Fungi and other organisms.…”

Section: Phylogenetic Hypotheses and Circumscription Of The True Fungimentioning

confidence: 91%

Relatedness, phylogeny, and evolution of the fungi

Sugiyama

1998

Mycoscience

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"Traditional studies of evolution have amply demonstrated that evolution at the phenotypic level is characterized by adaptation and opportunism, irregularity in pace, and inequality of rates among lineages. In contrast, studies of molecular evolution have revealed quite different features characterized by changes that are conservative in nature, random in pattern (independent of phenotypic characters), and quite regular in pace with equal rates among diverge [sic] lineages for a given protein". (Kimura, M. 1983. The neutral theory of molecular evolution, pp. 308-309, Cambridge University Press, Cambridge.) Accepted for publication 2 November 1998Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi including Basidiobolus, 3) detection of a major new lineage "Archiascomycetes,'' comprising Taphrina, Protomyces and Saitoella, Schizosaccharomyces, and Pneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genus Geosmithia, and 5) phylogenetic placement of Mixia osmundae, species correctly and incorrectly assigned to the genus Taphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated.

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Phylogenetic Relationships of Fungi, Plantae, and Animalia Inferred from Homologous Comparison of Ribosomal Proteins

Cited by 28 publications

References 65 publications

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

The complete set of ribosomal proteins from the marine sponge Suberites domuncula

Relatedness, phylogeny, and evolution of the fungi

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