The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise
Phylogenetic inference can be improved by the development and use of better models for inference given the data available, or by gathering more appropriate data given the potential inferences to be made. Numerous studies have demonstrated the crucial importance of selecting a best-fit model to condu...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-04-01
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| Series: | Frontiers in Ecology and Evolution |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fevo.2014.00011/full |
| _version_ | 1819053361188569088 |
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| author | Zhuo eSu Zheng eWang Zheng eWang Francesc eLopez-Giraldez Francesc eLopez-Giraldez Jeffrey Peter Townsend Jeffrey Peter Townsend Jeffrey Peter Townsend |
| author_facet | Zhuo eSu Zheng eWang Zheng eWang Francesc eLopez-Giraldez Francesc eLopez-Giraldez Jeffrey Peter Townsend Jeffrey Peter Townsend Jeffrey Peter Townsend |
| author_sort | Zhuo eSu |
| collection | DOAJ |
| description | Phylogenetic inference can be improved by the development and use of better models for inference given the data available, or by gathering more appropriate data given the potential inferences to be made. Numerous studies have demonstrated the crucial importance of selecting a best-fit model to conducting accurate phylogenetic inference given a data set, explicitly revealing how model choice affects the results of phylogenetic inferences. However, the importance of specifying a correct model of evolution for predictions of the best data to be gathered has never been examined. Here, we extend analyses of phylogenetic signal and noise that predict the potential to resolve nodes in a phylogeny to incorporate all time-reversible Markov models of nucleotide substitution. Extending previous results on the canonical four-taxon tree, our theory yields an analytical method that uses estimates of the rates of evolution and the model of molecular evolution to predict the distribution of signal, noise, and polytomy. We applied our methods to a study of 29 taxa of the yeast genus Candida and allied members to predict the power of five markers, COX2, ACT1, RPB1, RPB2, and D1/D2 LSU, to resolve a poorly supported backbone node corresponding to a clade of haploid Candida species, as well as nineteen other nodes that are reasonably short and at least moderately deep in the consensus tree. The use of simple, unrealistic models that did not take into account transition/transversion rate differences led to some discrepancies in predictions, but overall our results demonstrate that predictions of signal and noise in phylogenetics are fairly robust to model specification. |
| first_indexed | 2024-12-21T12:34:30Z |
| format | Article |
| id | doaj.art-76a5b3aec76b4755b10b0b7e52cb773c |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-21T12:34:30Z |
| publishDate | 2014-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-76a5b3aec76b4755b10b0b7e52cb773c2022-12-21T19:03:57ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2014-04-01210.3389/fevo.2014.0001183025The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noiseZhuo eSu0Zheng eWang1Zheng eWang2Francesc eLopez-Giraldez3Francesc eLopez-Giraldez4Jeffrey Peter Townsend5Jeffrey Peter Townsend6Jeffrey Peter Townsend7Yale UniversityYale UniversityYale UniversityYale UniversityYale UniversityYale UniversityYale UniversityYale UniversityPhylogenetic inference can be improved by the development and use of better models for inference given the data available, or by gathering more appropriate data given the potential inferences to be made. Numerous studies have demonstrated the crucial importance of selecting a best-fit model to conducting accurate phylogenetic inference given a data set, explicitly revealing how model choice affects the results of phylogenetic inferences. However, the importance of specifying a correct model of evolution for predictions of the best data to be gathered has never been examined. Here, we extend analyses of phylogenetic signal and noise that predict the potential to resolve nodes in a phylogeny to incorporate all time-reversible Markov models of nucleotide substitution. Extending previous results on the canonical four-taxon tree, our theory yields an analytical method that uses estimates of the rates of evolution and the model of molecular evolution to predict the distribution of signal, noise, and polytomy. We applied our methods to a study of 29 taxa of the yeast genus Candida and allied members to predict the power of five markers, COX2, ACT1, RPB1, RPB2, and D1/D2 LSU, to resolve a poorly supported backbone node corresponding to a clade of haploid Candida species, as well as nineteen other nodes that are reasonably short and at least moderately deep in the consensus tree. The use of simple, unrealistic models that did not take into account transition/transversion rate differences led to some discrepancies in predictions, but overall our results demonstrate that predictions of signal and noise in phylogenetics are fairly robust to model specification.http://journal.frontiersin.org/Journal/10.3389/fevo.2014.00011/fullNoiseBayesian inferenceModel selectionphylogenetic analysismaximum likelihoodPhylogenetic informativeness |
| spellingShingle | Zhuo eSu Zheng eWang Zheng eWang Francesc eLopez-Giraldez Francesc eLopez-Giraldez Jeffrey Peter Townsend Jeffrey Peter Townsend Jeffrey Peter Townsend The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise Frontiers in Ecology and Evolution Noise Bayesian inference Model selection phylogenetic analysis maximum likelihood Phylogenetic informativeness |
| title | The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| title_full | The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| title_fullStr | The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| title_full_unstemmed | The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| title_short | The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| title_sort | impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise |
| topic | Noise Bayesian inference Model selection phylogenetic analysis maximum likelihood Phylogenetic informativeness |
| url | http://journal.frontiersin.org/Journal/10.3389/fevo.2014.00011/full |
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