Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice

Genome Biology and Evolution

Volumn 5, Issue 4, 2013, Pages 681-687

  Grievink, Liat Shavit ^a   Penny, David ^b   Holland, Barbara R ^c  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b MASSEY UNIVERSITY   (New Zealand)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

Influential sites; Maximum likelihood; Mesostigma; Missing data; Site likelihood; Taxon sampling

Indexed keywords

MESOSTIGMA;

EID: 84876517039     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt032     Document Type: Article

References (23)

1. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
2. Allison PD. 2002. Missing data. Los Angeles (CA): Sage.
3. Bar-Hen A, Mariadassou M, Poursat MA, Vandenkoornhuyse P. 2008. Influence function for robust phylogenetic reconstruction. Mol Biol Evol. 25:869-873.
4. Cocquyt E, et al. 2009. Gain and loss of elongation factor genes in green algae. BMC Evol Biol. 9:39.
5. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:401-410.
6. Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH. 2005. Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol. 22:1813-1822.
7. Goremykin VV, Nikiforova SV, Bininda-Emonds OR. 2010. Automated removal of noisy data in phylogenomic analyses. J Mol Evol. 71: 319-331.
8. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
9. Hendy MD, Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst Zool. 38:297-309.
10. Huelsenbeck JP. 1991. When are fossils better than extant taxa in phylogenetic analysis? Syst Zool. 40:458-469.
11. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.
12. Lockhart P, et al. 2006. Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol. 23:40-45.
13. Philippe H. 2000. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci. 267:1213-1221.
14. Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol. 5:50.
15. Rodríguez-Ezpeleta N, Philippe H, Brinkmann H, Becker B, Melkonian M. 2007. Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta. Mol Biol Evol. 24:723-731.
16. Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ. 2007. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans. Mol Biol Evol. 24:54-62.
17. Roure B, Baurain D, Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic datasets. Mol Biol Evol. 30:197-214.
18. Schliep KP. 2010. phangorn: phylogenetic analysis in R. Bioinformatics 27: 592-593.
19. Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492-508.
20. Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
21. Turmel M, Otis C, Lemieux C. 2002. The complete mitochondrial DNA sequence of Mesostigma viride. Mol Biol Evol. 19:24-38.
22. Wiens JJ, Morrill MC. 2011. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst Biol. 60: 719-731.
23. Wiens JJ, Tiu J. 2012. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 7:e42925.