A Bayesian approach for evaluating the impact of historical events on rates of diversification

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

Volumn 106, Issue 11, 2009, Pages 4307-4312

  Moore, Brian R ^a   Donoghue, Michael J ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Adoxaceae; Extinction; Key innovations; Lupinus; Speciation

Indexed keywords

ADOXACEAE; ARTICLE; BAYES THEOREM; BIODIVERSITY; BIOGEOGRAPHY; CONTROLLED STUDY; HISTORY; LUPIN; MORPHOLOGICAL ADAPTATION; PREDICTION; PRIORITY JOURNAL; SPECIES; SPECIES DIFFERENCE; SPECIES DIVERSITY;

ADOXACEAE; BAYES THEOREM; BIODIVERSITY; EVOLUTION; GEOGRAPHY; KINETICS; LUPINUS; PLANTS;

ADOXACEAE; LUPINUS;

EID: 63149188584     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807230106     Document Type: Article

References (43)

1. Paradis E (2005) Statistical analysis of diversification with species traits. Evolution 59:1-12.
2. Ree RH (2005) Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59:257-265.
3. Maddison WP, Midford PE, Otto SP (2007) Evaluating a binary character's effect on speciation and extinction. Syst Biol 56:701-710.
4. Gelfand, AE (1996) Markov Chain Monte Carlo in Practice, eds Gilks WR, Richardson S, Spiegelhalter D (Chapman & Hall, New York), pp 145-161.
5. Gelman AE, Dey DK, Chang H (1992) Bayesian Statistics, eds Bernardo JM, Berger JO, Dawid AP, Smith AFM (Oxford Univ Press, New York), Vol 4, pp 147-167.
6. Nielsen R, Huelsenbeck JP (2002) Pacific Symposium on Biocomputing, Proceedings, eds Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE (World Scientific, Singapore), pp 576-588.
7. Bollback JP (2002) Bayesian model adequacy and choice in phylogenetics. Mol Biol Evol 19:1171-1180.
8. Nielsen R (2002) Mapping mutations on phylogenies. Syst Biol 51:729-739.
9. Huelsenbeck JP, Nielsen R, Bollback, JP (2003) Stochastic mapping of morphological characters. Syst Biol 52:131-158.
10. Kohavi R (1995)Astudyofcross-validation and bootstrap for accuracy estimation and model selection. Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, Vol 2, pp 1137-1143.
11. Harris TE (1964) The Theory of Branching Processes, Springer, Berlin.
12. Gelman A, Carlin JB, Stern HS, Rubin DB (1996) Bayesian Data Analysis, Chapman & Hall, London.
13. Meng X-L (1994) Posterior predictive P-values. Ann Stat 22:1142-1160.
14. Aris-Brosou S, Yang Z (2002) The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Syst Biol 51:703-714.
15. Aris-Brosou S, Yang Z (2003) Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Mol Biol Evol 20:1947-1954.
16. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
17. Rannala B, Yang Z (2007) Inferring speciation times underan episodic molecular clock. Syst Biol 56:453-466.
18. Huelsenbeck JP, Bollback JP (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol 50:351-366.
19. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
20. Pagel M, Meade A (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am Nat 167:808-825.
21. Bollback JP (2006) SIMMAP: stochastic character mapping of discrete traitson phylog-enies. BMC Bioinformatics 7:88.
22. Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673-684.
23. Huelsenbeck JP, Rannala B, Larget B (2000) A Bayesian framework for the analysis of cospeciation. Evolution 54:352-364.
24. Huelsenbeck JP, Rannala B, Larget B (2002) Tangled Trees: Phylogenies, Cospeciation, and Coevolution, ed Page RDM (Chicago Univ Press, Chicago), pp 93-119.
25. Ree RH, Moore BR, Donoghue MJ (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59:2299-2311.
26. Moore BR, Smith SA, Donoghue MJ (2009) Alikelihood model for incorporating fossil data in the inference of historical biogeography. Evolution, in press.
27. Moore BR, Donoghue MJ (2007) Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations. Am Nat 170:S28-S55.
28. Moore BR, Chan KMA, Donoghue MJ (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, ed Bininda-Emonds ORP (Kluwer Academic, Dordrecht, The Netherlands), pp 487-533.
29. Chan KMA, Moore BR (2005) Symme TREE: performing whole-tree tests of diversification rate variation. Bioinformatics 21:1709-1710.
30. Donoghue MJ, Bell CD, Winkworth RC (2003) The evolution of reproductive characters in Dipsacales. Int J Plant Sci 164:S453-S464.
31. Hughes C, Eastwood R (2006) Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proc Natl Acad Sci USA 103:10334-10339.
32. Ronquist F (1997) Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst Biol 46:195-203.
33. Nee S, Barraclough TG, Harvey PH (1996) Biodiversity: A Biology of Numbers and Differences, ed Gaston KJ (Blackwell Science, Oxford), pp 230-252.
34. Chan KMA, Moore BR (2002) Whole-tree methods for detecting differential diversification rates. Syst Biol 51:855-865.
35. Huelsenbeck JP, Rannala B, Masly JP (2000) Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349-2350.
36. Lutzoni F, Pagel M (1997) Accelerated molecular evolution as a consequence of transitions to mutualism. Proc Natl Acad Sci USA 94:11422-11427.
37. Yule GU (1924) A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis. Philos Trans R Soc Lond B 213:21-87.
38. de Queiroz A (1998) Interpreting sister-group tests of key innovation hypotheses. Syst Biol 47:710-718.
39. Maddison WP (2006) Confounding asymmetries in evolutionary diversification and character change. Evolution 60:1743-1746.
40. Donoghue MJ, Ree RH, Baum DA (1998) Phylogeny and the evolution of flower symmetryin the Asteridae. Trends Plants Sci 3:311-317.
41. Magallon S, Sanderson MJ (2001) Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
42. Kubo T, Iwasa Y (1995) Inferring rates of branching and extinction from molecular phylogenies. Evolution 49:694-704.
43. Donoghue MJ (2005) Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31:77-93.