Publications (in PDF) or links to open access articles for all but some in press publications. Please email me if you have trouble opening a file or want an article that lacks a PDF.
Sun, K., K.A. Meicklejohn, B. Faircloth, T. Glenn, E.L. Braun, and R.T. Kimball. In press. The evolution of peafowl and other taxa with ocelli (eyespots): A phylogenomic approach. In press. Proceedings of the Royal Society of London, B.
Crawford, D.J., M. Tadesse, R.T. Kimball, M.E. Mort, P. Carrillo-Reyes and I. Sanchez-Vega. In press. Coreopsis section Pseudoagarista (Asteraceae: Coreopsideae): Molecular phylogeny, chromosome numbers, and comments on taxonomy and distribution. Taxon.
Kimball, R.T. and E.L. Braun. 2014. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ 2:e361.
Meicklejohn, K.A., M.J. Danielson, E.L. Braun, B.C. Faircloth, T. C. Glenn, and R.T. Kimball. 2014. Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Molecular Phylogenetics and Evolution 78: 314-323. PDF
Kimball, R.T., N. Wang , C.N. Ferguson , V. Heimer-McGinn , and E.L. Braun. In Press. Identifying localized biases in large datasets: A case study using the Avian Tree of Life. Molecular Phylogenetics and Evolution. PDF
Patel, S., R.T. Kimball, E.L. Braun. In Press. Error in Phylogenetic Estimation for Bushes in the Tree of Life. Journal of Phylogenetics and Evolutionary Biology 1:110. PDF
Sun, K., L. Luo, R.T. Kimball, X. Wei, L. Jin, T. Jiang, G. Li and J. Feng. 2014. Geographic variation in the acoustic traits of greater horseshoe bats: testing the importance of drift and ecological selection in evolutionary processes. PLoS One: 8 e70368.
Wang, N., R.T. Kimball, E.L. Braun, B. Liang, Z. Zhang. 2013. Assessing phylogenetic relationships among Galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae. PLOS One: 8: e64312.
Yuri, T., R.T. Kimball, J. Harshman, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, K-L Han, Hackett, S.J., C.J. Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, D.W. Steadman, C.C. Witt, and E.L. Braun. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology 2: 419-444. PDF
Smith, J.V., E.L. Braun and R.T. Kimball. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology 62: 45-49. PDF
Wang, N. and R.T Kimball. 2012. Nestmate killing by obligate brood parasitic chicks: Is this linked to obligate siblicidal behavior? Journal of Ornithology 153: 825-31. PDF
Wang, N., E.L. Braun, and R.T. Kimball. 2012. Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset. Molecular Biology and Evolution 29: 737-750. PDF
Braun, E.L., R.T. Kimball, K-L Han, N.R. Iuhasz-Velez, A.J. Bonilla, J.L. Chojnowski, J.V. Smith, R.C.K. Bowie, M.J. Braun, Hackett, S.J., J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt and T. Yuri. 2011. Homoplastic microinversions and the avian tree of life. BMC Evolution 11: 141. PDF
Kimball, R.T., C.M. St. Mary, and E.L. Braun. 2011. A macroevolutionary perspective on multiple sexual traits in the Phasianidae (Galliformes). International Journal of Evolutionary Biology. Article ID: 423938, doi:10.4061/2011/423938. PDF
Han, K-L, E.L. Braun, R.T. Kimball, S. Reddy, R.C.K. Bowie, M. J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt and T. Yuri. 2011. Are transposable element insertions homoplasy free? An examination of the avian tree of life. Systematic Biology 60: 375-386. PDF
Haas, S.E., J.A. Cox, J.V. Smith, and R.T. Kimball. 2010. Fine-scale spatial genetic structure in the cooperatively breeding Brown-Headed Nuthatch (Sitta pusilla). Southeastern Naturalist. Southeastern Naturalist 9: 743-756. PDF
Lomáscolo, S., D. Levey, R.T. Kimball, and B. Bolker. 2010. Dispersers shape fruit diversity in the genus Ficus (Moraceae). Proceedings of the National Academy of Sciences 107: 14668-14672. PDF
Bonilla, A.J., E.L. Braun, and R.T. Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3’-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution 56: 536-542. PDF
Whiteman, N.K., S.V. Dosanjh, R. Palma, J. Hull, R.T. Kimball, P. Sanchez, J.H. Sarasola, P.G. Parker. 2009. Molecular and morphological divergence in a pair of bird species and their ectoparasites. Journal of Parasitology 95: 1372–1382. PDF
Kimball, R. T., E. L. Braun, R. C. K. Bowie, M. J. Braun, J.L. Chojnowsk, S. J. Hackett, K-L Han, J. Harshman, V. Heimer-Torres, C. J. Huddleston, B. D. Marks, K. J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, J. V. Smith, C. C. Witt, and T. Yuri. 2009. A well-tested set of resources to amplify nuclear regions across the avian genome. Molecular Phylogenetics and Evolution 50: 654-660. PDF
Krakauer, A. and R.T. Kimball. 2009. Interspecific brood parasitism in galliform birds. Ibis 151 373-381.
Haas, S.E., J.V. Smith, R.T. Kimball, and A.M. Clark. 2009. Isolation and characterization of polymorphic microsatellite markers for the brown-headed nuthatch (Sitta pusilla). Conservation Genetics 10: 1393-1395. PDF
Haas, S.E., R.T. Kimball, J. Martin, and W. Kitchens. 2008. Genetic divergence among snail kite subspecies: implications for the conservation of the endangered Florida snail kite (Rostrhamus sociabilis). Ibis 151: 181-185. PDF
Crawford, D.J., M. Tadesse, M.E. Mort, R.T. Kimball, and C.P. Randle. 2009. Coreopsideae. Pp. 713-730 in Systematics, Evolution, and Biogeography of Compositae. Funk, V.A., A. Susanna, T.F. Stuessy, and R.J. Bayer, eds. International Association of Plant Taxonomy (Sheridan Press, Ann Arbor). PDF
Funk, V.A., A.A. Anderberg, B.G. Baldwin, R.J. Bayer, M. Bonifacino, I. Breitwieser, L. Brouillet, R. Carbajal, R. Chan, A.X.P. Coutinho, D.J. Crawford, J.J.V. Crisci, M.O. Dillon, S.E. Freire, M. Galbany-Casals, N. Garcia-Jacas, B. Gemeinholzer, M. Gruenstaeudl, H.W. Lack, H.V. Hansen, S. Himmelreich, J.W. Kadereit, M. Källersjö, V. Karaman-Castro, P.O. Karis, L. Katinas, S. Keeley, N. Kilian, R.T. Kimball, T.K. Lowrey, J. Lundberg, R.J. McKenzie, M.E. Mort, B. Nordenstam, C. Oberprieler, S. Ortiz, J.L. Panero, P.B. Pelser, C.P. Randle, H. Robinson, N. Roque, G. Sancho, E. Schilling, J.C. Semple, M. Serrano, R. Smissen, T.F. Stuessy, A. Susanna, M. Tadesse, M. Unwin, L. Urbatsch, E. Urtubey, J. Vallès, R. Vogt, S. Wagstaff, J. Ward, and L.E. Watson. 2009. Compositae Meta-supertree: The Next Generation. Pp. 747-777in Systematics, Evolution, and Biogeography of Compositae. V.A. Funk, A. Susanna, T.F. Stuessy, and R. J. Bayer, eds. Vienna: International Association of Plant Taxonomy. (Printed by Sheridan Press, Ann Arbor). PDF
Hackett, S.*, R. T. Kimball*, S. Reddy*, R. Bowie, E. L. Braun, M. Braun, J.L. Chojnowski, W.A. Cox, K-L Han, J. Harshman, C. Huddleston, B. Marks, K. Miglia, W.S. Moore, F.H. Sheldon, D. Steadman,and C. Witt and T. Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768. PDF
* Authors contributed equally.
See related Science podcast and Science News Focus (Pennisi 2008)
Kimball, R.T., and E.L. Braun. 2008. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. Journal of Avian Biology 39: 438-445. PDF
Harshman, J. E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S. J. Hackett, K-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, S.J. Steppan, C. C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the
National Academy of Sciences 105:13462-13467. PDF
Hull, J.M., W.K. Savage, J.L. Bollmer, R.T. Kimball, P.G. Parker, N.K. Whiteman, H.B. Ernest. 2008. On the origin of the Galápagos hawk: an examination of phenotypic differentiation and mitochondrial paraphyly. Biological Journal of the Linnean Society 95: 779-789. PDF
Lomáscolo, S., P. Speranza , and R.T. Kimball. 2008. Correlated evolution of fig size and color in Ficus (Moraceae) supports the Dispersal Syndrome hypothesis. Oecologia 156:783-796. PDF
Mort, M.E., C.P. Randle, R.T. Kimball, M. Tadesse, and D.J. Crawford. 2008. Phylogeny of Coreopsideae (Asteraceae): Insights from nuclear and plastid sequences. Taxon. 57: 109-120.
Chojnowski, J., R.T. Kimball, and E.L. Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene. 410: 89-96. PDF
Yuri, T., R.T. Kimball, E.L. Braun and M.J. Braun. 2008. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution 25:352-361. PDF
Whiteman, N.K., R.T. Kimball, and P.G. Parker. 2007. Co-phylogeography and comparative population genetics of the threatened Galapagos hawk and three ectoparasite species: ecology shapes population histories within parasite communitites. Molecular Ecology 16: 4759-4773. PDF
Chojnowski, J.L., J. Franklin, Y. Katsu, T. Iguchi,L.J. Guillette Jr, R.T. Kimball and E.L. Braun. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian and crocodilian genes. Journal of Molecular Evolution 65: 259-266. PDF
Cox, W.A., R.T. Kimball, and E.L. Braun. 2007. Phylogenetic position of the New World quail (Odontophoridae): eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist tapestry. Auk 124: 71-84. PDF
Gibb, G.C., O. Kardailsky, R.T. Kimball, E.L. Braun, and D. Penny. 2007. Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution 24: 269-280. PDF
Kimball, R.T., E.L. Braun, J.D. Ligon, E. Randi, and V. Lucchini. 2006. Using molecular phylogenetics to interpret evolutionary changes in morphology and behavior in the Phasianidae. Acta Zoologica Sinica 52 (supplement): 362-365. PDF
Crowe, T.M., P. Bloomer, E. Randi, V. Lucchini, R. Kimball, E. Braun, and J.G. Groth. 2006. Supra-generic cladistics of landfowl (Order Galliformes). Acta Zoologica Sinica 52 (supplement): 358-361. PDF
Bollmer, J. L., R.T. Kimball, N. K. Whiteman, J. H. Sarasola, and P.G. Parker. 2006. Phylogeography of the Galápagos Hawk (Buteo galapagoensis): a recent arrival to the Galápagos Islands. Molecular Phylogenetics and Evolution 39: 237-247. PDF
Kimball, R.T. 2006. Hormonal control of avian coloration. Pp. 431-468. in Bird Coloration I: measurements and mechanisms. G. E. Hill and K. McGraw, eds. Harvard University Press. PDF
Crawford, D. J., E. Landolt, D. H. Les, and R.T. Kimball. 2005. Speciation in duckweeds (Lemnaceae): phylogenetic and ecological inferences. Aliso 22:229-240. PDF
Crawford, D. J., E. Landolt, D. H. Les, J. K. Archibald, and R.T. Kimball. 2005. Allozyme variation within and divergence between Lemna gibba and L. disperma: systematic and biogeographic implications. Aquatic Botany 83: 119-128. PDF
Kimball, R.T. and D.J. Crawford. 2004. Phylogeny of Coreopsideae (Asteraceae) using ITS sequences suggests lability in reproductive characters. Molecular Phylogenetics and Evolution 33: 127-139. PDF
Les, D.H., D.J. Crawford, R.T. Kimball, M.L. Moody, and E. Landolt. 2003. Biogeography of discontinuously distributed hydrophytes: a molecular appraisal of intercontinental disjunctions. International Journal of Plant Sciences 164: 917-932. PDF
Kimball, R.T., J.C. Bednarz, and P.G. Parker. 2003. Occurrence and evolution of cooperative breeding among diurnal raptors (Accipitridae and Falconidae). Auk 120: 717-729. PDF
Kimball, R.T., D.J. Crawford, D.H. Les, and E. Landolt. 2003. Out of Africa: molecular phylogenetics and biogeography of Wolffiella (Lemnaceae). Biological Journal of the Linnean Society 79: 565-576. PDF
Kimball, R.T., E.D. Smith, and D.J. Crawford. 2003. Molecular phylogeny and evolution of Coreocarpus (Asteraceae). Evolution 57: 52-61. PDF
Braun, E.L. and R.T. Kimball. 2002. Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling and Sequence Length. Systematic Biology 51:614-625. PDF
Les, D.H., D.J. Crawford, E. Landolt, J.D. Gabel, and R.T. Kimball. 2002. Phylogeny and systematics of Lemnaceae Dumortier, the duckweed family. Systematic Botany 27: 221-240. PDF
Kimball, R.T., D.J. Crawford, J.R. Page and P. J. Harmon. 2001. Intersimple Sequence Repeat (ISSR) diversity within Monarda fistulosa var. brevis (Lamiaceae) and divergence between var. brevis and var. fistulosa in West Virginia. Brittonia 53: 511-518. PDF
Crawford, D. J., E. Landolt , D. H. Les, and R. T. Kimball. 2001. Allozyme studies in Lemnaceae: variation and relationships in Lemna sections Alatae and Biformes. Taxon 50: 987-999. PDF
Crawford, D.J., R.T. Kimball, and M. Tadesse. 2001. The generic placement of a morphologically enigmatic species in Asteraceae: evidence from ITS sequences. Plant Systematics and Evolution 228: 63-69. PDF
Armstrong, M.H., E.L. Braun, and R.T. Kimball. 2001. Phylogenetic Utility of Avian Ovomucoid Intron G: A Comparison of Nuclear and Mitochondrial Phylogenies in the Galliformes. Auk 118: 799-804. PDF
Kimball, R.T., E.L. Braun, J.D. Ligon, E. Randi, and V. Lucchini. 2001. A Molecular Phylogeny of the Peacock-pheasants (Galliformes: Polyplectron spp.) Indicates Loss and Reduction of Ornamental Traits and Display Behaviors. Biological Journal of the Linnean Society 73: 187-198. PDF
Randi, E., V. Lucchini, A. Hennache, R.T. Kimball, E.L. Braun, and J.D. Ligon. 2001. Evolution of the mitochondrial DNA control-region and cytochrome b genes, and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Molecular Phylogenetics and Evolution 19: 187-201. PDF
Lowrey, T.K., C.J. Quinn, R.K. Taylor, R. Chan, R.T. Kimball, J.C. De Nardi. 2001. Molecular and morphological reassessment of relationships with the Vittadinia group of Astereae (Asteraceae). American Journal of Botany 88: 1279-1289. PDF
Braun, E.L., and R.T. Kimball. 2001. Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution: a reply to Walsh et al. (1999). Evolution 55: 1261-1263. PDF
Randi, E, V. Lucchini, T. Armijo-Prewitt, R.T. Kimball, E.L. Braun, and J.D. Ligon. 2000. Mitochondrial DNA phylogeny and speciation of the tragopans. Auk 117: 1003-1015. PDF
Kimball, R.T. and J.D. Ligon. 1999. Evolution of avian plumage dichromatism from a proximate perspective. American Naturalist 154: 182-193. PDF
Kimball, R.T., E.L. Braun, P. Zwartjes, T.M. Crowe, and J.D. Ligon. 1999. A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Molecular Phylogenetics and Evolution 11: 38-54. PDF
Furlow, F.B., R.T. Kimball, M.C. Marshall. 1998. Are rooster crows honest signals of fighting ability? Auk 115: 763-766. PDF
Ligon, J.D., R.T. Kimball, and M. Merola-Zwartjes. 1998. Mate choice in red junglefowl: the issues of multiple ornaments and fluctuating asymmetry. Animal Behaviour: 55: 41-50. PDF
Kimball, R.T. 1997. Male morphology and nest-site quality in House Sparrows. Wilson Bulletin 109: 711-719. PDF
Kimball, R.T., J.D. Ligon, and M. Merola-Zwartjes. 1997. Testicular asymmetry and secondary sexual characters in red junglefowl. Auk 114: 221-228. PDF
Kimball, R.T., E.L. Braun, and J.D. Ligon. 1997. Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma. Proceedings of the Royal Society of London B 264: 1517-1523. PDF
Kimball, R.T., J.D. Ligon, and M. Merola-Zwartjes. 1997. Fluctuating asymmetry in red junglefowl. Journal of Evolutionary Biology 10: 441-457. PDF
Hagelin, J.C. and R.T. Kimball. 1997. A female Gambel’s Quail with partial male plumage. Wilson Bulletin 109:544-546. PDF
Kimball, R.T. 1996. Female choice for male morphological traits in house sparrows, Passer domesticus. Ethology 102:639-648. PDF
Møller, A.P., R.T. Kimball, and J. Erritzoe. 1996. Sexual ornamentation, condition, and immune defense in the house sparrow Passer domesticus. Behavioral Ecology and Sociobiology 39: 317-322. PDF
Government Publications
Finch, D.M., J.L. Ganey, W. Yong, R. Kimball, and R. Sallabanks. 1997. Effects and interactions of fire, logging, and grazing. In Songbird Ecology in Southwestern Ponderosa Pine Forests: A literature review. USDA Forest Service Gen. Tech. Rep. RM-GTR-292: 103-136.
Mehlman, D., K. Gordon, D. Gray, R. Kimball, M.J. Mund-Meyerson. 1995. 1995 survey for and habitat characteristics of the southwestern willow flycatcher (Empidonax traillii extimus) in the Isleta-Belen reach of the Rio Grande, New Mexico. Report to the U.S. Army Corps of Engineers, Albuquerque District.
Mund, M.J., R. Kimball, D. Mehlman, K. Gordon, J. Travis, and D. Gray. 1994. Survey for the Southwestern Willow Flycatcher, Empidonax traillii extimus, in the Middle Rio Grande Flood Protection Project area, Isleta Pueblo to south of Belen. Report to the U.S. Army Corps of Engineers, Albuquerque District.