Skip to main content
NCBI home page
Proceedings of the Royal Society B: Biological Sciences logoLink to Proceedings of the Royal Society B: Biological Sciences
. 2002 Feb 7;269(1488):295–308. doi: 10.1098/rspb.2001.1883

A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data.

F Keith Barker 1, George F Barrowclough 1, Jeff G Groth 1
PMCID: PMC1690884  PMID: 11839199

Abstract

Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family-level relationships was available until recent analyses of DNA-DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA-hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG-1 and c-mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA-hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family-level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.

Full Text

The Full Text of this article is available as a PDF (203.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baker R. H., DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst Biol. 1997 Dec;46(4):654–673. doi: 10.1093/sysbio/46.4.654. [DOI] [PubMed] [Google Scholar]
  2. Baker R. H., Yu X., DeSalle R. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Mol Phylogenet Evol. 1998 Jun;9(3):427–436. doi: 10.1006/mpev.1998.0519. [DOI] [PubMed] [Google Scholar]
  3. Briskie J. V., Montgomerie R. Sperm size and sperm competition in birds. Proc Biol Sci. 1992 Feb 22;247(1319):89–95. doi: 10.1098/rspb.1992.0013. [DOI] [PubMed] [Google Scholar]
  4. Carlson L. M., Oettinger M. A., Schatz D. G., Masteller E. L., Hurley E. A., McCormack W. T., Baltimore D., Thompson C. B. Selective expression of RAG-2 in chicken B cells undergoing immunoglobulin gene conversion. Cell. 1991 Jan 11;64(1):201–208. doi: 10.1016/0092-8674(91)90221-j. [DOI] [PubMed] [Google Scholar]
  5. Christidis L., Leeton P. R., Westerman M. Were bowerbirds part of the New Zealand fauna? Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3898–3901. doi: 10.1073/pnas.93.9.3898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cibois A., Pasquet E., Schulenberg T. S. Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences. Mol Phylogenet Evol. 1999 Dec;13(3):581–595. doi: 10.1006/mpev.1999.0684. [DOI] [PubMed] [Google Scholar]
  7. Cooper A., Penny D. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science. 1997 Feb 21;275(5303):1109–1113. doi: 10.1126/science.275.5303.1109. [DOI] [PubMed] [Google Scholar]
  8. Cracraft J. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc Biol Sci. 2001 Mar 7;268(1466):459–469. doi: 10.1098/rspb.2000.1368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cracraft J., Feinstein J. What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree. Proc Biol Sci. 2000 Feb 7;267(1440):233–241. doi: 10.1098/rspb.2000.0992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Deutsch M., Long M. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 1999 Aug 1;27(15):3219–3228. doi: 10.1093/nar/27.15.3219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Edwards S. V., Arctander P., Wilson A. C. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc Biol Sci. 1991 Feb 22;243(1307):99–107. doi: 10.1098/rspb.1991.0017. [DOI] [PubMed] [Google Scholar]
  12. Goldman N., Anderson J. P., Rodrigo A. G. Likelihood-based tests of topologies in phylogenetics. Syst Biol. 2000 Dec;49(4):652–670. doi: 10.1080/106351500750049752. [DOI] [PubMed] [Google Scholar]
  13. Goldman N., Whelan S. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol Biol Evol. 2000 Jun;17(6):975–978. doi: 10.1093/oxfordjournals.molbev.a026378. [DOI] [PubMed] [Google Scholar]
  14. Groth J. G., Barrowclough G. F. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol Phylogenet Evol. 1999 Jul;12(2):115–123. doi: 10.1006/mpev.1998.0603. [DOI] [PubMed] [Google Scholar]
  15. Groth J. G. Molecular phylogenetics of finches and sparrows: consequences of character state removal in cytochrome b sequences. Mol Phylogenet Evol. 1998 Dec;10(3):377–390. doi: 10.1006/mpev.1998.0540. [DOI] [PubMed] [Google Scholar]
  16. Helm-Bychowski K., Cracraft J. 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. 1993 Nov;10(6):1196–1214. doi: 10.1093/oxfordjournals.molbev.a040072. [DOI] [PubMed] [Google Scholar]
  17. Huelsenbeck J. P., Larget B., Swofford D. A compound poisson process for relaxing the molecular clock. Genetics. 2000 Apr;154(4):1879–1892. doi: 10.1093/genetics/154.4.1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Johnson K. P. Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. Syst Biol. 2001 Feb;50(1):128–136. [PubMed] [Google Scholar]
  19. Lovette I. J., Bermingham E. c-mos variation in songbirds: molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation. Mol Biol Evol. 2000 Oct;17(10):1569–1577. doi: 10.1093/oxfordjournals.molbev.a026255. [DOI] [PubMed] [Google Scholar]
  20. McDonald D. B., Potts W. K. Cooperative display and relatedness among males in a lek-mating bird. Science. 1994 Nov 11;266(5187):1030–1032. doi: 10.1126/science.7973654. [DOI] [PubMed] [Google Scholar]
  21. Mindell D. P., Sorenson M. D., Dimcheff D. E., Hasegawa M., Ast J. C., Yuri T. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol. 1999 Mar;48(1):138–152. doi: 10.1080/106351599260490. [DOI] [PubMed] [Google Scholar]
  22. Nee S., Mooers A. O., Harvey P. H. Tempo and mode of evolution revealed from molecular phylogenies. Proc Natl Acad Sci U S A. 1992 Sep 1;89(17):8322–8326. doi: 10.1073/pnas.89.17.8322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Ota R., Waddell P. J., Hasegawa M., Shimodaira H., Kishino H. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol Biol Evol. 2000 May;17(5):798–803. doi: 10.1093/oxfordjournals.molbev.a026358. [DOI] [PubMed] [Google Scholar]
  24. doi: 10.1098/rspb.1998.0322. [DOI] [PMC free article] [Google Scholar]
  25. Posada D., Crandall K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998;14(9):817–818. doi: 10.1093/bioinformatics/14.9.817. [DOI] [PubMed] [Google Scholar]
  26. Robinson M., Gautier C., Mouchiroud D. Evolution of isochores in rodents. Mol Biol Evol. 1997 Aug;14(8):823–828. doi: 10.1093/oxfordjournals.molbev.a025823. [DOI] [PubMed] [Google Scholar]
  27. Saint K. M., Austin C. C., Donnellan S. C., Hutchinson M. N. C-mos, a nuclear marker useful for squamate phylogenetic analysis. Mol Phylogenet Evol. 1998 Oct;10(2):259–263. doi: 10.1006/mpev.1998.0515. [DOI] [PubMed] [Google Scholar]
  28. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  29. Schatz D. G., Oettinger M. A., Baltimore D. The V(D)J recombination activating gene, RAG-1. Cell. 1989 Dec 22;59(6):1035–1048. doi: 10.1016/0092-8674(89)90760-5. [DOI] [PubMed] [Google Scholar]
  30. Schmidt M., Oskarsson M. K., Dunn J. K., Blair D. G., Hughes S., Propst F., Vande Woude G. F. Chicken homolog of the mos proto-oncogene. Mol Cell Biol. 1988 Feb;8(2):923–929. doi: 10.1128/mcb.8.2.923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sueoka N. Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol. 1993 Aug;37(2):137–153. doi: 10.1007/BF02407349. [DOI] [PubMed] [Google Scholar]
  32. Takano-Shimizu T. Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol Biol Evol. 2001 Apr;18(4):606–619. doi: 10.1093/oxfordjournals.molbev.a003841. [DOI] [PubMed] [Google Scholar]
  33. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993 May;10(3):512–526. doi: 10.1093/oxfordjournals.molbev.a040023. [DOI] [PubMed] [Google Scholar]
  34. Watson R., Oskarsson M., Vande Woude G. F. Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4078–4082. doi: 10.1073/pnas.79.13.4078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. West M. J., King A. P. Female visual displays affect the development of male song in the cowbird. Nature. 1988 Jul 21;334(6179):244–246. doi: 10.1038/334244a0. [DOI] [PubMed] [Google Scholar]
  36. Yang Z. Estimating the pattern of nucleotide substitution. J Mol Evol. 1994 Jul;39(1):105–111. doi: 10.1007/BF00178256. [DOI] [PubMed] [Google Scholar]
  37. Yoder A. D., Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol. 2000 Jul;17(7):1081–1090. doi: 10.1093/oxfordjournals.molbev.a026389. [DOI] [PubMed] [Google Scholar]
  38. van Tuinen M., Hedges S. B. Calibration of avian molecular clocks. Mol Biol Evol. 2001 Feb;18(2):206–213. doi: 10.1093/oxfordjournals.molbev.a003794. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the Royal Society B: Biological Sciences are provided here courtesy of The Royal Society

RESOURCES