Michael Braun

Journal Article

• Long, Kira M., Rivera-Colón,Angel, G., Bennett, Kevin F. P., Catchen, Julian M., Braun, Michael J., and Brawn, Jeffrey D. 2024. "Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone." Evolution, https://doi.org/10.1093/evolut/qpae076.
• Vernasco, Ben J., Long, Kira M., Braun, Michael J., and Brawn, Jeffrey D. 2024. "Genetic and telomeric variability: Insights from a tropical avian hybrid zone." Molecular ecology, https://doi.org/10.1111/mec.17491.
• DeRaad, Devon A., Applewhite, Emily E., Tsai, Whitney L. E., Terrill, Ryan S., Kingston, Sarah E., Braun, Michael J., and McCormack, John E. 2023. "Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley's classic species conundrum in Pipilo towhees." Evolution, 77, (3) 852–869. https://doi.org/10.1093/evolut/qpac068.
• Rasband, Shauna A., Bolton, Peri E., Fang, Qi, Johnson, Philip L. F., and Braun, Michael J. 2023. "Evolution of the Growth Hormone Gene Duplication in Passerine Birds." Genome Biology and Evolution, 15, (3). https://doi.org/10.1093/gbe/evad033.
• White, Noor D., Batz, Zachary A., Braun, Edward L., Braun, Michael J., Carleton, Karen L., Kimball, Rebecca T., and Swaroop, Anand. 2021. "A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution." Molecular Ecology Resources, https://doi.org/10.1111/1755-0998.13496.
• Bennett, Kevin F. P., Lim, Haw Chuan, and Braun, Michael J. 2021. "Sexual Selection and Introgression in Avian Hybrid Zones: Spotlight on Manacus." Integrative and Comparative Biology, 61, (4) 1291–1309. https://doi.org/10.1093/icb/icab135.
• Braun, Michael J., Wilkinson, Gerald S., and Cade, Brian S. 2020. "Comment on "Female toads engaging in adaptive hybridization prefer high-quality heterospecifics as mates"." Science, 370, (6513). https://doi.org/10.1126/science.abd3905.
• Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold et al. 2020. "Dense sampling of bird diversity increases power of comparative genomics." Nature, 587, (7833) 252–257. https://doi.org/10.1038/s41586-020-2873-9.
• Lim, Haw Chuan, Shakya, Subir B., Harvey, Michael G., Moyle, Robert G., Fleischer, Robert C., Braun, Michael J., and Sheldon, Frederick H. 2020. "Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA." Ecology and Evolution, 10, (7) 3222–3247. https://doi.org/10.1002/ece3.5964.
• Sánchez‐Mercado, A., Cardozo‐Urdaneta, A., Moran, L., Ovalle, L., Arvelo, M. Á., Morales‐Campos, J., Coyle, Brian James, Braun, Michael J., and Rodríguez‐Clark, Kathryn M. 2020. "Social network analysis reveals specialized trade in an Endangered songbird." Animal Conservation, 23, (2) 132–144. https://doi.org/10.1111/acv.12514.

• Sanchez-Mercado, A., Cardozo-Urdaneta, A., Rodríguez-Clark, Kathryn M., Moran, L., Ovalle, L., Arvelo, M. Angel, Morales-Campos, J., Coyle, Brian J., and Braun, Michael J. 2020. "Illegal wildlife trade networks: finding creative opportunities for conservation intervention in challenging circumstances." Animal Conservation, 23, (2) 151–152. https://doi.org/10.1111/acv.12587.
• Chen, Albert, White, Noor D., Benson, Roger B. J., Braun, Michael J., and Field, Daniel J. 2019. "Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)." Diversity, 11, (9) 143. https://doi.org/10.3390/d11090143.
• Kimball, Rebecca T., Oliveros, Carl H., Wang, Ning, White, Noor D., Barker, F. Keith, Field, Daniel J., Ksepka, Daniel T., Chesser, R. Terry, 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 of cyto-nuclear discordance using avian mitogenomic data?" Molecular phylogenetics and evolution, 130 132–142. https://doi.org/10.1016/j.ympev.2018.10.008.
• White, Noor D. and Braun, Michael J. 2019. "Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)." Molecular phylogenetics and evolution, 141 Article 106611. https://doi.org/10.1016/j.ympev.2019.106611.
• 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. https://doi.org/10.58843/ornneo.v27i0.88.
• 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, Jesús 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;2.
• 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;2.
• 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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Book Chapter

• Arvelo, Miguel, Braun, Michael J., Coyle, Brian J., Davis, Sam, Diaz, Zirza, Fink, Jonathan, Lynch, Warren, Hansen, Paula, Marinari, Paul, Miranda, Jonathan, Monfort, Steven L., Ovalle-Moleiro, Leonel, Rodríguez, Jon Paul, Rodríguez-Clark, Kathryn M., Rodríguez-Ferraro, Adriana, Royer, Erica, Sánchez-Mercado, Ada Y., and Sucre, Bibiana. 2017. "The Red Siskin Initiative: Saving an Endangered Finch in Partnership with Aviculturists." In Finches ’17: White Papers from the Sixth International Finch Convention. Brisbane ed. 45–66. Queensland Finch Society, Ltd..
• Rodríguez-Clark, Kathryn M., Rojas-Suárez, F., Sharpe, Christopher J., Miranda, Jonathan, Ascanio, David, Lentino, Miguel, and Braun, Michael J. 2014. "Cardenalito, Sporagra cucullata." In Libro Rojo de la Fauna Venezolana, Edición en Linea. Rodríguez, Jon Paul and Rojas-Suárez, F., editors. Caracas, Venezuela: Provita, Conservación Internacional Venezuela and Fundación Empresas Polar.
• Cracraft, J., Barker, F. K., Braun, Michael J., Harshman, J., Dyke, G., Feinstein, J., Stanely, S., Cibois, A., Schikler, P., Beresford, P., Garcia-Moreno, J., Sorenson, Michael D., Yuri, T., and Mindell, D. P. 2004. "Phylogenetic relationships among modern birds (Neornithines): Toward and avian tree of life." In Assembling the Tree of Life. Cracraft, J. and Donoghue, M. J., editors. 468–490. New York: Oxford University Press.
• Braun, Michael J. 1999. "The Mockingbird." In Fifty Great Birds of Texas. O'Neill, John P. and Winckler, S., editors. 82–83. Austin, TX: University of Texas Press.
• Glenn, T. C., Ojerio, R. S., Stephan, W., and Braun, Michael J. 1997. "Microsatellite DNA loci for genetic studies of cranes." In Proceedings of the 7th North American Crane Workshop. Urbanek, R. P. and Stahlecker, D. W., editors. 36–45. North American Crane Working Group.
• Bowditch, B. M., Albright, D. G., Williams, J. G. K., and Braun, Michael J. 1993. "The use of randomly amplified polymorphic DNA markers in comparative genome studies." In Molecular Evolution: Producing the Biochemical Data (Methods in Enzymology 224.). Zimmer, Elizabeth Anne, Cann, R. L., and Wilson, A. C., editors. 294–309. San Diego: Academic Press.
• Suh, Y. B., Blake, J. A., and Braun, Michael J. 1993. "Equipping and organizing a molecular systematics laboratory." In Molecular Evolution: Producing the Biochemical Data (Methods in Enzymology 224.). Zimmer, Elizabeth Anne, Cann, R. L., and Wilson, A. C., editors. 3–22. San Diego: Academic Press.

Book

• Braun, Michael J., Finch, D. W., Robbins, M. B., and Schmidt, Brian K. 2007. A Field Checklist of the Birds of Guyana, 2nd Edition. Smithsonian Institution Press.
• Braun, Michael J., Finch, D. W., Robbins, M. B., and Schmidt, Brian K. 2000. A Field Checklist of the Birds of Guyana. Washington , D.C.: Smithsonian Institution.