Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes

Molecular Phylogenetics and Evolution

Volumn 33, Issue 2, 2004, Pages 321-332

  Ruiz Trillo, Iñaki ^a   Riutort, Marta ^a   Fourcade, H Matthew ^b   Baguñà, Jaume ^a   Boore, Jeffrey L ^b,c  

^a UNIVERSITY OF BARCELONA   (Spain)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Acoel; Evolution; Genome; Metazoa; Mitochondria; Platyhelminth

Indexed keywords

MITOCHONDRIAL DNA; TRANSFER RNA;

ANIMAL; ARTICLE; CLASSIFICATION; CODON; CONFORMATION; DNA SEQUENCE; GENE ORDER; GENETICS; GENOME; PHYLOGENY; PLATYHELMINTH; SEQUENCE ANALYSIS; TURBELLARIA;

ANIMALS; CODON; DNA, MITOCHONDRIAL; GENE ORDER; GENOME; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLATYHELMINTHS; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; TURBELLARIA;

ACOELOMORPHA; BILATERIA; METAZOA; MICROSTOMUM; MICROSTOMUM LINEARE; NEMERTODERMA; NEMERTODERMA WESTBLADI; NEMERTODERMATIDA; PARATOMELLA; PARATOMELLA RUBRA; PLATYHELMINTHES;

EID: 3142770785     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.06.002     Document Type: Article

References (59)

1. J. Adachi, and M. Hasegawa Model of amino acid substitution in proteins encoded by mitochondrial DNA J. Mol. Evol. 42 1996 459 468
2. A. Adoutte, G. Balavoine, N. Lartillot, O. Lespinet, B. Prud'homme, and R. de Rosa The new animal phylogeny: reliability and implications Proc. Natl. Acad. Sci. USA 97 2000 4453 4456
3. U. Arnason, and A. Janke Mitogenomic analyses of eutherian relationships Cytogenet. Genome Res. 96 2002 20 32
4. Ax, P., 1996. in: Multicellular Animals. A New Approach to the Phylogenetic Order in Nature, vol. I. Springer-Verlag, Berlin, Germany
5. J. Baguñà Planarian neoblasts Nature 290 1981 14 15
6. J. Baguñà, E. Saló, and C. Auladell Regeneration and pattern formation in planarians III. Evidence that neoblasts are totipotent stem cells Development 107 1989 77 86
7. J. Baguñà, and M. Riutort Molecular phylogeny of the platyhelminthes Can. J. Zool. 82 2004 168 193
8. W.M. Barnes PCR amplification of up to 35-kb DNA with high fidelity and high yield from bacteriophage templates Proc. Natl. Acad. Sci. USA 91 1994 2216 2220
9. J.R. Bayascas, E. Castillo, and E. Saló Platyhelminthes have a Hox code differentially activated during regeneration, with genes closely related to those of spiralian protostomes Dev. Genes Evol. 208 1998 467 473
10. C.T. Beagley, R. Okimoto, and D.R. Wolstenholme The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code Genetics 148 1998 1091 1108
11. M.J. Beaton, A.J. Roger, and T. Cavalier-Smith Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals J. Mol. Evol. 47 1998 697 708
12. J.L. Boore, and W.M. Brown Big trees from little genomes: mitochondrial gene order as a phylogenetic tool Curr. Opin. Genet. Dev. 8 1998 668 674
13. J.L. Boore Animal mitochondrial genomes Nucleic Acids Res. 27 1999 1767 1780
14. J.L. Boore, and W.M. Brown Mitochondrial genomes of Galatheolinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa Mol. Biol. Evol. 17 2000 87 106
15. J.L. Boore, and J.L. Staton The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca Mol. Biol. Evol. 19 2002 127 137
16. R.C. Brusca, and G.J. Brusca Invertebrates 1990 Sinauer Associates Sunderland
17. S. Carranza, J. Baguñà, and M. Riutort Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences Mol. Biol. Evol. 14 1997 485 497
18. C.E. Cook, E. Jimínez, M. Akam, and E. Saló The Hox complement of acoel flatworms, a basal bilaterian clade Evol. Dev. 6 2004 154 163
19. R. De Rosa, J.K. Grenier, T. Andreeva, C.E. Cook, A. Adoutte, M. Akam, S.B. Carroll, and G. Balavoine Hox genes in brachiopods and priapulids and protostome evolution Nature 399 1999 772 776
20. U. Ehlers Phylogenetic relationships within the Platyhelminthes S.C. Morris J.D. George R. Gibson H.M. Platt The Origin and Relationships of Lower Invertebrates Groups 1985 Oxford University Press Oxford 143 158
21. O. Folmer, M. Black, W. Hoeh, R. Lutz, and R. Vrijenhoek DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates Mol. Mar. Biol. Biotechnol. 3 1994 294 299
22. J.Q. Henry, M.Q. Martindale, and B.C. Boyer The unique developmental program of the acoel flatworm, Neochildia fusca Dev. Biol. 220 2000 285 295
23. L.H. Hyman The Invertebrates. II. Platyhelminthes and Rhynchocoela. The Acoelomate Bilateria 1951 McGraw-Hill New York
24. R.J. Hoffmann, J.L. Boore, and W.M. Brown A novel mitochondrial genome organization for the blue mussel, Mytilus edulis Genetics 131 1992 397 412
25. J.G. Inoue, M. Miya, and M. Nishida Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the ancient fish Mol. Phylogenet. Evol. 26 2003 110 120
26. U. Jondelius, I. Ruiz-Trillo, J. Baguñà, and M. Riutort The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes Zool. Scr. 31 2002 201 215
27. E.M. Keddie, T. Higazi, and T.R. Unnasch The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis Mol. Biochem. Parasitol. 95 1998 111 127
28. S. Kumar, K. Tamura, I.B. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 2001 1244 1245
29. T.H. Le, D. Blair, and D.P. McManus Mitochondrial genomes of parasitic flatworms Trends Parasitol. 18 2002 206 213
30. D.T.J. Littlewood, and P.D. Olson Small subunit rDNA and the Platyhelminthes: signal, noise and compromise D.T.J. Littlewood R.D. Bray The Interrelationships of the Platyhelminthes 2001 Taylor and Francis London 252 278
31. T.M. Lowe, and S.R. Eddy tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res. 25 5 1997 955 964
32. K. Lundin, and J. Hendelberg Is the sperm type of the Nemertodermatida close to that of the ancestral Platyhelminthes? Hydrobiologia 383 1998 197 205
33. M. Miya, H. Takeshima, H. Endo, N.B. Ishiguro, J.G. Inoue, T. Mukai, T.P. Satoh, M. Yamaguchi, A. Kawaguchi, K. Mabuchi, and M. Nishida Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences Mol. Phylogenet. Evol. 26 2003 121 138
34. Y. Murata, M. Nikaido, T. Sasaki, Y. Cao, Y. Fukumoto, and N. Okada Afrotherian phylogeny as inferred from complete mitochondrial genomes Mol. Phylogenet. Evol. 28 2003 253 260
35. M. von Nickisch-Rosenegk, W.M. Brown, and J.L. Boore Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that platyhelminthes are eutrochozoans Mol. Biol. Evol. 18 2001 721 730
36. D. Ojala, J. Montoya, and G. Attardi tRNA punctuation model of RNA processing in human mitochondria Nature 290 1981 470 474
37. R. Okimoto, J.L. MacFarlane, D.O. Clary, and D.R. Wolstenholme The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum Genetics 130 1992 471 498
38. H. Orii, K. Kato, Y. Umesono, T. Sakurai, K. Agata, and K. Watanabe The planarian HOM/HOX homeobox genes (Plox) expressed along the anteroposterior axis Dev. Biol. 210 1999 456 468
39. S.R. Palumbi Nucleic acids II: the polymerase chain reaction D.M. Hillis C. Moritz B.K. Mable Molecular Systematics 1996 Sinauer Sunderland, MA 205 247
40. A.E. Pasquinelli, A. McCoy, E. Jimenez, E. Salo, G. Ruvkun, M.Q. Martindale, and J. Baguñà Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol. Dev. 5 2003 372 378
41. N.T. Perna, and T.D. Kocher Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes J. Mol. Evol. 41 1995 353 358
42. O.I. Raikova, M. Reuter, E.A. Kotikova, and M.K.S. Gustafsson A commisural brain! The pattern of 5-HT immunoreactivity in Acoela (Platyhelminthes) Zoomorphology 118 1998 69 77
43. O.I. Raikova, M. Reuter, U. Jondelius, and M.K.S. Gustafsson The brain of the Nemertodermatida (Platyhelminthes) as revealed by anti-5HT and anti-FMRMamide immunostainings Tissue Cell 32 2000 358 365
44. O.I. Raikova, M. Reuter, and J.L. Justine Contributions to the phylogeny and systematics of the Acoelomorpha D.T.J. Littlewood R.A. Bray Interrelationships of the Platyhelminthes 2001 Taylor and Francis London 13 23
45. M. Reuter, O.I. Raikova, and M.K. Gustafsson An endocrine brain? The pattern of FMRF-amide immunoreactivity in Acoela (Plathelminthes) Tissue Cell 30 1998 57 63
46. R.M. Rieger, S. Tyler, J.P.S. Smith III, and G.E. Rieger Platyhelminthes: Turbellaria F.W. Harrison B.J. Bogitsh Microscopic Anatomy of Invertebrates. vol. 3: Platyhelminthes and Nemertinea 1991 Wiley-Liss New York 7 140
47. M. Robinson-Rechavi, and D. Huchon RRTree: relative-rate tests between groups of sequences on a phylogenetic tree Bioinformatics 16 2000 296 297
48. I. Ruiz-Trillo, M. Riutort, D.T.J. Littlewood, E.A. Herniou, and J. Baguñà Acoel flatworms: earliest extant bilaterian metazoans, not members of the Platyhelminthes Science 283 1999 1919 1923
49. I. Ruiz-Trillo, J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguñà, and M. Riutort A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians Proc. Natl. Acad. Sci. USA 99 2002 11246 11251
50. J.P.S. Smith, and S. Tyler The acoel turbellarians: kingpins of metazoan evolution or a specialized offshoot C. Conway Morris J.D. George R. Gibson H.M. Platt The Origins and Relationships of Lower Invertebrates 1985 Oxford University Press Oxford 123 142
51. J.P.S. Smith, S. Tyler, and R.R. Rieger Is the Turbellaria polyphyletic? Hydrobiologia 132 1986 13 21
52. S.W. Smith, R. Overbeek, C.R. Woese, W. Gilbert, and P.M. Gillevet The genetic data environment: an expandable GUI for multiple sequence-analysis Comp. Appl. Biosci. 10 1994 671 675
53. K. Strimmer, and A. von Haeseler Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 1996 964 969
54. M.J. Telford, E.A. Herniou, R.B. Russell, and D.T.J. Littlewood Changes in mitochondrial gene tic code as phylogenetic characters: two examples from the flatworms Proc. Natl. Acad. Sci. USA 97 2000 11359 11364
55. M.J. Telford, A.E. Lockyer, C. Cartwright-Finch, and D.T.J. Littlewood Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms Proc. R. Soc. (Lond.) B 270 2003 1077 1083
56. S. Tyler The early worm: origins and relationships of the lower flatworms D.T.J. Littlewood R. Bray Interrelationships of the Platyhelminthes 2001 Taylor & Francis London 3 12
57. S. Tyler, and R.M. Rieger Functional morphology of musculature in the acoelomate worm, Convoluta pulchra (Platyhelminthes) Zoomorphology 119 1999 127 141
58. D.R. Wolstenholme Genetic novelties in mitochondrial genomes of multicellular animals Curr. Opin. Genet. Dev. 2 1992 918 925
59. J. Zhang, and T.L. Madden Power BLAST: a new network BLAST application for interactive or automated sequence analysis and annotation Genome Res. 7 1997 649 656