Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny

Molecular Phylogenetics and Evolution

Volumn 57, Issue 1, 2010, Pages 466-470

  Nabholz, Benoit ^a   Jarvis, Erich D ^b   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Mitochondrial DNA; Molecular phylogeny; Muscicapoidae; Next generation sequencing; Paridae; Passerida; Passeriformes; Passeroidea; Songbirds; Sylvioidea

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; PHYLOGENY; SONGBIRD;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME, MITOCHONDRIAL; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AVES; MUSCICAPIDAE; PARIDAE; PASSERI; PASSERIDA; PASSERIFORMES; PASSEROIDEA;

EID: 77956227293     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.06.009     Document Type: Article

References (33)

1. Barker F.K., Barrowclough G.F., Groth J.G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. Biol. Sci. 2002, 269:295-308.
2. Barker F.K., Cibois A., Schikler P., Feinstein J., Cracraft J. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 2004, 101:11040-11045.
3. Berlin S., Tomaras D., Charlesworth B. Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome. Heredity 2007, 99:389-396.
4. Clements J.F. The Clements Checklist of Birds of the World 2007, Cornell University Press. sixth ed.
5. Delsuc F., Phillips M.J., Penny D. Comment on " Hexapod origins: monophyletic or paraphyletic?" Science 2003, 301:1482.
6. Ericson P.G.P., Johansson U.S. Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data. Mol. Phylogenet. Evol. 2003, 29:126-138.
7. Ericson P.G.P., Christidis L., Irestedt M., Norman J.A. Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds. Mol. Phylogenet. Evol. 2002, 25:53-62.
8. Ericson P.G.P., Christidis L., Cooper A., Irestedt M., Jackson J., Johansson U.S., Norman J.A. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc. Biol. Sci. B 2002, 269:235-241.
9. Gibb G.C., Kardailsky O., Kimball R.T., Braun E.L., Penny D. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol. Biol. Evol. 2007, 24:269-280.
10. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
11. Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
12. Hale M.C., Mccormick C.R., Jackson J.R., Dewoody J.A. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 2009, 10:203.
13. Harrison G.L., Mclenachan P.A., Phillips M.J., Slack K.E., Cooper A., Penny D. Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol. Biol. Evol. 2004, 21:974-983.
14. Hazkani-Covo E., Zeller R.M., Martin W. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 2010, 6:e1000834.
15. Jex A.R., Hu M., Littlewood D.T., Waeschenbach A., Gasser R.B. Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics 2008, 9:11.
16. Johansson U.S., Fjeldså J., Bowie R.C.K. Phylogenetic relationships within Passerida (Aves: Passeriformes): a review and a new molecular phylogeny based on three nuclear intron markers. Mol. Phylogenet. Evol. 2008, 48:858-876.
17. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
18. Künstner A., Wolf J.B., Backström N., Whitney O., Balakrishnan C.N., Day L., Edwards S.V., Janes D.E., Schlinger B.A., Wilson R.K., Jarvis E.D., Warrens W.C., Ellegren H. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol. Ecol. 2010, 19(Suppl. 1):266-276.
19. Meyer M., Stenzel U., Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 2008, 3:267-278.
20. Nabholz B., Glémin S., Galtier N. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol. Biol. 2009, 9:54.
21. Paton T., Haddrath O., Baker A.J. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. Biol. Sci. B 2002, 269:839-846.
22. Pereira S.L., Baker A.J. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evol. Biol. 2004, 4:17.
23. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
24. Pratt R.C., Gibb G.C., Morgan-Richards M., Phillips M.J., Hendy M.D., Penny D. Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol. Biol. Evol. 2009, 26:313-326.
25. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
26. Scarpulla R.C. Transcriptional paradigms in mammalian mitochondrial biogenesis and function. Physiol. Rev. 2008, 88:611-638.
27. Schwartz S., Kent W.J., Smit A., Zhang Z., Baertsch R., Hardison R.C., Haussler D., Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003, 13:103-107.
28. Scornavacca C., Berry V., Lefort V., Douzery E.J., Ranwez V. PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics 2008, 9:413.
29. Sibley C.G., Ahlquist J.E. Phylogeny and Classification of Birds: A Study in Molecular Evolution 1990, Yale University Press.
30. Slack K.E., Jones C.M., Ando T., Harrison G.L., Fordyce R.E., Arnason U., Penny D. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 2006, 23:1144-1155.
31. Sorenson M.D., Quinn T.W. Numts: a challenge for avian systematics and population biology. Auk 1998, 115:214-221.
32. Treplin S., Siegert R., Bleidorn C., Thompson H.S., Fotso R., Tiedemann R. Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci. Cladistics 2008, 24:328-349.
33. Zwickl, D., 2006. Ph.D. Thesis. University of Texas.