A cryptic, intergeneric cytochrome c oxidase i pseudogene in tyrant flycatchers (family: Tyrannidae)

Genome

Volumn 53, Issue 12, 2010, Pages 1103-1109

  Kerr, Kevin C R ^a,b  

^a UNIVERSITY OF GUELPH   (Canada)

^b SMITHSONIAN INSTITUTION   (United States)

Author keywords

Contopus; Cytochrome c oxidase; DNA barcode; Empidonax; Mitochondrial DNA; Pseudogene

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOGENE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SONGBIRD;

AMINO ACID SUBSTITUTION; ANIMALS; BASE SEQUENCE; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PSEUDOGENES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SONGBIRDS;

AVES; CONTOPUS; EMPIDONAX; TYRANNIDAE;

EID: 78650324292     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G10-085     Document Type: Article

References (33)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215 (3): 403-410. 2231712
2. Antunes, A., and Ramos, M.J. 2005. Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. Genomics, 86 (6): 708-717. 10.1016/j.ygeno.2005.08.002 16176867 (Pubitemid 41752952)
3. Bensasson, D., Zhang, D.X., Hartl, D.L., and Hewitt, G.M. 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16 (6): 314-321. 10.1016/S0169-5347(01)02151-6 11369110 (Pubitemid 32706648)
4. Chung, W.K., and Steiper, M.E. 2008. Mitochondrial COII introgression into the nuclear genome of Gorilla gorilla. Int. J. Primatol. 29 (5): 1341-1353. 10.1007/s10764-008-9303-4 19802374
5. Cicero, C., and Johnson, N.K. 2002. Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyrannidae): a test of W. E. Lanyon's hypothesis using mtDNA sequences. Mol. Phylogenet. Evol. 22 (2): 289-302. 10.1006/mpev.2001.1054 11820849 (Pubitemid 34973445)
6. Coin, L., and Durbin, R. 2004. Improved techniques for the identification of pseudogenes. Bioinformatics, 20 (suppl 1): i94-i100. 10.1093/bioinformatics/ bth942 15262786 (Pubitemid 41296676)
7. Dunshea, G., Barros, N.B., Wells, R.S., Gales, N.J., Hindell, M.A., and Jarman, S.N. 2008. Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system. Bull. Entomol. Res. 98 (3): 239-248. 10.1017/S0007485308005993 18439341 (Pubitemid 351693042)
8. Frézal, L., and Leblois, R. 2008. Four years of DNA barcoding: current advances and prospects. Infect. Genet. Evol. 8 (5): 727-736. 10.1016/j.meegid.2008.05.005 18573351
9. Goios, A., Prieto, L., Amorim, A., and Pereira, L. 2008. Specificity of mtDNA-directed PCR-influence of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques. Int. J. Legal Med. 122 (4): 341-345. 10.1007/s00414-007-0191-5 17874117 (Pubitemid 351799184)
10. Guindon, S., and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (5): 696-704. 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
11. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser., 41: 95-98.
12. Hebert, P.D.N., Cywinska, A., Ball, S.L., and DeWaard, J.R. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B. Biol. Sci. 270 (1512): 313-321. 10.1098/rspb.2002.2218 (Pubitemid 36228536)
13. s ratio: diagnosing the form of sequence evolution. Trends Genet. 18 (9): 486-487. 10.1016/S0168-9525(02)02722-1 12175810
14. Johnson, N.K., and Cicero, C. 2002. The role of ecologic diversification in sibling speciation of Empidonax flycatchers (Tyrannidae): multigene evidence from mtDNA. Mol. Ecol. 11 (10): 2065-2081. 10.1046/j.1365-294X.2002.01588.x 12296949 (Pubitemid 35156999)
15. Kerr, K.C.R., Stoeckle, M.Y., Dove, C.J., Weigt, L.A., Francis, C.M., and Hebert, P.D.N. 2007. Comprehensive DNA barcode coverage of North American birds. Mol. Ecol. Notes, 7 (4): 535-543. 10.1111/j.1471-8286.2007.01670.x 18784793 (Pubitemid 47035498)
16. Mirol, P.M., Mascheretti, S., and Searle, J.B. 2000. Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, rodentia) with either great similarity to or high divergence from the true mitochondrial sequence. Heredity, 84 (5): 538-547. 10.1046/j.1365-2540.2000.00689.x 10849078 (Pubitemid 30446090)
17. Moritz, C., and Cicero, C. 2004. DNA barcoding: promise and pitfalls. PLoS Biol. 2 (10): e354. 10.1371/journal.pbio.0020354 (Pubitemid 39532912)
18. Mundy, N.I., Pissinatti, A., and Woodruff, D.S. 2000. Multiple nuclear insertions of mitochondrial cytochrome b sequences in callitrichine primates. Mol. Biol. Evol. 17 (7): 1075-1080. 10889220
19. Pons, J., and Vogler, A.P. 2005. Complex pattern of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles. Mol. Biol. Evol. 22 (4): 991-1000. 10.1093/molbev/msi085 15647517 (Pubitemid 40471412)
20. Posada, D., and Crandall, K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817 9918953
21. Rodrguez, F., Albornoz, J., and Domnguez, A. 2007. Cytochrome b pseudogene originated from a highly divergent mitochondrial lineage in genus Rupicapra. J. Hered. 98 (3): 243-249. 10.1093/jhered/esm013 17416931 (Pubitemid 47343927)
22. Rozen, S., and Skaletsky, H.J. 2000. Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols: methods in molecular biology. Edited by S. Krawetz and S. Misener. Humana Press, Totowa, N.J. pp. 365-386.
23. Sanderson, M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19 (2): 301-302. 10.1093/bioinformatics/19.2.301 12538260 (Pubitemid 36181923)
24. Song, H., Buhay, J.E., Whiting, M.F., and Crandall, K.A. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc. Natl. Acad. Sci. U.S.A. 105 (36): 13486-13491. 10.1073/pnas.0803076105 18757756
25. Sorenson, M.D., and Quinn, T.W. 1998. Numts: A challenge for avian systematics and population biology. Auk, 115 (1): 214-221.
26. Spinks, P.Q., and Shaffer, H.B. 2007. Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci. Conserv. Genet. 8 (3): 641-657. 10.1007/s10592-006-9210-1 (Pubitemid 46682962)
27. Swofford, D.L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
28. Tamura, K., Dudley, J., Nei, M., and Kumar, S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (8): 1596-1599. 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
29. Torrents, D., Suyama, M., Zdobnov, E., and Bork, P. 2003. A genome-wide survey of human pseudogenes. Genome Res. 13 (12): 2559-2567. 10.1101/gr.1455503 14656963 (Pubitemid 37541144)
30. Triant, D.A., and DeWoody, J.A. 2008. Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents. Genetica, 132 (1): 21-33. 10.1007/s10709-007-9145-6 17333478 (Pubitemid 350172602)
31. Weir, J.T., and Schluter, D. 2008. Calibrating the avian molecular clock. Mol. Ecol. 17 (10): 2321-2328. 10.1111/j.1365-294X.2008.03742.x 18422932 (Pubitemid 351623774)
32. s through model selection and model averaging. Genomics Proteomics Bioinf. 4 (4): 259-263. 10.1016/S1672-0229(07)60007-2 17531802 (Pubitemid 46771391)
33. Zink, R.M., and Johnson, N.K. 1984. Evolutionary genetics of flycatchers. I. Sibling species in the genera Empidonax and Contopus. Syst. Zool. 33 (2): 205-216. 10.2307/2413021