Strong mitochondrial DNA support for a cretaceous origin of modern avian lineages

BMC Biology

Volumn 6, Issue , 2008, Pages

  Brown, Joseph W ^a   Rest, Joshua S ^b   García Moreno, Jaime ^c   Sorenson, Michael D ^d   Mindell, David P ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c Conservation International ^*  (Costa Rica)

^d Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BAYES THEOREM; BIRD; CENOZOIC; CLADISTICS; CONTROLLED STUDY; CRETACEOUS; EVOLUTION; FAMILIA; FOSSIL; FOWL; GENE SEQUENCE; GENETIC VARIABILITY; MOLECULAR GENETICS; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORDO; PALEONTOLOGY; PHYLOGENY; SPECIES EXTINCTION; TAXON; UNCERTAINTY; UNINDEXED SEQUENCE; ANIMAL; CLASSIFICATION; GENETICS; MOLECULAR EVOLUTION; SPECIES DIFFERENTIATION;

AVES;

ANIMALS; BAYES THEOREM; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FOSSILS; GENETIC SPECIATION; PHYLOGENY; VARIATION (GENETICS);

EID: 41049092682     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-6-6     Document Type: Article

References (109)

1. Archibald JD Deutschman DH Quantitative analysis of the timing of the origin and diversification of extant placental orders J Mamm Evol 2001, 8:107-124. 10.1023/A:1011317930838
2. Cooper A Fortey R Evolutionary explosions and the phylogenetic fuse Trends Ecol Evol 1998, 13:151-156. 10.1016/S0169-5347(97)01277-9
3. Penny D Phillips MJ The rise of birds and mammals: Are microevolutionary processes sufficient for macroevolution? Trends Ecol Evol 2004, 19:516-522. 10.1016/j.tree.2004.07.015 16701316
4. van Tuinen M Stidham TA Hadly EA Tempo and mode of modern bird evolution observed with large-scale taxonomic sampling Hist Biol 2006, 18:205-221. 10.1080/08912960600641174
5. Benton MJ Ayala FJ Dating the tree of life Science 2003, 300:1698-1700. 10.1126/science.1077795 12805535
6. Edwards SV Beerli P Perspective: Gene divergence, population divergence, and the variance in coalescent time in phylogeographic studies Evolution 2000, 54:1839-1854. 11209764
7. Rannala B Yang Z Inferring speciation times under an episodic molecular clock Syst Biol 2007, 56:453-466. 10.1080/10635150701420643 17558967
8. Feduccia A Explosive evolution in tertiary birds and mammals Science 1995, 267:637-638. 10.1126/science.267.5198.637 17745839
9. Feduccia A 'Big bang' for tertiary birds? Trends Ecol Evol 2003, 18:172-176. 10.1016/S0169-5347(03)00017-X
10. Clarke JA Tambussi CP Noriega JI Erikson GM Ketcham RA Definitive fossil evidence for the extant avian radiation in the Cretaceous Nature 2005, 433:305-308. 10.1038/nature03150 15662422
11. Bleiweiss R Fossil gap analysis supports early Tertiary origin of trophically diverse avian orders Geology 1998, 26:323-326. 10.1130/ 0091-7613(1998)026<0323:FGASET<2.3.CO;2
12. Chiappe LM Dyke GJ The Mesozoic radiation of birds Annu Rev Ecol Syst 2002, 33:91-124. 10.1146/annurev.ecolsys.33.010802.150517
13. Feduccia A The Origin and Evolution of Birds New Haven: Yale University Press 2 1999.
14. Fountaine TM Benton MJ Dyke GJ Nudds RL The quality of the fossil record of Mesozoic birds Proc R Soc Lond B Biol Sci 2005, 272:289-294. 15705554 10.1098/rspb.2004.2923
15. Mayr G The Paleogene fossil record of birds in Europe Biol Rev 2005, 80:515-542. 10.1017/S1464793105006779 16221327
16. Brown JW Payne RB Mindell DP Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: A comment on Ericson et al Biol Lett 2007, 3:257-259. 10.1098/rsbl.2006.0611 17389215
17. Cooper A Penny D Mass survival of birds across the Cretaceous-Tertiary boundary: Molecular evidence Science 1997, 275:1109-1113. 10.1126/ science.275.5303.1109 9027308
18. Hedges SB Parker PH Sibley CG Kumar S Continental breakup and the ordinal diversification of birds and mammals Nature 1996, 381:226-229. 10.1038/381226a0 8622763
19. Kumar S Hedges SB A molecular timescale for vertebrate evolution Nature 1998, 392:917-920. 10.1038/31927 9582070
20. van Tuinen M Hedges SB Calibration of avian molecular clocks Mol Biol Evol 2001, 18:206-213. 11158379
21. Paton T Haddrath O Baker AJ Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds Proc R Soc Lond B Biol Sci 2002, 269:839-846. 11958716 10.1098/ rspb.2002.1961
22. Paton TA Baker AJ Groth JG Barrowclough GF RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds Mol Phylogenet Evol 2003, 29:268-278. 10.1016/S1055-7903(03)00098-8 13678682
23. Pereira SL Baker AJ A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock Mol Biol Evol 2006, 23:1731-1740. 10.1093/molbev/msl038 16774978
24. Slack KE Jones CM Ando T Harrison GL Fordyce RE Penny D Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution Mol Biol Evol 2006, 23:1144-1155. 10.1093/molbev/msj124 16533822
25. Baker AJ Pereira SL Paton TA Phylogenetic relationships and divergence times of Charadriiformes genera: Multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds Biol Lett 2007, 3:205-209. 10.1098/rsbl.2006.0606 17284401
26. Rest JS Ast JC Austin CC Waddell PJ Tibbetts EA Hay JM Mindell DP Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome Mol Phylogenet Evol 2003, 29:289-297. 10.1016/ S1055-7903(03)00108-8 13678684
27. Benton MJ Vertebrate palaeontology London: Chapman and Hall 2 1997.
28. Benton MJ Wills MA Hitchin R Quality of the fossil record through time Nature 2000, 403:534-537. 10.1038/35000558 10676959
29. Foote M Hunter JP Janis CM Sepkoski JJ Jr Evolutionary and preservational constraints on origins of biologic groups: Divergence times of Eutherian mammals Science 1999, 283:1310-1314. 10.1126/ science.283.5406.1310 10037598
30. Foote M Sepkoski JJ Jr Absolute measures of the completeness of the fossil record Nature 1999, 398:415-417. 10.1038/18872 11536900
31. Tavaré S Marshall CR Will O Soligo C Martin RD Using the fossil record to estimate the age of the last common ancestor of extant primates Nature 2002, 416:726-729. 10.1038/416726a 11961552
32. Wills MA Fossil ghost ranges are most common in some of the oldest and some of the youngest strata Proc Natl Acad Sci USA 2007, 274:2421-2427. 17652067
33. Benton MJ Early origins of modern birds and mammals: Molecules vs. morphology BioEssays 1999, 21:1043-1051. 10.1002/ (SICI)1521-1878(199912)22:1<1043::AID-BIES8<3.0.CO;2-B 10580989
34. Padian K Chiappe LM The origin and early evolution of birds Biol Rev 1998, 73:1-42. 10.1017/S0006323197005100
35. Clarke JA Chiappe LM A new carinate bird from the late Cretaceous of Patagonia Am Mus Novit 2001, 3323:1-23. 10.1206/ 0003-0082(2001)323<0001:ANCBFT<2.0.CO;2
36. Stidham TA A lower jaw from a Cretaceous parrot Nature 1998, 396:29-30. 10.1038/23841
37. Chatterjee S The morphology and systematics of Polarornis, a Cretaceous loon (Aves: Gaviidae) from Antarctica Proceedings of the 5th Symposium of the Society of Avian Paleontology and Evolution: 1-4 June 2000; Beijing Beijing: Science Press Zhou Z, Zhang F 2002:125-155.
38. Dyke GJ Mayr G Did parrots exist in the Cretaceous period? Nature 1999, 399:317-318. 10.1038/20583
39. Dyke GJ van Tuinen M The evolutionary radiation of modern birds (Neornithes): Reconciling molecules, morphology and the fossil record Zool J Linn Soc 2004, 141:153-177. 10.1111/j.1096-3642.2004.00118.x
40. García-Moreno J Is there a universal molecular clock for birds? J Avian Biol 2004, 35:465-468. 10.1111/j.0908-8857.2004.03316.x
41. Mindell DP Knight A Baer C Huddleston CJ Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypotheses Mol Biol Evol 1996, 13:422-426.
42. Lovette IJ Mitochondrial dating a mixed support for the "2% rule" in birds Auk 2004, 121:1-6. 10.1642/ 0004-8038(2004)121[0001:MDAMSF]2.0.CO;2
43. Bromham L Penny D The modern molecular clock Nat Rev Genet 2003, 4:216-224. 10.1038/nrg1020 12610526
44. Magallón SA Dating lineages: Molecular and paleontological approaches to the temporal framework of clades Int J Plant Sci 2004, 165:S7-S21. 10.1086/383336
45. Rutschmann F Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times Divers Distrib 2006, 12:35-48. 10.1111/j.1366-9516.2006.00210.x
46. Welch JJ Bromham L Molecular dating when rates vary Trends Ecol Evol 2004, 20:320-327. 16701388 10.1016/j.tree.2005.02.007
47. Drummond AJ Ho SYW Phillips MJ Rambaut A Relaxed phylogenetics and dating with confidence PLoS Biol 2006, 4:e88. 1395354 16683862 10.1371/ journal.pbio.0040088
48. Ho SYW Phillips MJ Drummond AJ Cooper A Accuracy of rate estimation using relaxed-clock models with a critical focus on the early Metazoan radiation Mol Biol Evol 2005, 22:1355-1363. 10.1093/molbev/msi125 15758207
49. Easteal S Molecular evidence for the early divergence of placental mammals BioEssays 1999, 21:1052-1058. 10.1002/ (SICI)1521-1878(199912)22:1<1052::AID-BIES9<3.0.CO;2-6 10580990
50. Hug LA Roger AJ The impact of fossils and taxon sampling on ancient molecular dating analyses Mol Biol Evol 2007, 24:1889-1897. 10.1093/ molbev/msm115 17556757
51. Linder HP Hardy CR Rutschmann F Taxon sampling effects in molecular clock dating: An example from the African Restionaceae Mol Phylogenet Evol 2005, 35:569-582. 10.1016/j.ympev.2004.12.006 15878126
52. Pagel M Venditti C Meade A Large punctuational contribution of speciation to evolutionary divergence at the molecular level Science 2006, 314:119-121. 10.1126/science.1129647 17023657
53. Cracraft J Barker FK Braun M Harshman J Dyke GJ Feinstein J Stanley S Cibois A Schikler P Beresford P García-Moreno J Sorenson MD Yuri T Mindell DP Phylogenetic relationships among modern birds (Neornithes): Toward an avian tree of life Assembling the Tree of Life New York: Oxford University Press Cracraft J, Donoghue MJ 1 2004, 1:468-489.
54. Livezey BC Zusi RL Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion Zool J Linn Soc 2007, 149:1-95. 10.1111/ j.1096-3642.2006.00293.x
55. Mayr G Osteological evidence for paraphyly of the avian order Caprimulgiformes (nightjars and allies) J Ornithol 2002, 143:82-97. 10.1007/BF02465461
56. Barrowclough GF Groth JG Mertz LA The RAG-1 exon in the avian order Caprimulgiformes: Phylogeny, heterozygosity, and base composition Mol Phylogenet Evol 2006, 41:238-248. 10.1016/j.ympev.2006.05.013 16814574
57. Ericson PGP Anderson CL Britton T Elzanowski A Johansson US Källersjö M Ohlson JI Parsons TJ Zuccon D Mayr G Diversification of Neoaves: Integration of molecular sequence data and fossils Biol Lett 2006, 4:543-547. 17148284 10.1098/rsbl.2006.0523
58. Fain MG Houde P Parallel radiations in the primary clades of birds Evolution 2004, 58:2558-2573. 15612298
59. Griffiths CS Monophyly of the Falconiformes based on syringeal morphology Auk 1994, 111:787-805.
60. Mayr G Clarke J The deep divergences of neornithine birds: A phylogenetic analysis of morphological characters Cladistics 2003, 19:527-553. 10.1111/j.1096-0031.2003.tb00387.x
61. Sibley CG Ahlquist JE Phylogeny and Classification of Birds London: Yale University Press 1990.
62. Gibb GC Kardailsky O Kimball RT Braun EL Penny D Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations Mol Biol Evol 2007, 24:269-280. 10.1093/molbev/ msl158 17062634
63. Sorenson MD Oneal E Garcia-Moreno J Mindell DP More taxa, more characters: The hoatzin problem is still unresolved Mol Biol Evol 2003, 20:1484-1498. 10.1093/molbev/msg157 12777516
64. de Juana E Family Pteroclidae (Sandgrouse) Handbook of the Birds of the World. Sandgrouse to Cuckoos Barcelona: Lynx Edicions del Hoyo J, Elliott A, Sargatal J 1997, 4:30-49.
65. Slack KE Delsuc F McLenachan PA Arnason U Penny D Resolving the root of the avian mitogenomic tree by breaking up long branches Mol Phylogenet Evol 2007, 42:1-13. 10.1016/j.ympev.2006.06.002 16854605
66. Sanderson MJ r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock Bioinformatics 2003, 19:301-302. 10.1093/bioinformatics/19.2.301 12538260
67. Thorne JL Kishino H Painter IS Estimating the rate of evolution of the rate of evolution Mol Biol Evol 1998, 15:1647-1657. 9866200
68. Robertson DS McKenna MC Toon OB Hope S Lillegraven JA Survival in the first hours of the Cenozoic Geol Soc Am Bull 2004, 116:760-768. 10.1130/ B25402.1
69. Cracraft J Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event Proc R Soc Lond B Biol Sci 2001, 268:459-469. 11296857 10.1098/rspb.2000.1368
70. Eldredge N Gould SJ Punctuated equilibria: An alternative to phyletic gradualism Models in Paleobiology San Francisco: Freeman, Cooper, and Co Schopt TJM 1972:82-115.
71. Mayr E Change of genetic environment and evolution Evolution as a Process London: George Allen and Unwin Huxley J, Hardy AC, Ford EB 1954:157-180.
72. Barrachlough TG Savolainen V Evolutionary rates and species diversity in flowering plants Evolution 2001, 55:677-683. 10.1554/ 0014-3820(2001)055[0677:ERASDI]2.0.CO;2 11392385
73. Cubo J Evidence for speciational change in the evolution of ratites (Aves: Palaeognathae) Biol J Linn Soc 2003, 80:99-106. 10.1046/ j.1095-8312.2003.00222.x
74. Mindell DP Sites JW Jr Graur D Speciational evolution: A phylogenetic test with allozymes in Sceloporus (REPTILIA) Cladistics 1989, 5:49-61.
75. Bromham L Woolfit M Explosive radiations and the reliability of molecular clocks: Island endemic radiations as a test case Syst Biol 2004, 53:758-766. 10.1080/10635150490522278 15545253
76. Aris-Brosou S Yang Z Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa Mol Biol Evol 2003, 20:1947-1954. 10.1093/molbev/msg226 12949122
77. Dyke GJ The evolutionary radiation of modern birds: Systematics and patterns of diversification Geology Journal 2001, 36:305-315. 10.1002/ gj.878
78. Hope S The Mesozoic record of Neornithes (modern birds) Mesozoic Birds: Above the Heads of Dinosaurs Berkeley, CA: University of California Press Chiappe LM, Witmer LM 2002:339-388.
79. Smith AB Peterson KJ Dating the time of origin of major clades: molecular clocks and the fossil record Annu Rev Earth Planet Sci 2002, 30:65-88. 10.1146/annurev.earth.30.091201.140057
80. Marshall CR Fossil gap analysis supports early Tertiary origin of trophically diverse avian orders: Comment Geology 1999:27-95. 10.1130/ 0091-7613(1999)027<0095:FGASET<2.3.CO;2
81. Bininda-Emonds ORP Cardillo M Jones KE MacPhee RDE Beck RMD Grenyer R Price SA Vos RA Gittleman JL Purvis A The delayed rise of present-day mammals Nature 2007, 446:507-512. 10.1038/nature05634 17392779
82. Cutler DJ Estimating divergence times in the presence of an overdispersed molecular clock Mol Biol Evol 2000, 17:1647-1660. 11070053
83. Rannala B Yang Z Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci Genetics 2003, 164:1645-1656. 1462670 12930768
84. Ho SYW Calibrating molecular estimates of substitution rates and divergence times in birds J Avian Biol 2007, 38:409-414.
85. Yang Z Rannala B Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds Mol Biol Evol 2006, 23:212-226. 10.1093/molbev/msj024 16177230
86. Brochu CA Sumrall CD Theodor JM When clocks (and communities) collide: estimating divergence time from molecules and the fossil record J Paleontol 2004, 78:1-6. 10.1666/ 0022-3360(2004)078<0001:WCACCE<2.0.CO;2
87. Donoghue PCJ Benton MJ Rocks and clocks: Calibrating the Tree of Life using fossils and molecules Trends Ecol Evol 2007, 22:424-431. 10.1016/ j.tree.2007.05.005 17573149
88. Gill F Wright M Birds of the World: Recommended English Names Princeton, NJ: Princeton University Press 2006.
89. Sorenson MD Ast JC Dimcheff DE Yuri T Mindell DP Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates Mol Phylogenet Evol 1999, 12:105-114. 10.1006/mpev.1998.0602 10381314
90. Mindell DP Sorenson MD Huddleston CJ Miranda HCJ Knight A Sawchuk SJ Yuri T Phylogenetic relationships among and within select avian orders based on mitochondrial DNA Avian Molecular Evolution and Systematics San Diego, CA: Academic Press Mindell DP 1997:213-247.
91. Müller J Reisz RR Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates BioEssays 2005, 27:1069-1075. 10.1002/bies.20286 16163732
92. Sanders KL Lee MSY Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds Biol Lett 2007, 3:275-279. 10.1098/rsbl.2007.0063 17363358
93. Stamatakis A Ludwig T Meier H RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees Bioinformatics 2005, 21:456-463. 10.1093/bioinformatics/bti191 15608047
94. Felsenstein J PHYLIP (Phylogeny Inference Package) 3.6 Seattle, WA: Department of Genome Sciences, University of Washington 2004.
95. Swofford DL PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods) 4 (beta 10) Sunderland, MA: Sinauer Associates 2003.
96. Sanderson MJ Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach Mol Biol Evol 2002, 19:101-109. 11752195
97. Sanderson MJ A nonparametric approach to estimating divergence times in the absence of rate constancy Mol Biol Evol 1997, 14:1218-1231.
98. Britton T Anderson CL Jaquet D Lundqvist S Bremer K PATHd8 - a new method for estimating divergence times in large phylogenetic trees without a molecular clock 2006. http://www.math.su.se/PATHd8
99. Britton T Anderson CL Jacquet D Lundqvist S Bremer K Estimating divergence times in large phylogenetic trees Syst Biol 2007, 56:741-752. 10.1080/10635150701613783 17886144
100. Thorne JL MULTIDISTRIBUTE 2003. http://statgen.ncsu.edu/thorne/ multidivtime.html
101. Kishino H Thorne JL Bruno WJ Performance of a divergence time estimation method under a probabilistic model of rate evolution Mol Biol Evol 2001, 18:352-361. 11230536
102. Thorne JL Kishino H Divergence time and evolutionary rate estimation Syst Biol 2002, 51:689-702. 10.1080/10635150290102456 12396584
103. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13:555-556. 9367129
104. Cutler DJ Dating5 2000.
105. Drummond AJ Rambaut A BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214 17996036 2247476
106. Suchard MA Weiss RE Sinsheimer JS Bayesian selection of continuous-time Markov chain evolutionary models Mol Biol Evol 2001, 18:1001-1013. 11371589
107. Rambaut A Drummond AJ TreeAnnotator 1.4.5 2006. http://tree.bio.ed.ac.uk/ software/treeannotator/
108. Pagel M Venditti C Meade A Test for Punctuational Evolution and the Node-Density Artifact 2006. http://www.evolution.reading.ac.uk/pe/ index.html
109. Mayr G Old world fossil record of modern-type hummingbirds Science 2004, 304:861-864. 10.1126/science.1096856 15131303