Likelihood reinstates Archaeopteryx as a primitive bird

Biology Letters

Volumn 8, Issue 2, 2012, Pages 299-303

  Lee, Michael S Y ^a,b   Worthy, Trevor H ^c  

^a SOUTH AUSTRALIAN MUSEUM   (Australia)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Archaeopteryx; Bayesian inference; Bird origins; Maximum likelihood; Phylogeny; Theropoda

Indexed keywords

BAYESIAN ANALYSIS; BIRD; BOOTSTRAPPING; DINOSAUR; FLIGHT; FOSSIL RECORD; MAXIMUM LIKELIHOOD ANALYSIS; MORPHOLOGY; PARSIMONY ANALYSIS; PHYLOGENETICS; PHYLOGENY;

ARCHAEOPTERYX; AVES; DEINONYCHOSAURIA; THEROPODA;

EID: 84860338571     PISSN: 17449561     EISSN: 1744957X     Source Type: Journal    
DOI: 10.1098/rsbl.2011.0884     Document Type: Article

References (24)

1. Hecht, M. K., Ostrum, J. H., Viohl, G. & Wellnhofer, P. (eds) 1985 The beginnings of birds. In Proc. Int. Archaeopteryx Conf., Eichstätt, 1984, pp. 298-292. Eichstätt: Freunde des Jura-Museums Eichstätt.
2. Chiappe, L. M. & Witmer, L. M. (eds) 2002 Mesozoic birds: above the heads of dinosaurs. Berkeley/Los Angeles, CA: University of California Press.
3. Xu, X., You, H., Du, K. & Han, F. 2011 An Archaeopteryxlike theropod from China and the origin of Avialae. Nature 475, 460-465. (doi:10.1038/ nature10288)
4. Gauthier, J. 1986 Saurischian monophyly and the origin of birds. Mem. Calif. Acad. Sci. 8, 1-55.
5. Gauthier, J. & de Queiroz, K. 2001 Feathered dinosaurs, flying dinosaurs, crown dinosaurs, and the name 'Aves'. In New perspectives on the origin and early evolution of birds (eds J. Gauthier & L. F. Gall), pp. 7-41. New Haven, CT: Peabody Museum of Natural History.
6. Witmer, L. M. 2011 An icon knocked off its perch. Nature 475, 458-459. (doi:10.1038/475458a)
7. Felstenstein, J. 2004 Inferring phylogenies. Sunderland, MA: Sinauer Associates.
8. Kolaczkowski, B. & Thornton, J.W. 2004 Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431, 980-984. (doi:10.1038/nature02917) (Pubitemid 39434418)
9. Wagner, P. J. 2011 Modeling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates. Biol. Lett. 8, 143-146. (doi:10.1098/rsbl.2011.0523)
10. Swofford, D. L. 2002 PAUP*: phylogenetic analysis using parsimony (*and other methods) v. 4. Sunderland, MA: Sinauer Associates.
11. Lewis, P. O. 2001 A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913-925. (doi:10.1080/10635150175 3462876)
12. Stamatakis, A. 2006 RAXML-VI-HPC: maximum likelihood- based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. (doi:10.1093/bioinformatics/btl446) (Pubitemid 44642609)
13. Ronquist, F. & Huelsenbeck, J. P. 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. (doi:10.1093/bioinformatics/ btg180) (Pubitemid 37038874)
14. Wilgenbusch, J. C., Warren, D. L. & Swofford, D. L. 2004 AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. See http://ceb.csit.fsu.edu/awty.
15. Rambaut, A. & Drummond, A. J. 2004 TRACER v. 1.5. See http://beast.bio.ed.ac.uk/Tracer.
16. Farris, J. S. 1989 The retention index and the rescaled consistency index. Cladistics 5, 417-419. (doi:10.1111/ j.1096-0031.1989.tb00573.x)
17. Hu, D., Hou, L., Zhang, L. & Xu, X. 2009 A pre- Archaeopteryx troodontid theropod from China with long feathers on the metatarsus. Nature 461, 640-643. (doi:10.1038/nature08322)
18. Hennig, W. 1966 Phylogenetic systematics. Urbana, IL: University of Illinois Press.
19. Senter, P. 2007 A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda). J. Syst. Palaeont. 5, 429-463. (doi:10.1017/S1477201907002143) (Pubitemid 351651090)
20. Chatterjee, S. & Templin, R. J. 2003 The flight of Archaeopteryx. Naturwissenschaften 90, 27-32. (doi:10. 1007/s00114-002-0385-0) (Pubitemid 36207907)
21. Alexander, D. E., Gong, E., Martin, L. D., Burnham, D. A. & Falk, A. R. 2010 Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui. Proc. Natl Acad. Sci. USA 107, 2972-2976. (doi:10.1073/pnas.0911852107).
22. Xu, X., Zheng, X. & You, H. 2010 Exceptional dinosaur fossils show ontogenetic development of early feathers. Nature 464, 1338-1341. (doi:10.1038/ nature08965)
23. Alfaro, M. E. & Holder, M. T. 2006 The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Syst. 37, 19-42. (doi:10.1146/annurev. ecolsys.37. 091305.110021) (Pubitemid 44907611)
24. Clarke, J. A. & Middleton, K. M. 2008 Mosaicism, modules, and the evolution of birds: results from a Bayesian approach to the study of morphological evolution using discrete character data. Syst. Biol. 57, 185-202. (doi:10.1080/10635150802022231)