Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

Proceedings of the Royal Society B: Biological Sciences

Volumn 279, Issue 1747, 2012, Pages 4617-4625

  Haddrath, Oliver ^a,b   Baker, Allan J ^a,b  

^a DEPARTMENT OF NATURAL HISTORY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bird origins; Gene trees; Palaeognaths; Phylogenetics; Retroposon; Vicariance biogeography

Indexed keywords

BIOGEOGRAPHY; BIRD; CRETACEOUS; DINOSAUR; DISPERSAL; DIVERGENCE; EXTINCTION; GENE EXPRESSION; GENETIC ANALYSIS; PALEOGENE; PHYLOGENETICS; TAXONOMY; VICARIANCE;

EID: 84867569468     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2012.1630     Document Type: Article

References (58)

1. Cracraft, J. 1973 Continental drift, paleoclimatology, and the evolution and biogeography of birds. J. Zool. 169, 455-545. (doi:10.1111/j.1469-7998.1973.tb03122.x)
2. Sibley, C. G. & Ahlquist, J. E. 1990 Phylogeny and classification of birds: a study in molecular evolution. New Haven, CT: Yale University Press.
3. Haddrath, O. & Baker, A. J. 2001 Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268, 939-945. (doi:10.1098/rspb.2001.15)
4. Lee, K., Feinstein, J. & Cracraft, J. 1997 The phylogeny of ratite birds: resolving conflicts between molecular and morphological data sets. In Avian molecular evolution and systematics (ed. D. P. Mindell), pp. 173-211. San Diego, CA: Academic Press.
5. Cooper, A., Lalueza-Fox, C., Anderson, S., Rambaut, A., Austin, J. & Ward, R. 2001 Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409, 704-707. (doi:10.1038/35055536)
6. Harshman, J. et al. 2008 Phylogenomic evidence for multiple losses of flight in ratite birds. Proc. Natl Acad. Sci. USA 105, 13 462-13 467. (doi:10.1073/pnas. 0803242105)
7. Hackett, S. J. et al. 2008 A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768. (doi:10.1126/science.1157704)
8. Phillips, M. J., Gibb, G. C., Crimp, E. A. & Penny, D. 2009 Tinamous and moa flock together: mitochondrial genome sequence analysis reveal independent losses of flight among ratites. Syst. Biol. 59, 1-18. (doi:10.1093/sysbio/syp079)
9. Brown, J. W., Rest, J. S., García-Moreno, J., Sorenson, M. D. & Mindell, D. P. 2008 Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biol. 6, 6-24. (doi:10.1186/1741-7007-6-6)
10. Pereira, S. L. & Baker, A. J. 2006 A mitogenomics timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 23, 1731-1740. (doi:10.1098/rspb.2005.3260)
11. Paton, T., Haddrath, O. & Baker, A. J. 2002 Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. R. Soc. Lond. B 269, 839-846. (doi:10.1098/rspb.2002.1961)
12. Ericson, P. G. P. et al. 2006 Diversification of neoaves: integration of molecular sequence data and fossils. Biol. Lett. 2, 543-547. (doi:10.1098/rsbl.2006.0523)
13. Cooper, A. & Penny, D. 1997 Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275, 1109-1113. (doi:10.1126/science.275.5303.1109)
14. Fountaine, T. M. R., Benton, M. J., Dyke, G. J. & Nudds, R. L. 2005 The quality of the fossil record of Mesozoic birds. Proc. R. Soc. B 272, 289-294. (doi:10. 1098/rspb.2004.2923)
15. Rokas, A. & Carroll, S. B. 2006 Bushes in the tree of life. PLoS Biol. 4, 1899-1904. (doi:10.1371/journal.pbio. 0040352)
16. Edwards, S. V. 2009 Is a new and general theory of molecular systematics emerging? Evolution 63, 1-19. (doi:10. 1111/j.1558-5646.2008.00549.x)
17. Degnan, J. H. & Rosenberg, N. A. 2006 Discordance of species trees with their most likely gene trees. PLoS Genet. 2, 762-768. (doi:10.1371/journal.pgen.0020068)
18. Edwards, S. V., Liu, L. & Pearl, D. K. 2007 Highresolution species trees without concatenation. Proc. Natl Acad. Sci. USA 104, 5936-5941. (doi:10.1073/pnas.0607004104)
19. 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. (doi:10.1016/j.ympev.2006.10.020)
20. Kaiser, V., van Tuinen, M. & Ellegren, H. 2007 Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. Mol. Biol. Evol. 24, 338-347. (doi:10.1093/molbev/msl164)
21. Watanabe, M., Nikaido, M., Tsuda, T. T., Inoko, H., Mindell, D. P., Murata, K. & Okada, N. 2006 The rise and fall of the CR1 subfamily in the lineage leading to penguins. Gene 365, 57-66. (doi:10.1016/j.gene.2005.09.042)
22. Kriegs, J. O., Churakov, G., Kiefmann, M., Jordan, U., Brosius, J. & Schmitz, J. 2006 Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4, 537-544. (doi:10.1371/journal. pbio.0040091)
23. Nishihara, H., Maruyama, S. & Okada, N. 2009 Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc. Natl Acad. Sci. USA 106, 5235-5240. (doi:10.1073/pnas.0809297106)
24. Suh, A., Paus, M., Kiefmann, M., Churakjov, G., Franke, F. A., Brosius, J., Kriegs, J. O. & Schmitz, J. 2011 Mesozoic retroposons reveals parrots as the closest living relatives of the passerine birds. Nat. Commun. 2, 443. (doi:10.1038/ncomms1448)
25. Nylander, J. A. 2004 MrModeltest v. 2.0. Program distributed by the author. Uppsala, Sweden: Evolutionary Biology Centre, Uppsala University.
26. Lewis, P. O., Holder, M. T. & Swofford, D. L. 2008 Phycas: software for phylogenetic analysis. Storrs, CT: University of Connecticut. See www.phycas.org.
27. Fan, Y., Chen, M., Kuo, L. & Lewis, P. O. 2011 Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28, 523-532. (doi:10.1093/molbev/msq224)
28. Huelsenbeck, J. P. & Ronquist, F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (doi:10.1093/bioinformatics/17.8.754)
29. Miller, M. A., Pfeiffer, W. & Schwartz, T. 2010 Creating the CIPRES science gateway for inference of large phylogenetic trees. In Proc. Gateway Computing Environments Workshop (GCE), 14 November 2010, New Orleans, LA, pp. 1-8. Piscataway Township, NJ: Institute of Electrical and Electronics Engineers.
30. Rambaut, A. & Drummond, A. J. 2007 Tracer v. 1.5. See http://beast.bio.ed.ac.uk/Tracer.
31. Silvestro, D. & Michalak, I. 2011 RAXMLGUI: a graphical front-end for RAXML. Organ. Divers. Evol. (doi:10. 1007/s13127-011-0056-0)
32. Heled, J. & Drummond, A. 2010 Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27, 570-580. (doi:10.1093/molbev/msp274)
33. Liu, L., Yu, L. & Edwards, S. V. 2010 A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10, 302. (doi:10.1186/1471-2148-10-302)
34. Drummond, A. J. & Rambaut, A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
35. Yang, Z. & Rannala, B. 2006 Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212-226. (doi:10.1093/molbev/msj024)
36. Müller, J. & Reisz, R. R. 2005 Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. BioEssays 27, 1069-1075. (doi:10.1002/bies.20286)
37. Boles, W. E. 1992 Revision of Dromaius gidju Patterson and Rich 1987 from Riversleigh, northwestern Queensland, Australia, with a reassessment of its generic position. Nat. Hist. LA County Sci. Ser. 36, 195-208.
38. Clarke, J. A., Tambussi, C. P., Noriega, J. I., Erickson, G. M. & Ketcham, R. A. 2005 Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433, 305-306. (doi:10.1038/nature03150)
39. Slack, K. E., Jones, C. M., Ando, T., Harrison, G. L., Fordyce, R. E., Arnason, U. & Penny, D. 2006 Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 23, 1144-1155. (doi:10.1093/molbev/msj124)
40. Rasmussen, D. T., Olson, S. L. & Simmons, E. L. 1987 Fossil birds from the Oligocene Jebel Qatrani Formation, Fayum Province, Egypt. Smithsonian Contrib. Paleobiol. 62, 1-20. (doi:10.5479/si.00810266.62.1)
41. Smit, A. F. A., Hubley, R. & Green, P. 1996-2010 Repeat-Masker Open-3.0. See http://www.repeatmasker.org.
42. Felsenstein, J. 2005 PHYLIP v. 3.6. Seattle, WA: Department of Genome Science, University of Washington.
43. del Hoyo, J., Elliot, A. & Sargatal, J. 1992 Handbook of the birds of the world. Barcelona, Spain: Lynx Edicions.
44. Xia, X. & Xie, Z. 2001 DAMBE: data analysis in molecular biology and evolution. J. Hered. 92, 371-373. (doi:10. 1093/jhered/92.4.371)
45. Cracraft, J. 2001 Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. R. Soc. Lond. B 268, 459-469. (doi:10.1098/rspb.2000.1368)
46. Brocklehurst, N., Upchurch, P., Mannion, P. D. & O'Connor, J. 2012 The completeness of the fossil record of Mesozoic birds: implications for early avian evolution. PLoSONE7, e39056. (doi:10.1371/journal.pone.0039056)
47. Krause, D. W., O'Connor, P. M., Rogers, K. C., Sampson, S. D., Buckley, G. A. & Rogers, R. R. 2006 Late Cretaceous terrestrial vertebrates from Madagascar: implications for Latin American biogeography. Ann. Mon. Bot. Gard. 93, 178-208. (doi:10.3417/0026-6493(2006)93[178:LCTVFM]2.0.CO2)
48. Sereno, P. C., Wilson, J. A. & Conrad, J. L. 2004 New dinosaurs link southern landmasses in the Mid-Cretaceous. Proc. R. Soc. Lond. B 271, 1325-1330. (doi:10.1098/rspb. 2004.2692)
49. Cooper, R. A. & Millener, P. 1993 The New Zealand biota: historical background and new research. Trends Ecol. Evol. 8, 429-433. (doi:10.1016/0169-5347(93) 90004-9)
50. Burbidge, M. L., Colbourne, R. M., Roberston, H. A. & Baker, A. J. 2003 Molecular and other biological evidence supports the recognitions of at least three species of brown kiwi. Conserv. Genet. 4, 167-177. (doi:10.1023/A:1023386506067)
51. Baker, A. J., Huynen, L. J., Haddrath, O., Millar, C. D. & Lambert, D. M. 2005 Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand. Proc. Natl Acad. Sci. USA. 102, 8257-8262. (doi:10.1073/pnas.0409435102)
52. Landis, C. A., Campbell, H. J., Begg, J. G., Mildenhall, D. C., Paterson, A. M. & Trewick, S. A. 2008 The Waipounamu erosion surface: questioning the antiquity of the New Zealand land surface and terrestrial fauna and flora. Geol. Mag. 145, 173-197. (doi:10.1017/S0016756807004268)
53. Bunce, M. et al. 2009 The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proc. Natl Acad. Sci. USA 106, 20 646-20 651. (doi:10.1073/pnas.0906660106)
54. Barrett, P. M., McGowan, A. J. & Page, V. 2009 Dinosaur diversity and the rock record. Proc. R. Soc. B 276, 2667-2674. (doi:10.1098/rspb.2009.0352)
55. Baker, A. J., Pereira, S. L., Haddrath, O. & Edge, K. A. 2006 Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling. Proc. R. Soc. B 273, 11-17. (doi:10.1098/rspb.2005.3260)
56. 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, 11 040-11 045. (doi:10.1073/pnas.0401892101)
57. Boles, W. E. 1995 The world's oldest songbird. Nature 374, 21-22. (doi:10.1038/374021b0)
58. McCormack, J. E., Heled, J., Delaney, K. S., Peterson, A. T. & Knowles, L. L. 2011 Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 65, 184-202. (doi:10.1111/j.1558-5646.2010.01097.x)