Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders

Journal of Molecular Evolution

Volumn 47, Issue 3, 1998, Pages 307-322

  Cao, Ying ^a,b   Janke, Axel ^c,f   Waddell, Peter J ^b   Westerman, Michael ^d   Takenaka, Osamu ^e   Murata, Shigenori ^a   Okada, Norihiro ^a   Pääbo, Svante ^c   Hasegawa, Masami ^b  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c UNIVERSITY OF MUNICH   (Germany)

^d LA TROBE UNIVERSITY   (Australia)

^e KYOTO UNIVERSITY   (Japan)

^f LUND UNIVERSITY   (Sweden)

Author keywords

Convergent evolution; Mammalian phylogeny; Maximumlikelihood method; Mitochondrial proteins; ND1; Trees of individual proteins

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; EVOLUTION; HUMAN; MAMMAL; MARSUPIAL; MITOCHONDRION; MONOTREMATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; RODENT;

ANIMALS; BASE SEQUENCE; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX I; EVOLUTION, MOLECULAR; HUMANS; MAMMALS; MOLECULAR SEQUENCE DATA; NADH, NADPH OXIDOREDUCTASES; PHYLOGENY; PROTEINS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ARTIODACTYLA; CETACEA; EUTHERIA; MAMMALIA; METATHERIA; MONOTREMATA; PRIMATES; RODENTIA;

EID: 0031694349     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006389     Document Type: Article

References (74)

1. Adachi J, Hasegawa M (1995a) Phylogeny of whales: dependence of the inference on species sampling. Mol Biol Evol 12:177-179
2. Adachi J, Hasegawa M (1995b) Improved dating of the human-chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. J Mol Evol 40:622-628
3. Adachi J, Hasegawa M (1996a) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 42:459-468
4. Adachi J, Hasegawa M (1996b) MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput Sci Monogr Inst Stat Math 28:1-150
5. Adachi J, Hasegawa M (1996c) Instability of quartet analyses of molecular sequence data by the maximum likelihood method: The Cetacea/Artiodactyla relationships. Mol Phylogenet Evol 6:72-76
6. Adkins R, Honeycutt R (1993) A molecular examination of Archontan and chiropteran monophyly, Primates and Their Relatives. In: MacPhee R (ed) Phylogenetic perspective. Plenum Press, New York, pp 227-249
7. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Contr AC-19:716-723
8. Arnason U, Gullberg A (1996) Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol Biol Evol 13:407-417
9. Arnason U, Gullberg A, Xu X (1996a) A complete mitochondrial DNA molecule of the white-handed gibbon, Hylobates lar, and comparison among individual mitochondrial genes of all hominoid genera. Hereditas 124:185-189
10. Arnason U, Gullberg A, Janke A, Xu X (1996b) Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J Mol Evol 43:650-661
11. Arnason U, Gullberg A, Janke A (1997) Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and ferungulates. Mol Biol Evol 14:762-768
12. Bachman B, Luke W, Hunsmann (1990) Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Res 18:1309-1309
13. Bandelt H-J, Dress A (1992) Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1:242-252
14. Bull J, Huelsenbeck J, Cunningham C, Swofford D, Waddell P (1993) Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384-397
15. Bulmer M, Wolfe K, Sharp P (1991) Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proc Natl Acad Sci USA 88:5974-5978
16. Cao Y, Adachi J, Janke A, Pääbo S, Hasegawa M (1994a) Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J Mol Evol 39:519-527
17. Cao Y, Adachi J, Hasegawa M (1994b) Eutherian phylogeny as inferred from mitochondrial DNA sequence data. Jpn J Genet 69: 455-472
18. Cao Y, Okada N, Hasegawa M (1997) Phylogenetic position of guinea-pigs revisited. Mol Biol Evol 14:461-464
19. de Jong WW, Leunissen JAM, Wistow GJ (1993) Eye lens crystallins and the phylogeny of placental orders: evidence for a macroscelidpaenungulate clade? In: Szalay FS, Novacek MJ, McKenna MC (eds) Mammal phylogeny - placentals. Springer-Verlag, New York, pp 5-12
20. D'Erchia A, Gissi C, Pesole G, Saccone C, Arnason U (1996) The guinea-pig is not a rodent. Nature 381:597-600
21. Easteal S (1990) The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics 124:165-173
22. Felsenstein J (1996) PHYLIP, version 3.572. University of Washington, Seattle
23. Fischer Lindahl K, Hermel E, Loveland B, Wang C-R (1991) Maternally transmitted antigen of mice: a model transplantation antigen. Annu Rev Immunol 9:351-372
24. Gemmell N, Westerman M (1994) Phylogenetic relationships within the class Mammalia: a study using mitochondrial 12S RNA sequences. J Mammal Evol 2:3-23
25. Graur D, Gouy M, Duret L (1997) Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata. Mol Phylogenet Evol 7:195-200
26. Hasegawa M, Adachi J (1996) Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences. Mol Biol Evol 13:710-717
27. Hasegawa M, Kishino H (1994) Accuracies of the simple methods for estimating the bootstrap probability of a maximum likelihood tree. Mol Biol Evol 11:142-145
28. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
29. Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N (1995) The recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci USA 92:532-536
30. Höss M, Dilling A, Currant A, Pääbo S (1996) Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc Natl Acad Sci USA 93:181-185
31. Janke A, Feldmaier-Fuchs G, Thomas W, von Haeseler A, Pääbo S (1994) The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256
32. Janke A, Gemmell N, Feldmaier-Fuchs G, von Haeseler A, Pääbo S (1996) The complete mitochondrial genome of a monotreme, the platypus (Ornithorhynchus anatinus). J Mol Evol 42:153-159
33. Janke A, Xu X, Arnason U (1997) The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia and Eutheria. Proc Natl Acad Sci USA 94:1276-1281
34. Keohavong P, Thilly W (1989) Fidelity of DNA polymerase in DNA amplification. Proc Natl Acad Sci USA 86:9253-9257
35. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179
36. Kishino H, Miyata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts. J Mol Evol 31:151-160
37. Krettek A, Gullberg A, Arnason U (1995) Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J Mol Evol 41:952-957
38. Kuma K, Miyata T (1994) Mammalian phylogeny inferred from multiple protein data. Jpn J Genet 69:555-566
39. Lake J (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc Natl Acad Sci USA 91:1455-1459
40. Lecointre G, Philippe H, Lê H, Le Guyader H (1993) Species sampling has a major impact on phylogenetic inference. Mol Phylogenet Evol 2:205-224
41. Li W-H, Gouy M, Sharp P, O'hUigin C, Yang Y-W (1990) Molecular phylogeny of Rodentia, Lagomorpha. Primates, Artiodactyla, and Carnivora and molecular clocks. Proc Natl Acad Sci USA 87:6703-6707
42. Lockhart P, Steel M, Hendy M, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605-612
43. Lockhart P, Larkum A, Steel M, Waddell P, Penny D (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA 93:1930-1934
44. Lopez J, Culver M, Cevario S, O'Brien S (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA repeat (Numt) in the nuclear genome. Genomics, 33:229-246
45. Loveland B, Wang C-R, Yonekawa H, Hermel E, Fischer Lindahl K (1990) Maternally transmitted histocornpatibility antigen of mice: a hydrophobic peptide of a mitochondrially encoded protein. Cell 60:971-980
46. Luckett W (1994) Suprafamilial relationships within Marsupialia: resolution and discordance from multidisciplinary data. J Mammal Evol 2:255-283
47. Maddison W, Maddison D (1992) MacClade, version 3.0. Sinauer Associates, Sunderland, MA
48. Naylor G, Brown W (1997) Structural biology and phylogenetic estimation. Nature 388:527-528
49. Novacek M (1992) Mammalian phylogeny: shaking the tree. Nature 356:121-125
50. Penny D, Hasegawa M (1997) The platypus put in its place. Nature 387:549-550
51. Philippe H, Douzery E (1994) The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J Mammal Evol 2:133-152
52. Porter C, Goodman M, Stanhope M (1996) Evidence on mammalian phylogeny from sequences of exon 28 of the von Willebrand factor gene. Mol Phylogenet Evol 5:89-101
53. Reiss K (1997) Myology of the feeding apparatus of myrmecophagid anteaters (Xenarthra: Myrmecophagidae). J Mammal Evol 4:87-117
54. Retief J, Krajewski C, Westerman M, Winkfein R, Dixon G (1995) Molecular phylogeny and evolution of marsupial protamine P1 genes. Proc R Soc Lond 259:7-14
55. Sambrook E, Fritsch F, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Press, Cold Spring Harbor, NY
56. Sarich V, Wilson, A (1967) Immunological time scale for hominid evolution. Science 158:1200-1203
57. Sidow A, Nguyen T, Speed T (1992) Estimating the fraction of invariable codons with a capture-recapture method. J Mol Evol 35:253-260
58. Springer M, Westerman M, Kirsch J (1994) Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation. J Mammal Evol 2:85-115
59. Springer M, Cleven G, Madsen O, de Jong W, Waddell V, Amrine H, Stanhope M (1997) Endemic African mammals shake the phylogenetic tree. Nature 388:61-64
60. Stanhope M, Smith M, Waddell V, Porter C, Shivji M, Goodman M (1996) Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. J Mol Evol 43:83-92
61. Sullivan J, Swofford D (1997) Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J Mammal Evol 4:77-86
62. Swofford D (1996) PAUP*, version 4.0 (demonstration version 57). Sinauer Associates, Sunderland, MA (in press)
63. Swofford D, Olsen G, Waddell P, Hillis D (1996) Phylogenetic inference. In: Hillis D, Moritz C, Mable B (eds) Molecular systematics, 2nd ed. Sinauer Associates, Sunderland, MA, pp 407-514
64. Templeton A (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244
65. Tindall K, Kunkel T (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008-6013
66. Waddell P (1995) Statistical methods of phylogenetic analysis: including Hadamard conjugations, LogDet Transforms, and maximum likelihood, PhD dissertation. Massey University, New Zealand, Palmerston North
67. Waddell P, Penny D (1996) Evolutionary trees of apes and humans from DNA sequences. In: Lock A, Peters C (eds) Handbook of human symbolic evolution. Oxford University Press, Oxford, pp 53-73
68. Waddell P, Penny D, Moore T (1997) Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Mol Phylogenet Evol 8:33-50
69. Westerman M, Edwards D (1992) DNA hybridization and the phylogeny of monotremes. In: Augee M (ed) Platypus and echidnas. R Zool Soc New South Wales, Sydney, pp 28-34
70. Xu X, Arnason U (1994) The complete mitochondrial DNA sequence of the horse. Equus caballus: extensive heteroplasmy of the control region. Gene 148:357-362
71. Xu X, Arnason U (1996) The mitochondrial DNA molecule of Sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan. J Mol Evol 43:431-437
72. Xu X, Janke A, Arnason U (1996) The complete mitochondrial DNA sequences of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea). Mol Biol Evol 13:1167-1173
73. Yang Z (1996) Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol 42:294-307
74. Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11:316-324