RBrownie: An R package for testing hypotheses about rates of evolutionary change

Methods in Ecology and Evolution

Volumn 2, Issue 6, 2011, Pages 660-662

  Stack, J Conrad ^a   Harmon, Luke J ^b   O'Meara, Brian ^c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF IDAHO   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Bioinformatics; Comparative analysis; Evolutionary biology; Phylogenetics; Reconstruction; Software

Indexed keywords

EID: 84867688966     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2011.00112.x     Document Type: Article

References (11)

1. Ackerly, D. (2009) Conservatism and diversification of plant functional traits: evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences, 106(Suppl. 2), 19699-19706.
2. Bollback, J.P. (2006) Simmap: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.
3. Collar, D.C., O'Meara, B.C., Wainwright, P.C. & Near, T.J. (2009) Piscivory limits diversification of feeding morphology in centrarchid fishes. Evolution, 63, 1558-5646.
4. Gatesy, S.M. & Middleman, K.M. (1997) Bipedalism, flight, and the evolution of theropod locomotor diveristy. Journal of Vertebrate Paleontology, 17, 308-329.
5. Hackathon, R., Bolker, B., Butler, M., Cowan, P., de Vienne, D., Eddelbuettel, D., Holder, M., Jombart, T., Kembel, S., Michonneau, F., Orme, D., O'Meara, B., Paradis, E., Regetz, J. & Zwickl, D. (2010) Phylobase. R package version 0.6.2. http://CRAN.R-project.org/package=phylobase.
6. Huelsenbeck, J.P., Nielsen, R. & Bollback, J.P. (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-158.
7. Maddison, W.P. & Maddison, D. (2010) Mesquite: a modular system for evolutionary analysis. Version 2.73. http://mesquiteproject.org.
8. Maddison, D.R., Swofford, D.L. & Maddison, W.P. (1997) Nexus: an extensible file format for systematic information. Systematic Biology, 46, 590-621.
9. O'Meara, B.C. (2008) Using trees: myrmecocystus phylogeny and character evolution and new methods for investigating trait evolution and species delimitation (PhD Dissertation). Available from Nature Precedings.
10. O'Meara, B.C. (2010) New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59, 59-73.
11. O'Meara, B.C., Ané, C., Sanderson, M.J. & Wainwright, P. (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution, 60, 922-933.