Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci

Cladistics

Volumn 24, Issue 3, 2008, Pages 328-349

  Treplin, Simone ^a   Siegert, Romy ^a   Bleidorn, Christoph ^a   Thompson, Hazell Shokellu ^b   Fotso, Roger ^c   Tiedemann, Ralph ^a  

^a UNIVERSITY OF POTSDAM   (Germany)

^b ICIPE Campus   (Kenya)

^c Cameroon Biodiversity Project WCS   (Cameroon)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; GENETIC MARKER; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; SONGBIRD; TAXONOMY;

AVES; PARIDAE; PASSERI; PASSERIDA; PASSERIFORMES; PASSEROIDEA; TYRANNI;

EID: 43549119814     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2007.00178.x     Document Type: Article

References (86)

1. Alström, P., Ericson, P.G.P., Olsson, U., Sundberg, P., 2006. Phylogeny and classification of the avian superfamily Sylvioidea. Mol. Phylogenet. Evol. 38, 381 397.
2. Amadon, D., 1943. The genera of starlings and their relationships. Am. Mus. Novit. 1247, 1 16.
3. Ames, P., 1971. The morphology of the syrinx in passerine birds. Bull. Peabody Mus. Nat. Hist. 37, 194.
4. Baker, R.H., DeSalle, R., 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46, 654 673.
5. Baker, R.H., Yu, X.B., DeSalle, R., 1998. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Mol. Phylogenet. Evol. 9, 427 436.
6. Baker, R.H., Wilkinson, G.S., DeSalle, R., 2001. Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Syst. Biol. 50, 87 105.
7. Ball, G.F., Gentner, T.Q., 1998. They're playing our song: gene expression and birdsong perception. Neuron 21, 271 274.
8. Barker, F.K., Barrowclough, G.F., Groth, J.G., 2002. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. R. Soc. Lond. B Biol. Sci. 269, 295 308.
9. Barker, F.K., Cibois, A., Schikler, P., Feinstein, J., Cracraft, J., 2004. Phylogeny and diversification of the largest avian radiation. Proc. Natl Acad. Sci. USA 101, 11040 11045.
10. Beresford, P., Barker, F.K., Ryan, P.G., Crowe, T.M., 2005. African endemics span the tree of songbirds (Passeri): molecular systematics of several evolutionary "enigmas". Proc. R. Soc. Lond. B Biol. Sci. 272, 849 858.
11. Boles, W.E., 1995. The worlds oldest songbird. Nature 374, 21 22.
12. Christy, B.A., Lau, L.F., Nathans, D., 1988. A gene activated in mouse 3T3-cells by serum growth-factors encodes a protein with zinc finger sequences. Proc. Natl Acad. Sci. USA 85, 7857 7861.
13. Chubb, A.L., 2004a. New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i). Mol. Phylogenet. Evol. 30, 140 151.
14. Chubb, A.L., 2004b. Nuclear corroboration of DNA-DNA hybridization in deep phylogenies of hummingbirds, swifts, and passerines: the phylogenetic utility of ZENK (ii). Mol. Phylogenet. Evol. 30, 128 139.
15. Cibois, A., Cracraft, J., 2004. Assessing the passerine "Tapestry": phylogenetic relationships of the Muscicapoidea inferred from nuclear DNA sequences. Mol. Phylogenet. Evol. 32, 264 273.
16. Clayton, D.F., 1997. Role of gene regulation in song circuit development and song learning. J. Neurobiol. 33, 549 571.
17. Colless, D.H., 1980. Congruence between morphometric and allozyme data for Menidia species - A reappraisal. Syst. Zool. 29, 289 299.
18. Colless, D.H., 1981. Predictivity and stability in classifications - some comments on recent studies. Syst. Zool. 30, 325 331.
19. Degnan, J.H., Rosenberg, N.A., 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2, 762 768.
20. Delacour, J., Amadon, D., 1951. The systematic position of Picathartes. Ibis 93, 60 62.
21. Edwards, S.V., Boles, W.E., 2002. Out of Gondwana: the origin of passerine birds. Trends Ecol. Evol. 17, 347 349.
22. Edwards, S.V., Arctander, P., Wilson, A.C., 1991. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc. R. Soc. Lond. B Biol. Sci. 243, 99 107.
23. Edwards, S.V., Jennings, W.B., Shedlock, A.M., 2005. Phylogenetics of modern birds in the era of genomics. Proc. R. Soc. Biol. Sci. Ser. B 272, 979 992.
24. Ericson, P.G.P., Johansson, U.S., 2003. Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data. Mol. Phylogenet. Evol. 29, 126 138.
25. Ericson, P.G.P., Johansson, U.S., Parsons, T.J., 2000. Major divisions of oscines revealed by insertions in the nuclear gene c-myc: a novel gene in avian phylogenetics. Auk 117, 1077 1086.
26. Ericson, P.G.P., Christidis, L., Cooper, A., Irestedt, M., Jackson, J., Johansson, U.S., Norman, J.A., 2002a. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc. R. Soc. Lond. B Biol. Sci. 269, 235 241.
27. Ericson, P.G.P., Christidis, L., Irestedt, M., Norman, J.A., 2002b. Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds. Mol. Phylogenet. Evol. 25, 53 62.
28. Ericson, P.G.P., Irestedt, M., Johansson, U.S., 2003. Evolution, biogeography, and patterns of diversification in passerine birds. J. Avian Biol. 34, 3 15.
29. Farris, J.S., Kluge, A.G., Eckardt, M.J., 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19, 172 189.
30. Farris, J.S., Kallersjo, M., Kluge, A.G., Bult, C., 1995. Constructing a significance test for incongruence. Syst. Biol. 44, 570 572.
31. Feduccia, A., 1975. Morphology of the bony stapes (columella) in the Passeriformes and related groups: evolutionary implications. Miscellaneous Publication - University Kansas, Museum Natural History, 63, 1 34.
32. Feduccia, A., 1995. Explosive evolution in Tertiary birds and mammals. Science 267, 637 638.
33. Feduccia, A., 1996. The Origin and Evolution of Birds, 2nd edn. Yale University Press, New Haven, CT.
34. Felsenstein, J., 1981. Evolutionary trees from DNA-sequences - a maximum-likelihood approach. J. Mol. Evol. 17, 368 376.
35. Fuchs, J., Fjeldså, J., Bowie, R.C., Voelker, G., Pasquet, E., 2006. The African warbler genus Hyliota as a lost lineage in the oscine songbird tree: molecular support for an African origin of the Passerida. Mol. Phylogenet. Evol. 39, 186 197.
36. Groth, J.G., 1998. Molecular phylogenetics of finches and sparrows: consequences of character state removal in cytochrome b sequences. Mol. Phylogenet. Evol. 10, 377 390.
37. Groth, J.G., Barrowclough, G.F., 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12, 115 123.
38. Guindon, S., Gascuel, O., 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696 704.
39. Haffer, J., 1991. Familie Sylviidae - Zweigsänger (Grasmücken und Verwandte). In : Glutz von Blotzheim, U.N., Bauer, K.M. (Eds Handbuch der Vögel Mitteleuropas. AULA-Verlag, Wiebelsheim.
40. 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.
41. Hasegawa, M., Kishino, H., Yano, T.A., 1985. Dating of the human ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160 174.
42. Helbig, A.J., Seibold, I., 1999. Molecular phylogeny of Palearctic-African Acrocephalus and Hippolais warblers (Aves: Sylviidae). Mol. Phylogenet. Evol. 11, 246 260.
43. Huelsenbeck, J.P., Ronquist, F., 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754 755.
44. Huelsenbeck, J.P., Rannala, B., Masly, J.P., 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288, 2349 2350.
45. Irestedt, M., Johansson, U.S., Parsons, T.J., Ericson, P.G.P., 2001. Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data. J. Avian Biol. 32, 15 25.
46. Irestedt, M., Fjeldså, J., Johansson, U.S., Ericson, P.G.P., 2002. Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes). Mol. Phylogenet. Evol. 23, 499 512.
47. James, H.F., Ericson, P.G.P., Slikas, B., Lei, F.M., Gill, F.B., Olson, S.L., 2003. Pseudopodoces humilis, a misclassified terrestrial tit (Paridae) of the Tibetan Plateau: evolutionary consequences of shifting adaptive zones. Ibis 145, 185 202.
48. Johansson, U.S., Irestedt, M., Parsons, T.J., Ericson, P.G.P., 2002. Basal phylogeny of the tyrannoidea based on comparisons of cytochrome b and exons of nuclear c-myc and RAG-1 genes. Auk 119, 984 995.
49. Jønsson, K.A., Fjeldså, J., 2006a. Determining biogeographical patterns of dispersal and diversification in oscine passerine birds in Australia, Southeast Asia and Africa. J. Biogeogr. 33, 1155 1165.
50. Jønsson, K.A., Fjeldså, J., 2006b. A phylogenetic supertree of oscine passerine birds (Aves: Passeri). Zool. Scr. 35, 149 186.
51. Lanfear, J., Jowett, T., Holland, P.W.H., 1991. Cloning of fish zinc-finger genes related to Krox-20 and Krox-24. Biochem. Biophys. Res. Commun. 179, 1220 1224.
52. Larget, B., Simon, D.L., 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750 759.
53. Leisler, B., Heidrich, P., SchulzeHagen, K., Wink, M., 1997. Taxonomy and phylogeny of reed warblers (genus Acrocephalus) based on mtDNA sequences and morphology. J. Ornithol. 138, 469 496.
54. Long, K.D., Salbaum, J.M., 1998. Evolutionary conservation of the immediate-early gene ZENK. Mol. Biol. Evol. 15, 284 292.
55. Lowe, P.R., 1938. Some anatomical and other notes on the systematic position of the genus Picathartes, together with some remarks on the families Sturnidae and Eulabetidae. Ibis 14, 254 269.
56. Mau, B., Newton, M.A., 1997. Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6, 122 131.
57. Mau, B., Newton, M.A., Larget, B., 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1 12.
58. Mayr, G., 2005. The Paleogene fossil record of birds in Europe. Biol. Rev. 80, 515 542.
59. Mayr, G., Manegold, A., 2004. The oldest European fossil songbird from the early Oligocene of Germany. Naturwissenschaften 91, 173 177.
60. Mello, C.V., Vicario, D.S., Clayton, D.F., 1992. Song presentation induces gene-expression in the songbird forebrain. Proc. Natl Acad. Sci. USA 89, 6818 6822.
61. Milbrandt, J., 1987. A nerve growth-factor induced gene encodes a possible transcriptional regulatory factor. Science 238, 797 799.
62. Nixon, K.C., 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407 414.
63. Nylander, J.A.A., 2004. MrModeltest v2. Program distributed by the author.
64. Page, R.D.M., Holmes, E.C., 1998. Molecular Evolution. A Phylogenetic Approach. Blackwell Science, Oxford.
65. Posada, D., Buckley, T.R., 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53, 793 808.
66. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817 818.
67. Raikow, R.J., 1982. Monophyly of the Passeriformes - test of a phylogenetic hypothesis. Auk 99, 431 445.
68. Raikow, R.J., 1987. Hindlimb myology and evolution of the old world suboscine passerine birds (Acanthisittidae, Pittidae, Philepittidae, Eurylaimidae). Ornithol. Monogr. 41, 1 81.
69. Rannala, B., Yang, Z.H., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304 311.
70. Ribeiro, S., Mello, C.V., 2000. Gene expression and synaptic plasticity in the auditory forebrain of songbirds. Learn. Mem. 7, 235 243.
71. Rokas, A., Carroll, S.B., 2006. Bushes in the tree of life. PLoS Biol. 4, 1899 1904.
72. Sclater, W.L., 1930. Systema Avium Aethiopicarum. Taylor & Francis, London.
73. Sheldon, F.H., Gill, F.B., 1996. A reconsideration of songbird phylogeny, with emphasis on the evolution of titmice and their sylvioid relatives. Syst. Biol. 45, 473 495.
74. Sibley, C.G., Ahlquist, J.E., 1990. Phylogeny and Classification of Birds: a Study in Molecular Evolution. Yale University Press, New Haven, CT.
75. Sibley, C.G., Monroe, B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT.
76. Sikes, D.S., Lewis, P.O., 2001. PAUPRat: PAUP* Implementation of the Parsimony Ratchet. Distributed by the authors. Beta Software, Version 1. Department of Ecology and Evolutionary Biology. University of Connecticut, Storrs.
77. Sorenson, M.D., 1999. Treerot, Version 2. Boston University, Boston, MA.
78. Stork, O., Welzl, H., 1999. Memory formation and the regulation of gene expression. Cell. Mol. Life Sci. 55, 575 592.
79. Sukhatme, V.P., Cao, X.M., Chang, L.C., Tsaimorris, C.H., Stamenkovich, D., Ferreira, P.C.P., Cohen, D.R., Edwards, S.A., Shows, T.B., Curran, T., Lebeau, M.M., Adamson, E.D., 1988. A zinc finger-encoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization. Cell 53, 37 43.
80. Swofford, D.L., 2001. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0. Sinauer Associates, Sunderland, MA.
81. Tavaré, S., 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57 86.
82. Thompson, H.S., Fotso, R., 1995. Rockfowl, the genus Picathartes. Bull. Afr. Bird Club 2, 25 28.
83. Tischmeyer, W., Grimm, R., 1999. Activation of immediate early genes and memory formation. Cell. Mol. Life Sci. 55, 564 574.
84. Treplin, S., Tiedemann, R., 2007. Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae). Mol. Phylogenet. Evol. 43, 328 337.
85. Van der Meij, M.A.A., de Bakker, M.A.G., Bout, R.G., 2005. Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA. Mol. Phylogenet. Evol. 34, 97 105.
86. Voelker, G., Spellman, G.M., 2004. Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea. Mol. Phylogenet. Evol. 30, 386 394.