The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree

Journal of Molecular Evolution

Volumn 67, Issue 5, 2008, Pages 437-447

  Townsend, Jeffrey P ^a   López Giráldez, Francesc ^a   Friedman, Robert ^b  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Information; Phylogeny; Polytomy; Power; Rapid radiation; Vertebrate

Indexed keywords

ALBUMIN; CALMODULIN; CYTOCHROME B;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; DNA SEQUENCE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ONCOGENE C MYC; PHYLOGENETIC TREE;

ALGORITHMS; ANIMALS; CALMODULIN; CYTOCHROMES B; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENETIC VARIATION; PHYLOGENY; PROTO-ONCOGENE PROTEINS C-MYC; SERUM ALBUMIN; VERTEBRATES;

EUTHERIA; METAZOA; MUROIDEA; RODENTIA; VERTEBRATA;

EID: 56149119671     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9142-0     Document Type: Article

References (54)

1. F Abascal R Zardoya D Posada 2005 ProtTest: selection of best-fit models of protein evolution Bioinformatics 21 2104 2105
2. SF Altschul TL Madden AA Schaffer JH Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
3. U Arnason JA Adegoke K Bodin EW Born YB Esa A Gullberg M Nilsson RV Short XF Xu A Janke 2002 Mammalian mitogenomic relationships and the root of the eutherian tree Proc Natl Acad Sci USA 99 8151 8156
4. U Arnason A Janke 2002 Mitogenomic analyses of eutherian relationships Cytogenet Genome Res 96 20 32
5. TM Collins O Fedrigo GJP Naylor 2005 Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics Syst Biol 54 493 500
6. F Delsuc M Scally O Madsen MJ Stanhope WW de Jong FM Catzeflis MS Springer EJP Douzery 2002 Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting Mol Biol Evol 19 1656 1671
7. RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32 1792 1797
8. O Fedrigo DC Adams GJ Naylor 2005 DRUIDS-detection of regions with unexpected internal deviation from stationarity J Exp Zool B Mol Dev Evol 304 119 128
9. J Felsenstein 2001 Taking variation of evolutionary rates between sites into account in inferring phylogenies J Mol Evol 53 447 455
10. C Gissi D San Mauro G Pesole R Zardoya 2006 Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters Gene 366 228 237
11. GV Glazko M Nei 2003 Estimation of divergence times for major lineages of primate species Mol Biol Evol 20 424 434
12. A Graybeal 1994 Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates Syst Biol 43 174 193
13. M Hasegawa H Kishino T Yano 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA J Mol Evol 22 160 174
14. SB Hedges S Kumar 2003 Genomic clocks and evolutionary timescales Trends Genet 19 200 206
15. SB Hedges JE Blair ML Venturi JL Shoe 2004 A molecular timescale of eukaryote evolution and the rise of complex multicellular life BMC Evol Biol 4 2
16. DM Hillis DD Pollock JA McGuire DJ Zwickl 2003 Is sparse taxon sampling a problem for phylogenetic inference? Syst Biol 52 124 126
17. DT Jones WR Taylor JM Thornton 1992 The rapid generation of mutation data matrices from protein sequences Comput Appl Biosci 8 275 282
18. S Kumar SR Gadagkar 2001 Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences Genetics 158 1321 1327
19. MC Lara JL Patton MNF daSilva 1996 The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences Mol Phylogenet Evol 5 403 413
20. EP Lessa JA Cook 1998 The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation Mol Phylogenet Evol 9 88 99
21. Li W (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
22. I Mayrose D Graur N Ben-Tal T Pupko 2004 Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior Mol Biol Evol 21 1781 1791
23. A Meyer R Zardoya 2003 Recent advances in the (molecular) phylogeny of vertebrates Annu Rev Ecol Evol Syst 34 311 338
24. WJ Murphy E Eizirik WE Johnson YP Zhang OA Ryderk SJ O'Brien 2001 Molecular phylogenetics and the origins of placental mammals Nature 409 614 618
25. WJ Murphy E Eizirik SJ O'Brien O Madsen M Scally CJ Douady E Teeling OA Ryder MJ Stanhope WW de Jong MS Springer 2001 Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2348 2351
26. GJ Naylor WM Brown 1997 Structural biology and phylogenetic estimation Nature 388 527 528
27. M Nei S Kumar K Takahashi 1998 The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small Proc Natl Acad Sci USA 95 12390 12397
28. SL Pond SD Frost SV Muse 2005 HyPhy: hypothesis testing using phylogenies Bioinformatics 21 676 679
29. D Posada KA Crandall 1998 MODELTEST: testing the model of DNA substitution Bioinformatics 14 817 818
30. C Poux EJP Douzery 2004 Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP Am J Phys Anthropol 124 1 16
31. A Rokas SB Carroll 2005 More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy Mol Biol Evol 22 1337 1344
32. A Rokas N King J Finnerty SB Carroll 2003 Conflicting phylogenetic signals at the base of the metazoan tree Evol Dev 5 346 359
33. A Rokas BL Williams N King SB Carroll 2003 Genome-scale approaches to resolving incongruence in molecular phylogenies Nature 425 798 804
34. MS Rosenberg S Kumar 2001 Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well Mol Biol Evol 18 1823 1827
35. MS Rosenberg S Kumar 2001 Incomplete taxon sampling is not a problem for phylogenetic inference Proc Natl Acad Sci USA 98 10751 10756
36. MS Rosenberg S Kumar 2003 Taxon sampling, bioinformatics, and phylogenomics Syst Biol 52 119 124
37. CAM Russo N Takezaki M Nei 1996 Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny Mol Biol Evol 13 525 536
38. VM Sarich AC Wilson 1967 Rates of albumin evolution in primates Proc Natl Acad Sci USA 58 142
39. M Scally O Madsen CJ Douady WW de Jong MJ Stanhope MS Springer 2002 Molecular evidence for the major clades of placental mammals J Mammal Evol 8 239 277
40. HA Schmidt K Strimmer M Vingron A von Haeseler 2002 TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 502 504
41. MP Simmons 2000 A fundamental problem with amino-acid-sequence characters for phylogenetic analyses Cladistics Int J Willi Hennig Soc 16 274 282
42. MP Simmons H Ochoterena JV Freudenstein 2002 Conflict between amino acid and nucleotide characters Cladistics Int J Willi Hennig Soc 18 200 206
43. MP Simmons H Ochoterena JV Freudenstein 2002 Amino acid vs nucleotide characters: challenging preconceived notions Mol Phylogenet Evol 24 78 90
44. MP Simmons TG Carr K O'Neill 2004 Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters Mol Phylogenet Evol 32 913 926
45. MP Simmons A Reeves JI Davis 2004 Character-state space versus rate of evolution in phylogenetic inference Cladistics Int J Willi Hennig Soc 20 191 204
46. MS Springer WJ Murphy E Eizirik SJ O'Brien 2003 Placental mammal diversification and the Cretaceous-Tertiary boundary Proc Natl Acad Sci USA 100 1056 1061
47. N Takezaki T Gojobori 1999 Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences Mol Biol Evol 16 590 601
48. N Takezaki F Figueroa Z Zaleska-Rutczynska J Klein 2003 Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes Mol Biol Evol 20 287 292
49. N Takezaki F Figueroa Z Zaleska-Rutczynska N Takahata J Klein 2004 The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes Mol Biol Evol 21 1512 1524
50. EC Teeling MS Springer O Madsen P Bates SJ O'Brien WJ Murphy 2005 A molecular phylogeny for bats illuminates biogeography and the fossil record Science 307 580 584
51. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882
52. JP Townsend 2007 Profiling phylogenetic informativeness Syst Biol 56 222 231
53. ZH Yang 1996 Among-site rate variation and its impact on phylogenetic analyses Trends Ecol Evol 11 367 372
54. ZH Yang 1997 PAML: a program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 13 555 556