Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 32, 2009, Pages 13410-13414

  Alfaro, Michael E ^a   Santini, Francesco ^a   Brock, Chad ^b   Alamillo, Hugo ^b   Dornburg, Alex ^g   Rabosky, Daniel L ^c,d   Carnevale, Giorgio ^e   Harmon, Luke J ^f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c Department of Obstetrics Gynecology   (United States)

^d Fuller Evolutionary Biology Program   (United States)

^e UNIVERSITY OF PISA   (Italy)

^f UNIVERSITY OF IDAHO   (United States)

^g YALE UNIVERSITY   (United States)

Author keywords

Evolutionary radiation; Macroevolution; Phylogeny

Indexed keywords

ARTICLE; BIRD; BIRTH RATE; CICHLID; CORAL REEF; EVOLUTION; FISH; LIVING FOSSIL; LIZARD; MAMMAL; MORTALITY; NONHUMAN; PERCH; PHYLOGENY; PRIORITY JOURNAL; SNAKE; SPECIES DIVERSITY; SPECIES EXTINCTION; SPECIES RICHNESS; VERTEBRATE;

ANIMALS; BIODIVERSITY; EVOLUTION; JAW; LIKELIHOOD FUNCTIONS; PHYLOGENY; VERTEBRATES;

ANTHOZOA; AVES; CICHLIDAE; EUTHERIA; GNATHOSTOMATA (VERTEBRATE); MAMMALIA; OSTARIOPHYSAN; PISCES; SERPENTES; SQUAMATA; TELEOSTEI; TETRAPODA; VERTEBRATA;

EID: 69449089577     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811087106     Document Type: Article

References (47)

1. Mooers AO, Heard SB (1997) Inferring evolutionary process from the phylogenetic tree shape. Q Rev Biol 72:31-54.
2. Slowinski JB, Guyer C (1993) Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction. Am Nat 142:1019.
3. Schluter D (2000) The Ecology of Adaptive Radiation (Oxford Univ Press, New York).
4. Eldredge N, Stanley SM (1984) Living Fossils (Springer, New York).
5. Stanley SM (1979) Macroevolution: Pattern and Process (Freeman, San Francisco).
6. Raup DM, Gould SJ, Schopf TJM, Simberloff DS (1973) Stochastic models of phylogeny and the evolution of diversity. J Geol 81:525-542.
7. Bininda-Emonds OR, et al. (2007) The delayed rise of present-day mammals. Nature 446:507-512.
8. Ricklefs RE, Losos JB, Townsend TM (2007) Evolutionary diversification of clades of squamate reptiles. J Evol Biol 20:1751-1762.
9. Roelants K, et al. (2007) Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci USA 104:887-892. (Pubitemid 46154706)
10. Chan KM, Moore BR (2005) SYMMETREE: Whole-tree analysis of differential diversification rates. Bioinformatics 21:1709-1710.
11. Chan KM, Moore BR (2002) Whole-tree methods for detecting differential diversification rates. Syst Biol 51:855-865.
12. Nee S, May RM, Harvey PH (1994) The reconstructed evolutionary process. Phil Trans R Soc London, Ser B 344:305-311.
13. Rabosky DL, Donnellan SC, Talaba AL, Lovette IJ (2007) Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proc Biol Sci 274:2915-2923.
14. Woodburne MO, Rich TH, Springer MS (2003) The evolution of tribospheny and the antiquity of mammalian clades. Mol Phylogenet Evol 28:360-385.
15. Ostrom JH (1979) Bird flight: How did it begin? Am Sci 67:45-56.
16. Burnham KP, Anderson DR (2003) Model Selection and Multimodel Inference, A Practical Information-Theoretic Approach (Springer, New York).
17. Simpson GG (1944) Tempo and Mode in Evolution (Columbia Classics in Evolution Series) (Columbia Univ Press, New York), reprint Ed, 1984.
18. Darwin C (1859) On the Origin of Species-A Facsimile of the First Edition (Harvard Univ Press, Cambridge, MA).
19. Liow LH (2007) Lineages with long durations are old and morphologically average: An analysis using multiple datasets. Evolution 61:885-901.
20. Ricklefs RE (2005) Small clades at the periphery of passerine morphological space. Am Nat 165:651-659.
21. Strathmann RR, Slatkin M (1983) The improbability of animal phyla with few species. Paleobiology 9:97-106.
22. Evans SE, Chure D (1998) Paramacellodid lizard skulls from the Jurassic Morrison Formation at Dinosaur National Monument. Utah J Vert Paleont 18:99-114. (Pubitemid 128077076)
23. Forey PL (1998) History of the Coelacanth Fishes (Springer, London).
24. Markwick PJ (1998) Crocodilian diversity in space and time; the role of climate in paleoecology and its implication for understanding K/T extinctions. Paleobiology 24:470-497. (Pubitemid 128632517)
25. Grande L, Bemis W (1998) A Comprehensive Phylogenetic Study of Amiid Fishes (Amiidae) Based on Comparative Skeletal Anatomy: An Empirical Search for Interconnected Patterns of Natural History (Memoir) (Society of Vertebrate Paleontology, Lawrence, KS).
26. Etienne RS, Apol ME (2009) Estimating speciation and extinction rates from diversity data and the fossil record. Evolution 63:244-255.
27. Alroy J (2009) in Speciation and Patterns of Diversity (Cambridge Univ Press, Cambridge, MA), pp 301-323.
28. Nee S, Holmes EC, May RM, Harvey PH (1994) Extinction rates can be estimated from molecular phylogenies. Philos Trans R Soc London Ser B 344:77-82.
29. Paradis E (2004) Can extinction rates be estimated without fossils? J Theor Biol 229:19-30.
30. Rabosky DL (2009) Ecological limits on clade diversification in higher taxa. Am Nat 173:662-674.
31. Li C, Orti G (2007) Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 44:386-398. (Pubitemid 46829903)
32. Hugall AF, Foster R, Lee MS (2007) Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst Biol 56:543-563. (Pubitemid 47171630)
33. Brinkmann H, Venkatesh B, Brenner S, Meyer A (2004) Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates. Proc Natl Acad Sci USA 101:4900-4905. (Pubitemid 38469175)
34. Townsend TM, Larson A, Louis E, Macey JR (2004) Molecular phylogenetics of Squamata: The position of snakes, Amphisbaenians, and Dibamids, and the root of the Squamate tree. Syst Biol 53:735-757. (Pubitemid 39568276)
35. Schluter SF, Marchalonis JJ (2003) Cloning of shark RAG2 and characterization of the RAG1/RAG2 gene locus. FASEB J 17:470-472.
36. Venkatesh B, Erdmann MV, Brenner S (2001) Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc Natl Acad Sci USA 98:11382. (Pubitemid 32928737)
37. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
38. Drummond AJ, Rambaut (2007) A BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
39. Nelson JS (2006) Fishes of the World (Wiley, Hoboken, NJ).
40. Uetz P, et al., The Reptile Database, http://www.reptile-database.org, accessed May23, 2006.
41. Gill FG (2006) Ornithology (Freeman, New York).
42. Frost DR, Duellman WE (1985) Amphibian Species of the World : A Taxonomic and Geographical Reference (Allen/Association of Systematics Collections, Lawrence, KS).
43. Wilson DE, Reeder DAM (2005) Mammal Species of the World: A Taxonomic and Geographic Reference (Johns Hopkins Univ Press, Baltimore).
44. R Development Core Team (2005) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, www.R-project.org.
45. Paradis E, Claude J, Strimmer K (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290. (Pubitemid 38195693)
46. Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W (2008) GEIGER: Investigating evolutionary radiations. Bioinformatics 24:129-131.
47. Rabosky DL (2006) LASER: A maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinformatics 2:257-260.