Chloroplast genome phylogenetics: Why we need independent approaches to plant molecular evolution

Trends in Plant Science

Volumn 10, Issue 5, 2005, Pages 203-209

  Martin, William ^a   Deusch, Oliver ^a   Stawski, Nadine ^a   Grünheit, Nicole ^a   Goremykin, Vadim ^b  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 18144368560     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2005.03.007     Document Type: Article

References (41)

1. D.E. Soltis Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics Trends Plant Sci. 9 2004 477 483
2. V.V. Goremykin Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm Mol. Biol. Evol. 20 2003 1499 1505
3. V.V. Goremykin The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm Mol. Biol. Evol. 21 2004 1445 1454
4. S. Mathews, and M.J. Donoghue The root of angiosperm phylogeny inferred from duplicate phytochrome genes Science 286 1999 947 950
5. Y.L. Qiu The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes Nature 402 1999 404 407
6. C.L. Parkinson Multigene analyses identify the three earliest lineages of extant flowering plants Curr. Biol. 9 1999 1485 1488
7. T.J. Barkman Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny Proc. Natl. Acad. Sci. U. S. A. 97 2000 13166 13171
8. S.W. Graham, and R.G. Olmstead Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms Am. J. Bot. 87 2000 1712 1730
9. M.S. Rosenberg, and S. Kumar Incomplete taxon sampling is not a problem for phylogenetic inference Proc. Natl. Acad. Sci. U. S. A. 98 2001 10751 10756
10. Y-H. Lin Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling Mol. Biol. Evol. 19 2002 2060 2070
11. S. Stefanović Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol. 4 2004 35
12. J. Felsenstein Inferring Phylogenies 2004 Sinauer
13. C. Semple, and M.A. Steel Phylogenetics 2003 Oxford University Press
14. A.C. Driskell Prospects for building the tree of life from large sequence databases Science 306 2004 1172 1174
15. P.J. Lockhart Recovering evolutionary trees under a more realistic model of sequence evolution Mol. Biol. Evol. 11 1994 605 612
16. P.J. Lockhart Spectral analysis, systematic bias, and the evolution of chloroplasts Mol. Biol. Evol. 16 1999 573 576
17. M.J. Phillips Genome-scale phylogeny and the detection of systematic biases Mol. Biol. Evol. 21 2004 1455 1458
18. S.Y. Ho, and L. Jermiin Tracing the decay of the historical signal in biological sequence data Syst. Biol. 53 2004 623 637
19. J.A. Lake Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances Proc. Natl. Acad. Sci. U. S. A. 91 1994 1455 1459
20. D. Bryant, and V. Moulton Neighbor-Net: an agglomerative method for the construction of phylogenetic networks Mol. Biol. Evol. 21 2004 255 265
21. M. Thollesson LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences Bioinformatics 20 2004 416 418
22. F. Delsuc Comment on "Hexapod origins: monophyletic or paraphyletic?" Science 301 2003 1482
23. I. Hrdy Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I Nature 432 2004 618 622
24. G.J.P. Naylor, and W.M. Brown Structural biology and phylogenetic estimation Nature 388 1997 527 528
25. M.A. Steel Invariable site models and their use in phylogeny reconstruction Syst. Biol. 49 2000 225 232
26. N. Galtier, and M. Gouy Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis Mol. Biol. Evol. 15 1998 871 879
27. W.F. Fitch, and E. Markowitz An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem. Genet. 4 1970 579 593
28. D. Penny Mathematical elegance with biochemical realism: the covarion model of molecular evolution J. Mol. Evol. 53 2001 711 723
29. P.J. Lockhart A covariotide model explains the evolution of oxygenic photosynthesis Mol. Biol. Evol. 15 1998 1183 1188
30. P.J. Lockhart How molecules evolve in eubacteria Mol. Biol. Evol. 17 2000 835 838
31. H. Philippe Heterotachy and functional shift in protein evolution IUBMB Life 55 2003 257 265
32. Y. Inagaki Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 alpha phylogenies Mol. Biol. Evol. 21 2004 1340 1349
33. B. Kolaczkowski, and J.W. Thornton Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous Nature 431 2004 980 984
34. Ané, C. et al. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. (in press)
35. U. Bergthorsson Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella Proc. Natl. Acad. Sci. U. S. A. 101 2004 17747 17752
36. V. Goremykin Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: revised molecular estimates of two seed plant divergence times Pl. Syst. Evol. 206 1997 337 351
37. W. Martin Gene transfer to the nucleus and the evolution of chloroplasts Nature 393 1998 162 165
38. C. Vogl Probabilistic analysis indicates discordant gene trees in chloroplast evolution J. Mol. Evol. 56 2003 330 340
39. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
40. D.H. Huson SplitsTree: analyzing and visualizing evolutionary data Bioinformatics 14 1998 68 73
41. Y.L. Qiu Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya Mol. Biol. Evol. 18 2001 1745 1753