File Contents ------------- emberizoid.supertrees.RData An R workspace binary containing backbone and subclade trees and functions for generation of emberizoid pseudoposterior trees. The workspace contains the following objects: 1) backbone_contree: A multiPhylo object containing backbone trees generated by concatenated analysis (Barker et al. 2013). 2) backbone_sptree: A multiPhylo object containing backbone trees generated by species tree analysis (Barker et al. 2013). 3) base.list: A list of all emberizoid species in our base taxonomy. 4) calcariids: A multiPhylo object containing trees for the subclade Calcariidae (this study). 5) cardinals: A multiPhylo object containing trees for the subclade Cardinalidae (this study). 6) emberiza: A multiPhylo object containing trees for the subclade Emberizidae (this study, based on data from Alström et al. 2008). 7) graft.clade: A grafting function called by output.posterior (see below). 8) icterids: A multiPhylo object containing trees for the subclade Icteridae (Powell et al. 2014). 9) output.posterior: The base function used to generate grafted pseudoposterior trees. The code has loops and is very slow. 10) parulids: A multiPhylo object containing trees for the subclade Parulidae (Lovette et al. 2010). 11) passerellids: A multiPhylo object containing trees for the subclade Passerellidae (Klicka et al. 2014). 12) thraupids: A multiPhylo object containing trees for the subclade Thraupidae (Burns et al. 2014). References Alstrom, P., U. Olsson, F. Lei, H. T. Wang, W. Gao, and P. Sundberg (2008). Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes). Molecular Phylogenetics and Evolution 47:960-973. Barker, F.K. K.J. Burns, J. Klicka, S.M. Lanyon, and I.J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62(2): 298-320. Burns, K.J., A.J. Shultz, P.O. Title, N.A. Mason, F.K. Barker, J. Klicka, S.M. Lanyon, and I.J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75: 41-77. Klicka, J., F.K. Barker, K.J. Burns, S.M. Lanyon, I.J. Lovette, J.A. Chaves, and RW. Bryson, Jr. 2014. A comprehensive multilocus assessment of sparrow (Family Passerellidae) relationships. Molecular Phylogenetics and Evolution 77: 177-182. Lovette, I.J., J.L. Perez-Emán, J. Sullivan, R.C. Banks, I. Fiorentino, S. Córdoba-Córdoba, M. Echeverry-Galvis, F.K. Barker, K. Burns, J. Klicka, S.M. Lanyon, and E. Bermingham. 2010. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution 57: 753-770. Powell, A.F.L.A., F.K. Barker, Scott M. Lanyon, K.J. Burns, J. Klicka, and I.J.L. Lovette. 2014. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae). Molecular Phylogenetics and Evolution 71(1): 94-112.