Phylogenomics with incomplete taxon coverage: The limits to inference

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Sanderson, Michael J ^a   McMahon, Michelle M ^b   Steel, Mike ^c  

^a University of Arizona   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; GENOMICS; PHYLOGENETICS; TAXONOMY; THEORETICAL STUDY;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; DATA MINING; DNA SEQUENCE; GENE LIBRARY; GENETIC DATABASE; GENOMICS; METHODOLOGY; PHYLOGENY;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; GENOMIC LIBRARY; GENOMICS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 77952490857     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-155     Document Type: Article

References (57)

1. Homoplasy increases phylogenetic structure. M Kallersjo VA Albert JS Farris, Cladistics 1999 15 1 91 93
2. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. MM McMahon MJ Sanderson, Syst Biol 2006 55 818 836 10.1080/10635150600999150 17060202
3. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. SA Smith JM Beaulieu MJ Donoghue, BMC Evolutionary Biology 2009 9 37 10.1186/1471-2148-9-37 19210768
4. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. PA Goloboff SA Catalano JM Mirande CA Szumik JS Arias M Kallersjo JS Farris, Cladistics 2009 25 3 211 230 10.1111/j.1096-0031.2009.00255.x
5. Genome-scale approaches to resolving incongruence in molecular phylogenies. A Rokas B Williams N King S Carroll, Nature 2003 425 798 804 10.1038/nature02053 14574403
6. Prospects for building the tree of life from large sequence databases. AC Driskell C Ané JG Burleigh MM McMahon B O'Meara MJ Sanderson, Science (Washington D C) 2004 306 1172 1174 10.1126/science.1102036 (Pubitemid 39488993)
7. Genomics, biogeography, and the diversification of placental mammals. D Wildman M Uddin J Opazo G Liu V Lefort S Guindon O Gascuel L Grossman R Romero M Goodman, Proceedings of the National Academy of Sciences 2007 104 36 14395 14400 10.1073/pnas.0704342104 (Pubitemid 350003272)
8. Broad phylogenomic sampling improves resolution of the animal tree of life. CW Dunn A Hejnol DQ Matus K Pang WE Browne SA Smith E Seaver GW Rouse M Obst GD Edgecombe, et al. Nature 2008 452 7188 745 U745 10.1038/nature06614 18322464
9. Analysis of 142 genes resolves the rapid diversification of the rice genus. XH Zou FM Zhang JG Zhang LL Zang L Tang J Wang T Sang S Ge, Genome Biology 2008 9 3 10.1186/gb-2008-9-3-r49 18315873
10. Assessing the root of bilaterian animals with scalable phylogenomic methods. A Hejnol M Obst A Stamatakis M Ott GW Rouse GD Edgecombe P Martinez J Baguna X Bailly U Jondelius, et al. Proceedings of the Royal Society B-Biological Sciences 2009 276 1677 4261 4270 10.1098/rspb.2009.0896
11. Phylogenomic analysis from deep BAC-end sequence libraries in rice. KA Cranston B Hurwitz MJ Sanderson D Ware RA Wing L Stein, Syst Bot 2010
12. Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures. A Stamatakis M Ott, Philosophical Transactions of the Royal Society B-Biological Sciences 2008 363 1512 3977 3984 10.1098/rstb.2008.0163
13. Dealing with incongruence in phylogenomic analyses. N Galtier V Daubin, Philosophical Transactions of the Royal Society B-Biological Sciences 2008 363 1512 4023 4029 10.1098/rstb.2008.0144
14. Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. DA Pollard VN Iyer AM Moses MB Eisen, Plos Genetics 2006 2 10 1634 1647
15. Species Trees from Highly Incongruent Gene Trees in Rice. KA Cranston B Hurwitz D Ware L Stein RA Wing, Syst Biol 2009 58 5 489 500 10.1093/sysbio/ syp054 20525603
16. Fine-Scale Phylogenetic Discordance across the House Mouse Genome. MA White C Ane CN Dewey BR Larget BA Payseur, Plos Genetics 2009 5 11 10.1371/journal.pgen.1000729 19936022
17. Mapping human genetic ancestry. I Ebersberger P Galgoczy S Taudien S Taenzer M Platzer A von Haeseler, Mol Biol Evol 2007 24 10 2266 2276 10.1093/molbev/msm156 17660505
18. Inconsistency of phylogenetic estimates from concatenated data under coalescence. LS Kubatko JH Degnan, Syst Biol 2007 56 1 17 24 10.1080/10635150601146041 17366134
19. Maximum tree: a consistent estimator of the species tree. L Liu LL Yu DK Pearl, Journal of Mathematical Biology 2010 60 1 95 106 10.1007/s00285-009-0260- 0 19283383
20. A likelihood look at the supermatrix-supertree controversy. FR Ren H Tanaka ZH Yang, Gene 2009 441 1-2 119-125 18502054
21. Phylogenetic inference using whole Genomes. B Rannala ZH Yang, Annual Review of Genomics and Human Genetics 2008 9 217 231 10.1146/annurev.genom.9. 081307.164407 18767964
22. Is a new and general theory of phylogenetic inference emerging? SV Edwards, Evolution 2009 63 1 1 19 10.1111/j.1558-5646.2008.00549.x 19146594
23. Gene tree discordance, phylogenetic inference and the multispecies coalescent. JH Degnan NA Rosenberg, Trends Ecol Evol 2009 24 6 332 340 10.1016/j.tree.2009.01.009 19307040
24. Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes. LL Knowles, Syst Biol 2009 58 5 463 467 10.1093/sysbio/syp061 20525600
25. The evolution of supertrees. ORP Bininda-Emonds, Trends Ecol Evol 2004 19 6 315 322 10.1016/j.tree.2004.03.015 16701277
26. Inferring phylogeny despite incomplete lineage sorting. WP Maddison LL Knowles, Syst Biol 2006 55 1 21 30 10.1080/10635150500354928 16507521
27. High-resolution species trees without concatenation. SV Edwards L Liu DK Pearl, Proc Natl Acad Sci USA 2007 104 14 5936 5941 10.1073/pnas.0607004104 17392434
28. Phylogenomics of primates and their ancestral populations. A Siepel, Genome Res 2009 19 11 1929 1941 10.1101/gr.084228.108 19801602
29. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. LS Kubatko, Syst Biol 2009 58 5 478 488 10.1093/sysbio/syp055 20525602
30. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. C Meng LS Kubatko, Theoretical Population Biology 2009 75 1 35 45 10.1016/j.tpb.2008.10.004 19038278
31. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. MJ Sanderson AC Driskell RH Ree O Eulenstein S Langley, Mol Biol Evol 2003 20 1036 1042 10.1093/molbev/msg115 12777519
32. Gene family evolution across 12 Drosophila genomes. MW Hahn MV Han SG Han, Plos Genetics 2007 3 11 2135 2146 10.1371/journal.pgen.0030197 (Pubitemid 350291574)
33. Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. C Soderlund A Descour D Kudrna M Bomhoff L Boyd J Currie A Angelova K Collura M Wissotski E Ashley, et al. Plos Genetics 2009 5 11 10.1371/journal.pgen.1000740 19936069
34. The Importance of Fossils in Phylogeny Reconstruction. MJ Donoghue JA Doyle J Gauthier AG Kluge T Rowe, Annual Review of Ecology and Systematics 1989 20 431 460 10.1146/annurev.es.20.110189.002243
35. When are fossils better than extant taxa in phylogenetic analysis? JP Huelsenbeck, Syst Zool 1991 40 4 458 469 10.2307/2992240
36. Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions. M Kearney, Syst Biol 2002 51 2 369 381 10.1080/10635150252899824 12028738
37. Missing data, incomplete taxa, and phylogenetic accuracy. JJ Wiens, Syst Biol 2003 52 4 528 538 10.1080/10635150390218330 12857643
38. Phylogenomics of eukaryotes: Impact of missing data on large alignments. H Philippe E Snell E Bapteste P Lopez P Holland D Casane, Mol Biol Evol 2004 21 1740 1752 10.1093/molbev/msh182 15175415
39. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? S Hartmann TJ Vision, BMC Evolutionary Biology 2008 8 95 10.1186/1471-2148-8-95 18366758
40. The Use and Validity of Composite Taxa in Phylogenetic Analysis. V Campbell FJ Lapointe, Syst Biol 2009 58 6 560 572 10.1093/sysbio/syp056 20525609
41. The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference. AR Lemmon JM Brown K Stanger-Hall EM Lemmon, Syst Biol 2009 58 1 130 145 10.1093/sysbio/syp017 20525573
42. Phylogenomics. H Philippe F Delsuc H Brinkmann N Lartillot, Annual Review of Ecology Evolution and Systematics 2005 36 541 562 10.1146/annurev.ecolsys. 35.112202.130205 (Pubitemid 43068870)
43. The supermatrix approach to systematics. A de Queiroz J Gatesy, Trends Ecol Evol 2007 22 1 34 41 10.1016/j.tree.2006.10.002 17046100
44. Characterizing phylogenetically decisive taxon coverage. M Steel MJ Sanderson, Applied Mathematics Letters 2010 23 1 82 86 10.1016/j.aml.2009.08.009
45. Homoplasy and the choice among cladograms. PA Goloboff, Cladistics-the International Journal of the Willi Hennig Society 1991 7 3 215 232 10.1111/j.1096-0031.1991.tb00035.x
46. Phylogenetics. C Semple M Steel, New York: Oxford University Press 2003
47. The complexity of reconstructing trees from qualitative characters and subtrees. M Steel, J Classif 1992 9 91 116 10.1007/BF02618470
48. Combinatorial aspects of leaf-labelled trees. PJ Humphries, Christchurch, New Zealand: University of Canterbury 2008
49. Algorithmic aspects of tree amalgamation. S Böcker D Bryant AWM Dress MA Steel, J Algorithms 2000 37 2 522 537 10.1006/jagm.2000.1116
50. Extension operations on sets of leaf-labelled trees. D Bryant M Steel, Advances in Applied Mathematics 1995 16 4 425 453 10.1006/aama.1995.1020
51. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). DL Swofford, Sunderland, MA: Sinauer 4 2002 12504223
52. The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research. MJ Sanderson D Boss D Chen KA Cranston A Wehe, Syst Biol 2008 57 335 346 10.1080/10635150802158688 18570030
53. Missing data and the design of phylogenetic analyses. JJ Wiens, Journal of Biomedical Informatics 2006 39 1 34 42 10.1016/j.jbi.2005.04.001 15922672
54. Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics. JG Gibbons EM Janson CT Hittinger M Johnston P Abbot A Rokas, Mol Biol Evol 2009 26 12 2731 2744 10.1093/molbev/msp188 19706727
55. The 1kp Project. http://www.onekp.com/essential.html
56. Groves of phylogenetic trees. C Ane O Eulenstein R Piaggio-Talice MJ Sanderson, Annals of Combinatorics 2009 13 139 167 10.1007/s00026-009-0017-x
57. Fragmentation of large data sets in phylogenetic analysis. MJ Sanderson C Ane O Eulenstein D Fernandez-Baca J Kim MM McMahon R Piaggio-Talice, Reconstructing evolution: new mathematical and computational advances Oxford: Oxford University Press, Gascuel O, Steel M, 2007