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Browsing by Author "Braun, Edward L."

Browsing by Author "Braun, Edward L."

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  • Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life 
    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.; Yuri, Tamaki (2011)
  • Comparative genomics reveals insights into avian genome evolution and adaptation 
    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; Fonseca, Rute R. da; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N.; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth P.; Warren, Wesley; Wilson, Richard K.; Li, Shengbin; Ray, David A.; Green, Richard E.; O'Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. T.; Wang, Jun; Ye, Chen; Liang, Shaoguang; Yan, Zengli; Zepeda, M. L.; Campos, Paula F.; Velazquez, Amhed Missael Vargas; Samaniego, José Alfredo; Avila-Arcos, Mar; Martin, Michael D.; Barnett, Ross; Ribeiro, Angela M.; Mello, Claudio V.; Lovell, Peter V.; Almeida, Daniela; Maldonado, Emanuel; Pereira, Joana; Sunagar, Kartik; Philip, Siby; Dominguez-Bello, Maria; Bunce, Michael; Lambert, David; Brumfield, Robb T.; Sheldon, Frederick H.; Holmes, Edward C.; Gardner, Paul P.; Steeves, Tammy E.; Stadler, Peter F.; Burge, Sarah W.; Lyons, Eric; Smith, Jacqueline; McCarthy, Fiona; Pitel, Frederique; Rhoads, Douglas; Froman, David P. (2014)
    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant ...
  • Dense sampling of bird diversity increases power of comparative genomics 
    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; Fjeldså, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F.; Sicheritz-Ponten, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C.; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J.; Cowen, Saul J.; Njoroge, Peter; Dumbacher, John Philip; Ryder, Oliver A.; Fuchs, Jérôme; Bunce, Michael; Burt, David W.; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J.; Ryan, Peter G.; Jønsson, Knud Andreas; Jamieson, Ian G.; da Fonseca, Rute R.; Braun, Edward L.; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B.; van der Zwan, Henriette; van der Sluis, Rencia; Visser, Carina; Balakrishnan, Christopher N.; Clark, Andrew G.; Fitzpatrick, John W.; Bowman, Reed; Chen, Nancy; Cloutier, Alison; Sackton, Timothy B.; Edwards, Scott V.; Foote, Dustin J.; Shakya, Subir B.; Sheldon, Frederick H.; Vignal, Alain; Soares, André E. R.; Shapiro, Beth; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalén, Love; Urrutia, Araxi O.; Székely, Tamás; Liu, Yang; Campana, Michael G.; Corvelo, André; Fleischer, Robert C.; Rutherford, Kim M.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Milá, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Ángela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas Lee; Schlinger, Barney A.; Loiselle, Bette A.; Blake, John G.; Lim, Haw Chuan; Day, Lainy B.; Fuxjager, Matthew J.; Baldwin, Maude W.; Braun, Michael J.; Wirthlin, Morgan; Dikow, Rebecca B.; Ryder, T. B.; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Mark E.; Louder, Matthew I. M.; Witt, Christopher C.; McGuire, Jimmy A.; Mudge, Joann; Megna, Libby C.; Carling, Matthew D.; Wang, Biao; Taylor, Scott A.; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, M. T.; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie (2020)
    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a ...
  • Duplication and Accelerated Evolution of Growth Hormone Gene in Passerine Birds 
    Yuri, Tamaki; Kimball, Rebecca T.; Braun, Edward L.; Braun, Michael J. (2008)
  • Earth history and the passerine superradiation 
    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.; Robbins, Mark B.; Sheldon, Frederick H.; Silveira, Luís Fábio; Smith, Brian Tilston; White, Noor D.; Moyle, Robert G.; Faircloth, Brant C. (2019)
    Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds ...
  • Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae) 
    Zhao, Min; Kurtis, Sarah M.; White, Noor D.; Moncrieff, Andre E.; Leite, Rafael N.; Brumfield, Robb T.; Braun, Edward L.; Kimball, Rebecca T. (2022)
    Abstract Abstract.-Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to ...
  • Homoplastic microinversions and the avian tree of life 
    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.; Yuri, Tamaki (2011)
    Background: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free ...
  • A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution 
    White, Noor D.; Batz, Zachary A.; Braun, Edward L.; Braun, Michael J.; Carleton, Karen L.; Kimball, Rebecca T.; Swaroop, Anand (2021)
  • Phylogenomic evidence for multiple losses of flight in ratite birds 
    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.; Yuri, T. (2008)
  • A Phylogenomic Study of Birds Reveals Their Evolutionary History 
    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.; Yuri, Tamaki (2008)
    Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined [~]32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 ...
  • A Phylogenomic Supertree of Birds 
    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; Braun, Edward L. (2019)
    It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear ...
  • Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes 
    St John, John A.; Braun, Edward L.; Isberg, Sally R.; Miles, Lee G.; Chong, Amanda Y.; Gongora, Jaime; Dalzell, Pauline; Moran, Christopher; Bed'Hom, Bertrand; Abzhanov, Arhat; Burguess, Shane C.; Cooksey, Amanda M.; Castoe, Todd A.; Crawford, Nicholas G.; Densmore, Llewellyn D.; Drew, Jennifer C.; Edwards, Scott V.; Faircloth, Brant C.; Fujita, Matthew K.; Greenwold, Matthew J.; Hoffman, Federico G.; Howard, Jonathan M.; Iguchi, Taisen; Janes, Daniel E.; Khan, Shaid Yar; Kohno, Satomi; deKoning, AP Jason; Lance, Stacey L.; McCarthy, Fiona M.; McCormack, John E.; Merchant, Mark E.; Peterson, Daniel G.; Pollock, David D.; Pourmand, Nader; Raney, Brian J.; Roessler, Kyria A.; Sanford, Jeremy R.; Sawyer, Roger H.; Schmidt, Carl J.; Triplett, Eric W.; Tuberville, Tracey D.; Venegas-Anaya, Miryam D.; Howard, Jason T.; Jarvis, Erich D.; Guillette Jr., Louis J.; Glenn, Travis C.; Green, Richard E.; Ray, David A. (2012)
  • Systems biology as a framework to understand the physiological and endocrine bases of behavior and its evolution—From concepts to a case study in birds 
    Fuxjager, Matthew J.; Ryder, T. B.; Moody, Nicole M.; Alfonso, Camilo; Balakrishnan, Christopher N.; Barske, Julia; Bosholn, Mariane; Boyle, W. A.; Braun, Edward L.; Chiver, Ioana; Dakin, Roslyn; Day, Lainy B.; Driver, Robert; Fusani, Leonida; Horton, Brent M.; Kimball, Rebecca T.; Lipshutz, Sara; Mello, Claudio V.; Miller, Eliot T.; Webster, Michael S.; Wirthlin, Morgan; Wollman, Roy; Moore, Ignacio T.; Schlinger, Barney A. (2023)
    Organismal behavior, with its tremendous complexity and diversity, is generated by numerous physiological systems acting in coordination. Understanding how these systems evolve to support differences in behavior within and ...
  • Tempo and Pattern of Avian Brain Size Evolution 
    Ksepka, Daniel T.; Balanoff, Amy M.; Smith, N. Adam; Bever, Gabriel S.; Bhullar, Bhart-Anjan S.; Bourdon, Estelle; Braun, Edward L.; Burleigh, J. Gordon; Clarke, Julia A.; Colbert, Matthew W.; Corfield, Jeremy R.; Degrange, Federico J.; De Pietri, Vanesa L.; Early, Catherine M.; Field, Daniel J.; Gignac, Paul M.; Gold, Maria Eugenia Leone; Kimball, Rebecca T.; Kawabe, Soichiro; Lefebvre, Louis; Marugan-Lobon, Jesus; Mongle, Carrie S.; Morhardt, Ashley; Norell, Mark A.; Ridgely, Ryan C.; Rothman, Ryan S.; Scofield, R. Paul; Tambussi, Claudia P.; Torres, Christopher R.; van Tuinen, Marcel; Walsh, Stig A.; Watanabe, Akinobu; Witmer, Lawrence M.; Wright, Alexandra K.; Zanno, Lindsay E.; Jarvis, Erich D.; Smaers, Jeroen B. (2020)
    Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship ...
  • A well-tested set of primers to amplify regions spread across the avian genome 
    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.; Yuri, Tamaki (2009)
  • What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? 
    Tamashiro, Ryan A.; White, Noor D.; Braun, Michael J.; Faircloth, Brant C.; Braun, Edward L.; Kimball, Rebecca T. (2019)
    Conflicts between nuclear and mitochondrial phylogenies have led to uncertainty for some relationships within the tree of life. These conflicts have led some to question the value of mitochondrial DNA in phylogenetics now ...
  • Whole-genome analyses resolve early branches in the tree of life of modern birds 
    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; Capella-Gutiérrez, Salvador; Huerta-Cepas, Jaime; Rekepalli, Bhanu; Munch, Kasper; Schierup, Mikkel; Lindow, Bent; Warren, Wesley C.; Ray, David; Green, Richard E.; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Li, Shengbin; Li, Ning; Huang, Yinhua; Derryberry, Elizabeth P.; Bertelsen, Mads Frost; Sheldon, Frederick H.; Brumfield, Robb T.; Mello, Claudio V.; Lovell, Peter V.; Wirthlin, Morgan; Schneider, Maria Paula Cruz; Prosdocimi, Francisco; Samaniego, José Alfredo; Velazquez, Amhed Missael Vargas; Alfaro-Núñez, Alonzo; Campos, Paula F.; Petersen, Bent; Sicheritz-Ponten, Thomas; Pas, An; Bailey, Tom; Scofield, Paul; Bunce, Michael; Lambert, David M.; Zhou, Qi; Perelman, Polina; Driskell, Amy C.; Shapiro, Beth; Xiong, Zijun; Zeng, Yongli; Liu, Shiping; Li, Zhenyu; Liu, Binghang; Wu, Kui; Xiao, Jin; Yinqi, Xiong; Zheng, Qiuemei; Zhang, Yong; Yang, Huanming; Wang, Jian; Smeds, Linnea; Rheindt, Frank E.; Braun, Michael J.; Fjeldsa, Jon; Orlando, Ludovic; Barker, F. K.; Jønsson, Knud Andreas; Johnson, Warren E.; Koepfli, Klaus-Peter; O'Brien, Stephen; Haussler, David; Ryder, Oliver A.; Rahbek, Carsten; Willerslev, Eske; Graves, Gary R.; Glenn, Travis C.; McCormack, John; Burt, Dave; Ellegren, Hans; Alström, Per; Edwards, Scott V.; Stamatakis, Alexandros; Mindell, David P.; Cracraft, Joel; Braun, Edward L.; Warnow, Tandy; Jun, Wang; Gilbert, M. T.; Zhang, Guojie (2014)
    To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered ...
  • Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling 
    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; Braun, Edward L. (2017)
    Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that ...

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