Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and Mammalian phylogenomic data sets.
Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To...
| Publicado en: | BioMed Research International Vol. 2013; pp. 621604 - 621605 |
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| Autores principales: | , , |
| Formato: | Journal Article |
| Publicado: |
Wiley-Blackwell
2013
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104083235&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104083235 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 2013 vid: 2013 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 104083235 2012194674 NLM23878813 PMC3708382 104083235 ppf: 621604 ppct: 1 formats: fmt: @attributes: type: P tig: atl: Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and Mammalian phylogenomic data sets. aug: au: López-Giráldez, Francesc Moeller, Andrew H Townsend, Jeffrey P affil: Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA. sug: subj: Chromosome Mapping Methods Resource Databases Evolution Genetic Markers Genome Models, Biological Animals Computer Simulation Molecular Structure Fungi Mammals Sequence Analysis Methods ab: Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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