Phylogenetic bias in the likelihood method caused by missing data coupled with among-site rate variation: An analytical approach

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8492 LNBI, Issue , 2014, Pages 12-23

  Xia, Xuhua ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

likelihood; missing data; phylogenetic bias; pruning algorithm; supermatrix

Indexed keywords

FORESTRY;

LIKELIHOOD; MISSING DATA; PHYLOGENETIC BIAS; PRUNING ALGORITHMS; SUPERMATRIX;

BIOINFORMATICS;

ALGORITHMS; DATA PROCESSING; FORESTRY; GENETICS; INFORMATION RETRIEVAL;

EID: 84958535882     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-08171-7_2     Document Type: Conference Paper

References (29)

1. Hackett, S.J., Kimball, R.T., Reddy, S., Bowie, R.C., Braun, E.L., Braun, M.J., Chojnowski, J.L., Cox, W.A., Han, K.L., Harshman, J., Huddleston, C.J., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Yuri, T.: A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768 (2008)
2. Perelman, P., Johnson, W.E., Roos, C., Seuanez, H.N., Horvath, J.E., Moreira, M.A., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., Schneider, M.P., Silva, A., OBrien, S.J., Pecon-Slattery, J.: A molecular phylogeny of living primates. PLoS Genet. 7, e1001342 (2011)
3. Regier, J.C., Shultz, J.W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J.W., Cunningham, C.W.: Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463, 1079-1083 (2010)
4. Regier, J.C., Shultz, J.W., Ganley, A.R., Hussey, A., Shi, D., Ball, B., Zwick, A., Stajich, J.E., Cummings, M.P., Martin, J.W., Cunningham, C.W.: Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst. Biol. 57, 920-938 (2008)
5. Sanderson, M.J., Ane, C., Eulenstein, O., Fernandez-Baca, D., Kim, J., McMahon, M.M., Piaggio-Talice, R.: Fragmentation of large data sets in phylogenetic analysis. In: Gascuel, O., Steel, M. (eds.) Reconstructing Evolution: New Mathematical and Computational Advances, pp. 199-216. Oxford University Press, Oxford (2007)
6. Wiens, J.J., Tiu, J.: Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 7, e42925 (2012)
7. Lemmon, A.R., Brown, J.M., Stanger-Hall, K., Lemmon, E.M.: The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 58, 130-145 (2009)
8. Wiens, J.J.: Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52, 528-538 (2003)
9. Roure, B., Baurain, D., Philippe, H.: Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets. Mol. Biol. Evol. 30, 197-214 (2013)
10. Rubin, B.E., Ree, R.H., Moreau, C.S.: Inferring phylogenies from RAD sequence data. PLoS One 7, e33394 (2012)
11. Cho, S., Zwick, A., Regier, J.C., Mitter, C., Cummings, M.P., Yao, J., Du, Z., Zhao, H., Kawahara, A.Y., Weller, S., Davis, D.R., Baixeras, J., Brown, J.W., Parr, C.: Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)? Syst. Biol. 60, 782-796 (2011)
12. Felsenstein, J.: Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22, 240-249 (1973)
13. Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376 (1981)
14. Felsenstein, J.: Inferring phylogenies. Sinauer, Sunderland (2004)
15. Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, pp. 21-123. Academic Press, New York (1969)
16. Kishino, H., Hasegawa, M.: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179 (1989)
17. Yang, Z.: Computational molecular evolution. Oxford University Press, Oxford (2006)
18. Shimodaira, H., Hasegawa, M.: Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference. Mol. Biol. Evol. 16, 1114-1116 (1999)
19. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468 (1994)
20. Xia, X., Lemey, P.: Assessing substitution saturation with DAMBE. In: Lemey, P., Salemi, M., Vandamme, A.M. (eds.) The Phylogenetic Handbook, pp. 615-630. Cambridge University Press, Cambridge (2009)
21. Xia, X.H., Xie, Z., Salemi, M., Chen, L., Wang, Y.: An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26, 1-7 (2003)
22. Van de Peer, Y., Neefs, J.M., De Rijk, P., De Wachter, R.: Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J. Mol. Evol. 37, 221-232 (1993)
23. Xia, X.H., Xie, Z., Kjer, K.M.: 18S ribosomal RNA and tetrapod phylogeny. Syst. Biol. 52, 283-295 (2003)
24. Xia, X., Hafner, M.S., Sudman, P.D.: On transition bias in mitochondrial genes of pocket gophers. J. Mol. Evol. 43, 32-40 (1996)
25. Xia, X.: The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. Mol. Biol. Evol. 15, 336-344 (1998)
26. Marin, A., Xia, X.: GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand bias. J. Theor. Biol. 253, 508-513 (2008)
27. Xia, X.: DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Current Genomics 13, 16-27 (2012)
28. Xia, X.: DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. Mol. Biol. Evol. 30, 1720-1728 (2013)
29. Siddall, M.E.: Success of Parsimony in the Four-Taxon Case: Long-Branch Repulsion by Likelihood in the Farris Zone. Cladistics 14, 209-220 (1998)