An Application of Supertree Methods to Mammalian Mitogenomic Sequences
Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree metho...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2010-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S4527 |
| _version_ | 1819048342560178176 |
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| author | Véronique Campbell François-Joseph Lapointe |
| author_facet | Véronique Campbell François-Joseph Lapointe |
| author_sort | Véronique Campbell |
| collection | DOAJ |
| description | Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context. |
| first_indexed | 2024-12-21T11:14:44Z |
| format | Article |
| id | doaj.art-70498804d2134b4c9c8e3d1d4753fa6a |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-21T11:14:44Z |
| publishDate | 2010-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-70498804d2134b4c9c8e3d1d4753fa6a2022-12-21T19:05:58ZengSAGE PublishingEvolutionary Bioinformatics1176-93432010-01-01610.4137/EBO.S4527An Application of Supertree Methods to Mammalian Mitogenomic SequencesVéronique Campbell0François-Joseph Lapointe1Université de Montréal, Département de sciences Biologiques, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada.Université de Montréal, Département de sciences Biologiques, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada.Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.https://doi.org/10.4137/EBO.S4527 |
| spellingShingle | Véronique Campbell François-Joseph Lapointe An Application of Supertree Methods to Mammalian Mitogenomic Sequences Evolutionary Bioinformatics |
| title | An Application of Supertree Methods to Mammalian Mitogenomic Sequences |
| title_full | An Application of Supertree Methods to Mammalian Mitogenomic Sequences |
| title_fullStr | An Application of Supertree Methods to Mammalian Mitogenomic Sequences |
| title_full_unstemmed | An Application of Supertree Methods to Mammalian Mitogenomic Sequences |
| title_short | An Application of Supertree Methods to Mammalian Mitogenomic Sequences |
| title_sort | application of supertree methods to mammalian mitogenomic sequences |
| url | https://doi.org/10.4137/EBO.S4527 |
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