View Item 

Show simple item record

BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

dc.contributor.authorRabosky, Daniel L.en_US
dc.contributor.authorGrundler, Michaelen_US
dc.contributor.authorAnderson, Carlosen_US
dc.contributor.authorTitle, Pascalen_US
dc.contributor.authorShi, Jeff J.en_US
dc.contributor.authorBrown, Joseph W.en_US
dc.contributor.authorHuang, Huatengen_US
dc.contributor.authorLarson, Joanna G.en_US
dc.date.accessioned2014-08-06T16:49:41Z
dc.date.availableWITHHELD_12_MONTHSen_US
dc.date.available2014-08-06T16:49:41Z
dc.date.issued2014-07en_US
dc.identifier.citationRabosky, Daniel L.; Grundler, Michael; Anderson, Carlos; Title, Pascal; Shi, Jeff J.; Brown, Joseph W.; Huang, Huateng; Larson, Joanna G. (2014). " BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees." Methods in Ecology and Evolution 5(7): 701-707.en_US
dc.identifier.issn2041-210Xen_US
dc.identifier.issn2041-210Xen_US
dc.identifier.urihttps://hdl.handle.net/2027.42/108027
dc.publisherR Foundation for Statistical Computingen_US
dc.publisherWiley Periodicals, Inc.en_US
dc.subject.otherMacroevolutionen_US
dc.subject.otherComputational Biologyen_US
dc.subject.otherBayesianen_US
dc.subject.otherStatisticsen_US
dc.subject.otherSpeciationen_US
dc.subject.otherExtinctionen_US
dc.subject.otherTraitsen_US
dc.titleBAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic treesen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelEcology and Evolutionary Biologyen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/108027/1/mee312199.pdf
dc.identifier.doi10.1111/2041-210X.12199en_US
dc.identifier.sourceMethods in Ecology and Evolutionen_US
dc.identifier.citedreferenceKass, R.E., Raftery & A.E. ( 1995 ) Bayes factors. Journal of the American Statistical Association, 90, 773 – 795.en_US
dc.identifier.citedreferenceLartillot, N. & Phillipe, H. ( 2006 ) Computing Bayes factors using thermodynamic integration. Systematic Biology, 55, 195 – 207.en_US
dc.identifier.citedreferenceMahler, D.L., Revell, L.J., Glor, R.E. & Losos, J.B. ( 2010 ) Ecological opportunity and the rate of morphological evolution in the diversification of greater Antillean anoles. Evolution, 64, 2731 – 2745.en_US
dc.identifier.citedreferenceNewton, M.A. & Raftery, A.E. ( 1994 ) Approximate Bayesian inference by the weighted likelihood bootstrap. Journal of the Royal Statistical Society B, 56, 3 – 48.en_US
dc.identifier.citedreferenceParadis, E., Claude, J. & Strimmer, K. ( 2004 ) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289 – 290.en_US
dc.identifier.citedreferencePopescu, A.A., Huber, K.T. & Paradis, E. ( 2012 ) ape 3.0: new tools for distance‐based phylogenetics and evolutionary analysis in R. Bioinformatics, 28, 1536 – 1537.en_US
dc.identifier.citedreferenceR Development Core Team ( 2014 ) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.en_US
dc.identifier.citedreferenceRabosky, D.L. ( 2014 ) Automatic detection of key innovations, rate shifts, and diversity‐dependence on phylogenetic trees. PLoS One, 9, e89543.en_US
dc.identifier.citedreferenceRabosky, D.L., Santini, F., Eastman, J.M., Smith, S.A., Sidlauskas, B., Chang, J. & Alfaro, M.E. ( 2013 ) Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications, 4, 1958. doi: 10.1038/ncomms2958.en_US
dc.identifier.citedreferenceRabosky, D.L. & Glor, R.E. ( 2010 ) Equilibrium speciation dynamics in a model adaptive radiation of island lizards. Proceedings of the National Academy of Sciences of the United States of America, 107, 22178 – 22183.en_US
dc.identifier.citedreferenceAdams, D.C., Berns, C.M., Kozak, K.H. & Wiens, J.J. ( 2009 ) Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society B‐Biological Sciences, 276, 2729 – 2738.en_US
dc.identifier.citedreferenceBurbrink, F.T., Chen, X., Myers, E.A., Brandley, M.C. & Pyron, R.A. ( 2012 ) Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proceedings of the Royal Society of London Series B – Biological Sciences, 279, 4817 – 4826.en_US
dc.identifier.citedreferenceFitzJohn, R.G. ( 2012 ) Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution, 3, 1084 – 1092.en_US
dc.identifier.citedreferenceGoldberg, E.E., Lancaster, L.T. & Ree, R.H. ( 2011 ) Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology, 60, 451 – 465.en_US
dc.identifier.citedreferenceHardy, N.B. & Cook, L.G. ( 2012 ) Testing for ecological limitation of diversification: a case study using parasitic plants. American Naturalist, 180, 438 – 449.en_US
dc.identifier.citedreferenceHarmon, L.J., Schulte, J.A., Larson, A. & Losos, J.B. ( 2003 ) Tempo and mode of evolutionary radiation in iguanian lizards. Science, 301, 961 – 964.en_US
dc.identifier.citedreferenceHarmon, L.J., Weir, J.T., Brock, C., Glor, R.E. & Challenger, W.E. ( 2008 ) GEIGER: investigating evolutionary radiations. Bioinformatics, 24, 129 – 131.en_US
dc.identifier.citedreferenceIngram, T. & Mahler, D.L. ( 2013 ) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion. Methods in Ecology and Evolution, 4, 416 – 425.en_US
dc.identifier.citedreferenceThomas, G.H. & Freckleton, R.P. ( 2012 ) MOTMOT: models of trait macroevolution on trees. Methods in Ecology and Evolution, 3, 145 – 151.en_US
dc.identifier.citedreferenceRolland, J., Condamine, F.L., Jiguet, F. & Morlon, H. ( 2014 ) Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biology, 12, e1001775.en_US
dc.identifier.citedreferenceSteeman, M.E., Hebsgaard, M.E., Fordyce, R.E., Ho, S.W.Y., Rabosky, D.L., Nielsen, R. et al. ( 2009 ) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573 – 585.en_US
dc.identifier.citedreferenceSeddon, N., Merrill, R.M. & Tobias, J.A. ( 2008 ) Sexually selected traits predict patterns of species richness in a diverse clade of suboscine birds. American Naturalist, 171, 620 – 631.en_US
dc.identifier.citedreferenceRevell, L.J. ( 2013 ) Two new graphical methods for mapping trait evolution on phylogenies. Methods in Ecology and Evolution, 4, 754 – 759.en_US
dc.identifier.citedreferenceRevell, L.J. ( 2012 ) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217 – 223.en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
mee312199.pdf
Size:
1.399MB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.