Mitochondrial DNA phylogeny of babblers (Timaliidae)

Auk

Volumn 120, Issue 1, 2003, Pages 35-54

  Cibois, Alice ^a,b,c  

^a Service de Systématique moléculaire   (France)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^c MUSÉUM D HISTOIRE NATURELLE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; PASSERINE; PHYLOGENY;

AVES; BABAX; GARRULAX; KAKAMEGA POLIOTHORAX; PASSERI; PASSERIFORMES; PTERUTHIUS; SYLVIA; SYLVIIDAE; TIMALIIDAE; ZOSTEROPIDAE; ZOSTEROPS;

EID: 0037227077     PISSN: 00048038     EISSN: None     Source Type: Journal    
DOI: 10.2307/4090138     Document Type: Article

References (103)

1. ALVAREZ, B., M. D. CRISP, F. DRIVER, J. N. A. HOOPER, AND R. W. M. VAN SOEST. 2000. Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data. Zoologica Scipta 29:169-198.
2. AMES, P. L. 1971. The morphology of the syrinx in passerine birds. Yale University, Peabody Museum of Natural History Bulletin, no. 37.
3. AMES, P. L. 1975. The application of syringeal morphology to the classification of the Old World insect eaters (Muscicapidae). Bonner Zoologishe Beiträge 26:107-134.
4. BANNERMAN, D. 1923. Remarks on the genera Turdinus and Alcippe. Bulletin of the British Ornithologists' Club 44:24-26.
5. BARKER, F. K., G. F. BARROWCLOUGH, AND J. G. GROTH. 2002. A phylogenetic hypothesis for passerine birds: Taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proceedings of the Royal Society of London, Series B 269:295-308.
6. BERLIOZ, J. 1930. Révision systématique du genre Garrulax Lesson. L'Oiseau 11:1-27, 78-105, 128-159.
7. BERNARDI, G., D. R. ROBERTSON, K. E. CLIFTON, AND E. AZZURRO. 2000. Molecular systematics, zoogeography and evolutionary ecology of the Atlantic parrotfish genus Sparisoma. Molecular Phylogenetics and Evolution 15:292-300.
8. BOCK, W. J. 1994. History and nomenclature of avian family-group names. Bulletin of the American Museum of Natural History, no. 222.
9. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
10. BREMER, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
11. BROWN, J. L. 1959. Method of head-scratching in the Wrentit and other species. Condor 61:53.
12. BUCKLEY, T. R., C. SIMON, H. SHIMODAIRA, AND G. K. CHAMBERS. 2001. Evaluating hypotheses on the origin and evolution of the New Zealand Alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology. Molecular Biology and Evolution 18:223-234.
13. CHAPIN, J. P. 1953. The birds of the Belgian Congo, Part. 3. Bulletin of the American Museum of Natural History, no. 75A.
14. CIBOIS, A. 2000. Phylogénie et biogéographie des Timaliidae (Aves: Passeriformes). Ph.D. dissertation, Muséum National d'Histoire Naturelle, Paris.
15. CIBOIS, A., M. V. KALYAKIN, L.-X. HAN, AND E. PASQUET. 2002. Molecular phylogenetics of babblers (Timaliidae): Reevaluation of the genera Yuhina and Stachyris. Journal of Avian Biology 33:380-390.
16. CIBOIS, A., E. PASQUET, AND T. S. SCHULENBERG. 1999. Molecular systematics of the Malagasy babblers (Passeriformes: Timaliidae) and warblers (Passeriformes: Sylviidae), based on cytochrome b and 16S rRNA sequences. Molecular Phylogenetics and Evolution 13:581-595.
17. CIBOIS, A., B. SLIKAS, T. S. SCHULENBERG, AND E. PASQUIT. 2001. An endemic radiation of Malagasy songbirds is revealed by mitochondrial DNA sequence data. Evolution 55:1198-1206.
18. CUNNINGHAM, C. W. 1997. Can tree incongruence tests predict when data should be combined? Molecular Biology and Evolution 17:733-740.
19. DEIGNAN, H. G. 1964. Timaliinae, Panurinae, Picathartinae. Pages 240-442 in A Check-list of Birds of the World: A Continuation of the Work of James L. Peters (E. Mayr and R. A. Paynter, Jr., Eds.). Museum of Comparative Zoology, Cambridge, Massachusetts.
20. DELACOUR, J. 1927. New birds from Indo-China. Bulletin of the British Ornithologists' Club 47:151-170.
21. DELACOUR, J. 1946. Les Timaliinés. L'Oiseau 16:7-36.
22. DELACOUR, J. 1950. Les Timaliinés: Additions et modifications. L'Oiseau 20:186-191.
23. DELACOUR, J., AND D. AMADON. 1951. The systematic position of Picathartes. Ibis 93:60-62.
24. DIXON, M. T., AND D. M. HILLIS. 1993. Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Molecular Biology and Evolution 10:256-267.
25. DOWSETT, R. J., AND A. D. FORBES-WATSON. 1993. Checklist of Birds of the Afrotropical and Magalasy Regions. Turaco Press, Liège, Belgium.
26. ERICKSON, M. M. 1938. Territory, annual cycle and numbers in a population of Wrentits (Chamaea fasciata). University of California Publications in Zoology 42:247-334.
27. ERICKSSON, T. 1997. "AUTODECAY" version 2.9.9 (Hypercard stack distributed by the author). Botaniska Institutionen, University of Stockholm, Stockholm.
28. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40:366-375.
29. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1995. Testing significance of incongruence. Cladistics 10:315-319.
30. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39:783-791.
31. FELSENSTEIN, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetic 22:521-565.
32. FJELDSÅ, J., S. M. GOODMAN, T. S. SCHULENBERG, AND B. SLIKAS. 1999. Molecular evidence for relationships of Malagasy birds. Pages 3084-3094 in Proceedings of the 22nd International Ornithological Congress (N. J. Adams and R. H. Slotow, Eds.). BirdLife South Africa, Johannesburg.
33. GALTIER, N., AND M. GOUY. 1998. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology and Evolution 15:871-879.
34. GASTON, A. J. 1977. Social behavior within groups of Jungle Babblers Turdoides striatus. Animal Behaviour 25:828-848.
35. GOLDMAN, N., J. P. ANDERSON, AND A. G. RODRIGO. 2000. Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49:652-676.
36. GOLDMAN, N., AND S. WHELAN. 2000. Statistical tests of gamma-distributed rate in heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution 17:975-978.
37. GOTO, S. G., AND M. T. KIMURA. 2001. Phylogenetic utilities of mitochondrial COI and nuclear Gpdh genes in Drosophila. Molecular Phylogenetics and Evolution 18:404-422.
38. GRIMES, L. G. 1976. Co-operative breeding in African birds. Pages 667-672 in Proceedings 16th International Ornithological Congress (H. J. Frith and J. H. Calaby, Eds.). Australian Academy of Science, Canberra.
39. HALL, B. P., AND R. E. MOREAU. 1970. An atlas of speciation in African passerine birds. British Museum of Natural History Publication, no. 680.
40. HARRISON, C. J. O. 1986a. A reassessment of the affinities of some small Oriental babblers Timaliidae. Forktail 1:81-83.
41. HARRISON, C. J. O. 1986b. A reassignment of two small babblers at present in the genus Yuhina. Journal of the Bombay Natural History Society 83:202-206.
42. HARSHMAN, J. 2001. Does the T-TPT test tell us anything we want to know? Systematic Biology 50:284-289.
43. HARTERT, E. 1910. Die Vögel der Paläarktischen Fauna. R. Friedlander, Berlin, Germany.
44. HELLMAR, L. E. 1903. Paridae, Sittidae, and Certhiidae. Das Tierreich, no. 18. Friedlander und Sohn, Berlin, Germany.
45. HORSFIELD, T. 1822. Systematic arrangement and description of birds from the island of Java. Transactions of the Linnean Society of London 13:133-200.
46. HOWARD, R., AND A. MOORE. 1994. A Complete Checklist of the Birds of the World, 2nd ed. Academic Press, London.
47. HUELSENBECK, J. P., D. M. HILLIS, AND R. JONES. 1996. Parametric bootstrapping in molecular phylogenetics: Applications and performance. Pages 19-45 in Molecular Zoology: Advances, Strategies, and Protocols (J. D. Ferraris and S. R. Palumbi, Eds.). Wiley-Liss, New York.
48. IRWIN, M. P. S. 1983. The Malagasy species of Timaliidae (babblers). Honeyguide 116:26-31.
49. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution 29:170-179.
50. LACK, D. 1968. Ecological Adaptation for Breedings in Birds. Methuen, London.
51. LANYON, S. M. 1992. Review of Phylogeny and Classification of Birds: A Study in Molecular Evolution by C. G. Sibley and J. E. Ahlquist. Condor 94:304-310.
52. LOCKART, P. J., M. A. STEEL, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution 11:605-612.
53. LOWE, P. R. 1938. Some anatomical and other notes on the systematic position of the genus Picathartes, together with some remarks on the families Strurnidae and Eulabetidae. Ibis 1938:254-269.
54. MADDISON, W. P., AND D. R. MADDISON. 1992. MACCLADE: Analysis of phylogeny and character evolution, version 3.04. Sinauer and Associates, Sunderland, Massachusetts.
55. MAIDAK, B. L., N. LARSEN, M. J. MCCAUGHEY, R. OVERBEEK, G. J. OLSEN, K. FOGEL, J. BLANDY, AND C. R. WOESE. 1994. The Ribosomal Database Project. Nucleic Acids Research 22:3485-3487.
56. MANN, C. F., P. J. K. BURTON, AND I. LENNERSTEDT. 1978. A re-appraisal of the systematic position of Trichastoma poliothorax (Timaliidae, Muscicapidae). Bulletin of the British Ornithologists' Club 98:131-140.
57. MAYR, E., AND D. AMADON. 1951. A classification of recent birds. American Museum Novitates, no. 1496.
58. MAYR, E., AND J. C. GREENWAY, Jr. 1956. Sequence of passerine families (Aves). Breviora 58:1-11.
59. MCCLURE, H. E. 1974. Migration and Survival of the Birds in Asia. U.S. Army Component, SEATO Medical Research Laboratory, Bagkok, Thailand.
60. MEES, G. F. 1957. A systematic review of the Indo-Australasian Zosteropidae, Part I. Zoologische Verhandelingen, no. 35.
61. MEES, G. F. 1961. A systematic review of the Indo-Australasian Zosteropidae, Part II. Zoologische Verhandelingen, no. 50.
62. MEES, G. F. 1969. A systematic review of the Indo-Australasian Zosteropidae, Part III. Zoologische Verhandelingen, no. 102.
63. MINDELL, D. P. 1992. "DNA-DNA hybridization and avian phylogeny." Review of Phylogeny and Classification of Birds: A Study in Molecular Evolution by C. G. Sibley and J. E. Ahlquist. Systematic Biology 41:126-134.
64. MINDELL, D. P., M. D. SORENSON, C. J. HUDDLESTON, H. C. MIRANDA, JR., A. KNIGHT, S. J. SAWCHUK, AND Y. TAMAKI. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. Pages 213-247 in Avian Molecular Evolution and Systematics (D. P. Mindell, Ed.). Academic Press, London.
65. MORONY, J. J., JR., W. J. BOCK, AND J. FARRAND, JR. 1975. Reference List of the Birds of the World. Department of Ornithology, American Museum of Natural History, New York.
66. MORRISON, D. A., AND J. T. ELLIS. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S r DNAs of Apicomplexa. Molecular Biology and Evolution 14:428-441.
67. PASQUET, E., A. CIBOIS, F. BAILLON, AND C. ERARD. 1999. Relationships between the ant-thrushes Neocossyphus and the flycatcher-thrushes Stizorhina, and their position relative to Myadestes, Entomodestes and some other Turdidae (Passeriformes). Journal of Zoological Systematics and Evolutionary Research 37:177-183.
68. PAYNTER, R. A., Jr., ED. 1967. Check-list of Birds of the World, vol. 12. Museum of Comparative Zoology, Cambridge, Massachusetts.
69. PHILIPPE, H. 1993. MUST: A computer package of management utilities for sequences and trees. Nucleic Acids Research 21:5264-5272.
70. POSADA, D., AND K. A. CRANDALL. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
71. RAMBAUT, A., AND N. C. GRASSLY. 1997. SEQ-GEN: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, version 1.2.5. Computer Applications in the Biosciences 13:235-238.
72. REICHENOW, A. 1900. Zwei neue Arten von Kamerun. Ornithologische Monatsberichte 8:6.
73. REICHENOW, A. 1914. Die Vögel, vol. 2. Ferdinand Enke, Stuttgart, Germany.
74. RIDGWAY, R. 1904. Birds of North and Middle America, family Chamaedae. Bulletin of the Smithsonian Institution, U.S. National Museum 50:683-691.
75. RIPLEY, S. D., AND B. M. BEEHLER. 1985. A revision of the babbler genus Trichastoma and its allies (Aves: Timaliidae). Ibis 127:495-509.
76. ROBINSON, H. C., AND C. B. KLOSS. 1919. On birds from South Annam and Cochin China. Part II. Pycnonotidae-Dicaeidae. Ibis 11th series, vol. 1:565-625.
77. SAMBROOK, J., E. F. FRITSH, AND T. MANIATIS. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
78. SANGER, F., S. NICKLEN, AND A. R. COULSON. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA 74:5463-5467.
79. SCLATER, W. L. 1930. Systema Avium Aethiopicarum, part 2. Taylor and Francis, London.
80. SERLE, W. 1950. The British Cameroons. Ibis 92:343-376, 602-638.
81. SHELDON, F. H., AND F. B. GILL. 1996. A reconsideration of songbird phylogeny, with emphasis on the evolution of titmice and their sylvioid relatives. Systematic Biology 45:473-495.
82. SHIMODAIRA, H., AND M. HASEGAWA. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 13:964-969.
83. SIBLEY, C. G., AND J. E. AHLQUIST. 1982. The relationships of the Wrentit as indicated by DNA-DNA hybridization. Condor 84:40-44.
84. SIBLEY, C. G., AND J. E. AHLQUIST. 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press, New Haven, Connecticut.
85. SIBLEY, C. G., AND B. L. MONROE, Jr. 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, Connecticut.
86. SIMMONS, K. E. L. 1963. Some behaviour characters of the babblers (Timaliidae). Avicultural Magazine 69:183-193.
87. SLIKAS, B., I. B. JONES, S. R. DERRICKSON, AND R. C. FLEISCHER. 2000. Phylogenetic relationships of Micronesian white-eyes based on mitochondrial sequence data. Auk 117:355-365.
88. SMITH, A. B. 1994. Rooting molecular trees: Problems and strategies. Biological Journal of the Linnean Society 51:279-292.
89. STURMBAUER, C., B. BERGER, R. DALLINGER, AND M. FÖGER. 1998. Mitochondrial phylogeny of the genus Regulus and implications on the evolution of breeding behaviour in sylvioid songbirds. Molecular Phylogenetics and Evolution 10:144-149.
90. SWOFFORD, D. L. 1999. PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods), version 4.068. Sinauer Associates, Sunderland, Massachusetts.
91. SWOFFORD, D. L., G. J. OLSEN, P. J. WADELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular Systematics, 2nd ed. (D. M. Hillis, C. Moritz, and B. K. Mable, Eds.). Sinauer Associates, Sunderland, Massachusetts.
92. TEMPLETON, A. R. 1983. Phytogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
93. THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673-4680.
94. VAN DE WEGHE, J. P. 1988. The validity of Kupeornis Serle. Bulletin of the British Ornithologists' Club 108:54-58.
95. VIGORS, N. A.1830-31. Observations on a collection of birds from the Himalayas Mountains, with characters of new genera and species. Zoological Society of London, Committee of Science and Correspondence 1:22.
96. VOOUS, K. H. 1977. List of Holarctic bird species. Passerines. Ibis 119:223-250, 376-406.
97. WEBB, C. S. 1949. Some notes on the Grey-necked Picathartes (Picathartes oreas). Avicultural Magazine 55:11-154.
98. WETMORE, A. 1960. A classification for the birds of the world. Smithsonian Miscellaneous Collections, no. 139.
99. WINNEPENNINCKX, B., T. BACKELJAU, AND R. De WACHTER. 1993. Extraction of high molecular weight DNA from mollusks. Trends in Genetics 9:407.
100. WOLTERS, H. E. 1975-1982. Die Vogelarten der Erde. Parey, Berlin.
101. YODER, A. D., J. A. IRWIN, AND B. A. PAYSEUR. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology 50:408-424.
102. ZAHAVI, A. 1976. Co-operative breeding in Eurasian birds. Pages 685-693 in Proceedings of the 16th International Ornithological Congress (H. J. Frith and J. H. Calaby, Eds.). Australian Academy of Science, Canberra.
103. ZARDOYA, R., Y. CAO, M. HASEGAWA, AND A. MEYER. 1998. Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data. Molecular Biology and Evolution 15:506-517.