Molecular phylogenetics of babblers (Timaliidae): Revaluation of the genera Yuhina and Stachyris

Journal of Avian Biology

Volumn 33, Issue 4, 2002, Pages 380-390

  Cibois, Alice ^a,d   Kalyakin, Mikhail V ^b   Lian Xian, Han ^c   Pasquet, Eric ^a  

^a Serv de Systematique Molec   (France)

^b Zoological Mus of Moscow L S U   (Russian Federation)

^c Department of Forest Conservation ^*  (China)

^d MUSÉUM D HISTOIRE NATURELLE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR ANALYSIS; PHYLOGENY; TAXONOMY;

AVES; PASSERI; STACHYRIS; TIMALIIDAE; YUHINA; YUHINA ZANTHOLEUCA;

EID: 0036945151     PISSN: 09088857     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1600-048X.2002.02882.x     Document Type: Article

References (89)

1. Arctander, P. 1995. Comparison of a mitochondrial gene and a corresponding nuclear pseudogene. - Proc. R. Soc. Lond. B 262: 13-19.
2. Beecher, W. J. 1978. Feeding adaptations and evolution in the starlings. - Bull. Chicago Acad. Sci. 11: 269-298.
3. Belshaw, R. and Quicke, D. L. J. 1997. A molecular phylogeny of the Aphidiinae (Hymenoptera: Braconidae). - Mol. Phyl. Evol. 7: 281-293.
4. Blyth, E. 1844. Appendix to Mr. Blyth's report. - J. Asiat. Soc. Bengal 13: 378-380.
5. Bock, W. J. 1962. The pneumatic fossa of the humerus in the Passeres. - Auk 79: 425-443.
6. Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. - Evolution 42: 795-803.
7. Bremer, K. 1994. Branch support and tree stability. - Cladistics 10: 295-304.
8. Brown, W. M., Prager, E. M., Wang, A. and Wilson, A. C. 1982. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. - J. Mol. Evol. 18: 225-239.
9. Cibois, A., Pasquet, E. and Schulenberg, T. S. 1999. Molecular systematics of the Malagasy babblers (Passeriformes: Timaliidae) and warblers (Passeriformes: Sylviidae), based on cytochrome b and 16S rRNA sequences. - Mol. Phyl. Evol. 13: 581-595.
10. Cibois, A., Slikas, B., Schulenberg, T. S. and Pasquet, E. 2001. An endemic radiation of Malagasy songbirds is revealed by mitochondrial DNA sequence data. - Evolution: 1198-1206.
11. Cicero, C. and Johnson, N. K. 1995. Speciation in sapsuckers (Sphyrapicus): III Mitochondrial DNA sequence divergence at the cytochrome b locus. - Auk 112: 547-563.
12. De Schauensee, R. M. 1984. The Birds of China. - Oxford University Press, Oxford.
13. Deignan, H. G. 1964. Timaliinae, Panurinae, Picathartinae. In: Mayr, E. and Paynter, R. A., Jr. (eds). A Checklist of Birds of the World: a continuation of the work of James L. Peters, Vol. 10. Museum of Comparative Zoology, Cambridge, MA, pp. 240-442.
14. Delacour, J. 1946. Les Timaliinés. - L'Oiseau 16: 7-36.
15. Delacour, J. and Jabouille, P. 1931. Les Oiseaux de l'Indochine Française. - Impr. du Cantal républicain, Aurillac.
16. Desjardin, 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.
17. Dickinson, E. C., Kennedy, R. S. and Parkes, K. C. 1991. The Birds of the Philippines: An Annotated Check-list. B.O.U. Check-list No. 12. - British Ornithologists' Union, Herts.
18. Dixon, M. T. and Hillis, D. M. 1993. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. - Mol. Biol. Evol. 10: 256-267.
19. Doyle, J. J. and Doyle, J. L. 1987. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. - Phytochem. Bull. 19: 11-15.
20. Dzerzhinski, F. Y., Kalyakin, M. V. and Korzun, L. P. 1992. The experience of morpho-functional screening in study of trophic adaptations of tropical forest birds. - Tropcenter-91. Moscow-Hanoi-Hosimin-Nyachang. Part 1: 25-27.
21. Eames, J. C., Trai, L. T. and Cu, N. 1999a. A new species of laughingthrush (Passeriformes: Garrulacinea) from the Western highlands of Vietnam. - Bull. Br. Ornithol. Club. 119: 4-15.
22. Eames, J. C., Trai, L. T., Cu, N. and Eve, R. 1999b. New species of Barwing Actinodura (Passeriformes: Sylviinae: Timaliini) from the Western Highlands of Vietnam. - Ibis 141: 1-10.
23. Eriksson, T. 1997. "Autodecay" 2.9.10 (Hypercard stack distributed by the author). - Department of Botany, Stockholm University, Stockholm.
24. Farris, J. S., Källersjö, M., Kluge, A. G. and Bult, C. 1995. Testing significance of incongruence. - Cladistics 10: 315-319.
25. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. - Syst. Zool. 27: 401-410.
26. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using bootstrap. - Evolution 39: 783-791.
27. Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. - Annu. Rev. Genet. 22: 521-565.
28. Gaston, A. J. 1977. Social behaviour within groups of jungle babblers Turdoides striatus. - Anim. Behav. 25: 828-848.
29. Gaston, A. J. 1978. Demography of the jungle babbler Turdoides striatus. - J. Anim. Ecol. 47: 845-870.
30. Gonzales, P. C. and Kennedy, R. S. 1990. A new species of Stachyris babbler (Aves: Timaliidae) from the island of Panay, Philippines. - Wilson Bull. 102: 367-570.
31. Griffiths, C. S. 1997. Correlation of functional domains and rates of nucleotide substitution in cytochrome b. - Mol. Phyl. Evol. 7: 352-365.
32. Harrison, C. J. O. 1986a. A re-assessment of the affinities of some small oriental babblers Timaliidae. - Forktail 1: 81-83.
33. Harrison, C. J. O. 1986b. A re-assignment of two small babblers at present in the genus Yuhina. - J. Bombay Nat. Hist. Soc. 83: 202-206.
34. Helm-Bychowski, K. and Cracraft, J. 1993. Recovering phylogenetic signal from DNA sequences: relationships within the Corvine assemblage (Class Aves) as inferred from complete sequences of the mitochondrial DNA cytochrome b gene. - Mol. Biol. Evol. 10: 1196-1214.
35. Hendy, M. D. and Penny, D. 1989. A framework for the quantitative study of evolutionary trees. - Syst. Zool. 38: 297-309.
36. Hickson, R. E., Simon, C., Cooper, A., Spicer, G. S., Sullivan, J. and Penny, D. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. - Mol. Biol. Evol. 13: 150-169.
37. Hill, W. E., Dahlberg, A., Garrett, R. A., Moore, P. B., Schessinger, D. and Warner, J. R. 1990. The Ribosome, Structure, Function, and Evolution. - American Society for Microbiology, Washington, D.C.
38. Hillis, D. M., Moritz, C. and Mable, B. K. 1996. Molecular Systematics, 2nd edn. - Sinauer Associates, Inc., Sunderland, MA.
39. Hodgson, B. H. 1836. A new genus and 3 new species of the Sylviadae. - Asiatic Res. 19: 165-167.
40. Howard, R. and Moore, A. 1994. A Complete Checklist of the Birds of the World, 2nd edn. - Academic Press, London.
41. Inskipp, T., Lindsey, N. and Duckworth, W. 1996. An Annotated Checklist of the Birds of the Oriental Region. - Oriental Bird Club, Bedfordshire.
42. Irwin, D. M., Kocher, T. D. and Wilson, A. C. 1991. Evolution of the cytochome b gene of mammals. - J. Mol. Evol. 32: 128-144.
43. Irwin, M. P. S. 1983. The Malagasy species of Timaliidae (babblers). - Honeyguide 116: 26-31.
44. Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. - Syst. Biol. 45: 363-374.
45. Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. - Mol. Phyl. Evol. 4: 314-330.
46. Krajewski, C. and King, D. G. 1996. Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes. - Mol. Biol. Evol. 13: 21-30.
47. MacKinnon, J. and Philipps, K. 1993. A Field Guide to the Birds of Borneo, Sumatra, Java and Bali. - Oxford University Press, Oxford.
48. Maddison, W. P. and Maddison, D. R. 1992. MacClade: Analysis of phylogeny and character evolution. Version 3.04. - Sinauer, Sunderland, MA.
49. Maidak, B. L., Larsen, N., McCaughey, M. J., Overbeek, R., Olsen, G. J., Fogel, K., Blandy, J. and Woese, C. R. 1994. The Ribosomal Database Project. - Nucleic Acids Res. 22: 3485-3487.
50. Mayr, E. and Amadon, D. 1951. A classification of recent birds. - Am. Mus. Novit. 1496: 1-42.
51. Meyer, A. 1994. Shortcomings of the cytochrome b gene as a molecular marker. - Trends Ecol. Evol. 9: 278-280.
52. Mindell, D. P. and Honeycutt, R. L. 1990. Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annu. Rev. Ecol. Syst. 21: 541-566.
53. Mindell, D. P., Sorenson, M. D., Huddleston, C. J., Miranda, H. C., Jr., Knight, A., Sawchuk, S. J. and Tamaki, Y. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. - In: Mindell, D. P. (ed.). Avian Molecular Evolution and Systematics. Academic Press, London, pp. 213-247.
54. Moore, W. S. and DeFilippis, V. R. 1997. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b. - In: Mindell, D. P. (ed.). Avian Molecular Evolution and Systematics. Academic Press, London, pp. 83-120.
55. Morrison, D. A. and Ellis, J. T. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S r DNAs of Apicomplexa. - Mol. Biol. Evol. 14: 428-441.
56. Noller, H. F. 1984. Structure of ribosomal RNA. - Annu. Rev. Biochem. 53: 119-162.
57. Nunn, G. B. and Cracraft, J. 1996. Phylogenetic relationships among the major lineages of the birds-of-paradise (Paradisaeidae) using mitochondrial DNA gene sequences. - Mol. Phyl. Evol. 5: 445-459.
58. Olsen, G. J. 1988. Phylogenetic analysis using ribosomal RNA. - Methods Enzymol. 164: 793-812.
59. Philippe, H. 1993. MUST: A computer package of management utilities for sequences and trees. - Nucleic Acids Res. 21: 5264-5272.
60. Posada, D. and Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. - Bioinformatics 14: 817-818.
61. Rand, A. L. 1970. Species formation in the blue monarch flycatchers genus Hypothymis. - Nat. Hist. Bull. Siam. Soc. 23: 353-365.
62. Ripley, S. D. and Beehler, B. M. 1985a. A revision of the babbler genus Trichastoma and its allies (Aves: Timaliidae). - Ibis 127: 495-509.
63. Ripley, S. D. and Beehler, B. M. 1985b. A new subspecies of the babbler genus Malacocincla abbotti from the Eastern Ghats, India. - Bull. Br. Ornithol. Club 105: 66-67.
64. Sambrook, J., Fritsch, E. F. and Maniatis, T. 1989. Molecular cloning: a laboratory manual. - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
65. Sanger, F., Nicklen, S. and Coulson, A. R. 1977. DNA sequencing with chain-terminating inhibitors. - Proc. Natl. Acad. Sci. USA 74: 5463-5467.
66. Sibley, C. G. and Ahlquist, J. E. 1985. The phylogeny and classification of Australo-Papuan passerine birds. - Emu 85: 1-14.
67. Sibley, C. G. and Ahlquist, J. E. 1990. Phylogeny and Classification of Birds: a study in molecular evolution. - Yale University Press, New Haven.
68. Sibley, C. G. and Monroe, B. L., Jr. 1990. Distribution and Taxonomy of Birds of the World. - Yale University Press, New Haven.
69. Simmons, K. E. L. 1963. Some behaviour characters of the babblers (Timaliidae). - Avicult. Mag. 69: 183-193.
70. Smith, A. B. 1989. RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution. - Cladistics 5: 321-344.
71. Smith, A. B. 1994. Rooting molecular trees: problems and strategies. - Biol. J. Linn. Soc. 51: 279-292.
72. Smythies, B. E. 1981. The Birds of Borneo. - Sabah Society with the Malayan Nature Society, Kuala Lumpur.
73. Springer, M. S. and Douzery, E. 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. - J. Mol. Evol. 43: 357-373.
74. Springer, M. S., Hollar, L. J. and Burk, A. 1995. Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. - Mol. Biol. Evol. 12: 1138-1150.
75. Swofford, D. L. 1999. PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Version 4.0. - Sinauer, Sunderland, MA.
76. Swofford, D. L., Olsen, G. J., Wadell, P. J. and Hillis, D. M. 1996. Phylogenetic inference. - In: Hillis, D. M., Moritz, C. and Mable, B. K. (eds). Molecular Systematics, 2nd ed. Sinauer, Sunderland, MA, pp. 407-514.
77. Van de Weghe, J. P. 1988. The validity of Kupeornis Serle. Bull. Brit. Ornithol. Club 108: 54-58.
78. Vawter, L. and Brown, W. M. 1993. Rates and patterns of change in the small subunit ribosomal RNA gene. Genetics 134: 597-608.
79. Voelker, G. and Edwards, S. V. 1998. Can weighting improve bushy trees? Models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Aves: Motacillidae). - Syst. Biol. 47: 589-603.
80. Walters, M. 1996. Check List of Birds. - Domino Books LTD, London.
81. Wheeler, W. C. 1995. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44: 321-332.
82. Wheeler, W. and Gladstein, D. 1994. MALIGN: a multiple sequence alignment program. - J. Hered. 85: 417.
83. Winnepenninckx, B. and Backeljau, T. 1996. 18S rRNA alignments derived from different secondary structure models can produce alternative phylogenies. - J. Zool. Syst. Evol. Res. 34: 135-143.
84. Winnepenninckx, B., Backeljau, T. and De Wachter, R. 1993. Extraction of high molecular weight DNA from mollusks. - Trends Genet. 9: 407.
85. Wolters, H. E. 1975-1982. Die Vogelarten der Erde. - Parey, Berlin.
86. Xu, W.-S., Zhao, Z.-K., Zheng, G.-M., Yan, C.-W. and Tan, Y.-K. 1996. A Field Guide to the Birds of China. - Kingfisher Press, Taiwan.
87. Yang, Z. 1994. Estimating the pattern of nucleotide substitution. - J. Mol. Evol. 39: 105-111.
88. Yoder, A. D., Irwin, J. A. and Payseur, B. A. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. - Syst. Biol. 50: 408-424.
89. Zhang, D.-X. and Ryder, O. A. 1993. Mitochondrial DNA sequence evolution in the Artoidea. - Proc. Natl. Acad. Sci. USA 90: 9557-9561.