Michael Braun

Article

• Kimball, Rebecca T., Oliveros, Carl H., Wang, Ning, White, Noor D., Barker, F. K., Field, Daniel J., Ksepka, Daniel T., Chesser, R. T., Moyle, Robert G., Braun, Michael J., Brumfield, Robb T., Faircloth, Brant C., Smith, Brian Tilston, and Braun, Edward L. 2019. "A Phylogenomic Supertree of Birds." Diversity 11 (7):109. https://doi.org/10.3390/d11070109
• Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. K., Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. T. et al. 2019. "Earth history and the passerine superradiation." Proceedings of the National Academy of Sciences of the United States of America 116 (16):7916–7925. https://doi.org/10.1073/pnas.1813206116
• Tamashiro, Ryan A., White, Noor D., Braun, Michael J., Faircloth, Brant C., Braun, Edward L., and Kimball, Rebecca T. 2019. "What are the roles of taxon sampling and model fit in tests ofcyto-nuclear discordance using avian mitogenomic data?." Molecular phylogenetics and evolution 130:132–142. https://doi.org/10.1016/j.ympev.2018.10.008
• Costa, Thiago V. V., Whitney, Bret M., Braun, Michael J., White, Noor D., Silveira, Luís Fábio, and Cleere, Nigel. 2018. "A systematic reappraisal of the Rufous Potoo Nyctibius bracteatus (Nyctibiidae) and description of a new genus." Journal of Ornithology 159 (2):367–377. https://doi.org/10.1007/s10336-017-1511-2
• Rodríguez-Clark, Kathryn M., Davidson, Brian, Kingston, Sarah, Coyle, Brian J., Duchesne, Pierre, and Braun, Michael J. 2018. "Evaluating a potential source of founders for ex situ conservation efforts: genetic differentiation between disjunct populations of the Endangered red siskin Spinus cucullatus." Endangered Species Research 36:183–196. https://doi.org/10.3354/esr00898
• Sánchez-Mercado, Ada, Rodríguez-Clark, Kathryn M., Miranda, Jhonathan, Ferrer-Paris, José Rafael, Coyle, Brian, Toro, Samuel, Cardozo-Urdaneta, Arlene, and Braun, Michael J. 2018. "How to deal with ground truthing affected by human-induced habitat change?: Identifying high-quality habitats for the Critically Endangered Red Siskin." Ecology and Evolution 8 (2):841–851. https://doi.org/10.1002/ece3.3628
• Kingston, Sarah E., Parchman, T. L., Gompert, Z., Buerkle, C. A., and Braun, Michael J. 2017. "Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees." Journal of Evolutionary Biology 30 (3):474–485. https://doi.org/10.1111/jeb.13033
• Reddy, Sushma, Kimball, Rebecca T., Pandey, Akanksha, Hosner, Peter A., Braun, Michael J., Hackett, Shannon J., Han, Kin-Lan, Harshman, John, Huddleston, Christopher J., Kingston, Sarah, Marks, Ben D., Miglia, Kathleen J., Moore, William S., Sheldon, Frederick H., Witt, Christopher C., Yuri, Tamaki, and Braun, Edward L. 2017. "Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling." Systematic Biology 66 (5):857–879. https://doi.org/10.1093/sysbio/syx041
• White, Noor D., Mitter, Charles, and Braun, Michael J. 2017. "Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)." Journal of Avian Biology 48 (6):872–880. https://doi.org/10.1111/jav.01313
• Lim, Haw Chuan and Braun, Michael J. 2016. "High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements." Molecular Ecology Resources 16 (5):1204–1223. https://doi.org/10.1111/1755-0998.12568

• White, Noor D., Barrowclough, George F., Groth, Jeff G., and Braun, Michael J. 2016. "A multi-gene estimate of higher-level phylogenetic relationships among Nightjars (Aves: Caprimulgidae)." Ornitología Neotropical 27:223–236.
• Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y. W., Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., Fonseca, Rute R. da, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni et al. 2014. "Whole-genome analyses resolve early branches in the tree of life of modern birds." Science 346 (6215):1320–1331. https://doi.org/10.1126/science.1253451
• Kingston, Sarah E., Navarro-Sigüenza, Adolfo G., García-Trejo, Erick A., Vázquez-Miranda, Hernán, Fagan, William F., and Braun, Michael J. 2014. "Genetic differentiation and habitat connectivity across towhee hybrid zones in Mexico." Evolutionary Ecology 28 (2):277–297. https://doi.org/10.1007/s10682-013-9673-8
• Reynolds, Sheila M., Uy, J. Albert C., Patricelli, Gail L., Coleman, Seth W., Braun, Michael J., and Borgia, Gerald. 2014. "Tests of the kin selection model of mate choice and inbreeding avoidance in satin bowerbirds." Behavioral Ecology 25 (4):1005–1014. https://doi.org/10.1093/beheco/aru065
• Coyle, Brian J., Braun, Michael J., Rodríguez-Clark, Kathryn M., and Moleiro, Leonel Ovalle. 2013. "Recovering the endangered Red Siskin." Journal of the National Finch and Softbill Society 30–38.
• Davidson, Brian S., Sattler, Gene D., Via, Sara, and Braun, Michael J. 2013. "Reproductive isolation and cryptic introgression in a sky island enclave of Appalachian birds." Ecology and Evolution 3 (8):2485–2496. https://doi.org/10.1002/ece3.604
• Parchman, T. L., Gompert, Z., Braun, Michael J., Brumfield, R. T., McDonald, D. B., Uy, J., Jarvis, E. D., Schlinger, B. A., and Buerkle, C. A. 2013. "The genomic consequences of adaptive divergence and reproductive isolation between species of manakins." Molecular ecology 22 (12):3304–3317. https://doi.org/10.1111/mec.12201
• Yuri, Tamaki, Kimball, Rebecca, Harshman, John, Bowie, Rauri, Braun, Michael J., Chojnowski, Jena, Han, Kin-Lan, Hackett, Shannon, Huddleston, Christopher, Moore, William, Reddy, Sushma, Sheldon, Frederick, Steadman, David, Witt, Christopher, and Braun, Edward. 2013. "Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals." Biology 2 (1):419–444. https://doi.org/10.3390/biology2010419
• Kingston, Sarah E., Jernigan, Robert W., Fagan, William F., Braun, David R., and Braun, Michael J. 2012. "Genomic variation in cline shape across a hybrid zone." Ecology and Evolution 2 (11):2737–2748. https://doi.org/10.1002/ece3.375
• Pravosudov, V. V., Roth, T. C., Forister, M. L., LaDage, L. D., Burg, T. M., Braun, Michael J., and Davidson, Brian S. 2012. "Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees." Molecular Ecology 21 (18):4486–4497. https://doi.org/10.1111/j.1365-294X.2012.05721.x
• Braun, Edward L., Kimball, Rebecca T., Han, Kin-Lan, Iuhasz-Velez, Naomi R., Bonilla, Amber J., Chojnowski, Jena L., Smith, Jordan V., Bowie, Rauri C. K., Braun, Michael J., Hackett, Shannon J., Harshman, John, Huddleston, Christopher J., Marks, Ben D., Miglia, Kathleen J., Moore, William S., Reddy, Sushma, Sheldon, Frederick H., Witt, Christopher C., and Yuri, Tamaki. 2011. "Homoplastic microinversions and the avian tree of life." Bmc Evolutionary Biology 11:141. https://doi.org/10.1186/1471-2148-11-141
• Han, Kin-Lan, Braun, Edward L., Kimball, Rebecca T., Reddy, Sushma, Bowie, Rauri C. K., Braun, Michael J., Chojnowski, Jena L., Hackett, Shannon J., Harshman, John, Huddleston, Christopher J., Marks, Ben D., Miglia, Kathleen J., Moore, William S., Sheldon, Frederick H., Steadman, David W., Witt, Christopher C., and Yuri, Tamaki. 2011. "Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life." Systematic Biology 60 (3):375–386. https://doi.org/10.1093/sysbio/syq100
• Rodríguez-Clark, Kathryn M., Maldonado, Jesus E., Ascanio, David, Gamero, Emperatriz, Ovalle Moleiro, Leonel, Pérez-Emán, Jorge, and Braun, Michael J. 2011. "Using genetics to understand and conserve the Red Siskin (Carduelis cucullata)." Journal of the National Finch and Softbill Society 25.
• Braun, Michael J. and Huddleston, Christopher J. 2010. "Response to Mayr and Manegold." Molecular phylogenetics and evolution 55 (1):345–346. https://doi.org/10.1016/j.ympev.2009.12.014
• Han, Kin-Lan, Robbins, Mark B., and Braun, Michael J. 2010. "A Multi-gene Estimate of Phylogeny in the Nightjars and Nighthawks (Caprimulgidae)." Molecular phylogenetics and evolution 55 (2):443–453. https://doi.org/10.1016/j.ympev.2010.01.023
• Olson, Jennifer R., Cooper, Sheldon J., Swanson, David L., Braun, Michael J., and Williams, Joseph B. 2010. "The Relationship of Metabolic Performance and Distribution in Black-Capped and Carolina Chickadees." Physiological and Biochemical Zoology 83 (2):263–275.
• Braun, Michael J. and Huddleston, Christopher J. 2009. "A Molecular Phylogenetic Survey of Caprimulgiform Nightbirds Illustrates the Utility of Non-coding Sequences." Molecular phylogenetics and evolution 53 (3):948–960. https://doi.org/10.1016/j.ympev.2009.08.025
• Kimball, Rebecca T., Braun, Edward L., Barker, F. Keith, Bowie, Rauri C. K., Braun, Michael J., Chojnowski, Jena L., Hackett, Shannon J., Han, Kin-Lan, Harshman, John, Heimer-Torres, Victoria, Holznagel, Wallace, Huddleston, Christopher J., Marks, Ben D., Miglia, Kathleen J., Moore, William S., Reddy, Sushma, Sheldon, Frederick H., Smith, Jordan V., Witt, Christopher C., and Yuri, Tamaki. 2009. "A well-tested set of primers to amplify regions spread across the avian genome." Molecular phylogenetics and evolution 50 (3):654–660. https://doi.org/10.1016/j.ympev.2008.11.018
• Meares, Kate, Dawson, Deborah A., Horsburgh, Gavin J., Glenn, Travis C., Jones, Kenneth L., Braun, Michael J., Perrin, Mike R., and Taylor, Tiawanna D. 2009. "Microsatellite loci characterized in three African crane species (Gruidae, Aves)." Molecular Ecology Resources 9 (1):308–311.
• Reynolds, Sheila M., Christman, Mary C., Uy, J. Albert C., Patricelli, Gail L., Braun, Michael J., and Borgia, Gerald. 2009. "Lekking satin bowerbird males aggregate with relatives to mitigate aggression." Behavioral Ecology 20 (2):410–415. https://doi.org/10.1093/beheco/arn146
• Yuri, Tamaki, Jernigan, Robert W., Brumfield, Robb T., Bhagabati, Nirmal K., and Braun, Michael J. 2009. "The effect of marker choice on estimated levels of introgression across an avian (Pipridae: Manacus) hybrid zone." Molecular Ecology 18 (23):4888–4903. https://doi.org/10.1111/j.1365-294X.2009.04381.x
• Hackett, Shannon J., Kimball, Rebecca T., Reddy, Sushma, Bowie, Rauri C. K., Braun, Edward L., Braun, Michael J., Chojnowski, Jena L., Cox, W. Andrew, Han, Kin-Lan, Harshman, John, Huddleston, Christopher J., Marks, Ben D., Miglia, Kathleen J., Moore, William S., Sheldon, Frederick H., Steadman, David W., Witt, Christopher C., and Yuri, Tamaki. 2008. "A Phylogenomic Study of Birds Reveals Their Evolutionary History." Science 320 (5884):1763–1768. https://doi.org/10.1126/science.1157704
• Harshman, J., Braun, Edward L., Braun, Michael J., Huddleston, Christopher J., Bowie, R. C. K., Chojnowski, J. L., Hackett, S. J., Han, K., Kimball, R. T., Marks, B. D., Miglia, K. J., Moore, W. S., Reddy, S., Sheldon, F. H., Steadman, D. W., Steppan, Scott J., Witt, C. C., and Yuri, T. 2008. "Phylogenomic evidence for multiple losses of flight in ratite birds." Proceedings of the National Academy of Sciences of the United States of America 105 (36):13462–13467. https://doi.org/10.1073/pnas.0803242105
• Yuri, Tamaki, Kimball, Rebecca T., Braun, Edward L., and Braun, Michael J. 2008. "Duplication and Accelerated Evolution of Growth Hormone Gene in Passerine Birds." Molecular Biology and Evolution 25:352–361.
• Cleere, N., Kratter, A. W., Steadman, D. W., Braun, Michael J., Huddleston, Christopher J., and Filardi, C. E. 2007. "A new genus of frogmouth (Podargidae) from the Solomon Islands results from a taxonomic review of Podargus ocellatus inexpectatus Hartert 1901." Ibis 149 (2):271–286. https://doi.org/10.1111/j.1474-919X.2006.00626.x
• Reynolds, S. M., Dryer, K., Bollback, J., Uy, A. C., Patricelli, Gail L., Robson, T., Borgia, Gerald, and Braun, Michael J. 2007. "Behavioral paternity predicts genetic paternity in Satin Bowerbirds (Ptilonorhynchus violaceus), a species with a non-resource-based mating system." The Auk 124 (3):857–867. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO
• Robbins, M. B., Braun, Michael J., Milensky, Christopher M., Schmidt, Brian K., Prince, W., Rice, N. H., Finch, D. W., and O'Shea, B. J. 2007. "Avifauna of the Upper Essequibo River and Acary Mountains, Southern Guyana." Ornitologia Neotropical 18 (3):339–368.
• Sattler, G. D., Sawaya, P., and Braun, Michael J. 2007. "An assessment of song admixture and its reliability as an indicator of genetic ancestry in Black-capped and Carolina Chickadees." The Auk 124 (3):926–944. https://doi.org/10.1642/0004-8038(2007)124[926:AAOSAA]2.0.CO
• Braun, Michael J., Isler, Morton L., Isler, Phyllis R., Bates, J., and Robbins, M. B. 2005. "Avian speciation in the Pantepui: The case of the Roraiman Antbird (Percnostola[Schistocichla] "leucostigma" saturata." The Condor 107 (2):327–341.
• Bronson, C. L., Grubb, T. C., Sattler, G. D., and Braun, Michael J. 2005. "Reproductive success across the Black-capped chickadee (Poecile atricapillus) and Carolina chickadee (P. carolinensis) hybrid zone in Ohio." The Auk 122:759–772.
• Helbig, A. J., Kocum, A., Seibold, I., and Braun, Michael J. 2005. "A multi-gene phylogeny of Aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level." Molecular Phylogenetics and Evolution 35:147–164.
• Robbins, M. B., Braun, Michael J., Huddleston, Christopher J., Finch, Davis W., and Milensky, Christopher M. 2005. "First Guyana records, natural history and systematics of the White-naped Seedeater Dolospingus fringilloides." Ibis 147 (2):334–341.
• Robbins, M. B., Braun, Michael J., and Finch, D. W. 2004. "Avifauna of the Guyana southern Rupununi, with comparisons to other savannas of northern South America." Ornitologia Neotropical 15:173–200.
• Braun, Michael J., Robbins, M. B., Milensky, Christopher M., O'Shea, B. J., Barber, B. R., Hinds, W., and Prince, W. S. 2003. "New birds for Guyana from Mts Roraima and Ayanganna." Bulletin of the British Ornithologists' Club 123 (1):24–33.
• Bronson, C. L., Grubb, T. C., and Braun, Michael J. 2003. "A test of the endogenous and exogenous selection hypotheses for the maintenance of a narrow avian hybrid zone." Evolution 57 (3):630–637.
• Bronson, C. L., Grubb, T. C., Sattler, G. D., and Braun, Michael J. 2003. "Mate preference: A possible causal mechanism for a moving hybrid zone." Animal Behaviour 65:489–500.
• Brumfield, Robb T., Jernigan, R. W.,Jr., McDonald, D. B., and Braun, Michael J. 2003. "Erratum correcting "Evolutionary implications of divergent clines in a manakin (Manacus, Aves) hybrid zone." Evolution 57:2919.
• Harshman, J., Huddleston, Christopher J., Bollback, J. P., Parsons, T. J., and Braun, Michael J. 2003. "True and false gharials: a nuclear gene phylogeny of Crocodylia." Systematic Biology 52 (301-238):386–402.
• Robbins, M. B., Braun, Michael J., and Finch, D. W. 2003. "Discovery of a population of the endangered Red Siskin (Carduelis cucullata) in Guyana." The Auk 120 (2):291–298.
• Brumfield, Robb T. and Braun, Michael J. 2001. "Phylogenetic Relationships in Bearded Manakins (Pipridae: Manacus) Indicate That Male Plumage Color Is a Misleading Taxonomic Marker." The Condor (2): 248–258.
• Brumfield, Robb T., Jernigan, Robert W., McDonald, David B., and Braun, Michael J. 2001. "Evolutionary Implications of Divergent Clines in an Avian (Manacus: Aves) Hybrid Zone." Evolution 55 (10):2070–2087.
• McDonald, David B., Clay, Robert P., Brumfield, Robb T., and Braun, Michael J. 2001. "Sexual Selection on Plumage and Behavior in an Avian Hybrid Zone: Experimental Tests of Male-Male Interactions." Evolution 55 (7):1443–1451.
• Sattler, G. D. and Braun, Michael J. 2000. "Morphometric variation as an indicator of genetic interactions between Black-capped and Carolina chickadees at their contact zone in the Appalachian Mountains." The Auk 117:427–444.
• Winker, Kevin, Graves, Gary R., and Braun, Michael J. 2000. "Genetic differentiation among populations of a migratory songbird: Limnothlypis swainsonii." Journal of Avian Biology 31 (3):319–328.
• Glenn, T. C., Stephan, W., and Braun, Michael J. 1999. "Effect of a population bottleneck on mitochondrial DNA variation in Whooping Cranes." Conservation Biology 13 (5):1097–1107.
• Steppan, Scott J., Akhverdyan, M. R., Lyapunova, E. A., Fraser, D. G., Vorontsov, N. N., Hoffmann, Robert S., and Braun, Michael J. 1999. "Molecular phylogeny of the marmots (Rodentia:Sciuridae): Tests of evolutionary and biogeographic hypotheses." Systematic Biology 48 (4):715–734.
• Braun, Michael J. and Brumfield, Robb T. 1998. "Enigmatic phylogeny of skuas: an alternative hypothesis." Proceedings of the Royal Society B: Biological Sciences 265:995–999.
• Glenn, T. C., Dessauer, H. C., and Braun, Michael J. 1998. "Characterization of microsatellite DNA loci in American alligators." Copeia 1998 (3):591–601.
• Brumfield, Robb T., Swofford, David L., and Braun, Michael J. 1997. "Evolutionary relationships among the potoos (Nyctibiidae) based on isozymes." Ornithological Monographs 48:129–145.
• Glenn, T. C., Stephan, W., Dessauer, H. C., and Braun, Michael J. 1996. "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.
• Mariaux, J. and Braun, Michael J. 1996. "A molecular phylogenetic survey of the nightjars and allies (Caprimulgiformes) with special emphasis on the potoos (Nyctibiidae)." Molecular Phylogenetics and Evolution 6:228–244.
• Winker, Kevin, Braun, Michael J., and Graves, Gary R. 1996. "Voucher specimens and quality control in avian molecular studies." Ibis 138 (2):345–346.
• Glenn, T. C., Waller, D. R., and Braun, Michael J. 1994. "Increasing proportions of uracil in DNA substrates increases inhibition of restriction enzyme digests." BioTechniques 17:1086–1090.
• Parsons, Thomas J., Olson, Storrs L., and Braun, Michael J. 1994. "Hybrid Zones and Sexual Selection." Science 265 (5168):122–123.
• Rhymer, J. M., Williams, M. J., and Braun, Michael J. 1994. "Mitochondrial analysis of gene flow between New Zealand Mallards (Anas platyrhynchos) and Grey Ducks (A. superciliosa)." The Auk 111:970–978.
• Parsons, T. J., Olson, Storrs L., and Braun, Michael J. 1993. "Unidirectional spread of secondary sexual plumage traits across an avian hybrid zone." Science 260:1643–1646.
• Wilkerson, Richard C., Parsons, T. J., Albright, D. G., Klein, T. A., and Braun, Michael J. 1993. "Random amplified polymorphic DNA (RAPD) markers readily distinguish cryptic mosquito species (Diptera: Culicidae: Anopheles)." Insect molecular biology 1 (4):205–211.
• Glenn, T. C. and Braun, Michael J. 1992. "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.
• Graves, Gary R. and Braun, Michael J. 1992. "Museums: Storehouses of DNA?." Science 255 (5050):1335–1336. https://doi.org/10.1126/science.255.5050.1335-d
• Krajewski, C., Driskell, Amy C., Baverstock, P. R., and Braun, Michael J. 1992. "Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials: evidence from cytochrome b DNA sequences." Proceedings of the Royal Society B: Biological Sciences 250:19–27.
• Braun, Michael J. 1991. "The flowering of molecular systematics. Review of "Molecular Systematics", D. M. Hillis and C. Moritz (eds.)." Systematic zoology 40:111–114.
• Garvey, Kevin J., Oberste, M. Steven, Elser, John E., Braun, Michael J., and Gonda, Matthew A. 1990. "Nucleotide sequence and genome organization of biologically active proviruses of the bovine immunodeficiency-like virus." Virology 175 (2):391–409.
• Morton, Eugene S., Forman, Lisa, and Braun, Michael J. 1990. "Extra Pair Fertilizations and the Evolution of Colonial Breeding in Purple Martins." The Auk 107 (2):275–283. https://doi.org/10.2307/4087610
• Braun, Michael J., Lahn, S., Boyd, A. L., Kost, T. T., and Nagashima, K. G. 1988. "Molecular Cloning of Biologically Active Proviruses of Bovine Immunodeficiency-like Virus." Virology 167 (2):515–523.
• Houde, P. and Braun, Michael J. 1988. "Museum Collections as a Source of DNA for Studies of Avian Phylogeny." The Auk 105:773–776.

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