ModelFinder: fast model selection for accurate phylogenetic estimates

Abstract

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.

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Figure 1: ModelFinder obtains accurate phylogenetic estimates.
Figure 2: Advantages provided by ModelFinder.

References

  1. 1

    Eisen, J.A. Genome Res. 8, 163–167 (1998).

  2. 2

    Hardy, M.P., Owczarek, C.M., Jermiin, L.S., Ejdebäck, M. & Hertzog, P.J. Genomics 84, 331–345 (2004).

  3. 3

    dos Reis, M. et al. Proc. R. Soc. B 279, 3491–3500 (2012).

  4. 4

    Prum, R.O. et al. Nature 526, 569–573 (2015).

  5. 5

    Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E. & Burleigh, J.G. BMC Evol. Biol. 14, 23 (2014).

  6. 6

    Salichos, L. & Rokas, A. Nature 497, 327–331 (2013).

  7. 7

    Andersen, K.G. et al. Cell 162, 738–750 (2015).

  8. 8

    Tay, W.T. et al. Sci. Rep. 7, 45302 (2017).

  9. 9

    Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. Nat. Methods 9, 772 (2012).

  10. 10

    Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. Bioinformatics 27, 1164–1165 (2011).

  11. 11

    Lanfear, R., Calcott, B., Ho, S.Y.W. & Guindon, S. Mol. Biol. Evol. 29, 1695–1701 (2012).

  12. 12

    Yang, Z. J. Mol. Evol. 39, 306–314 (1994).

  13. 13

    Yang, Z. Genetics 139, 993–1005 (1995).

  14. 14

    Nguyen, L.-T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. Mol. Biol. Evol. 32, 268–274 (2015).

  15. 15

    Dempster, A.P., Laird, N.M. & Rubin, D.B. J. R. Stat. Soc. Series B Stat. Methodol. 39, 1–38 (1977).

  16. 16

    Fletcher, W. & Yang, Z. Mol. Biol. Evol. 26, 1879–1888 (2009).

  17. 17

    Le, S.Q. & Gascuel, O. Mol. Biol. Evol. 25, 1307–1320 (2008).

  18. 18

    Robinson, D.F. & Foulds, L.R. Math. Biosci. 53, 131–147 (1981).

  19. 19

    Wu, D. et al. Nature 462, 1056–1060 (2009).

  20. 20

    Kass, R.E. & Raftery, A.E. J. Am. Stat. Assoc. 90, 773–795 (1995).

  21. 21

    Sanderson, M.J., Donoghue, M.J., Piel, W. & Eriksson, T. Am. J. Bot. 81, 183 (1994).

  22. 22

    Jayaswal, V., Wong, T.K.F., Robinson, J., Poladian, L. & Jermiin, L.S. Syst. Biol. 63, 726–742 (2014).

  23. 23

    Posada, D. & Crandall, K.A. Bioinformatics 14, 817–818 (1998).

  24. 24

    Chiotis, M., Jermiin, L.S. & Crozier, R.H. Mol. Phylogenet. Evol. 17, 108–116 (2000).

  25. 25

    Abascal, F., Zardoya, R. & Posada, D. Bioinformatics 21, 2104–2105 (2005).

  26. 26

    Keane, T.M., Creevey, C.J., Pentony, M.M., Naughton, T.J. & Mclnerney, J.O. BMC Evol. Biol. 6, 29 (2006).

  27. 27

    Posada, D. Nucleic Acids Res. 34, W700–W703 (2006).

  28. 28

    Posada, D. Mol. Biol. Evol. 25, 1253–1256 (2008).

  29. 29

    Santorum, J.M., Darriba, D., Taboada, G.L. & Posada, D. Bioinformatics 30, 1310–1311 (2014).

  30. 30

    Whelan, S., Allen, J.E., Blackburne, B.P. & Talavera, D. Syst. Biol. 64, 42–55 (2015).

  31. 31

    Soubrier, J. et al. Mol. Biol. Evol. 29, 3345–3358 (2012).

  32. 32

    Fletcher, R. Practical Methods of Optimization 2nd edn (John Wiley & Sons, 2000).

  33. 33

    Guindon, S. et al. Syst. Biol. 59, 307–321 (2010).

  34. 34

    Guindon, S. Syst. Biol. 62, 22–34 (2013).

  35. 35

    Bouckaert, R. et al. PLoS Comp. Biol. 10, e1003537 (2014).

  36. 36

    Brent, R.P. Algorithms for Minimization without Derivatives (Prentice Hall, 1973).

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Acknowledgements

We thank D.Y. Wu, J.A. Eisen, P. Donoghue and A. Rokas for access to their data; E. Susko for discussions about the EM algorithm; and V. Jayaswal for constructive feedback. B.Q.M. and A.v.H. were supported by the Austrian Science Fund (FWF I-2805-B29).

Author information

S.K., T.K.F.W. and L.S.J. conceived the method and executed a pilot study to assess the method's likely impact on model selection. B.Q.M. and T.K.F.W. implemented the method in IQ-TREE with contributions from S.K., L.S.J. and A.v.H. S.K., T.K.F.W., L.S.J. and B.Q.M. assessed the performance and accuracy of the method. S.K., T.K.F.W. and L.S.J. carried out the analyses of simulated and real data. L.S.J., S.K., T.K.F.W., B.Q.M. and A.v.H. wrote the paper.

Correspondence to Lars S Jermiin.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Table 2 (PDF 298 kb)

Supplementary Table 1 (XLSX 54 kb)

Supplementary Software

IQ-TREE-1.4.2.tar.gz (ZIP 4685 kb)

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Kalyaanamoorthy, S., Minh, B., Wong, T. et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14, 587–589 (2017). https://doi.org/10.1038/nmeth.4285

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