Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes

Proceedings of the Royal Society B: Biological Sciences

Volumn 266, Issue 1433, 1999, Pages 2043-2052

  Stechmann, Alexandra ^a   Schlegel, Martin ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Brachiopod phylogeny; Gene order; Lophotrochozoa; Mitochondrial genome; Sequence analysis

Indexed keywords

MITOCHONDRIAL DNA;

ANNELID WORM; ARTICLE; DNA SEQUENCE; GENE ORDER; GENE SEQUENCE; METAZOON; MOLLUSC; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ANNELIDA; BRACHIOPODA; KATHARINA TUNICATA; LITTORINA SAXATILIS; LOPHOTROCHOZOA; METAZOA; MOLLUSCA; POLYPLACOPHORA; RETUSA; TEREBRATULINA RETUSA; UROCHORDATA;

EID: 0033595767     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.1999.0885     Document Type: Article

References (64)

1. Adachi, J. & Hasegawa, M. 1996 Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42, 459-468.
2. Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A. & Lake, J. A. 1997 Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 189-493.
3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. L. 1995 Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Asakawa, S., Himeno, H., Miura, K. & Watanabe, K. 1995 Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics 140, 1047-1060.
5. Backeljau, T., Winnepenninckx, B. & De Bruyn, L. 1993 Cladistic analysis of metazoan relationships: a reappraisal. Cladistics 9, 167-181.
6. Balavoine, G. & Adoutte, A. 1998 One or three Cambrian radiations? Science 280, 397-398.
7. Boore, J. L. 1999 Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767-1780.
8. Boore, J. L. & Brown, W. M. 1994a Mitochondrial genomes and the phylogeny of mollusks. Nautilus 2(Suppl.), 61-78.
9. Boore, J. L. & Brown, W. M. 1994b Complete DNA sequence of the mitochondrial genome of the black chiton Katharina tunicata. Genetics 138, 423-443.
10. Boore, J. L. & Brown, W. M. 1995 Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics 141, 305-319.
11. Boore, J. L. & Brown, W. M. 1998 Big tress from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8, 668-674.
12. Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L. & Brown, W. M. 1995 Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376, 163-165.
13. Boore, J. L., Lavrov, D. V. & Brown, W. M. 1998 Gene translocation links insects and crustaceans. Science 392, 667-668.
14. Brusca, R. C. & Brusca, G. J. 1990 Invertebrates. Sunderland, MA: Sinauer Associates.
15. Cantatore, P., Gadaleta, M. N., Roberti, M., Saccone, C. & Wilson A. C. 1987 Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329, 853-855.
16. Castresana, J., Feldmaier-Fuchs, G., Yokobori, S., Satoh, N. & Pääbo, S. 1998 The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 150, 1115-1123.
17. Clary, D. O. & Wolstenholme, D. R. 1985 The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organisation and genetic code. J. Mol. Evol. 22, 252-271.
18. Cohen, B. L. & Gawthrop, A. B. 1997 The brachiopod genome. In Treatise on invertebrate paleontology. Brachiopoda, revised (ed. A. Williams), pp. 189-211. Lawrence, KS: Geological Society of America and University of Kansas Press.
19. Cohen, B. L., Balfe, P. & Cohen, M. 1991 Molecular evolution and morphological speciation in North Atlantic brachiopods (Terebratulina ssp.). Can. J. Zool. 69, 2903-2911.
20. Cohen, B. L., Gawthrop, A. & Cavalier-Smith, T. 1998a Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences. Proc. R. Soc. Lond. B 353, 2039-2061.
21. Cohen, B. L., Stark, S., Gawthrop, A. B., Burke, M. E. & Thayer, C. W. 1998b Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa). Proc. R. Soc. Lond. B 265, 475-482.
22. Conway-Morris, S. 1995 Nailing the Lophophorates. Science 375, 365-366.
23. Conway-Morris, S. 1998 Metazoan phylogenies: falling into place or falling to pieces? A palaeontological perspective. Curr. Opin. Genet. Dev. 8, 662-667.
24. Conway-Morris, S. & Peel, S. 1995 Articulated balkieriids from the Lower Cambrian of North Greenland and their role in early protostome evolution. Phil. Trans. R. Soc. Lond. B 347, 305-358.
25. Conway-Morris, S., Cohen, B. L., Gawthrop, A. B., Cavalier-Smith, T. & Winnepenninckx, B. 1996 Lophophorate phylogeny. Science 272-282.
26. Eernisse, D. J., Albert, J. S. & Anderson, F. E. 1992 Annelida and Arthropoda are not sister-taxa: a phylogenetic analysis of spiralian metazoan morphology. Syst. Biol. 41, 305-330.
27. Emig, C. 1976 Le Lophophore-structure significative des Lophophorates (Brachiopoda, Bryozoa, Phoronida). Zool. Sci. 5, 133-137.
28. Emig, C. 1984 On the origin of the Lophophorata. Z. Zool. Syst. Evolut.-Forsch. 22, 91-94.
29. Felsenstein, J. & Churchill, G. A. 1996 A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13, 93-104.
30. Field, K. G., Olsen, G. J., Lane, D. J., Giovannoni, S. J., Ghiselin, M. T., Raff, E. C., Pace, N. R. & Raff, R. A. 1988 Molecular phylogeny of the animal kingdom. Science 239, 748-753.
31. Halanych, K. M. 1993 Suspension feeding by the lophophore-like apparatus of the pterobranch hemichordate Rhabdopleura normani. Biol. Bull. 185, 417-427.
32. Halanych, K. M. 1995 The phylogenetic position of the pterobranch hemichordates based on 18SrDNA sequence data. Mol. Phyl. Evol. 4, 72-76.
33. Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M. A., Liva, S. M., Hillis, D. M. & Lake, J. A. 1995 Evidence from 18S ribosomal DNA that the Lophophorates are protostome animals. Science 267, 1641-1643.
34. Hasegawa, M. & Fujiwara, M. 1993 Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phyl. Evol. 2, 1-5.
35. Hatzoglou, E., Rodakis, G. C. & Lecanidou, R. 1995 Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coeralea. Genetics 140, 1353-1366.
36. Hennig, W. 1966 Phylogenetic systematics. Urbana, IL: University of Illinois Press.
37. Hoffmann, R. J., Boore, J. L. & Brown, W. M. 1992 A novel mitochondrial gene organization for the blue mussel, Mytilus edulis. Genetics 131, 397-412.
38. Jacobs, H. T., Balfe, P., Cohen, B. L., Farquharson, A. & Comito, L. 1988 Phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA. In Echinoderm phylogeny and evolutionary biology (ed. C. R. C. Paul & A. B. Smith), pp. 121-137. Oxford, UK.: Clarendon Press.
39. Kimura, M. 1983 The neutral theory of molecular evolution. Cambridge University Press.
40. 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.
41. Kyle, J. & Doolilttle, R. F. 1982 A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
42. Lake, J. A. 1990 Origin of the metazoz. Proc. Natl Acad. Sci. USA 87, 763-766.
43. Lee, W. J. & Kocher, T. D. 1995 Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139, 873-887.
44. Mackey, L. Y., Winnepenninckx, B., De Wachter, R., Backeljau, T., Emschermann, P. & Garey, J. R. 1996 18SrRNA suggests that Entoprocta are protostomes, unrelated to Ectoprocta. J. Mol. Evol. 42, 552-559.
45. Moritz, C., Dowling, T. E. & Brown, W. M. 1987 Evolution of animal mitochondrial DNA: relevance for population biology and systematic. A. Rev. Ecol. Syst. 18, 269-292.
46. Nielsen, C. 1987 Structure and function of metazoan ciliary bands and their phylogenetic significance. Acta Zool. 68, 205-262.
47. Nielsen, C. 1995 Animal evolution. Interrelationships of the living phyla. Oxford University Press.
48. Palumbi, S., Martin, A., Romano, W. O., Srice, L. & Grabowski, G. 1991 The simple fools guide to PCR, version 2.0. Honolulu: University of Hawaii.
49. Ruiz-Trillo, I., Riutort, M., Littlewood, D. T. J., Herniou, E. A. & Baguna, J. 1999 Acoel flatworms: earliest extant bilaterian metazoans, not members of platyhelminthes. Science 283, 1919-1923.
50. Salvini-Plawen, L. V. 1982 A paedomorphic origin of the oligomerous animals? Zool. Scr. 11, 77-81.
51. Sambrook, J., Fritsch, E. T. & Maniatis, T. 1989 Molecular cloning. A laboratory manual, 2nd edn. New York: Cold Spring Harbor Laboratory Press.
52. Sasuga, J., Yokobori, S., Kaifu, M., Ueda, T., Nishikawa, K. & Watanabe, K. 1999 Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J. Mol. Evol. 48, 692-702.
53. Smith, M. J., Arndt, A., Gorski, S. & Fajber, E. 1993 The phylogeny of echinoderm classes based on mitochondrial gene arrangements. J. Mol. Evol. 36, 545-554.
54. Spruyt, N., Delarbre, C., Gachelin, G. & Laudet, V. 1998 Complete sequence of the amphioxus (Branchiostoma lanceo-latum) mitochondrial genome: relations to vertebrates. Nucl. Acids Res. 26, 3279-3285.
55. Staton, J. L., Daehler, L. L. & Brown, W. M. 1997 Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol. Biol. Evol. 14, 867-874.
56. Strimmer, K. & Von Haeseler, A. 1996 Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 240-247.
57. Strimmer,K. & Von Haeseler,A. 1997 Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl Acad. Sci. USA 94, 6815-6819.
58. Tajima,F. & Nei,M. 1984 Estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 1, 269-285.
59. Terrett, J. A., Miles, S. & Thomas, R. H. 1996 Complete DNA sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda: Pulmonata). J. Mol. Evol. 42, 160-168.
60. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
61. Van de Peer, Y. & De Wachter, R. 1991 TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10, 569-570.
62. Wilding, C. S., Mill, P. J. & Grahame, J. 1999 Partial sequence of the mitochondrial genome of Littorina saxatilis: relevance to gastropod phylogenetics. J. Mol. Evol. 48, 348-359.
63. Wolstenholme, D. R. 1992 Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173-216.
64. Yamazaki, N. (and II others) 1997 Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organization of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145, 749-758.