Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
Motivation: Through the most extensive phylogenomic analysis carried out to date, complete genomes of 11 eukaryotic species have been examined in order to find the homologous of more than 25 000 amino acid sequences. These sequences correspond to the exons of more than 3000 genes and were used as pr...
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| Veröffentlicht in: | Bioinformatics 2004-08, Vol.20 (suppl-1), p.i116-i121 |
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| creator | Dopazo, Hernán Santoyo, Javier Dopazo, Joaquín |
| description | Motivation: Through the most extensive phylogenomic analysis carried out to date, complete genomes of 11 eukaryotic species have been examined in order to find the homologous of more than 25 000 amino acid sequences. These sequences correspond to the exons of more than 3000 genes and were used as presence/absence characters to test one of the most controversial hypotheses concerning animal evolution, namely the Ecdysozoa hypothesis. Distance, maximum parsimony and Bayesian methods of phylogenetic reconstruction were used to test the hypothesis. Results: The reliability of the ecdysozoa, grouping arthropods and nematodes in a single clade was unequivocally rejected in all the consensus trees. The Coelomata clade, grouping arthropods and chordates, was supported by the highest statistical confidence in all the reconstructions. The study of the dependence of the genomes' tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies. Previous studies supporting ecdysozoa, could not guarantee an accurate phylogeny because the number of characters used was clearly below the minimum required. |
| doi_str_mv | 10.1093/bioinformatics/bth902 |
| format | Article |
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These sequences correspond to the exons of more than 3000 genes and were used as presence/absence characters to test one of the most controversial hypotheses concerning animal evolution, namely the Ecdysozoa hypothesis. Distance, maximum parsimony and Bayesian methods of phylogenetic reconstruction were used to test the hypothesis. Results: The reliability of the ecdysozoa, grouping arthropods and nematodes in a single clade was unequivocally rejected in all the consensus trees. The Coelomata clade, grouping arthropods and chordates, was supported by the highest statistical confidence in all the reconstructions. The study of the dependence of the genomes' tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies. 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Previous studies supporting ecdysozoa, could not guarantee an accurate phylogeny because the number of characters used was clearly below the minimum required.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Biological Evolution</subject><subject>Chromosome Mapping - methods</subject><subject>Coelomata</subject><subject>Ecdysozoa</subject><subject>Eucarya</subject><subject>Exons - genetics</subject><subject>Genetic Code</subject><subject>Humans</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Reproducibility of Results</subject><subject>Sensitivity and Specificity</subject><subject>Species Specificity</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkVFvFCEUhYnR2Fr9CRrig29jYWAYeDTVdU2a2DQ1Mb4QYC5d2plhC0zi_nvZ7EZjX_rEDfc7B-49CL2l5CMlip3bEMPsY5pMCS6f27JRpH2GTikXpGlJp57Xmom-4ZKwE_Qq5ztCOso5f4lOaNeKtpfqFKWrzW6MtzDHqdpgMw-4bADPy2Qh4eix25hkXIGUcYKHJSQYcH0WR1tMmMN8WzXYOLckUwBvj267vRSWe5N2sV5PcYAR5y24APk1euHNmOHN8TxDP1Zfbi7WzeX3r98uPl02jnNZGtsxo4yXdRZPmWRceWuNkkJQ4_0giGWD6RiX0JKBtrZWRlBGe6eAkF6yM_Th4LtN8WGBXPQUsoNxNDPEJWsh-pZK9jRIe6WooKqC7x-Bd3FJcx1C0_3HiGz3bt0BcinmnMDrbQpTXYSmRO-j0_9Hpw_RVd27o_liJxj-qY5ZVaA5ACEX-P23b9K9Fj3rO73--Uuz1ecrdb1a6479AdHgqv8</recordid><startdate>20040804</startdate><enddate>20040804</enddate><creator>Dopazo, Hernán</creator><creator>Santoyo, Javier</creator><creator>Dopazo, Joaquín</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20040804</creationdate><title>Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species</title><author>Dopazo, Hernán ; 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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; Alma/SFX Local Collection |
| subjects | Animals Base Sequence Biological Evolution Chromosome Mapping - methods Coelomata Ecdysozoa Eucarya Exons - genetics Genetic Code Humans Models, Genetic Molecular Sequence Data Phylogeny Reproducibility of Results Sensitivity and Specificity Species Specificity |
| title | Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species |
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