Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds

Genome

Volumn 47, Issue 3, 2004, Pages 535-545

  Pereira, Sergio L ^a,b   Grau, Erwin T ^a   Wajntal, Anita ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b DEPARTMENT OF NATURAL HISTORY   (Canada)

Author keywords

Aves; Cracidae; Mitochondrial control region; Molecular evolution

Indexed keywords

DNA; PRIMER DNA;

ANIMAL; ARTICLE; BIRD; GENETICS; MITOCHONDRION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; BIRDS; DNA; DNA PRIMERS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

AVES; CRACIDAE;

EID: 4143101642     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g04-009     Document Type: Article

References (51)

1. Anderson, S., Bankier, A.T., Barrel, B.G., de Bruijn, M.H., Coulson, A.R. et al. 1981. Sequence and organization of the human mitochondrial genome. Nature (London), 290: 457-465.
2. Aquadro, C.F., and Greenberg, B.D. 1983. Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics, 103: 287-312.
3. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Niegel, J.E., Reeb, C.A., and Saunders, N.C. 1987. Intraespecific phylogeography: the mitochondrial bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18: 489-522.
4. Baker, A.J., and Marshall, H.D. 1997. Mitochondrial control region sequences as tools for understanding evolution. In Avian molecular systematics. Edited by D.P. Mindell. Academic Press, San Diego, Calif. pp. 51-82.
5. Berg, T., Moum, T., and Johansen, S. 1995. Variable number of simple tandem repeats make birds of the order Ciconiformes heteroplasmic in their mitochondrial genomes. Curr. Genet. 27: 257-262.
6. Brown, G.G., Gadaleta, G., Pepe, G., Saccone, C., and Sbisá, E. 1986. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192: 503-511.
7. Buehler, D.M., and Baker, A.J. 2003. Characterization of the red knot (Calidris canutus) mitochondrial control region. Genome, 46: 565-572.
8. Cann, R.L., Brown, W.M., and Wilson, A.C. 1984. Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics, 106: 479-499.
9. Cheng, S., Higuchi, R., and Stoneking, M. 1994. Complete mitochondrial genome amplification. Nat. Genet. 7: 350-351.
10. Crochet, P.A., and Desmarais, E. 2000. Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae). Mol. Biol. Evol. 17: 1797-1806.
11. Desjardins, P., and Morais, R. 1990. Sequence and gene organization of the chicken mitochondrial genome - a novel gene order in higher vertebrates. J. Mol. Biol. 212: 599-634.
12. Desjardins, P., and Morais, R. 1991. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J. Mol. Evol. 32: 153-161.
13. Doda, J.N., Wright, C.T., and Clayton, D.A. 1981. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA. 78: 6116-6120.
14. Douzery, E., and Randi, E. 1997. The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content. Mol. Biol. Evol. 14: 1154-1166.
15. Dufresne, C., Mignotte, F., and Guéride, M. 1996. The presence of tandem repeats and the initiation of replication in rabbit mitochondrial DNA. Eur. J. Biochem. 235: 593-600.
16. Eberhard, J.R., Wringht, T.F., and Bermingham, E. 2001. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol. Biol. Evol. 18: 1330-1342.
17. Grau, E.T., Pereira, S.L., Silveira, L.F., and Wajntal, A. 2003. Molecular markers contribute to a breeding programme of the extinct in the wild Alagoas Curassow Mitu mitu and confirm the validity of the species. Bird Conserv. Int. 13: 115-126.
18. Haddrath, O., and Baker, A.J. 2001. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and vicariance biogeography hypothesis. Proc. R. Soc. Lond. B Biol. Sci. 268: 939-945.
19. Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21: 160-174.
20. Kimball, R.T., Braun, E.L., and Ligon, J.D. 1997. Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma. Proc. R. Soc. Lond. B Biol. Sci. 264: 1517-1523.
21. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X., and Wilson, A.C. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA. 86: 6196-6200.
22. Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: molecular evolutionary genetics analysis software. Arizona State University, Tempe, Ariz.
23. L'Abbé, D.L., Duhaime, J.-F., Lang, B.F., and Morais, R. 1991. The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850.
24. Maddison, D.R., and Maddison, W.P. 2000. MacClade 4.0. Sinauer Associates, Inc., Sunderland, Mass.
25. Miyaki, C.Y., Matioli, S.R., Burke, T., and Wajntal, A. 1998. Parrot evolution and paleogeographical events: mitochondrial DNA evidence. Mol. Biol. Evol. 15: 544-551.
26. Pereira, S.L. 2000. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23: 745-752.
27. Pereira, S.L., and Baker, A.J. 2004. A vicariant hypothesis for the speciation of curassows (Aves, Cracidae) based on mitochondrial DNA phylogeny. Auk, 121: In press.
28. Pereira, S.L., Baker, A., and Wajntal, A. 2002. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). Syst. Biol. 51: 946-958.
29. Posada, D., and Crandall, K.A. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics, 14: 817-818.
30. Quinn, T.W., and Wilson, A.C. 1993. Sequence evolution in and around the mitochondrial control region in birds. J. Mol. Evol. 37: 417-425.
31. Randi, E., and Lucchini, V. 1998. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449-462.
32. Rest, J.S., Ast, J.C., Austin, C.C., Waddell, P.J., Tibbetts, E.A., Hay, J.M., and Mindell, D.P. 2003. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol. Phylogenet. Evol. 29: 289-297.
33. Ritchie, P.A., and Lambert, D.M. 2000. A repeat complex in the mitochondrial control region of Adélie penguins from Antarctica. Genome, 43: 613-618.
34. Rodriguéz, F., Oliver, J.L., Marín, A., and Medina, J.R. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501.
35. Ruokonen, M., and Kvist, L. 2002. Structure and evolution of the avian mitochondrial control region. Mol. Phylogenet. Evol. 23: 422-432.
36. Saccone, C., De Giorgio, C., Gissi, C., Pesole, G., and Reyes, A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene, 238: 195-209.
37. Sambrook, J., Fritsch, F., and Maniats, T. 1989. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
38. Sanderson, M.J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19: 101-109.
39. Saunders, M.A., and Edwards, S.V. 2000. Dynamics and phylogenetic implications of mtDNA control region sequences in New World jays (Aves: Corvidae). J. Mol. Evol. 51: 97-109.
40. Sbisá, E., Tanzariello, F., Reyes, A., Pesole, G., and Saccome, C. 1997. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene, 205: 125-140.
41. Slack, K.E., Janke, A., Penny, D., and Arnason, U. 2003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene, 302: 43-52.
42. Sorenson, M.D., Ast, J.C., Dimcheff, E.D., Yuri, T., and Mindell, D.P. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12: 105-114.
43. Steinborn, R., Muller, M., and Brem, G. 1998. Genetic variation in functionally important domains of the bovine mtDNA control region. Biochim. Biophys. Acta, 1397: 295-304.
44. Strimmer, K., and von Haeseler, A. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.
45. Swofford, D.L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and related methods). Version 4.10b. Sinauer Associates, Sunderland, Mass.
46. Taanman, J.-W. 1999. The mitochondrial genome: structure, transcription, translation and replication. Biochim. Biophys. Acta, 1410: 103-123.
47. Tamura, K., and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
48. van Tuinen, M., and Dyke, G.J. 2004. Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol. Phylogenet. Evol. 30: 74-86.
49. van Tuinen, M., and Hedges, S.B. 2001. Calibration of avian molecular clocks. Mol. Biol. Evol. 18: 206-213.
50. Vawter, L., and Brown, W.M. 1986. Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science (Washington, D.C.), 234: 194-196.
51. Zink, R.M., Weller, S.J., and Blackwell, R.C. 1998. Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty. Mol. Phylogenet. Evol. 10: 191-201.