Publications

Listed by year of publication

2017    Kingston SE, Parchman TL, Gompert Z, Buerkle CA and Braun MJ. Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees. Journal of Evolutionary Biology 30: 474–485.

2017    White ND, Mitter CM and Braun MJ. Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae). Journal of Avian Biology, published online January 16, 2017.

2016    White, N. D., G. F. Barrowclough, J. G. Groth and M. J. Braun. A multi-gene estimate of higher-level phylogenetic relationships among nightjars (Aves: Caprimulgidae). Ornitología Neotropical 27:223-236.

2016    Lim, H. C. and M. J. Braun. High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements.  Molecular Ecology Resources 16:1204-1223 (doi: 10.1111/1755-0998.12568).

2014    Jarvis, E. D., and 104 others including M. J. Braun. Whole Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds. Science 346:1320-1331.

2014    Reynolds, S. M., J. A. C. Uy, G. Patricelli, S. Coleman, M. J. Braun and G. Borgia. Tests of the kin selection model of mate choice and inbreeding avoidance in satin bowerbirds. Behavioral Ecology 25:1005-1014 (doi:10.1093/beheco/aru065).

2014    Kingston, S. E., A. G. Navarro-Sigüenza, E. A. García-Trejo, H. Vázquez-Miranda, W. F. Fagan, and M. J. Braun. Genetic differentiation and habitat connectivity across towhee hybrid zones in Mexico. Evolutionary Ecology 28: 277-297.

2014    S.R. Reynolds, J.A.C. Uy, G.L. Patricelli, S.W. Coleman, M.J. Braun, and G. Borgia.  Tests of the kin selection model of mate choice and inbreeeding avoidance in satin bowerbirds. Behavioral Ecology 00: 1-10.

2013    T.L. Parchman, Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. McDonald, J. A. C. Uy, G. Zhang, E. D. Jarvis, B. A. Schlinger and C. A. Buerkle. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology 22: 3304-3317.

2013    Coyle B.J., M.J. Braun, K.M. Rodriguez-Clark, L. Ovalle. Recovering the Red Siskin. Journal of the National Finch and Softbill Society July/August 2013: 30-38.

2013    Brian S. Davidson, Gene D. Sattler, Sara Via and Michael J. Braun. Reproductive isolation and cryptic introgression in a sky island enclave of Appalachian birds. Ecology and Evolution 3(8): 2485-2496.

2013    Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C. K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, and Edward L. Braun. Parsimony and Model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology 2: 419-444.

2012    Kingston, S. E., R. W. Jernigan W. F. Fagan, D. Braun and M. J. Braun. Genomic variation in cline shape across a hybrid zone. Ecology and Evolution 2(11): 2737-2748 (doi: 10.1002/ece3.375).

2011    Rodríguez-Clark, K. M., J. E. Maldonado, D. Ascanio, E. Gamero, L. Ovalle, J. Pérez-Emán and M. J. Braun. Using genetics to understand and conserve the Red Siskin (Carduelis cucullata). Journal of the National Finch and Softbill Society July/August 2011: 25-30.

2011*    Braun, E. L., R. T. Kimball, K.-L. Han, N. R. Iuhasz, A. J. Bonilla, J. L. Chojnowski, J. V. Smith, R. C. K Bowie, M. J. Braun, S.J. Hackett, J. Harshman, C. J. Huddleston, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, C. C. Witt, T. Yuri. Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology 11:141.*Recognized by BioMed Central as a “Highly Accessed” article in Sept 2011.

2011    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. Are Transposable Element Insertions Homoplasy Free? An Examination Using the Avian Tree of Life. Systematic Biology 60(3): 375-86.

2010    Han, K.-L., M. B. Robbins and M. J. Braun. A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae).  Molecular Phylogenetics and Evolution 55: 443-453.

2010    Braun, M. J., and C. J. Huddleston. Response to Mayr and Manegold. Molecular Phylogenetics and Evolution 55: 345-346.

2010    Olson, J. R., S. J. Cooper, D. L. Swanson, M. J. Braun, and J. B. Williams.  The relationship of metabolic performance and distribution in Black-capped and Carolina Chickadees. Physiological and Biochemical Zoology 83: 263-275.

2009    Yuri, T., R. W. Jernigan, R. T. Brumfield, N. K. Bhagabati, and M. J. Braun. The effect of marker choice on estimated levels of introgression across an avian (Pipridae: Manacus) hybrid zone. Molecular Ecology 18: 4888-4903.

2009    Braun, M. J., and C. J. Huddleston. A molecular phylogenetic survey of caprimulgiform nightbirds illustrates the utility of non-coding sequences. Molecular Phylogenetics and Evolution 53: 948-960.

2009    Kimball, R. T., E. L. Braun, F. K. Barker, R. C. K. Bowie, M. J. Braun, J. L. Chojnowski, S. J. Hackett, K.-L. Han, J. Harshman, V. Heimer-Torres, W. Holznagel, 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.  A well-tested set of primers to amplify regions spread across the avian genome. Molecular Phylogenetics and Evolution 50: 654-660.

2009   Reynolds, S. M., M. C. Christman, J. A. C. Uy, G. L. Patricelli, M. J. Braun, and G. Borgia. Lekking satin bowerbird males aggregate with relatives to mitigate aggression. Behavioral Ecology 20(2): 410-5.

2009    Meares, K., D. A. Dawson, G. J. Horsburgh, T. C. Glenn, K. L. Jones, M. J. Braun, M. R. Perrin and T. D. Taylor. Microsatellite loci characterized in three African crane species (Gruidae, Aves). Molecular Ecology Resources 9: 308–311.

2008    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, D. W. Steadman, S. J. Steppan, C. C. Witt, T. Yuri.  Phylogenomic evidence for multiple losses of flight in ratite birds.  Proceedings of the National Academy of Science USA 105: 13462-13467. *These authors contributed equally to the production of the manuscript.

2008    Hackett, S.J., Kimball, R.T., Reddy, S., Bowie, R.C.K., Braun, E.L., Braun, M.J., Chojnowski, J.L., Cox, W.A., Han, K., Harshman, J., Huddleston, C.J., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C. and Yuri, T.  A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768.

2008    Yuri, T., R. T. Kimball, E. L. Braun and M. J. Braun.  Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution 25: 352-361.

2007    Robbins, M. B., M. J. Braun, C. M. Milensky, B. K. Schmidt, W. Prince, N. H. Rice, D. W. Finch and B. J. O’Shea.  Avifauna of the upper Essequibo River and Acary Mountains, Southern Guyana.  Ornitologia Neotropical 18: 339-368.

2007    Reynolds, S. M., K. Dryer, J. Bollback, J. A. C. Uy, G. L. Patricelli, T. Robson, G. Borgia and M. J. Braun.  Behavioral paternity predicts genetic paternity in Satin Bowerbirds (Ptilonorhynchus violaceus), a species with a non-resource-based mating system. Auk 124(3): 857-867.

2007    Braun, M. J., D. W. Finch, M. B. Robbins and B. K. Schmidt. A Field Checklist of the Birds of Guyana, 2nd Ed.  Smithsonian Institution, Washington, D.C.

2007    Cleere, N., A. W. Kratter, D. W. Steadman, M. J. Braun, C. J. Huddleston and C. E. Filardi. A new genus of frogmouth (Podargidae) from the Solomon Islands – results from a taxonomic review of Podargus ocellatus inexpectatus Hartert 1901. Ibis 149: 271-286.

2007    Sattler. G. D., P. Sawaya and M. J. Braun.  An assessment of song admixture as an indicator of hybridization in Black-capped Chickadees (Poecile atricapillus) and Carolina Chickadees (P. carolinensis). Auk 124: 926-944.

2005    Bronson, C. L., T. C. Grubb, Jr., G. D. Sattler, and M. J. Braun. Reproductive success across the Black-capped (Poecile atricapillus) and Carolina chickadee (P. carolinensis) hybrid zone in Ohio. Auk 122: 759-772.

2005    Helbig, A. J., A. Kocum, I. Seibold and M. J. Braun.  A multi-gene phylogeny of Aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level.  Molecular Phylogenetics and Evolution 35:147-164.

2005    Braun, M. J., M. L. Isler, P. R. Isler, J. M. Bates and M. B. Robbins. Avian speciation in the Pantepui: The case of the Roraiman Antbird (Percnostola[Schistocichla] “leucostigma” saturata). Condor 107: 329-343.

2005    Robbins, M. B., M. J. Braun, Christopher J. Huddleston, Davis W. Finch, & Christopher M. Milensky. First Guyana records, natural history, and systematics of the White-naped Seedeater (Dolospingus fringilloides). Ibis 147: 334-341.

2004    Robbins, M. B., M. J. Braun and D. W. Finch. Avifauna of the Guyana southern Rupununi, with comparisons to other savannas of northern South America. Ornitologia Neotropical 15:173-200.

2004    Cracraft, J., F. K. Barker, M. J. Braun, J. Harshman, G. Dyke, J. Feinstein, S. Stanley, A. Cibois, P. Schikler, P. Beresford, J. García-Moreno, M. D. Sorenson, T. Yuri, and D. P. Mindell. “Phylogenetic relationships among modern birds (Neornithes): Toward an avian tree of life”, Chap. 28 in Assembling the Tree of Life, Cracraft, J. and M. J. Donoghue (eds.). Oxford Univ. Press, New York.

2003    Robbins, M. B., M. J. Braun and D. W. Finch. Discovery of a population of the endangered Red Siskin (Carduelis cucullata) in Guyana. Auk 120: 291-298.

2003    Harshman, J., C. J. Huddleston, J. P. Bollback, T. J. Parsons, and M. J. Braun.  True and false gharials: a nuclear gene phylogeny of Crocodylia. Systematic Biology 52: 386-402.

2003    Braun, M. J., M. B. Robbins, C. M. Milensky, B. J. O’Shea, B. R. Barber, W. Hinds and W. S. Prince.  New birds for Guyana from Mts. Roraima and Ayanganna. Bulletin of the British Ornithologist’s Club 123: 24-33.

2003a  Bronson, C. L., T. C. Grubb, Jr., and M. J. Braun. A test of the endogenous and exogenous selection hypotheses for the maintenance of a narrow avian hybrid zone.    Evolution 57:630-637.

2003b  Bronson, C. L., T. C. Grubb, Jr., G. D. Sattler and M. J. Braun.  Mate preference:  A possible causal mechanism for a moving hybrid zone.  Animal Behaviour 65: 489-500.

2003    Brumfield, R. T., R. W. Jernigan, D.B. McDonald and M. J. Braun.  Erratum correcting “Evolutionary implications of divergent clines in a manakin (Manacus; Aves) hybrid zone.” Evolution 57: 2919.

2001    Brumfield, R. T., R. W. Jernigan, D.B. McDonald and M. J. Braun.  Evolutionary implications of divergent clines in a manakin (Manacus; Aves) hybrid zone. Evolution 55: 2070-2087.

2001    McDonald, D. B., R. P. Clay, R. T. Brumfield and M. J. Braun.  Sexual selection on plumage  and behavior  in an avian hybrid zone: experimental tests of male-male interactions. Evolution 55:1443–1451.

2001    Brumfield, R. T. and M. J. Braun.  Phylogenetic relationships in bearded manakins  (Pipridae:Manacus ) indicate that male plumage color is a misleading taxonomic marker.  Condor 103:248-258.

2000    Braun, M. J., D. W. Finch, M. B. Robbins and B. K. Schmidt.  A Field Checklist of the Birds of Guyana.  Smithsonian Institution, Washington , D.C.

2000    Sattler, G. D. and M. J. Braun.  Morphometric variation as an indicator of genetic interactions between Black-capped and Carolina chickadees at their contact zone in the Appalachian Mountains.  Auk 117:427-444.

2000    Winker, K., G. R. Graves and M. J. Braun.  Population genetic differentiation in a migratory songbird: Limnothlypis swainsonii. Journal of Avian Biology 31: 319-328.

1999    Steppan, S. J., M. R. Akhverdyan, E. A. Lyapunova, D. G. Fraser, N. N. Vorontsov, R. S. Hoffmann, and M. J. Braun.  Molecular phylogeny of the marmots (Rodentia:Sciuridae): Tests of evolutionary and biogeographic hypotheses. Systematic Biology 48(4): 715-734.

1999    Glenn, T. C., W. Stephan, and M. J. Braun.  Effect of a population bottleneck on mitochondrial DNA variation in Whooping Cranes. Conservation Biology 13(5):1097-1107.

1999    Braun, M. J.  “The Mockingbird”.  Pp. 82-83  in “Fifty Great Birds of Texas” by  J. P. O’Neill.  S. Winckler, ed. University of Texas Press.

1998    Glenn, T. C., H. C. Dessauer, and M. J. Braun.  Characterization of microsatellite DNA loci in American alligators. Copeia 1998(3): 591-601.

1998    Braun, M. J. and R. T. Brumfield. 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.  Evolutionary relationships among the potoos (Nyctibiidae) based on isozymes. Ornithological Monographs 48:129-145.

1997    Glenn, T. C., R. S. Ojerio, W. Stephan, and M. J. Braun.  Microsatellite DNA loci for genetic studies of cranes.  Pp. 36-45 in “Proceedings of the 7th North American Crane Workshop”, R.P. Urbanek and D.W. Stahlecker (eds.). North American Crane Working Group.

1996    Glenn, T. C., W. Stephan, H. C. Dessauer, and M. J. Braun.  Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability. Molecular Biology and Evolution 13:1151-1154.

1996    Mariaux, J. and M. J. Braun.  A molecular phylogenetic survey of the nightjars and allies (Caprimulgiformes) with special emphasis on the potoos (Nyctibiidae). Molecular Phylogenetics and Evolution 6: 228-244.

1996    Winker, K., G. Graves and M.J. Braun.  Voucher specimens and quality control in avian molecular studies. Ibis 138: 345-346.

1994    Rhymer, J. M., M. J. Williams and M. J. Braun.  Mitochondrial DNA analysis of gene flow between New Zealand Mallards (Anas platyrhynchos) and Grey Ducks (A. superciliosa). Auk: 111: 970-978.

1994    Parsons, T. J., S. L. Olson, and M. J. Braun. Hybrid zones and sexual selection.  Science 265:122-123.

1994    Glenn, T. C., D. R. Waller and M. J. Braun.  Increasing proportions of uracil in DNA substrates increases inhibition of restriction enzyme digests. Biotechniques 17: 1086-1090.

1992    Graves, G. and M.J. Braun. Museums: Storehouses of DNA? Science 255:1335.

1992    Glenn, T. C. and M. J. Braun.  Toward the elimination of contamination from ancient DNA amplicons: use of 2′-deoxyuridine-5′-triphosphate and uracil DNA glycosylase to eliminate carryover PCR products. Ancient DNA Newsletter 1(2):28-31.

1991    Braun, M. J.  The flowering of molecular systematics.  Review of “Molecular Systematics”, D. M. Hillis and C. Moritz (eds.). Systematic Zoology 40:111-114.

1993    Parsons,T. J., S. L. Olson, and M. J. Braun.  Undirectional spread of secondary sexual plumage traits across an avian hybrid zone. Science 260: 1643-1646.

1993    Wilkerson, R. C., T. J. Parsons, D. G. Albright, T. A. Klein, M. J. Braun.  Random amplified polymorphic DNA (RAPD) markers readily distinguish cryptic mosquito species (Diptera:Culicidae: Anopheles). Insect Molecular Biology 1:205-211.

1993    Suh, Y. B., J. A. Blake, and M. J. Braun.  Equipping and organizing a molecular systematics laboratory.  Pp. 3-22 in “Molecular Evolution: Producing the Biochemical Data”, E. A. Zimmer, T. J. White, R. L. Cann, and A.C. Wilson (eds.).  Methods in Enzymology 224. Academic Press, San Diego.

1993    Bowditch, B. M., D. G. Albright, J. G. K. Williams, and M. J. Braun.  The use of randomly amplified polymorphic DNA markers in comparative genome studies.  Pp. 294-309 in “Molecular Evolution: Producing the Biochemical Data”, E. A. Zimmer, T. J. White, R. L. Cann, and A. C. Wilson (eds.). Methods in Enzymology 224. Academic Press, San Diego.

1992    Krajewski, C., A. C. Driskell, P. R. Baverstock, and M. J. Braun.  Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials: evidence from  cytochrome b DNA sequences. Proceedings of the Royal Society of London B 250:19-27.

1990    Morton, E. S., L. Forman, and M. J. Braun.  Extra pair fertilizations and the evolution of colonial breeding in purple martins. Auk 107:275-283.

1990    Garvey, K. J., M. S. Oberste, J. E. Elser, M. J. Braun, and M. A. Gonda.  Nucleotide sequence and genome organization of biologically active proviruses of the bovine immunodeficiency-like virus. Virology 175:391-409.

1988    Braun, M. J., S. Lahn, A. L. Boyd, T. A. Kost, K. Nagashima, and M. A. Gonda.  Molecular cloning of biologically active proviruses of bovine immunodeficiency-like virus.  Virology 167:515-523.

1988    Houde, P., and M. J. Braun. Museum collections as a source of DNA for studies of avian phylogeny.  Auk 105:773-776.

1988    Le, S.-Y., J.-H. Chen, M. J. Braun, M. A. Gonda, and J. V. Maizel.  Stability of RNA Stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-I). Nucleic Acids Research 16:5153-5168.

1988    Braun, M. J. Northern Gannet on I-65: Second record for Kentucky, first record for Tennessee. Kentucky Warbler 64:34-36.

1988    Dessauer, H. C., and M. J. Braun.  Species conservation of substrate requirements for peptidases. Isozyme Bulletin 21:188.

1987    Braun, M. J., M. A. Gonda, D. G. George, J. F. Bazan, R. J. Fletterick, and S. B. Prusiner. The burden of proof in linking AIDS to scrapie. Nature 330:525-526.

1987    Gonda, M. A., M. J. Braun, S. G. Carter, T. A. Kost, J. W. Bess, Jr., L. O. Arthur, and M. J. Van Der Maaten. Characterization and molecular cloning of a bovine lentivirus related to human immunodeficiency virus. Nature 330:388-391.

1987    Park, M., M. Dean, K. Kaul, M. J. Braun, M. A. Gonda, and G. Vande Woude.  Sequence of the MET proto-oncogene cDNA has features characteristic of the tyrosine kinase family of growth-factor receptors. Proceedings of the National Academy of Sciences USA 84:6379-6383.

1987    Braun, M. J., J. E. Clements, and M. A. Gonda.  The visna virus genome:  evidence for a hypervariable site in the env gene and sequence homology between lentivirus envelope proteins. Journal of Virology 61:4046-4054.

1987    Braun, M. J., and M. A. Gonda. Is scrapie PrP 27-30 related to the AIDS virus?  Nature 325:113-114.

1987    Braun, M. J., and D. E. Wolf. Recent records of vagrant South American land birds in Panama. Bulletin of the British Ornithologist’s Club 107:115-117.

1987    Baker, C. C., W. C. Phelps, V. Lindgren, M. J. Braun, M. A. Gonda and P. M. Howley.  Structural and transcriptional analysis of human papilloma virus type16 sequences in cervical carcinoma cell lines. Journal of Virology 61:962-971.

1986    Braun, M. J., and M. B. Robbins.  Extensive protein similarity of the hybridizing chickadees Parus atricapillus and P. carolinensis. Auk 103: 667-675.

1986    Robbins, M. B., M. J. Braun, and E. A. Tobey.  Morphological and vocal variation across a contact zone between the chickadees Parus atricapillus and P. carolinensis. Auk 103: 655-666.

1986    Gonda, M. A., M. J. Braun, J. E. Clements, J. M. Pyper, F. Wong-Staal, R. C. Gallo, and R. V. Gilden.  Human T-cell lymphotropic virus type III shares sequence homology with a family of pathogenic lentiviruses.  Proceedings of the National Academy of Sciences USA 83: 4007-4011.

1986    Braun, M. J., D. D. Braun, and S. B. Terrill.  Winter records of the Golden-cheeked Warbler (Dendroica chrysoparia) from Mexico. American Birds 10: 564-566.

1985    Braun, M. J., P. L. Deininger, and J. W. Casey.  Nucleotide sequence of a transduced myc gene from a defective feline leukemia provirus. Journal of Virology 55: 177-183.

1985    Braun, M. J., and T. A. Parker, III.  Molecular, morphological, and behavioral evidence concerning the taxonomic relationships of “Synallaxis” gularis  and other synallaxines.  Pp. 333-346 in “Neotropical Ornithology”, P. A. Buckley, M. S. Foster, E. S. Morton, R. S. Ridgely, and F. G. Buckley (eds.). Ornithological Monographs, No. 36.

1985    Parker, T. A., T. S. Schulenberg, G. R. Graves, and M. J. Braun.  The avifauna of the Huancabamba region, northern Peru.  Pp. 169-197 in “Neotropical Ornithology”,.P. A. Buckley, M. S. Foster, E. S. Morton, R. S. Ridgely, and F. G. Buckley (eds.). Ornithological Monographs, No. 36.

1984    Braun, D., G. B. Kitto, and M. J. Braun.  Molecular population genetics of Tufted and Black-crested forms of Parus bicolor. Auk 101: 170-173.

1983    Dessauer. H. C., M. J. Braun, and S. Neville. A simple hand centrifuge for field use. Isozyme Bulletin 16: 91-92.

1982    Braun, M.J., and V.L. Emanuel. Records of the Crimson collared Grosbeak (Rhodothraupis celaeno) from Texas. Auk 99: 787.

1981  Braun, M. J. Hybridization and high protein variability in finches of the genus Pipilo.  Isozyme Bulletin 14: 90.