The DOI matches its Crossref record; 82 of the 82 references it cites were found in a registry or an index.
Model selection may not be a mandatory step for phylogeny reconstruction
Open accessAbstract
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection.
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Cites
A new look at the statistical model identification
Akaike, H. (1974) · IEEE Transactions on Automatic Control · doi:10.1109/tac.1974.1100705 · Cited by 51,879
Estimating the Dimension of a Model
Schwarz, G. (1978) · The Annals of Statistics · doi:10.1214/aos/1176344136 · Cited by 47,033
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,647
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,806
jModelTest 2: more models, new heuristics and parallel computing
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012) · Nature Methods · doi:10.1038/nmeth.2109 · Cited by 16,785
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
(1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,229
Cited by
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
Darriba, D., Posada, D., Kozlov, A. M., Stamatakis, A., Morel, B., & Flouri, T. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz189 · Cited by 2,105
Incongruence in the phylogenomics era
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 259
Catanach, T. A., Halley, M. R., & Pirro, S. (2025) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blae028 · Cited by 76
Duchêne, D. A., Tong, K. J., Foster, C. S. P., Duchêne, S., Lanfear, R., & Ho, S. Y. W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz291 · Cited by 53
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome
Whelan, F. J., Hall, R. J., & McInerney, J. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab139 · Cited by 46
Metadata
- Authors
- Abadi, S., Azouri, D., Pupko, T., & Mayrose, I.
- Venue
- Nature Communications
- Published
- 2019-02-25
- Volume
- 10
- Issue
- 1
- Pages
- 934-934
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2915395120
- Cited by
- 406
- References
- 82
- FWCI
- 14.54
- Type
- journal article
- Language
- en
- Open access
- gold
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- Abadi, S., Azouri, D., Pupko, T., & Mayrose, I. (2019). Model selection may not be a mandatory step for phylogeny reconstruction. Nature Communications. https://doi.org/10.1038/s41467-019-08822-w
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