Rooted triple consensus and anomalous gene trees

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Ewing, Gregory B ^a   Ebersberger, Ingo ^a   Schmidt, Heiko A ^a   Von Haeseler, Arndt ^a  

^a MAX F PERUTZ LABORATORIES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ANOMALOUS GENE TREE; ARTICLE; CONSENSUS; METAZOON; PHYLOGENY; SIMULATION; SPECIES DIFFERENCE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; METHODOLOGY; MOLECULAR EVOLUTION; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

METAZOA;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 43549090646     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-118     Document Type: Article

References (50)

1. Statistical Inference of Phylogenies. J Felsenstein, J Royal Statist Soc A 1983 146 246 272 10.2307/2981654
2. Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Y Kuroki A Toyoda H Noguchi TD Taylor T Itoh DS Kim DW Kim SH Choi IC Kim HH Choi YS Kim Y Satta N Saitou T Yamada S Morishita M Hattori Y Sakaki HS Park A Fujiyama, Nat Genet 2006 38 158 167 10.1038/ng1729 16388311
3. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Felsenstein, J Mol Evol 1981 17 368 376 10.1007/BF01734359 7288891
4. Evolution of protein molecules. TH Jukes CR Cantor, Evolution of protein molecules 1969 3 21 132
5. Genome-scale approaches to resolving incongruence in molecular phylogenies. A Rokas BL Williams N King SB Carroll, Nature 2003 425 798 804 10.1038/nature02053 14574403
6. Molecular Phylogenetics at the Felsenstein Zone: Approaching the Strepsiptera Problem Using 5.8S and 28S rDNA Sequences. UW Hwang W Kim D Tautz M Friedrich, Mol Phylogenet Evol 1998 9 470 480 10.1006/mpev.1998.0518 9667995
7. Is the Felsenstein Zone a Fly Trap. JP Huelsenbeck, Syst Biol 1997 46 69 74 10.2307/2413636 11975354
8. Information Content of Individual Genetic Sequences. TD Schneider, J Theor Biol 1997 189 427 441 10.1006/jtbi.1997.0540 9446751
9. Analysis of Information Content for Biological Sequences. J Zhang, J Comput Biol 2002 9 487 503 10.1089/106652702760138583 12162888
10. Synonymous Nucleotide Divergence: What Is "Saturation"? J Maynard Smith NH Smith, Genetics 1996 142 1033 1036 8849908
11. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Jc Avise JE Neigel J Arnold, J Mol Evol 1984 20 99 105 10.1007/BF02257369 6433037
12. Relationships between gene trees and species trees. P Pamilo M Nei, Mol Biol Evol 1988 5 568 583 3193878
13. Molecular Phylogeny of the Hominoids: Inferences from Multiple Independent DNA Sequence Data Sets. M Ruvolo, Mol Biol Evol 1997 14 248 265 9066793
14. Likelihood and Bayes Estimation of Ancestral Population Sizes in Hominoids Using Data From Multiple Loci. Z Yang, Genetics 2002 162 1811 1823 12524351
15. Chimpanzee Genome. I Ebersberger, Encyclopedia of Molecular Cell Biology and Molecular Medicine Wiley-vch, Robert A. Meyers, 2004 551 678 ISBN: 3-527-30544-0
16. Discordance of Species Trees with Their Most Likely Gene Trees. JH Degnan NA Rosenberg, PloS Genet 2006 2 762 769 10.1371/journal.pgen.0020068
17. Genetic evidence for complex speciation of humans and chimpanzees. N Patterson DJ Richter S Gnerre ES Lander D Reich, Nature 2006 441 1103 8 10.1038/nature04789 16710306
18. Mapping Human Genetic Ancestry. I Ebersberger P Galgoczy S Taudien S Taenzer M Platzer A von Haeseler, Mol Biol Evol 2007 24 1 10 10.1093/molbev/msm156 17043087
19. Numerical Methods for Inferring Evolutionary Trees. J Felsenstein, Q Rev Biol 1982 57 379 404 10.1086/412935
20. A classification of consensus methods for phylogenetics. D Bryant, A classification of consensus methods for phylogenetics 2003 55 66
21. On consensus, confidence, and "total evidence". RDM Page, Cladistics 1996 12 83 92
22. PHYLIP - Phylogeny Inference Package (Version 3.2). J Felsenstein, Cladistics 1989 5 164 166
23. Phylogenetic Trees from Large Datasets. HA Schmidt, PhD thesis 2003
24. Against Consensus. M Barrett MJ Donoghue E Sober, Syst Zool 1991 40 486 493 10.2307/2992242
25. Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right? J Gatesy RH Baker, Syst Biol 2005 54 483 492 10.1080/10635150590945368 16012113
26. The Probabilities fo Rooted Tree-Shapes Generated by Random Bifurcation. EF Harding, Adv Appl Prob 1971 3 44 77 10.2307/1426329
27. Probabilities of Evolutionary Trees. JKM Brown, Syst Biol 1994 43 78 91 10.2307/2413582
28. Evolutionary Relationship of DNA Sequences in Finite Populations. F Tajima, Genetics 1983 105 437 460 6628982
29. Gene genealogy and variance of interpopulational nucleotide differences. N Takahata M Nei, Genetics 1985 110 2 325 44 4007484
30. A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S. GU Yule, Phil Trans R Soc B 1924 213 21 87 10.1098/rstb.1925. 0002
31. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. DJ Aldous, Stat Sci 2001 16 23 34 10.1214/ss/998929474
32. Properties of phylogenetic trees generated by Yule-type speciation models. A McKenzie M Steel, Math Biosci 2001 170 91 112 10.1016/S0025-5564(00) 00061-4 11259805
33. Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence. LS Kubatko JH Degnan, Syst Biol 2007 56 17 24 10.1080/ 10635150601146041 17366134
34. Animal Evolution and the Molecular Signature of Radiations Compressed in Time. A Rokas D Kruger SB Carroll, Science 2005 310 1933 1938 10.1126/science.1116759 16373569
35. The Coalescent. JFC Kingman, Stoch Proc Appl 1982 13 235 248 10.1016/0304-4149(82)90011-4
36. On the genealogy of large populations. JFC Kingman, J Appl Prob 1982 19A 27 43 10.2307/3213548
37. Inferring Phylogeny Despite Incomplete Lineage Sorting. WP Maddison LL Knowles, Syst Biol 2006 55 21 30 10.1080/10635150500354928 16507521
38. Gene Trees in Species Trees. WP Maddison, Syst Biol 1997 46 523 536 10.2307/2413694
39. Multiple maternal origins of chickens: Out of the Asian jungles. YP Liu GS Wu YG Yao YW Miao G Luikart M Baig A Beja-Pereira ZL Ding MG Palanichamy YP Zhang, Mol Phylogenet Evol 2006 38 12 19 10.1016/j.ympev.2005.09.014 16275023
40. High-resolution species trees without concatenation. SV Edwards L Liu DK Pearl, Proc Natl Acad Sci 2007 104 5936 41 17392434 10.1073/pnas.0607004104
41. Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers. BC Carstens LL Knowles, Syst Biol 2007 56 3 400 411 10.1080/10635150701405560 17520504
42. Bayesian Estimation of Concordance Among Gene Trees. C Ané B Larget DA Baum SD Smith A Rokas4, Mol Biol Evol 2007 24 2 412 426 10.1093/molbev/msl170 17095535
43. Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies. K Strimmer A von Haeseler, Mol Biol Evol 1996 13 964 969
44. T-Coffee: A novel method for fast and accurate multiple sequence alignment. C Notredame DG Higgins J Heringa, J Mol Biol 2000 302 205 17 10.1006/jmbi.2000.4042 10964570
45. A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
46. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. YI Wolf IB Rogozin EV Koonin, Genome Res 2004 14 29 36 14707168 10.1101/gr.1347404
47. Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. IB Rogozin YI Wolf L Carmel EV Koonin, Mol Biol Evol 2007 24 1080 90 10.1093/molbev/msm029 17299026
48. Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. H Philippe N Lartillot H Brinkmann, Mol Biol Evol 2005 22 1246 1253 10.1093/molbev/msi111 15703236
49. Genome-scale evidence of the nematode-arthropod clade. H Dopazo J Dopazo, Genome Biol 2005 6 R41 15892869 10.1186/gb-2005-6-5-r41
50. 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 2007 2 10 e173 10.1371/journal.pgen.0020173