How good are deep phylogenetic trees?

Current Opinion in Genetics and Development

Volumn 8, Issue 6, 1998, Pages 616-623

  Philippe, Hervé ^a   Laurent, Jacqueline ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW;

EID: 0031737821     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(98)80028-2     Document Type: Article

References (68)

1. Zischler H, Geisert H, von Haeseler A, Paabo S. A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans. Nature. 378:1995;489-492.
2. Donoghue MJ, Mathews S. Duplicate genes and the root of angiosperms, with an example using phytochrome sequences. of special interest Mol Phylogenet Evol. 9:1998;489-500 Starting from the observation that the root of angiosperms has not been determined despite intensive work, the authors look for the use of duplicated genes as an alternative approach.
3. Roger AJ, Sandblom O, Doolittle WF, Philippe H. An evaluation of Elongation Factor 1α as a phylogenetic marker for Eukaryotes. of special interest Mol Biol Evol. 1998; A detailed study of the impact of tree reconstruction methods and of species sampling. An important conclusion is that EF-1α is highly saturated and that the methods for correcting multiple substitutions are not efficient, rendering the phylogeny based on EF-1α questionable.
4. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 87:1990;4576-4579.
5. Brown JR, Doolittle WF. Archaea and the prokaryote-to-eukaryote transition. of special interest Microbiol Mol Biol Rev. 61:1997;456-502 The most exhaustive review of the phylogenies linking the three domains. Unfortunately, the tree reconstruction method used - distance with Dayhoff correction - is not very efficient, rendering the interpretation of the phylogenies difficult.
6. Pennisi E. Genome data shake tree of life. Science. 280:1998;672-674.
7. Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. of outstanding interest Nature. 387:1997;708-713 Uses the physical location of the duplicated genes to demonstrate that a whole-genome duplication occurred recently in a yeast ancestor. Interestingly, only 13% of the duplicated genes were retained.
8. Lawrence JG, Ochman H. Molecular archaeology of the Escherichia coli genome. of outstanding interest Proc Natl Acad Sci USA. 95:1998;9413-9417 The use of codon usage bias allows the authors to demonstrate that ~18% of the Eschericha coli genome was acquired by horizontal transfers after the divergence from Salmonella: a conclusive example of the importance of horizontal transfer in prokaryotic evolution.
9. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:1978;401-410.
10. D'Erchia A, Gissi C, Pesole G, Saccone C, Arnason U. The guinea-pig is not a rodent. Nature. 381:1996;597-600.
11. Philippe H. Rodent monophyly: pitfalls of molecular phylogenies. of outstanding interest J Mol Evol. 45:1997;712-715 Shows that the paraphyly of rodents based on the complete mitochondrial genome disappears when species are added and suggests that paraphyly is a result of the increased evolutionary rate of rodents. Moreover, it is shown that the slow-evolving positions relevant to the question of the rodent monophyly are very rare (6 out of 3733) and contradictory.
12. Philippe H, Adoutte A. The molecular phylogeny of Eukaryota: solid facts and uncertainties. of outstanding interest Coombs G, Vickerman K, Sleigh M, Warren A. Evolutionary Relationships Among Protozoa. 1998;25-56 Chapman & Hall, London, Suggests for the first time that all the lineages that emerge early in the rRNA tree are misplaced because of the long branch attraction artefact. A clear correlation between high evolutionary rate and deep branching is shown for actin, tubulin and rRNA.
13. Gupta RS, Johari V. Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus - Thermus group and cyanobacteria. J Mol Evol. 46:1998;716-720.
14. Klenk H-P, Meier T-D, Durovic P, Schwass V, Lottspeich F, Dennis PP, Zillig W. RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC-operon and the extreme thermophilic bacteria. J Mol Evol. 1998;. in press.
15. Gupta RS. What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol. 229:1998;695-708.
16. Gray M, Spencer D. Organellar evolution. Roberts D, Sharp P, Alderson G, Collins M. Evolution of Microbial Life. 1996;109-126 Cambridge University Press, Cambridge.
17. Huelsenbeck JP. Is the Felsenstein zone a fly trap? of outstanding interest Syst Biol. 46:1997;69-74 Using empirical examples, the author shows that LBA is actually a source of error in phylogenetic analysis. He performs a simulation showing that the maximum parsimony method is very sensitive to LBA but if among-site variation is taken into account, the impact of this artefact is reduced.
18. Hwang UW, Kim W, Tautz D, Friedrich M. Molecular phylogenetics at the Felsenstein zone: approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences. of outstanding interest Mol Phylogenet Evol. 9:1998;470-480 Similar results as [17] but with another gene. Computer simulations show the inconsistency of the ML method when ignoring among-site rate variation, especially when four species are used.
19. Philippe H, Forterre P. The rooting of the universal tree of life is not reliable. J Mol Evol. 1998;. in press.
20. Meyer TE, Cusanovich MA, Kamen MD. Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc Natl Acad Sci USA. 83:1986;217-220.
21. Shoemaker JS, Fitch WM. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol. 6:1989;270-289.
22. Ayala FJ, Rzhetsky A, Ayala FJ. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates. of outstanding interest Proc Natl Acad Sci USA. 95:1998;606-611 This careful analysis demonstrates that previous date estimates from molecular data are flawed by several methodological biases, especially the use of slow-evolving vertebrates as a calibration point.
23. Wray GA, Levinton J, Shapiro L. Molecular evidence for deep precambrian divergences among metazoan phyla. Science. 274:1996;568-573.
24. Sorhannus U. Higher ribosomal RNA substitution rates in Bacillariophyceae and Dasycladales than in Mollusca Echinodermata, and Actinistia-Tetrapoda. Mol Biol Evol. 13:1996;1032-1038.
25. Ayala FJ. Vagaries of the molecular clock. Proc Natl Acad Sci USA. 94:1997;7776-7783.
26. Pawlowski J, Bolivar I, Fahrni JF, de Vargas C, Gouy M, Zaninetti L. Extreme differences in rates of molecular evolution of Foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. of outstanding interest Mol Biol Evol. 14:1997;498-505 The use of the fossil record allows the authors to demonstrate, for the first time, the extreme rate variation of rRNA evolution (up to 100 times faster in some lineages). Interestingly, no obvious biological reasons can explain these variations.
27. Dayhoff MO, Shwartz RM, Orcutt BC. A model of evolutionary change in proteins. Atlas Protein Struct. 5:1978;345-352. (Suppl 3).
28. Sullivan J, Swofford DL. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. of outstanding interest J Mam Evol. 4:1997;77-86 A demonstration that the improvement in the fit of the data by taking into account among-site rate variation - even with a simple model invariable plus variable sites - is more important than that by taking into account the nucleotide substitution model. The phylogeny inferred with the best model does not allow one to robustly locate hedgehog, mouse, rat and guinea-pig phylogenetically, which are robustly misplaced in the tree inferred with simple models (see [10]).
29. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA. Evidence for a clade of nematodes, arthropods and other moulting animals. of outstanding interest Nature. 387:1997;489-493 The authors sequenced rRNA of 20 different nematodes finding three slow-evolving ones. The use of these three sequences demonstrates that nematodes do not emerge at the base of Bilateria but could be closely related to arthropods. This last result, however, is obtained using only 17 species and is not statistically supported when more species are added.
30. Hendy M, Penny D. A framework for the quantitative study of evolutionary trees. Syst Zool. 38:1989;297-309.
31. Halanych KM. Lagomorphs misplaced by more characters and fewer taxa. of special interest Syst Biol. 47:1998;138-146 Shows that the previously observed clustering of primates and rabbit is strictly an artefact of a phylogenetic philosophy using a 'more data' approach at the expense of taxonomic representation.
32. Philippe H, Douzery E. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J Mam Evol. 2:1994;133-152.
33. Moreira D, Le Guyader H, Philippe H. Unusually high evolutionary rate of the elongation factor 1α genes from the ciliophora and its impact on the phylogeny of eukaryotes. of outstanding interest Mol Biol Evol. 1998; The importance of sequence addition and taxonomic sampling is analysed upon the eukaryotic phylogeny based on elongation factor 1α sequences, with special attention on the fast-evolving sequences from ciliates. Sequence addition increases the symmetry of the tree, suggesting that the asymmetrical base is caused by a LBA phenomenon.
34. Rice KA, Donoghue MJ, Olmstead RG. Analyzing large data sets: rbcL 500 revisited. Syst Biol. 46:1997;554-563.
35. Kim J. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst Biol. 45:1996;363-374.
36. Rannala B, Huelsenbeck JP, Yang Z, Nielsen R. Taxon Sampling and the accuracy of large phylogenies. of special interest Syst Biol. 1998; The accuracy of large phylogenies, studied with simulation only, is still a matter of debate. The authors here show that the assumptions of the simulation can severely bias the results.
37. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem? of special interest Syst Biol. 47:1998;9-17 Computer simulation shows that improvement of phylogenies is easier by adding taxa than by adding characters, in agreement with studies based on real data (see [32]).
38. Germot A, Philippe H, Le Guyader H. Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol. 87:1997;159-168.
39. Hirt RP, Healy B, Vossbrinck CR, Canning EU, Embley TM. A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that Microsporidia once contained mitochondria. Curr Biol. 7:1997;995-998.
40. Budin K, Philippe H. New insights into the phylogeny of eukaryotes based on ciliate HSP70 sequences. of outstanding interest Mol Biol Evol. 15:1998;943-956 In addition to a detailed analysis of the phylogeny of eukaryotes, it is shown that, for eukaryotes, the distance to the outgroup for the HSP70 is much smaller than for the rRNA. Interestingly, it was shown that the duplications of HSP70 genes within the eukaryotes occurred either before the divergence of all eukaryotes or within limited phyla, in agreement with the big-bang hypothesis (see [12]).
41. Germot A, Philippe H. Critical analysis of eukaryotic phylogeny: a case study based on HSP70 family. of outstanding interest J Euk Microbiol. 1998; Shows that the addition of species increases the symmetry of the trees, in agreement with the hypothesis that the asymmetrical base of eukaryotic phylogeny is caused by the long branch attraction. More importantly, it shows that the number of variable sites is different for the different types of HSP70 - in agreement with the covarion model - and most important, that fast-evolving species have more variable sites than slow-evolving ones, amplifying the long branch attraction artefact.
42. Rivera MC, Lake JA. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science. 257:1992;74-76.
43. Baldauf SL, Palmer JD. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA. 90:1993;11558-11562.
44. Hashimoto T, Sanchez LB, Shirakura T, Muller M, Hasegawa M. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. of outstanding interest Proc Natl Acad Sci USA. 95:1998;6860-6865 The finding that the VaIRS sequences of two amitochondriate protists are of the eukaryotic type (i.e. of mitochondrial origin) gives further evidence that, among the extant eukaryotes, there is no representative of a premitochondrial stage of eukaryotic evolution. A beautiful example of an incorrect phylogeny constructed with classic methods but for which the correct topology can be inferred from an insertion signature.
45. Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M, Munechika I, Okada N. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. of outstanding interest Nature. 388:1997;666-670 The use of new types of molecular phylogenetic markers, unique retropositional events, reliably resolves a question that is controversial with classical molecular phylogenies (see [32]). Supporting and completing previous molecular phylogenetic analysis, this approach, which can be considered noise-free, might be more convincing for morphologists and prompt them to reconsider their view of morphological transformations in whales and artiodactyls.
46. Qiu Y-L, Cho Y, Cox JC, Palmer JD. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. of special interest Nature. 394:1998;671-674 Whereas different phylogenetic analyses led to an unresolved polytomy at the base of land plants, the unique insertion of mitochondrial introns unambiguously identifies liverworts as the first emerging land plants. Like green algae, they do not possess the introns that are present in mosses, hornworts and all other lineages of vascular plants.
47. Wägele J. First principles of phylogenetic systematics, basis for numerical methods used for morphological and molecular characters. Vie et Milieu. 46:1996;125-138.
48. Kamaishi T, Hashimoto T, Nakamura Y, Nakamura F, Murata S, Okada N, Okamoto K, Shimizu M, Hasegawa M. Protein phylogeny of translation elongation factor EF-1 alpha suggests microsporidians are extremely ancient eukaryotes. J Mol Evol. 42:1996;257-263.
49. of outstanding interest Boore JL, Lavrov DV, Brown WM. Gene translocation links insects and crustaceans. of special interest Nature. 392:1998;667-668 As in [45,46], a new type of molecular marker - gene translocation - helps to solve a difficult phylogenetic problem, in this case the sisterhood of insects and crutaceans.
50. Lopez P, Forterre P, Philippe H. A method for extracting ancient phylogenetic signal: the rooting of the universal tree of life based on elongation factors. of outstanding interest J Mol Evol. 1998; A new statistical test shows that more than half of the elongation factor 1α and 2 residues conform to the covarion model. Accordingly, with a new method handling the covarion structure, the basal position of Eubacteria in the tree of Life inferred from these markers is shown to be an LBA artefact because of the higher evolutionary rate of Eubacteria.
51. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 11:1996;367-370.
52. Naylor GJP, Brown WM. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. of outstanding interest Syst Biol. 47:1998;61-76 This report shows that an incorrect phylogeny can be inferred even when very long sequences are used, contrary to the claim of the 'total evidence parsimony' school.
53. Halpern AL, Bruno WJ. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. of special interest Mol Biol Evol. 15:1998;910-917 Demonstrates that ignoring site-specific residues frequencies leads to a significant underestimation of evolutionary distances. Unfortunately, only simulation studies are presented and it would be very interesting to know if the proposed method can improve real phylogenies.
54. Lockhart PJ, Steel MA, Barbrook AC, Huson D, Charleston MA, Howe CJ. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. of outstanding interest Mol Biol Evol. 15:1998;1183-1188 Introduces a statistical test for substitution heterogeneity (interestingly different from that proposed in [50]) supporting the covarion model for rRNA and EF-Tu evolution. A correlation between the tree topology and the covarion structure is shown.
55. Russo CA, Takezaki N, Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol. 13:1996;525-536.
56. Waddell PJ, Steel MA. General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. of special interest Mol Phylogenet Evol. 8:1997;398-414 After developing new mathematical objects to deal with complex evolutionary models, the authors conclude that very slow evolving positions - although mathematically near equivalent to invariant sites - contain very important phylogenetic information.
57. Lockhart PJ, Larkum AW, Steel M, Waddell PJ, Penny D. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA. 93:1996;1930-1934.
58. Fitch WM. The nonidentity of invariable positions in the cytochromes c of different species. Biochem Genet. 5:1971;231-241.
59. Miyamoto MM, Fitch WM. Constraints on protein evolution and the age of the eubacteria/eukaryote split. Syst Biol. 45:1996;568-575.
60. Philippe H, Lecointre G, Lê HLV, Le Guyader H. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram. Mol Biol Evol. 13:1996;1174-1186.
61. Tuffley C, Steel M. Modeling the covarion hypothesis of nucleotide substitution. of special interest Math Biosci. 147:1998;63-91 The first mathematical interpretation of the covarion model. The recent date of this paper underlines the difficulty of laying down a mathematical framework for the 30 years old covarion hypothesis.
62. Waddell PJ, Penny D, Moore T. Hadamard conjugations and modeling sequence evolution with unequal rates across sites. of special interest Mol Phylogenet Evol. 8:1997;33-50 In addition to a new mathematical implementation of among-site rate variation in phylogenetic analysis, the authors discuss which selection pressure can create the among-site rate variation. They suggest that only the covarion model is able to explain that reversions did not hinder all the ancient substitutions.
63. Goldman N, Thorne JL, Jones DT. Assessing the impact of secondary structure and solvent accessibility on protein evolution. of outstanding interest Genetics. 149:1998;445-458 Development of a maximum likelihood approach handling both secondary structure and solvent accessibility, demonstrating that this yields to a much better fit of the data. Interestingly, the solvent accessibility appears to be more important than the secondary structure. The application of this method to real phylogenetic problems would be very interesting.
64. Bortoli-German I, Haiech J, Chippaux M, Barras F. Informational suppression to investigate structural functional and evolutionary aspects of the Erwinia chrysanthemi cellulase EGZ. J Mol Biol. 246:1995;82-94.
65. Philippe H, Adoutte A. What can phylogenetic patterns tell us about the evolutionary processes generating biodiversity? Hochberg M, Ciobert J, Barbault R. Aspects of the Genesis and Maintenance of Biological Diversity. 1996;41-59 Oxford University Press, Oxford.
66. Gu X, Li W-H. Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution. Proc Natl Acad Sci USA. 95:1998;5899-5905.
67. Reyes A, Pesole G, Saccone C. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly. Mol Biol Evol. 15:1998;499-505.
68. Yang Z. How often do wrong models produce better phylogenies? Mol Biol Evol. 144:1997;105-108.