Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data

Systematic Biology

Volumn 60, Issue 5, 2011, Pages 719-731

  Wiens, John J ^a   Morrill, Matthew C ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIA; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; EVOLUTION; GENETICS; NOTE; PHYLOGENY; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; URODELA;

EID: 80052006478     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr025     Document Type: Note

References (56)

1. Alfaro M.E., Zoller S., Lutzoni F. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confdence. Mol. Biol. Evol. 20:255-266. (Pubitemid 36237384)
2. Anderson J.S. 2001. The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda). Syst. Biol. 50:170-193.
3. Bossuyt F., Brown R.M., Hillis D.M., Cannatella D.C., Milinkovitch M.C. 2006. Phylogeny and biogeography of a cosmopolitan frog radiation: Late Cretaceous diversifcation resulted in continent-scale endemism in the family Ranidae. Syst. Biol. 55:579-594.
4. Cobbett A., Wilkinson M., Wills M.A. 2007. Fossils impact as hard as living taxa in parsimony analyses of morphology. Syst. Biol. 56:753-766.
5. Donoghue M.J., Doyle J.A., Gauthier J., Kluge A.G., Rowe T. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20:431-460.
6. Dragoo J.W., Honeycutt R.L. 1997. Systematics of mustelid-like carnivores. J. Mammal. 78:426-443. (Pubitemid 29160337)
7. Driskell A.C., Ané C., Burleigh J.G., McMahon M.M., O'Meara B.C., Sanderson M.J. 2004. Prospects for building the Tree of Life from large sequence databases. Science. 306:1172-1174. (Pubitemid 39488993)
8. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confdence. PLoS Biol. 4:e88.
9. Dunn K.A., McEachran J.D., Honeycutt R.L. 2003. Molecular phyloge-netics of myliobatiform fshes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. Mol. Phylogenet. Evol. 27:259-270. (Pubitemid 36521970)
10. Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
11. Edwards S.V., Liu L., Pearl D.K. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 104:5936-5941. (Pubitemid 47175637)
12. Frost D.R., Grant T., Faivovich J., Bain R.H., Haas A., Haddad C.F.B., de Sá R.O., Channing A., Wilkinson M., Donnellan S.C., Raxworthy C.J., Campbell J.A., Blotto B.L., Moler P., Drewes R.C., Nussbaum R.A., Lynch J.D., Green D.M., Wheeler W.C. 2006. The amphibian tree of life. Bull. Am. Mus. Nat. Hist. 297:1-370. (Pubitemid 44348578)
13. Gouveia-Oliveira R., Sackett P.W., Pedersen A.G. 2007. MaxAlign: maximizing usable data in an alignment. BMC Bioinformatics. 8:312.
14. Hartmann S., Vision T.J. 2008. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol. Biol. 8:95.
15. Hua X., Fu C., Li J., Nieto-Montes de Oca A., Wiens J.J. 2009. A revised phylogeny of Holarctic treefrogs (genus Hyla) based on nuclear and mitochondrial DNA sequences. Herpetologica. 65:246-259.
16. Huelsenbeck J.P. 1991. When are fossils better than extant taxa in phy-logenetic analysis? Syst. Zool. 40:458-469.
17. Huelsenbeck J.P. 1995. The performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
18. Huelsenbeck J.P., Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics. 17:754-755.
19. Huelsenbeck J.P., Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities. Syst. Biol. 53:904-913.
20. Kearney M. 2002. Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions. Syst. Biol. 51:369-381. (Pubitemid 35180714)
21. Kozak K.H., Mendyk R.W., Wiens J.J. 2009. Can parallel diversifca-tion occur in sympatry? Repeated patterns of body-size evolution in co-existing clades of North American salamanders. Evolution. 63:1769-1784.
22. Lemmon A.R., Brown J.M., Stanger-Hall K., Moriarty-Lemmon E. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 58:130-145.
23. Lewis P.O., Holder M.T., Holsinger K.E. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253 (Pubitemid 40707806)
24. Lynch V.J., Wagner G.P. 2010. Did egg-laying boas break Dollo Law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae). Evolution. 64:207-216.
25. Manos P.S., Soltis P.S., Soltis D.E., Manchester S.R., Oh S.-H., Bell C.D., Dilcher D.L., Stone D.E. 2007. Phylogeny of extant and extinct Jug-landaceae inferred from the integration of molecular and morphological data sets. Syst. Biol. 56:412-430.
26. Mueller R.L., Macey J.R., Jaekel M., Wake D.B., Boore J.L. 2004. Morphological homoplasy, life history evolution, and historical bio-geography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc. Natl. Acad. Sci. U.S.A. 101:13820-13825. (Pubitemid 39298491)
27. Novacek M.J. 1992. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Syst. Biol. 41:58-73.
28. Parra-Olea G., Wake D.B. 2001. Extreme morphological and ecological homoplasy in tropical salamanders. Proc. Natl. Acad. Sci. U.S.A. 98:7888-7891. (Pubitemid 32642657)
29. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W.H., Casane D. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21:1740-1752. (Pubitemid 39096890)
30. Platnick N.I., Griswold C.E., Coddington J.A. 1991. On missing entries in cladistic analysis. Cladistics. 7:337-343.
31. Poe S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol. 52:423-428. (Pubitemid 36844329)
32. Pyron R.A., Burbrink F.T., Colli G.R., Nieto Montes de Oca A., Vitt L.J., Kuczynski C.A., Wiens J.J. 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol. Phylogenet. Evol. 58:329-342.
33. Rannala B., Huelsenbeck J.P., Yang Z., Nielsen R. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710. (Pubitemid 128370907)
34. Sanderson M.J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109. (Pubitemid 34008052)
35. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688-2690. (Pubitemid 44642609)
36. Stanger-Hall K.F., Lloyd J.E., Hillis D.M. 2007. Phylogeny of North American frefies (Coleoptera: Lampyridae): implications for the evolution of light signals. Mol. Phylogenet. Evol. 45:33-49. (Pubitemid 47380415)
37. Thomson R.C., Shaffer H.B. 2010. Sparse supermatrices for phyloge-netic inference: Taxonomy, alignment, rogue taxa, and the phy-logeny of living turtles. Syst. Biol. 59:42-58
38. Wiens J.J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640. (Pubitemid 128370902)
39. Wiens J.J. 2003a. Incomplete taxa, incomplete characters, and phyloge-netic accuracy: what is the missing data problem? J. Vertebr. Pale-ontol. 23:297-310.
40. Wiens J.J. 2003b. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538. (Pubitemid 36990380)
41. Wiens J.J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. 54:731-742. (Pubitemid 43142293)
42. Wiens, J.J. 2006. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 39:34-42. (Pubitemid 43138915)
43. Wiens J.J. 2007. Global patterns of species richness and diversifcation in amphibians. Am. Nat. 170:S86-S106. (Pubitemid 47221675)
44. Wiens J.J. 2009. Paleontology, genomics, and combined-data phyloge-netics: can molecular data improve phylogeny estimation for fossil taxa? Syst. Biol. 58:87-99.
45. Wiens J.J., Fetzner J.W., Parkinson C.L., Reeder T.W. 2005. Hylid frog phylogeny and sampling strategies for speciose clades. Syst. Biol. 54:719-748. (Pubitemid 43142292)
46. Wiens J.J., Kuczynski C.A., Arif S., Reeder T.W. 2010. Phylogenetic relationships of phrynosomatid lizards based on nuclear and mi-tochondrial data, and a revised phylogeny for Sceloporus. Mol. Phylogenet. Evol. 54:150-161.
47. Wiens J.J., Kuczynski C., Duellman W.E., Reeder T.W. 2007. Loss and re-evolution of complex life cycles in marsupial frogs: can ancestral trait reconstruction mislead? Evolution 61:1886-1899. (Pubitemid 47220939)
48. Wiens J.J., Kuczynski C.A., Smith S.A., Mulcahy D.G., Sites J.W., Townsend T.M., Reeder T.W. 2008. Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst. Biol. 57:420-431. (Pubitemid 351882203)
49. Wiens J.J., Kuczynski C.A., Stephens P.R. 2010. Discordant mito-chondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation. Biol. J. Linn. Soc. 99: 445-461.
50. Wiens J.J., Kuczynski C.A., Townsend T., Reeder T.W., Mulcahy D.G., Sites J.W. Jr. 2010. Combining phylogenomics and fossils in higher level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Syst. Biol. 59:674-688.
51. Wiens J.J., Moen D.S. 2008. Missing data and the accuracy of Bayesian phylogenetics. J. Syst. Evol. 46:307-314.
52. Wiens J.J., Parra-Olea G., Garcia-Paris M., Wake D.B. 2007. Phyloge-netic history underlies elevational patterns of biodiversity in tropical salamanders. Proc. R. Soc. Lond. B 274:919-928. (Pubitemid 47056741)
53. Wiens J.J., Reeder T.W. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558. (Pubitemid 126021228)
54. Wiens J.J., Sukumaran J., Pyron R.A., Brown R.M. 2009. Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae). Evolution 63:1217-1231.
55. Wilcox T.P., Zwickl D.J., Heath T.A., Hillis D.M. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371. (Pubitemid 35343620)
56. Wilkinson M. 1995. Coping with abundant missing entries in phyloge-netic inference using parsimony. Syst. Biol. 44:501-514. (Pubitemid 126021225)