Publications
2023
Moncrieff, A. E., B. C. Faircloth, R. C. Remsen, A. E. Hiller, C. Felix, A. P. Capparella, A. Aleixo, T. Valqui, and R. T. Brumfield. In press. Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin. Evolution.
Corbett, E. C., R. T. Brumfield, and B. C. Faircloth. In press. The mechanistic, genetic and evolutionary causes of bird eye colour variation. Ibis.
Seeholzer, G. F., and R. T. Brumfield. In press. Speciation-by-extinction. Systematic Biology. DOI: 10.1093/syad049
Rego, M. A., G. Del-Rio, and R. T. Brumfield. In press. Subspecies level distribution maps for birds of the Amazon basin and adjacent areas. Journal of Biogeography.
Salter, J. F., R. T. Brumfield, and B. C. Faircloth. 2023. An island “endemic” born out of hybridization between introduced lineages. Molecular Ecology. 10.1111/mec.16990
Elizondo, E. C., B. C. Faircloth, R. T. Brumfield, S. B. Shakya, V. A. Ellis, C. J. Schmidt, A. I. Kovach, and W. G. Shriver. 2023. A high quality de novo genome assembly for clapper rail (Rallus crepitans). G3: Genes, Genomes, Genetics 13:jkad097. DOI: 10.1093/g3journal/jkad097
Martínez-Gómez S. C., C. E. Lara, J. V. Remsen, Jr., R. T. Brumfield, and A. M. Cuervo. 2023. Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low. Ornithology 140:1-14. https://doi.org/10.1093/ornithology/ukad028.
Johnson, O., C. C. Ribas, A. Aleixo, L. N. Naka, M. G. Harvey, and R. T. Brumfield. 2023. Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Molecular Ecology 32:2186-2205. 10.1111/mec.16886.
Smith, B. T., J. Merwin, K. L. Provost, G. Thom, R. T. Brumfield, M. Ferreira, W. M. Mauck, R. G. Moyle, T. F. Wright, and L. Joseph. 2023. Phylogenomic analysis of the parrots of the world distinguishes artifactual biological sources of gene tree discordance. Systematic Biology 72:228-241. 10.1093/sysbio/syac055.
2022
Buainain, N., M. Ferreira, J. E. Avendaño, C. D. Cadena, B. C. Faircloth, R. T. Brumfield, J. Cracraft, and C. C. Ribas. 2022. Biogeography of a neotropical songbird radiation reveals similar diversification dynamics between montane and lowland clades. Journal of Biogeography 49:1260-1273. 10.1111/jbi.14379.
Zhao, S. M. Kurtis, N. D. White, A. E. Moncrieff, R. T. Brumfield, E. L. Braun, and R. T. Kimball. 2023. Exploring conflicts in whole genome phylogenetics: a case study within manakins. Systematic Biology 72:161-178. 10.1093/sysbio/syac062.
Salter, J. A., P. A. Hosner, W. L. E. Tsai, J. E. McCormack, E. L. Braun, R. T. Kimball, R. T. Brumfield, and B. C. Faircloth. 2022. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Molecular Phylogenetics and Evolution. 175:107559. 10.1016/j.ympev.2022.107559.
Moncrieff, A. E., B. C. Faircloth, and R. T. Brumfield. 2022. Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers. Molecular Phylogenetics and Evolution 173. 10.1016/j.ympev.2022.107525
Musher, L. J., M. Giakoumis, J. Albert, G. Del-Rio, M. Rego, G. Thom, A. Aleixo, C. C. Ribas, R. T. Brumfield, B. T. Smith, J. Cracraft. 2022. River network rearrangements promote speciation in lowland Amazonian birds. Science Advances 8: eabn1099. DOI: 10.1126/sciadv.abn1099.
Del-Rio, G., M. A. Rego, B. M. Whitney, F. Schunck, L. F. Silveira, B. C. Faircloth, and R. T. Brumfield. 2022. Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian interfluve. Evolution 76:455-475. DOI:10.1111/evo.14377
2021
Singhal, S., G. E. Derryberry, G. A. Bravo, E. P. Derryberry, R. T. Brumfield, and M. G. Harvey. 2021. The dynamics of introgression across an avian radiation. Evolution Letters 5-6:568-581.
Hiller, A. E., R. T. Brumfield, and B. C. Faircloth. 2021. A reference genome for the nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris). G3: jkab271.
Buainain, N., M. F. A. Maximiano, M. Ferreira, A. Aleixo, B. C. Faircloth, R. T. Brumfield, J. Cracraft, and C. C. Ribas. 2021. Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae). Molecular Phylogenetics and Evolution 162:107206.
Marcondes, R. S., J. A. Nations, G. F. Seeholzer, and R. T. Brumfield. 2021. Rethinking Gloger’s Rule: Climate, light environments, and color in a large family of tropical birds (Furnariidae). American Naturalist 197:592-606.
Bravo, G. A., B. M. Whitney, R. Belmonte-Lopes, M. R. Bornschein, N. Aristizábal, R. Beco, J. Battilana, L. N. Naka, A. Aleixo, M. R. Pie, L. F. Silveira, E. P. Derryberry, and R. T. Brumfield. 2021. Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi. Ornithology 138:1-16.
Johnson, O., J. T. Howard, and R. T. Brumfield. 2021. Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae: Epinecrophylla). Molecular Phylogenetics and Evolution 154:106962.
Leite, R. N., R. T. Kimball, E. L. Braun, E. P. Derryberry, P. A. Hosner, G. E. Derryberry, M. Anciães, J. McKay, D. Meyer, A. Aleixo, C. C. Ribas, R. T. Brumfield, J. Cracraft. 2021. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness. Molecular Phylogenetics and Evolution 155:107013.
2020
Harvey, M. G., G. A. Bravo, S. Claramunt, A. M. Cuervo, G. E. Derryberry, J. Battilana, G. F. Seeholzer, J. Shearer McKay, B. C. O’Meara, B. C. Faircloth, S. V. Edwards, J. Pérez-Emán, R. G. Moyle, F. H. Sheldon, A. Aleixo, B. T. Smith, R. T. Chesser, L. F. Silveira, J. Cracraft, R. T. Brumfield, E. P. Derryberry. 2020. The evolution of a tropical biodiversity hotspot. Science 370:1343-1348.
Feng, S., et al. 2020. Dense sampling of bird diversity increases power of comparative genomics. 2020. Nature 587:252-257.
Marcondes, R. S., and R. T. Brumfield. 2020. A simple index to quantify and compare the magnitude of intraspecific geographic plumage colour variation in typical antbirds (Aves: Passeriformes: Thamnophilidae). Biological Journal of the Linnean Society 130:239-246. DOI 10.1093/biolinnean/blaa041.
Marcondes, R. S., K. F. Stryjewski, and R. T. Brumfield. 2020. Testing the simple and complex versions of Gloger’s rule in the Variable Antshrike (Thamnophilus caerulescens, Thamnophilidae). Auk. DOI 10.1093/auk/ukaa026.
Imfeld, T. S., F. K. Barker, and R. T. Brumfield. 2020. Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the bizarre Euphonia and Chlorophonia finches (Passeriformes: Fringillidae). Auk 137:1-25. DOI 10.1093/auk/ukaa016.
Bolívar-Leguizamón, S.D., L. F. Silveira, E. P. Derryberry, R. T Brumfield, and G. A. Bravo. 2020. Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients. Molecular Phylogenetics and Evolution 148:106810. DOI 10.1016/j.ympev.2020.106810.
Settlecowski, A. E., A. M. Cuervo, J. G. Tello, M. G. Harvey, R. T. Brumfield, and E. P. Derryberry. 2020. Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae). Molecular Phylogenetics and Evolution 147:106779. DOI 10.1016/j.ympev.2020.106779.
Cadena, C. D., A. M. Cuervo, L. N. Céspedes, G. A. Bravo, N. Krabbe, T. S. Schulenberg, G. E. Derryberry, L. F. Silveira, E. P. Derryberry, R. T. Brumfield, and J. Fjeldså. 2020. Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds. Auk 137:1-30. DOI 10.1093/auk/ukaa003.
Salter, J. F., C. H. Oliveros, P. A. Hosner, J. D. Manthey, M. B. Robbins, R. G. Moyle, R. T. Brumfield, and B. C. Faircloth. 2020. Extensive paraphyly in the typical owl family (Strigidae). Auk 137. DOI 10.1093/auk/ukz070.
2019
Cadena, C. D., A. M. Cuervo, L. N. Céspedes, G. A. Bravo, N. Krabbe, T. S. Schulenberg, G. E. Derryberry, L. F. Silveira, E. P. Derryberry, R. T. Brumfield, and J. Fjeldså. In press. Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds. Auk.
Salter, J. F., C. H. Oliveros, P. A. Hosner, J. D. Manthey, M. B. Robbins, R. G. Moyle, R. T. Brumfield, and B. C. Faircloth. In press. Extensive paraphyly in the typical owl family (Strigidae). Auk.
Salter, J. F., O. Johnson, N. J. Stafford, III, W. F. Herrin, Jr., D. Schilling, C. Cedotal, R. T. Brumfield, and B. C. Faircloth. 2019. Genome Report: A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus). G3: Genes|Genomes|Genetics. DOI:10.1534/g3.119.400609.
Schultz, E. D., J. Pérez-Emán, A. Aleixo, C. Y. Miyaki, R. T. Brumfield, J. Cracraft, and C. C. Ribas. 2019. Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): insights from broad geographic sampling. Molecular Phylogenetics and Evolution 140:106581 DOI: 10.1016/j.ympev.2019.106581.
Kimball, R. T., C. H. Oliveros, N. Wang, N. D. White, F. K. Barker, D. J. Field, D. T. Ksepka, R. T. Chesser, R. G. Moyle, M. J. Braun, R. T. Brumfield, B. C. Faircloth, B. T. Smith, and E. L. Braun. 2019. A phylogenomic supertree of birds. Diversity 11:109. DOI: 10.3390/d11070109.
Oliveros, C. H., D. J. Field, D. T. Ksepka, F. K. Barker, A. Aleixo, M. J. Andersen, P. Alström, B. W. Benz, E. L. Braun, M. J. Braun, G. A. Bravo, R. T. Brumfield, R. T. Chesser, S. Claramunt, J. Cracraft, A. M. Cuervo, E. P. Derryberry, T. C. Glenn, M. G. Harvey, P. A. Hosner, L. Joseph, R. Kimball, A. L. Mack, C. M. Miskelly, A. T. Peterson, M. B. Robbins, F. H. Sheldon, L. F. Silveira, B. T. Smith, N. D. White, R. G. Moyle, and B. C. Faircloth. 2019. Earth history and the passerine superradiation. PNAS 116:7916-7925. DOI: 10.1073/pnas.1813206116.
Marcondes, R. S., and R. T. Brumfield. 2019. Fifty shades of brown: Macroevolution of plumage brightness in a large clade of Neotropical passerines. Evolution 73:704-719. DOI: 10.1111/evo.13707.
Oswald, J. A., M. G. Harvey, R. C. Remsen, D. P. U. Foxworth, D. L. Dittmann, S. W. Cardiff, and R. T. Brumfield. 2019. Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World. Molecular Ecology 28:1675-1691. DOI: 10.1111/mec.15008.
2018
Naka, L. N., and R. T. Brumfield. 2018. The dual role of Amazonian rivers in the generation and maintenance of avian diversity. Science Advances 4:eaar8575. DOI 10.1126/sciadv.aar8575.
Derryberry, E. P., N. Seddon, G. E. Derryberry, S. Claramunt, G. F. Seeholzer†, R. T. Brumfield, and J. A. Tobias. 2018. Ecological drivers of song evolution in birds: Disentangling the effects of habitat and morphology. Ecology and Evolution 8:1890-1905. DOI: 10.1002/ece3.3760.
Ribas, C. C., A. Aleixo, C. Gubili, F. M. d’Horta, R. T. Brumfield, and J. Cracraft. 2018. Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary. Journal of Biogeography 45:917-928. DOI: 10/1111/jbi.13169.
Seeholzer, G. F., and R. T. Brumfield. 2018. Isolation-by-distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line-cheeked Spinetail) despite near three-fold body size change across an environmental gradient. Molecular Ecology. 27:279-296. DOI: 10.1111/mec.14429
2017
Harvey, M. G., A. Aleixo, C. C. Ribas, and R. T. Brumfield. 2017. Habitat association predicts genetic diversity and population divergence in Amazonian birds. American Naturalist 190:631-648. DOI: 10.1086/693856.
Harvey, M. G., G. F. Seeholzer, B. T. Smith, D. L. Rabosky, A. M. Cuervo, and R. T. Brumfield. 2017. Positive association between population genetic differentiation and speciation rates in New World birds. PNAS 114:6328-6333. DOI: 10.1073/pnas.1617397114.
Smith, B. T., G. F. Seeholzer, M. G. Harvey, A. M. Cuervo, and R. T. Brumfield. 2017. A latitudinal phylogeographic diversity gradient in birds. PLoS Biology 15:e2001073.
Seeholzer, G. F., S. Claramunt, and R. T. Brumfield. 2017. Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae). Evolution. doi: 10.1111/evo.13177.
Lipshutz, S. E., I. A. Overcast, M. J. Hickerson, R. T. Brumfield, and E. P. Derryberry. 2017. Behavioral response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys). Molecular Ecology.
Schultz, E. D., C. W. Burney, R. T. Brumfield, E. M. Polo, J. Cracraft, and C. C. Ribas. 2017. Systematics and biogeography of the Automolus infuscatus complex (Aves; Furnariidae): Cryptic diversity reveals western Amazonia as the origin of a transcontinental radiation. Molecular Phylogenetics and Evolution 107:503-515. doi: 10.1016/j.ympev.2016.12.023.
2016
Harvey, M. G., B. T. Smith, T. C. Glenn, B. C. Faircloth, and R. T. Brumfield. 2016. Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Systematic Biology doi: 10.1093/sysbio/syw036
Cadena, C. D., C. A. Pedraza, and R. T. Brumfield. 2016. Climate, habitat associations and the potential distributions of Neotropical birds: implications for diversification across the Andes. Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales. 40. doi: 10.18257/raccefyn.280.
Oswald, J. A., M. G. Harvey, R. C. Remsen, D. U. Foxworth, S. W. Cardiff, D. L. Dittmann, L. C. Megna, M. D. Carling, and R. T. Brumfield. 2016. Willet be one species or two? A genomic view of the evolutionary history of Tringa semipalmata. Auk 133:593-614. doi: 10.1642/auk-15-232.1
Zucker, M. R., M. G. Harvey, J. A. Oswald, A.M. Cuervo, E. P. Derryberry, and R. T. Brumfield. 2016. The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck. Molecular Phylogenetics and Evolution 101:294-302. doi: 10.1016/j.ympev.2016.04.031.
2015
Hird, S. M., C. Sánchez, B. C. Carstens, and R. T. Brumfield. 2015. Comparative gut microbiota of 59 Neotropical bird species. Front. Microbiol. 6:1403. doi: 10.3389/fmicb.2015.01403.
Harvey, M. G., Judy C. D., Seeholzer, G. F., Maley, J. M., Graves G. R., and Brumfield, R. T. 2015. Similarity thresholds used in short read assembly reduce the comparability of population histories across species. PeerJ 3:e895; doi: 10.7717/peerj.895
Harvey, M. G., and R. T. Brumfield. 2015. Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow. Molecular Phylogenetics and Evolution 83:305-316. doi: 10.1016/j.ympev.2014.10.023
2014
Zhang, G., et al. 2014. Comparative genomics across modern bird species reveal insights into avian genome evolution and adaptation. Science 346:1320-1331. doi: 10.1126/science.1251385
Jarvis, E. D., et al. 2014. Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346:1320-1331. doi: 10.1126/science.1253451
Isler, M. L., G. A. Bravo, and R. T. Brumfield. 2014. Systematics of the obligate ant-following clade of antbirds (Aves: Passeriformes: Thamnophilidae). Wilson Journal of Ornithology 126:635-648.
Smith, B. T., J. E. McCormack, A. M. Cuervo, M. J. Hickerson, A. Aleixo, C. D. Cadena, J. Pérez-Emán, C. W. Burney, X. Xie, M. G. Harvey, B. C. Faircloth, T. C. Glenn, E. P. Derryberry, J. Prejean, S. Fields, and R. T. Brumfield. 2014. The drivers of tropical speciation. Nature 515:406-409.
Cerame, B., J. A. Cox, R. T. Brumfield, J. W. Tucker, and S. S. Taylor. 2014. Adaptation to ephemeral habitat may overcome natural barriers and severe habitat fragmentation in a fire-dependent species, the Bachman’s Sparrow (Peucaea aestivalis). PLoS One. 9(9): e105782. doi:10.1371/journal.pone.0105782
Bravo, G. A., J. V. Remsen, Jr., and R. T. Brumfield. 2014. Adaptive processes drive convergent evolution of body size in antwrens (Thamnophilidae). Evolution 68:2757-74.
Valderrama, E., J. L. Pérez-Emán, R. T. Brumfield, A. M. Cuervo, and C. D. Cadena. 2014. The influence of the complex topography and dynamic history of the montane Neotropics on the evolutionary differentiation of a cloud forest bird (Premnoplex brunnescens, Furnariidae). Journal of Biogeography 41(8):1533-1546.
Isler, M. L., G. A. Bravo, and R. T. Brumfield. 2014. Inundicola Bravo, Isler, and Brumfield 2013 is a junior synonym of Akletos Dunajewski 1948 (Aves: Passeriformes: Thamnophilidae). Zootaxa 3779:399-400.
Hird, S. M., B. C. Carstens, S. W. Cardiff, D. L. Dittmann, and R. T. Brumfield. 2014. Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater). PeerJ 2:e321.
Tobias, J. A., C. K. Cornwallis, E. P. Derryberry, S. Claramunt, R. T. Brumfield, and N. Seddon. 2014. Species coexistence and the dynamics of phenotypic evolution in adaptive radiation. Nature 506:359-363. doi: 10.1038/nature12874
Derryberry, E. P., G. E. Derryberry, J. M. Maley, and R. T. Brumfield. 2014. HZAR: Hybrid zone analysis using an R software package. Molecular Ecology Resources.
Smith, B. T., M. G. Harvey, B. C. Faircloth, T. C. Glenn, and R. T. Brumfield. 2014. Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales. Systematic Biology 63:83-95.
2013
Brackett, C. L., J. M. Maley, R. T. Brumfield, and S. B. McRae. 2013. Characterization of microsatellite loci for a threatened species, the King Rail, Rallus elegans, using a next-generation sequencing protocol. Conservation Genetics Resources 5:1189-1191.
Isler, M. L, G. A. Bravo, and R. T. Brumfield. 2013. Taxonomic revision of Myrmeciza (Aves: Passeriformes: Thamnophilidae) into 12 genera based on phylogenetic, morphological, behavioral, and ecological data. Zootaxa 3717:469-497.
Claramunt, S., E. P. Derryberry, C. D. Cadena, A. M. Cuervo, C. Sanín, and R. T. Brumfield. 2013. Phylogeny and classification of Automolus foliage-gleaners and allies (Furnariidae). Condor 115:375-385.
Maley, J. M., and R. T. Brumfield. 2013. Mitochondrial and next-generation sequence data used to infer phylogenetic relationships and species limits in the Clapper/King Rail complex. Condor 115:316-329.
Parchman, T. L., Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. McDonald, J. A. C. Uy, E. D. Jarvis, B. A. Schlinger, and C. A. Buerkle. 2013. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology.
McCormack, J. E., M. G. Harvey, B. C. Faircloth, N. G. Crawford, T. C. Glenn, and R. T. Brumfield. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 8:e54848
Rheindt, F. E., Cuervo, A. M., and R. T. Brumfield. 2013. Rampant polyphyly indicates cryptic diversity in a clade of Neotropical flycatchers (Aves: Tyrannidae). Biological Journal of the Linnean Society 108:889-900.
d’Horta, F. M., A. M. Cuervo, C. C. Ribas, R. T. Brumfield, and C. Y. Miyaki. 2013. Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveals constant and cryptic diversification in an old radiation of rainforest understory specialists. Journal of Biogeography 40:37-49.
McCormack, J. E., S. M. Hird, A. J. Zellmer, B. C. Carstens, and R. T. Brumfield. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66:526-538.
2012
Tobias, J. A., J. D. Brawn, R. T. Brumfield, E. P. Derryberry, A. N. G. Kirschel, and N. Seddon. 2012. The importance of neotropical suboscine birds as study systems in ecology and evolution. Ornitologia Neotropical 23:259-272.
Belmonte-Lopes, Ricardo, G. A. Bravo, M. R. Bornschein, G. N. Maurício, M. R. Pie, and R. T. Brumfield. 2012. Genetic and morphological data support placement of Myrmotherula gularis (Spix) in the monotypic genus Rhopias Cabanis and Heine (Aves: Passeriformes: Thamnophilidae). Molecular Phylogenetics and Evolution 3451:1-16.
Bravo, G. A., J. V. Remsen, Jr., B. M. Whitney, and R. T. Brumfield. 2012. DNA sequence data reveal a subfamily-level divergence within the Thamnophilidae (Aves: Passeriformes). Molecular Phylogenetics and Evolution 65:287-293.
Brumfield, R. T. 2012. Inferring the origins of lowland Neotropical birds. Auk 129:367-376.
Crawford, N. G., B. C. Faircloth, J. E. McCormack, R. T. Brumfield, K. Winker, and T. C. Glenn. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters 8:783-786.
Isler, M. L., A. M. Cuervo†, G. A. Bravo and R. T. Brumfield. 2012. An integrative approach to species-level systematics reveals the depth of diversification in an Andean thamnophilid, the Long-tailed Antbird. Condor 114:571-583.
Gutiérrez-Pinto, N., A. M. Cuervo, J. Miranda, J. L. Pérez-Emán, R. T. Brumfield and C. D. Cadena. 2012. Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus Aves: Parulidae). Molecular Phylogenetics and Evolution 64:156-165.
Claramunt, S., E. P. Derryberry, J. V. Remsen, Jr., and R. T. Brumfield. 2012. High dispersal ability inhibits speciation in a continental radiation of passerine birds. Proc. Roy. Soc. London Series B 279:1567-1574.
Claramunt, S., E. P. Derryberry, R. T. Brumfield, and J. V. Remsen, Jr. 2012. Ecological opportunity and diversification in a continental radiation of birds: Climbing adaptations and cladogenesis in the Furnariidae. American Naturalist 179:649-666.
Derryberry, E. P., N. Seddon, S. Claramunt, J. A. Tobias, A. Baker, A. Aleixo, and R. T. Brumfield. 2012. Correlated evolution of beak morphology and song in the Neotropical woodcreeper radiation. Evolution 67:2784-2797.
Naka, L. N., C. L. Bechtoldt, L. M. P. Henriques, and R. T. Brumfield. 2012.The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern Amazonia. American Naturalist. E article. 179
McCormack, J. E., B. C. Faircloth, N. G. Crawford, P. A. Gowaty, R. T. Brumfield, and T. C. Glenn. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Research 22:746-754.
Faircloth, B. C., J. E. McCormack, N. G. Crawford, M. G. Harvey, R. T. Brumfield, and T. C. Glenn. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61:717-726.
Bravo, G. A., R. T. Chesser, and R. T. Brumfield. 2012. Isleria, a new genus of antwren (Aves: Passeriformes: Thamnophilidae). Zootaxa 3195:61-67.
McCormack, J. E., J. M. Maley, S. M. Hird, E. P. Derryberry, G. R. Graves, and R. T. Brumfield. 2012. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution 62:397-406.
2011
Claramunt, S., E. P. Derryberry, J. V. Remsen, Jr., and R. T. Brumfield. 2011. High dispersal ability inhibits speciation in a continental radiation of passerine birds. Proc. Roy. Soc. London B.
Cheviron, Z. A., and R. T. Brumfield. 2012. Genomic insights into adapation to high-altitude environments. Heredity 108:354-361.
Hird, S. M., R. T. Brumfield, and B. C. Carstens. 2011. PRGmatic: an efficient pipeline for collating genome-enriched second generation sequencing data using a ‘provisional-reference genome.’ Molecular Ecology Resources 11:743-748.
Cheviron, Z. A., M. D. Carling, and R. T. Brumfield. 2011. Effects of postmortem interval and preservation method on RNA isolated from field-preserved avian tissues. Condor 113:483-489.
Derryberry, E. P., S. Claramunt, G. Derryberry, R. T. Chesser, J. Cracraft, A. Aleixo, J. Pérez-Emán, J. V. Remsen, Jr., and R. T. Brumfield. 2011. Lineage diversification and morphological evolution in a large-scale continental radiation: the Neotropical ovenbirds and woodcreepers (Aves: Furnariidae). Evolution 65:2973-2986.
2010
Brumfield, R. T. 2010. Speciation genetics of biological invasions with hybridization. Molecular Ecology 19:5079-5083.
Tobias, J. A., J. Aben, E. P. Derryberry, R. T. Brumfield, W. Halfwerk, H. Slabbekoorn, and N. Seddon. 2010. Song divergence by sensory drive in Amazonian birds. Evolution 64:2820-2839.
Gómez, J. P., G. A. Bravo, R. T. Brumfield, J. G. Tello, and C. D. Cadena. 2010. A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds. Journal of Animal Ecology 79:1181-1192.
Brumfield, R.T. and M.D. Carling. 2010. The influence of hybrid zones on species tree inference in manakins. Pp. 115-128 in Estimating species trees: Practical and theoretical aspects (L.L. Knowles and L.S. Kubatko, eds.) Wiley-Blackwell, Hoboken, NJ.
Pérez-Emán, J. L., L. L. Hernandez, and R. T. Brumfield. 2010. Phylogenetic relationships of the White-throated Barbtail, Premnoplex tatei (Furnariidae): taxonomic and biogeographical implications. Condor 112:561-570.
Carling, M. D., I. J. Lovette, and R. T. Brumfield. 2010. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings. Evolution 64:1762-1772.
Claramunt, S., E. P. Derryberry, R. T. Chesser, A. Aleixo, and R. T. Brumfield. 2010. Polyphyly of Campylorhamphus with the description of a new genus for C. pucherani. Auk 127:430-439.
Derryberry, E., S. Claramunt, K. E. O’Quin, A. Aleixo, R. T. Chesser, J. V. Remsen, Jr., and R. T. Brumfield. 2010. Pseudasthenes, a new genus of ovenbird (Aves: Passeriformes: Furnariidae). Zootaxa 2416:61-68.
Derryberry, E., S. Claramunt, R. T. Chesser, A. Aleixo, J. Cracraft, R. G. Moyle, and R. T. Brumfield. 2010. Certhiasomus, a new genus of woodcreeper (Aves: Passeriformes: Dendrocolaptidae). Zootaxa 2416:44-50.
Mackay, A. J., W. L. Kramer, J. K. Meece, R. T. Brumfield, and L. D. Foil. 2010. Host feeding patterns of Culex mosquitos (Diptera: Culicidae) in East Baton Rouge Parish. Journal of Medical Entomology 47:238-248.
2009
Yuri, T., R. W. Jernigan, R. T. Brumfield, N. K. Bhagabati, and M. J. Braun. 2009. The effect of marker choice on estimated levels of introgression across an avian (Pipridae: Manacus) hybrid zone. Molecular Ecology 18:4888-4903.
Chesser, R. T., S. Claramunt, E. Derryberry, and R. T. Brumfield. 2009. Geocerthia, a new genus of terrestrial ovenbird (Aves: Passeriformes: Furnariidae). Zootaxa 2213:64-68.
Burney, C. W., and R. T. Brumfield. 2009. Ecology predicts levels of genetic differentiation in Neotropical birds. American Naturalist 174:358-368.
Moyle, R. G., R. T. Chesser, R. T. Brumfield, J. G. Tello, D. J. Marchese, and J. Cracraft. 2009. Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides). Cladistics 25:1-20.
Cheviron, Z. A., and R. T. Brumfield. 2009. Migration-selection balance and local adaptation of mitochondrial haplotypes in Rufous-collared Sparrows (Zonotrichia capensis) along an elevational gradient. Evolution 63:1593-1605.
Carling, M. D., and R. T. Brumfield. 2009. Speciation in Passerina buntings: introgression patterns of sex-linked loci identify a candidate gene region for reproductive isolation. Molecular Ecology 18:834-847.
Lance, S. L., C. Hagen, T. C. Glenn, R. T. Brumfield, K. Faust Stryjewski, and G. R. Graves. 2009. Fifteen polymorphic microsatellite loci from Jamaican streamertail hummingbirds (Trochilus). Conservation Genetics 10:1195-1198.
2008
Cheviron, Z. A., A. Whitehead, and R. T. Brumfield. 2008. Transcriptomic variation and plasticity in Rufous-collared Sparrows (Zonotrichia capensis) along an altitudinal gradient. Molecular Ecology 17:4556-4569.
Carling, M. D., and R. T. Brumfield. 2008. Haldane’s Rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone. Evolution 62:2600-2615.
Brumfield, R. T., L. Liu, D. E. Lum, and S. V. Edwards. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Systematic Biology 57:719-731.
Liu, L., D. K. Pearl, R. T. Brumfield, and S. V. Edwards. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080-2091.
Bates, J. M., C. D. Cadena, J. G. Tello, and R. T. Brumfield. 2008. Diversification in the Neotropics: Phylogenetic patterns and historical processes. Ornitologia Neotropical 19:427-432.
Carling, M. D., and R. T. Brumfield. 2008. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics 178:363-377.
2007
Peterson, A. T., R. T. Brumfield, R. G. Moyle, A. S. Nyári, J. V. Remsen Jr., and M. B. Robbins. 2007. The need for proper vouchering in phylogenetic studies of birds. Molecular Phylogenetics and Evolution 45:1042-1044.
Brumfield, R. T., and O. Maillard Z. 2007. Birds of the central Río Paracti valley, a humid montane forest in departamento Cochabamba, Bolivia. Ornitologia Neotropical 18:321-337.
Brumfield, R. T., J. G. Tello, Z. A. Cheviron, M. D. Carling, N. Crochet, and K. V. Rosenberg. 2007. Phylogenetic conservatism and antiquity of a tropical specialization: army-ant-following in the typical antbirds (Thamnophilidae). Molecular Phylogenetics and Evolution 45:1-13.
Chesser, R. T., and R. T. Brumfield. 2007. Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America. Proceedings of the Biological Society of Washington 120:337-339.
Chesser, R. T., F. K. Barker, and R. T. Brumfield. 2007. Four-fold polyphyly of the genus formerly known as Upucerthia, with notes on the systematics and evolution of the avian subfamily Furnariinae. Molecular Phylogenetics and Evolution 44:1320-1332.
Brumfield, R. T., and S. V. Edwards. 2007. Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution 61:346-367.
Carling, M. D., and R. T. Brumfield. 2007. Gene sampling strategies for multi-locus population estimates of genetic diversity (theta). PLoS ONE 2:e160.
2006
Isler, M. I., D. R. Lacerda, P. R. Isler, S. J. Hackett, K. V. Rosenberg, and R. T. Brumfield. 2006. Epinecrophylla, a new genus of antwrens (Aves: Passeriformes: Thamnophilidae). Proceedings of the Biological Society of Washington 119:522-527.
Cheviron, Z. A., S. H. Hackett, and R. T. Brumfield. 2006. Sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R) is not associated with plumage variation in the Blue-crowned Manakin (Lepdiothrix coronata). Proceedings of the Royal Society of London Series B 273:1613-1618.
Berg, K. S., R. T. Brumfield, and V. A. Apanius. 2006. Phylogenetic and ecological determinants of the Neotropical dawn chorus. Proceedings of the Royal Society of London Series B 273:999-1005.
2005
Edwards, S. V., S. Birks, R. T. Brumfield, and R. Hanner. 2005. The future of avian genetic resources collections: archives of evolutionary and environmental history. Auk 122:979-984.
Brumfield, R. T. 2005. Mitochondrial variation in Bolivian populations of the Variable Antshrike (Thamnophilus caerulescens). Auk 122:414-432.
Isler, M. L., P. R. Isler, and R. T. Brumfield. 2005. Clinal variation in vocalizations of an antbird (Thamnophilidae) and implications for defining species limits. Auk 122:433-444.
Brumfield, R. T. 2005. Review: The speciation and biogeography of birds. Condor 107:477-478.
Sheldon, F. H., J. V. Remsen, and R. T. Brumfield. 2005. Letter concerning Academy of Natural Science Job Cuts.
2004
Whitney, B. M., D. C. Oren, and R. T. Brumfield. 2004. A new species of Thamnophilus antshrike (Aves: Thamnophilidae) from the Serra do Divisor, Acre, Brazil. Auk 121:1031-1039.
Brumfield, R. T., O. Maillard Z., R. C. Faucett, G. Sánchez, V. G. Rohwer, J. C. Catari, C. G. Schmitt, D. C. Schmitt, R. Strem, and A. M. Mamani. 2004. Birds of the Laguna Kaucaya area, a semi-humid valley in the Andean foothills of departamento Santa Cruz, Bolivia. Ornitologia Neotropical 15:381-398.
Witt, C. C., and R. T. Brumfield. 2004. Comment on “Are rates of speciation and molecular evolution correlated?” Science 303:173b.
2003
Brumfield, R. T., P. Beerli, D. A. Nickerson, and S. V. Edwards. 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18:249-256.
2001
Weicker, J., R. T. Brumfield, and K. Winker. 2001. Estimating the unbiased estimator theta for population genetic survey data. Evolution 55:2601-2605.
Brumfield, R. T., R. W. Jernigan, D. B. McDonald, and M. J. Braun. 2001. Evolutionary implications of divergent clines in an avian (Manacus; Aves) hybrid zone. Evolution 55:2070-2087.
McDonald, D. B., M. J. Braun, R. T. Brumfield, and R. P. Clay. 2001. Sexual selection on plumage and behavior in an avian hybrid zone: experimental tests of male-male interactions. Evolution 55:1443-1451.
Brumfield, R. T., and M. J. Braun. 2001. Phylogenetic relationships in bearded manakins (Pipridae; Manacus) indicate that male plumage color is a misleading taxonomic marker. Condor 103:248-258.
2000
Brumfield, R. T. 2000. Book review: Molecular evolution: a phylogenetic approach. American Zoologist 40:707.
1998
Remsen, J. V., Jr., and R. T. Brumfield. 1998. Two new subspecies of Cinnycerthia fulva (Aves: Troglodytidae) from the southern Andes. Proceedings of the Biological Society of Washington 111:1008-1015.
Braun, M. J., and R. T. Brumfield. 1998. Enigmatic phylogeny of skuas: An alternative hypothesis. Proceedings of the Royal Society of London B 265:995-999.
1997
Brumfield, R. T., D. L. Swofford, and M. J. Braun. 1997. Evolutionary relationships among the potoos (Nyctibiidae) based on isozymes. Ornithological Monographs 48:129-145.
1996
Brumfield, R. T., and A. P. Capparella. 1996. Historical diversification of birds in northwestern South America: A molecular perspective on the role of vicariant events. Evolution 50:1607-1624.
Brumfield, R. T., and A. P. Capparella. 1996. Genetic differentiation and taxonomy in the Troglodytes aedon (House Wren) species group. Condor 98:547-556.
Brumfield, R. T., and J. V. Remsen, Jr. 1996. Geographic variation and species limits in Cinnycerthia wrens of the Andes. Wilson Bulletin 108:205-227.