Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

Molecular Phylogenetics and Evolution

Volumn 57, Issue 3, 2010, Pages 1268-1275

  Dong, Feng ^a   Li, Shou Hsien ^b   Yang, Xiao jun ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

Author keywords

Historical diversification; Mitochondrial genes; Nuclear introns; Pomatorhinus; Taxonomic revision

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; ASIA; BAYES THEOREM; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETICS; INTRON; MOLECULAR EVOLUTION; PHYLOGENY; SONGBIRD; STATISTICAL MODEL;

ANIMALS; ASIA; BAYES THEOREM; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; INTRONS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AVES; POMATORHINUS; TIMALIIDAE; XIPHIRHYNCHUS;

EID: 78649675645     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.09.023     Document Type: Article

References (54)

1. Abzhanov A., Kuo W.P., Hartmann C., Grant B.R., Grant P.R., Abin C.J. The calmodulin pathway and evolution of elongated beak morphology in Darwin's fnches. Nature 2006, 442:563-567.
2. Ali S., Ripley S.D. Handbook of the Birds of India and Pakistan 1971, vol. 1. Oxford University Press, London, pp. 129-151.
3. Avise J.C., Arnold J., Ball R.M., Bermingham E., Lamb T., Neigel J.E., Reeb C.A., Saunders N.C. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 1987, 18:489-522.
4. 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.
5. Barker F.K., Vandergon A.J., Lanyon S.M. Assessment of species limits among yellow-breasted meadowlarks (Sturnella spp.) using mitochondrial and sex-linked markers. Auk 2008, 125:869-879.
6. Bǒhme M. The miocene climatic optimum: evidence from ectothermic vertebrates of Central Europe. Palaeogeogr. Palaeoclimatol. Palaeoecol. 2003, 195:389-401.
7. Cerling T.E., Harris J.M., MacFadden B.J., Leakey M.G., Quade J., Eisenmann V., Ehleringer J.R. Global vegetation changes through the Miocene/Pliocene boundary. Nature 1997, 389:153-158.
8. Cibois A. Mitochondrial DNA phylogeny of babblers (Timaliidae). Auk 2003, 120:35-540.
9. Cibois A., Kalyakin M.V., Han L.X., Pasquet E. Molecular phylogenetics of babblers (Timaliidae): revaluation of the genera Yuhina and Stachyris. J. Avian Biol. 2002, 33:380-390.
10. Cibois A., Pasquet E., Schulenberg T. Molecular systematics of the Malagasy babblers (Passeriformes: Timaliidae) and warblers (Passeriformes: Sylviidae), based on cytochrome b and 16s rRNA sequences. Mol. Phyl. Evol. 1999, 13:581-595.
11. Cicero C., Johnson N.K. Higher-level phylogeny of new world vireos (Aves: Vireonidae) based on sequences of multiple mitochondrial DNA genes. Mol. Phyl. Evol. 2001, 20:27-40.
12. Collar N.J. Subspecies of Taiwan birds-first impressions. BirdingASIA 2004, 2:71-87.
13. Collar N.J. A partial revision of the Asian babblers (Timaliidae). Forktail 2006, 22:85-112.
14. Collar N.J., Robson C. Family Timaliidae (babblers). Handbook of the Birds of the World 2007, vol. 12:165-171. Lynx Edicions, Birdlife International.
15. Deignan H.G. Timaliinae, Panurinae, Picathartinae. A Checklist of Birds of the World: A Continuation of the Work of James L. Peters 1964, vol. 10:266-283. Museum of Comparative Zoology, Cambridge.
16. Delacour J. Les Timaliinés. L'Oiseau 1946, 16:7-36.
17. Delacour J. Les Timaliinés: Additions et modifi cations. L'Oiseau 1950, 20:186-191.
18. Delacour, J., Greenway Jr., J.C., 1940. Notes critiques sur certain oiseaux indochinois. L'Oiseau R.f.O. 10, 60-77.
19. deMenocal P.B. African climate change and faunal evolution during the Pliocene-Pleistocene. Earth Planet. Sci. Lett. 2004, 220:3-24.
20. Dickinson E.C. The Howard and Moore Complete Checklist of the Birds of the World 2003, Princeton University Press, London, pp. 602-604. third ed.
21. Dong F., Wu F., Liu L.M., Yang X.J. Molecular phylogeny of the barwings (Aves: Timaliidae: Actinodura), a paraphyletic group, and its taxonomic implications. Zool. Stud. 2010, 49:703-709.
22. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
23. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
24. Duckworth J.W., Timmins R.J., Thewlis R.M., Robichaud W.G., Evans T.D. Ornithological records from Laos, October 1994-August 1995. Forktail 1998, 13:33-68.
25. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1994, 10:315-319.
26. Futuyma D. Evolutionary Biology 1998, Sinauer Associates, Sunderland, MA. third ed.
27. Gelang M., Cibois A., Pasquet E., Olsson U., Alstrom P., Ericson G.P. Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification. Zoo. Scri. 2009, 38:225-236.
28. Gill F.B., Slikas B., Sheldon F.H. Phylogeny of Titmice (Paridae): II. Species relationships based on sequences of the Mitochondrial Cytochrome-b gene. Auk 2005, 122:121-143.
29. Horsfield T.M.D. Dr.Horsfield's systematic arrangement and description of bird from the island of Java. Trans. Linn. Soc. London 1821, 13:133-200.
30. Huelsenbeck J.P., Ronquist F. Mrbayes: bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
31. Inskipp T., Lindsey N., Duckworth W. An annotated checklist of the birds of the Oriental region 1996, Oriental Bird Club, Sandy, UK.
32. Irwin D.E., Irwin J.H., Price T.D. Ring species as bridges between microevolution and speciation. Genetica 2001, 112-113:223-243.
33. Luo X., Qu Y.H., Han L.X., Li S.H., Lei F.M. A phylogenetic analysis of laughingth rushes (Timaliidae: Garrulax) and allies based on mitochondrial and nuclear DNA sequences. Zoo. Scri. 2009, 38:9-12.
34. Maddison W.P., Donoghue M.J., Maddison D.R. Outgroup analysis and parsimony. Syst. Zool. 1984, 33:83-103.
35. Mayr E., Bock W.J. Classifications and other ordering systems. J. Zool. Syst. Evol. Res. 2002, 40:169-194.
36. Moyle R.G., Filardi C.E., Smith C.E., Diamond J. Explosive Pleistocene diversification and hemispheric expansion of a "great speciator" Proc. Natl. Acad. Sci. USA 2009, 106:1863-1868.
37. Pasquet E., Bourdon E., Kalyakin M.V., Cibois A. The fulvettas (Alcippe, Timaliidae, Aves): a polyphyletic group. Zoo. Scri. 2006, 35:559-566.
38. Pennington R.T., Lavin M., Prado D.E., Pendry C.A., Pell S.K., Butterworth C.A. Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification Philos. Trans. Biol. Sci. 2004, 359:515-538.
39. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
40. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
41. Ramsay W., F.Z.S.M.B.O.U. A synopsis of the genus Pomatorhinus 1887, 20:129-145.
42. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Available from: http://beast.bio.ed.ac.uk/Tracer.
43. Ravelo A.C., Andreasen D.H., Lyle M., Lyle A.O., Wara M.W. Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature 2004, 429:263-267.
44. Sambrook E., Fritsch F., Maniatis T. Molecular Cloning 1989, Cold Spring Harbor Press, Cold Spring Harbor.
45. Sibley C.G., Monroe B.L.Jr. Distribution and Taxonomy of Birds of the World 1990, Yale University Press, New Haven and London.
46. Smythies B.E. The Birds of Myanmar 1986, Nimrod Press LTD and Canada: Silvio Mattacchione and CO, Pickering, England, pp. 303-305. third ed.
47. Stanford J.K., Ticehurst C.B. Notes on some new or rarely recorded Burmese birds-Part I. IBIS 1935, 13:38-65.
48. Swofford D.L. Paup*. Phylogenetic analysis using parsimony (* and other methods), v. 4b10 2002, Sinauer, Sunderland.
49. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
50. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The clustal x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res. 1997, 24:4876-4882.
51. Wolters, H.E., 1975-2. Die Vogelarten der Erde, Hamburg and Berlin, Paul Parey, pp. 391-392.
52. Zachos J., Pagani M.N., Sloan L., Thomas E., Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to Present. Science 2001, 292:686-693.
53. Zhang S.X., Yang L., Yang X.J., Yang J.X. Molecular phylogeny of the yuhinas (Sylviidae: Yuhina): a paraphyletic group of babblers including Zosterops and Philippine Stachyris. J. Avian Biol. 2007, 148:216-417.
54. Zheng H.B., Chris M.P., David K.R., Wang J.L., Wang P.X. Late Miocene and mid-Pliocene enhancement of the East Asian monsoon as viewed from the land and sea. Glob. Planet Change 2004, 41:147-155.