The impact of missing data on species tree estimation

Molecular Biology and Evolution

Volumn 33, Issue 3, 2016, Pages 838-860

  Xi, Zhenxiang ^a   Liu, Liang ^b   Davis, Charles C ^a  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

coalescent methods; concatenation methods; gene rate heterogeneity; incomplete lineage sorting; missing data; species tree estimation

Indexed keywords

EMPIRICISM; MAXIMUM LIKELIHOOD METHOD; PHYLOGENOMICS; SAMPLING; SPECIES; TAXON; COMPUTER SIMULATION; GENOMICS; INFORMATION PROCESSING; PHYLOGENY; PROCEDURES;

COMPUTER SIMULATION; DATASETS AS TOPIC; GENOMICS; PHYLOGENY;

EID: 84964555311     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv266     Document Type: Article

References (102)

1. Agnarsson I, May-Collado LJ. (2008). The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Mol Phylogenet Evol. 48: 964-985
2. Baum BR. (1992). Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41: 3-10
3. Bayzid MS, Warnow T. (2013). Naive binning improves phylogenomic analyses. Bioinformatics 29: 2277-2284
4. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. (2015). GenBank. Nucleic Acids Res. 43: D30-D35
5. Bevan RB, Lang BF, Bryant D. (2005). Calculating the evolutionary rates of different genes: A fast, accurate estimator with applications to maximum likelihood phylogenetic analysis. Syst Biol. 54: 900-915
6. Bryant D, Steel M. (2001). Constructing optimal trees from quartets. J Algorithms. 38: 237-259
7. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. (2009). TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973
8. Carling MD, Brumfield RT. (2008). Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics 178: 363-377
9. Cho S, ZwickA, Regier JC, Mitter C, Cummings MP, Yao JX, Du ZL, Zhao H, Kawahara AY, Weller S, et al. (2011). Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)'. Syst Biol 60: 782-796
10. Davis CC, Webb CO, Wurdack KJ, Jaramillo CA, Donoghue MJ. (2005). Explosive radiation of Malpighiales supports a mid-Cretaceous origin of modern tropical rain forests. Am Nat. 165: E36-E65
11. De Koning AP, Keeling PJ. (2006). The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biol. 4: 12
12. De la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, KatariMS, Coruzzi GM, DeSalle R. (2009). The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One 4: e5764
13. De Queiroz A, Gatesy J. (2007). The supermatrix approach to systematics. Trends Ecol Evol. 22: 34-41
14. Degnan JH, Rosenberg NA. (2006). Discordance of species trees with their most likely gene trees. PLoS Genet. 2: e68
15. Degnan JH, Rosenberg NA. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 24: 332-340
16. Driskell AC, Ane C, Burleigh JG, McMahon MM, O'Meara BC, Sanderson MJ. (2004). Prospects for building the tree of life from large sequence databases. Science 306: 1172-1174
17. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, et al. (2008). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749
18. Edgar RC. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797
19. Edwards EJ, Smith SA. (2010). Phylogenetic analyses reveal the shady history of C4 grasses. Proc Natl Acad Sci U S A. 107: 2532-2537
20. Edwards SV. (2009). Is a new and general theory of molecular systematics emerging'. Evolution 63: 1-19
21. Fulton TL, Strobeck C. (2006). Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Mol Phylogenet Evol. 41: 165-181
22. Gatesy J, Springer MS. (2014). Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol. 80: 231-266
23. Goremykin VV, Nikiforova SV, Biggs PJ, Zhong BJ, Delange P, Martin W, Woetzel S, Atherton RA, McLenachan PA, Lockhart PJ. (2013). The evolutionary root of flowering plants. Syst Biol. 62: 50-61
24. Goremykin VV, Viola R, Hellwig FH. (2009). Removal of noisy characters from chloroplast genome-scale data suggests revision of phylogenetic placements of Amborella and Ceratophyllum. J Mol Evol. 68: 197-204
25. Hartmann S, Vision TJ. (2008). Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment'. BMC Evol Biol 8: 95
26. Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñá J, Bailly X, Jondelius U, et al. (2009). Assessing the root of bilaterian animals with scalable phylogenomicmethods. Proc R Soc Lond B Biol Sci. 276: 4261-4270
27. Heled J, Drummond AJ. (2010). Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27: 570-580
28. Hovmeoller R, Knowles LL, Kubatko LS. (2013). Effects of missing data on species tree estimation under the coalescent. Mol Phylogenet Evol. 69: 1057-1062
29. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, et al. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331
30. Jiang W, Chen S-Y, Wang H, Li D-Z, Wiens JJ. (2014). Should genes with missing data be excluded from phylogenetic analyses'. Mol Phylogenet Evol 80: 308-318
31. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers J, McKain M, McNeal J, Rolf M, Ruzicka D, Wafula E, Wickett N, et al. (2012). A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13: R3
32. Jukes TH, Cantor CR. (1969). Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. p. 21-132
33. Katinka MD, Duprat S, Cornillot E, Méténier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, et al. (2001). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414: 450-453
34. Kjer KM, Carle FL, Litman J, Ware J. (2006). A molecular phylogeny of Hexapoda. Arthropod Syst Phylogeny. 64: 35-44
35. Kubatko LS, Carstens BC, Knowles LL. (2009). STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25: 971-973
36. Kupczok A, Schmidt HA, von Haeseler A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol Biol. 5: 37
37. Kvist S, Siddall ME. (2013). Phylogenomics of Annelida revisited: A cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data. Cladistics 29: 435-448
38. Leaché AD, Rannala B. (2011). The accuracy of species tree estimation under simulation: A comparison of methods. Syst Biol. 60: 126-137
39. 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
40. Lemmon EM, Lemmon AR. (2013). High-Throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst. 44: 99-121
41. Liu L. (2008). BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543
42. Liu L, Xi Z, Davis CC. (2015). Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting. Mol Biol Evol. 32: 791-805
43. Liu L, Xi Z, Wu S, Davis CC, Edwards SV. (2015). Estimating phylogenetic trees from genome-scale data. Ann N Y Acad Sci. 1360: 36-53
44. Liu L, Yu L. (2011). Estimating species trees from unrooted gene trees. Syst Biol. 60: 661-667
45. Liu L, Yu L. (2010). Phybase: An R package for species tree analysis. Bioinformatics 26: 962-963
46. Liu L, Yu L, Edwards SV. (2010). A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 10: 302
47. Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV. (2009). Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol. 53: 320-328
48. Liu L, Yu L, Pearl DK, Edwards SV. (2009). Estimating species phylogenies using coalescence times among sequences. Syst Biol. 58: 468-477
49. Maddison WP. (1997). Gene trees in species trees. Syst Biol. 46: 523-536
50. Mardis ER. (2013). Next-generation sequencing platforms. Annu Rev Anal Chem. 6: 287-303
51. McMahon MM, Sanderson MJ. (2006). Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst Biol. 55: 818-836
52. McNeal JR, Kuehl JV, Boore JL, De Pamphilis CW. (2007). Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol. 7: 57
53. Mirarab S, Bayzid MS, Warnow T 2014. Evaluating summary methods formulti-locus species tree estimation in the presence of incomplete lineage sorting. Syst Biol. doi: 10.1093/sysbio/syu063
54. Mirarab S, Reaz R, Bayzid MS, Zimmermann T, SwensonMS, Warnow T. (2014). ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30: i541-i548
55. Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, et al. (2014). Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol. 31: 793-803
56. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, Casane D. (2004). Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol. 21: 1740-1752
57. Pyron RA, Wiens JJ. (2011). A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol. 61: 543-583
58. RaganMA. (1992). Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1: 53-58
59. Rambaut A, Grassly NC. (1997). Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13: 235-238
60. Rannala B, Yang Z. (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656
61. Robinson DF, Foulds LR. (1981). Comparison of phylogenetic trees. Math Biosci. 53: 131-147
62. Roure B, Baurain D, Philippe H. (2013). Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 30: 197-214
63. Saitou N, Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4: 406-425
64. Sakharkar KR, Dhar PK, Chow VTK. (2004). Genome reduction in prokaryotic obligatory intracellular parasites of humans: A comparative analysis. Int J Syst Evol Microbiol. 54: 1937-1941
65. Salichos L, Rokas A. (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331
66. Sanderson MJ, McMahon MM, Steel M. (2010). Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10: 155
67. Sanderson MJ, McMahon MM, Steel M. (2011). Terraces in phylogenetic tree space. Science 333: 448-450
68. Seo T-K. (2008). Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol Biol Evol. 25: 960-971
69. Simmons MP. 2012a. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol Phylogenet Evol. 62: 472-484
70. Simmons MP. 2012b.Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 28: 208-222
71. Simmons MP. (2014). A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Mol Phylogenet Evol. 80: 267-280
72. Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ. (2011). Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot. 98: 404-414
73. Springer MS, Gatesy J. (2014). Land plant origins and coalescence confusion. Trends Plant Sci. 19: 267-269
74. Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-Analysis of large phylogenies. Bioinformatics 30: 1312-1313
75. Steel M, Sanderson MJ. (2010). Characterizing phylogenetically decisive taxon coverage. Appl Math Lett. 23: 82-86
76. Streicher JW, Schulte JA, Wiens JJ. (2015). How should genes and taxa be sampled for phylogenomic analyses with missing data'. An empirical study in iguanian lizards. Syst Biol. doi: 10.1093/sysbio/syv058
77. Swofford DL. (2002). PAUP: phylogenetic analysis using parsimony (and other methods) 4.0 beta. Sunderland (MA): Sinauer Associates
78. Thomson RC, Shaffer HB. (2010). Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst Biol. 59: 42-58
79. Thomson RC, Shedlock AM, Edwards SV, Shaffer HB. (2008). Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol. 49: 514-525
80. Tonini J, Moore A, Stern D, Shcheglovitova M, Ortí G. (2015). Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLoS Curr. doi: 10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be
81. Tsagkogeorga G, Parker J, Stupka E, Cotton JA, Rossiter SJ. (2013). Phylogenomic analyses elucidate the evolutionary relationships of bats. Curr Biol. 23: 2262-2267
82. Turner EH, Ng SB, Nickerson DA, Shendure J. (2009). Methods for genomic partitioning. Annu Rev Genomics Hum Genet. 10: 263-284
83. Waddell PJ. (2005). Measuring the fit of sequence data to phylogenetic model: Allowing for missing data. Mol Biol Evol. 22: 395-401
84. Whelan S, Goldman N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18: 691-699
85. Whitfield JB, Kjer KM. (2008). Ancient rapid radiations of insects: challenges for phylogenetic analysis. Annu Rev Entomol. 53: 449-472
86. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, et al. (2014). Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. 111: E4859-E4868
87. Wiens JJ. (2003). Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol. 52: 528-538
88. Wiens JJ. (2005). Can incomplete taxa rescue phylogenetic analyses from long-branch attraction'. Syst Biol 54: 731-742
89. Wiens JJ, Moen DS. (2008). Missing data and the accuracy of Bayesian phylogenetics. J Syst Evol. 46: 307-314
90. Wiens JJ, Morrill MC. (2011). Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst Biol. 60: 719-731
91. Wiens JJ, Tiu J. (2012). Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 7: e42925
92. William J, Ballard O. (1996). Combining data in phylogenetic analysis. Trends Ecol Evol. 11: 334
93. Wolfe KH, Morden CW, Palmer JD. (1992). Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci U S A. 89: 10648-10652
94. Wu Y. (2012). Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66: 763-775
95. Xi Z, Liu L, Rest JS, Davis CC. (2014). Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst Biol. 63: 919-932
96. Xi Z, Rest JS, Davis CC. (2013). Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One 8: e80870
97. Xi Z, Ruhfel BR, Schaefer H, Amorim AM, Sugumaran M, Wurdack KJ, Endress PK, Matthews ML, Stevens PF, Mathews S, et al. (2012). Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc Natl Acad Sci U S A. 109: 17519-17524
98. Xia X. (2014). Phylogenetic bias in the likelihood method caused by missing data coupled with among-site rate variation: An analytical approach. In: Basu M, Pan Y, Wang J, editors. Bioinformatics research and applications. New York: Springer Publishing Company. p. 12-23
99. Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, et al. (2014). Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89-92
100. Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ, Atherton RA, Nikiforova SV, Lockhart PJ. (2011). Systematic error in seed plant phylogenomics. Genome Biol Evol. 3: 1340-1348
101. Zhong B, Liu L, Penny D. (2014). The multispecies coalescent model and land plant origins: A reply to Springer and Gatesy. Trends Plant Sci. 19: 270-272
102. Zhou X, Xu S, Xu J, Chen B, Zhou K, Yang G. (2012). Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. Syst Biol. 61: 150-164