Research Overview


My research foci include efforts to reconstruct the Tree of Life and understand patterns of genome evolution. A small number of representative publications are listed below and a more complete list is proved at the bottom of this page. Other recent scholarly work associated with the Braun lab include:

  • The "EARLY BIRD" project:
    • Details of the publications produced by the "Early Bird" project along with links to the data matrices and trees generated by the project.
    • A short description of the "Early Bird" project for the public appears in an American Paleontologist feature on the tree of life.
  • The "GATOR GENOME" project:
    • The UF portion of the Crocodialian Genome Project
    • This project integrates research and genomics education.
  • Also see below for links to my other scholarly work, including data matrices, computer programs, other publications, and web sites related to my work.

Representative Publications


I have highlighted a few publications from various periods in my career that I have selected to illustrate my interests. These publications are divided into three groups and links to the full citation are provided:

  • Phylogenetics and the Tree of Life
  1. Smith et al. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology, 62:35-49. [full citation]
  2. Yuri et al. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444. [full citation]
  3. Braun et al. 2011. Homoplastic microinversions and the Avian Tree of Life. BMC Evol Biol, 11:141. [full citation]
  4. Chojnowski et al. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410:89-96. [full citation]
  5. Harshman et al. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. PNAS, 105:13462-13467. [full citation]
  6. Braun & Kimball. 2002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling and sequence length. Syst Biol, 51:614-625. [full citation]
  • Molecular evolution and gene families
  1. Feller et al. 2011. Evolutionary and comparative genomics of MYB and bHLH plant transcription factors. Plant J, 66:94-116. [full citation]
  2. Chojnowski et al. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol, 65: 259-266. [full citation]
  3. Georgelis et al. 2007. The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria. Plant Cell, 19: 1458-1472. [full citation]
  4. Braun & Grotewold. 2001. Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains. Mol Biol Evol, 18:1401-1412.  [full citation]
  • Genomics and Phylogenomics
  1. Shaffer et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, in press. [full citation]
  2. St John et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology, 13:415. [full citation]
  3. Braun and Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. J Phycol, 44:2-6. [full citation]
  4. Braun. 2003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution. Applied Bioinf, 2:13-34.  [full citation] [full text]
  5. Galagan et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422: 859-868. [full citation]
  6. Braun et al. 2000. Large scale comparison of fungal sequence information reveals innovation in the filamentous fungus Neurospora crassa and gene loss in the budding yeast Saccharomyces cerevisiae. Genome Res, 10:416-430. [full citation]
See below for a complete list of peer-reviewed philosophy.

Links and Other Scholarly Works


Other work produced by myself and other members of the Braun lab includes:

Additional materials are forthcoming.

Complete Publication List


Full list of peer reviewed publications. Undergraduate co-authors are indicated with an asterisk.

  1. Shaffer, HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela, J Abramyan, CT Amemiya, D Badenhorst, KK Biggar, GM Borchert, CW Botka, RM Bowden, EL Braun, AM Bronikowski, BG Bruneau, LT Buck, B Capel, TA Castoe, M Czerwinski, KD Delehaunty, SV Edwards, CC Fronick, MK Fujita, L Fulton, TA Graves, RE Green, W Haerty, R Hariharan, O Hernandez, LW Hillier, AK Holloway, D Janes, FJ Janzen, C Kandoth, L Kong, APJ de Koning, Y Li, R Literman, SE McGaugh, L Mork, M O’Laughlin, RT Paitz, DD Pollock, CP Ponting, S Radhakrishnan, BJ Raney, JM Richman, J St John, T Schwartz, A Sethuraman, PQ Spinks, KB Storey, N Thane, T Vinar, LM Zimmerman, WC Warren, ER Mardis & RK Wilson. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, in press.
  2. Smith, JV, EL Braun & RT Kimball. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology, 62:35-49.
  3. Yuri, T, RT Kimball, J Harshman, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, K-L Han, SJ Hackett, CJ Huddleston, WS Moore, S Reddy, FH Sheldon, DW Steadman, CC Witt & EL Braun. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444.
  4. Castoe, TA, EL Braun, AM Bronikowski, CL Cox, AR Davis Rabosky, APJ de Koning, J Dobry, MK Fujita, MW Giorgianni, A Hargreaves, CV Henkel, SP Mackessy, D O’Meally, DR Rokyta, SM Secor, JW Streicher, KP Wray, KD Yokoyama & DD Pollock. 2012. Report from the first Snake Genomics and Integrative Biology meeting. Standards in Genomic Sciences, 7:1.
  5. Chojnowski, JL & EL Braun. 2012. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics,
  6. Ponciano, JM, JG Burleigh, EL Braun & ML Taper. 2012. Assessing parameter identifiability in phylogenetic models using Data Cloning. Systematic Biology, 61:955-972.
  7. St John, JA, EL Braun, SR Isberg, LB Miles, AY Chong, J Gongora, P Dalzell, C Moran, B Bed'hom, A Abzhanov, SC Burgess, AM Cooksey, TA Castoe, NG Crawford, LD Densmore, JC Drew, SV Edwards, BC Faircloth, MK Fujita, MJ Greenwold, FG Hoffmann, JM Howard, T Iguchi, DE Janes, SY Khan, S Kohno, APJ de Koning, SL Lance, FM McCarthy, JE McCormack, ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, RH Sawyer, CJ Schmidt, EW Triplett, TD Tuberville, M Venegas-Anaya, JT Howard, ED Jarvis, LJ Guillette Jr, TC Glenn, RE Green & DA Ray. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology, 13:415.
  8. Wang, N, EL Braun & RT Kimball. 2012. Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset. Molecular Biology and Evolution, 29:737-750.
  9. Braun, EL, RT Kimball, K-L Han, NR Iuhasz*, AJ Bonilla*, JL Chojnowski, JV Smith*, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, CC Witt & T Yuri. 2011. Homoplastic microinversions and the Avian Tree of Life. BMC Evolutionary Biology, 11:141.
  10. Feller, A, K Machemer, EL Braun & E Grotewold. 2011. Evolutionary and comparative genomics of MYB and bHLH plant transcription factors. The Plant Journal, 66:94-116. [abstract]
  11. Han, K-L, EL Braun, RT Kimball, S Reddy, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, CC Witt & T Yuri. 2011. Are transposable element insertions homoplasy free? An examination using the Avian Tree of Life. Systematic Biology, 60:375-386.
  12. Kimball, RT, CM St Mary & EL Braun. 2011. A macroevolutionary perspective on multiple sexual traits in the Phasianidae (Galliformes). International Journal of Evolutionary Biology, Article ID 423938, 16 pages.[full text html] [full text pdf]
  13. Lim, CH, T Hamazaki, EL Braun, J Wade & N Terada. 2011. Evolutionary genomics indicates a specific function of Slc25a31 in mammalian and anole lizard germ cells. PLoS ONE, 6:e23122.
  14. Bonilla, AJ*, EL Braun & RT Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3'-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution, 50:654-660. [abstract]
  15. Zhu, J, EL Braun, S Kohno, M Antenos, EY Xu, RW Cook, SJ Lin, BC Moore, LJ Guillette Jr, TS Jardetzky & TK Woodruff. 2010. Phylogenomic analyses reveal the evolutionary origin of the inhibin α-subunit, a unique TGFβ superfamily antagonist. PLoS ONE, 5:e9457. [abstract] [full text].
  16. Katsu, Y, EL Braun, LJ Guillette Jr & T Iguchi. 2009. From reptilian phylogenomics to reptilian genomes: Analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenetic and Genome Research, 127:79-93. [abstract]
  17. Kimball, RT, EL Braun, FK Barker, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, K-L Han, J Harshman, V Heimer-Torres*, W Holznagel, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, JV Smith*, CC Witt & T Yuri. 2009. A well-tested set of primers to amplify regions spread across the avian genome. Molecular Phylogenetics and Evolution, 50:654-660. [abstract]
  18. Braun, EL & N Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. Journal of Phycology, 44:2-6. [abstract]
  19. Chojnowski, JL & EL Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48:454-462. [abstract]
  20. Chojnowski, JL, RT Kimball & EL Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410:89-96. [abstract]
  21. Georgelis N, EL Braun & LC Hannah. 2008. Duplication and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evolutionary Biology, 8:232. [abstract] [full text pdf].
  22. Hackett, SJ, RT Kimball, S Reddy, RCK Bowie, EL Braun, MJ Braun, JL Chojnowski, WA Cox*, K-L Han, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, CC Witt & T Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320:1763-1768. [abstract]
  23. Harshman, J, EL Braun, MJ Braun, CJ Huddleston, S Reddy, RCK Bowie, JL Chojnowski, K-L Han, SJ Hackett, RT Kimball, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, SJ Steppan, CC Witt & T Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences USA, 105:13462-13467. [abstract]
  24. Kimball, RT & EL Braun. 2008. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. Journal of Avian Biology, 39:438-445. [abstract]
  25. Phillips, N, S Calhoun, A Moustafa, D Bhattacharya & EL Braun. 2008. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaephyceae. Journal of Phycology, 44:15-18. [abstract]
  26. Yuri, T, RT Kimball, EL Braun & MJ Braun. 2008. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution, 25:352-361. [abstract]
  27. Chojnowski, JL, J Franklin*, Y Katsu, T Iguchi, LJ Guillette Jr, RT Kimball & EL Braun. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. Journal of Molecular Evolution, 65: 259-266. [abstract]
  28. Cox, WA*, EL Braun & RT Kimball. 2007. Phylogenetic position of the New World Quail (Odontophoridae): Eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist Tapestry. The Auk, 124: 71-84. [abstract]
  29. Georgelis, N, EL Braun, JR Shaw & LC Hannah. 2007. The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria. Plant Cell, 19: 1458-1472. [abstract]
  30. Gibb, GC, O Kardailsky, RT Kimball, EL Braun & D Penny. 2007. Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution, 24: 269-280. [abstract]
  31. Sassi, SO, EL Braun & SA Benner SA. 2007. The evolution of seminal ribonuclease: Pseudogene reactivation or multiple gene inactivation events? Molecular Biology and Evolution, 24: 1012-1024. [abstract]
  32. Crowe, TM, P Bloomer, E Randi, V Lucchini, RT Kimball, EL Braun & JG Groth. 2006. Supra-generic cladistics of landfowl (Order Galliformes). Acta Zoologica Sinica, 52(Supplement): 358-361. [abstract] [full text pdf].
  33. Kimball, RT, EL Braun, JD Ligon, E Randi & V Lucchini. 2006. Using molecular phylogenetics to interpret evolutionary changes in morphology and behavior in the Phasianidae. Acta Zoologica Sinica, 52(Supplement): 362-365. [abstract] [full text pdf].
  34. Braun, EL, DO Natvig, M Werner-Washburne & MA Nelson. 2004. Genomics in Neurospora crassa: From One-Gene-One-Enzyme to 10,000 Genes. Applied Mycology and Biotechnology, Volume 4. Fungal Genomics (DK Arora & GG Khachatourians, editors), pp. 295-313. [abstract] [full text pdf].
  35. Katsu, Y, DS Bermudez, EL Braun, C Helbing, S Miyagawa, MP Gunderson, S Kohno, TA Bryan, LJ Guillette Jr, & T Iguchi. 2004. Molecular cloning of the estrogen and progesterone receptors of the American alligator. General and Comparative Endocrinology, 136: 122-133. [abstract]
  36. Braun, EL. 2003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution. Applied Bioinformatics, 2:13-34. [abstract] [full text pdf].
  37. Dias, AP, EL Braun, MD McMullen & E Grotewold. 2003. Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiology, 131: 610-620. [abstract]
  38. Galagan, JE, et al. (76 co-authors). 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422: 859-868. [abstract]
  39. Braun, EL & RT Kimball. 2002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling and sequence length. Systematic Biology, 51:614-625. [description]
  40. Armstrong, MH*, EL Braun & RT Kimball. 2001. Phylogenetic utility of avian ovomucoid intron G: A comparison of nuclear and mitochondrial phylogenies in the Galliformes. The Auk, 118:799-804. [abstract] [full text pdf].
  41. Bean, LE*, WH Dvorachek Jr, EL Braun, A Errett*, GS Saenz, M Giles*, M Werner-Washburne, MA Nelson & DO Natvig. 2001. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: Correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics, 157:1067-1075. [abstract]
  42. Braun, EL, AP Dias, TJ Matulnik & E Grotewold. 2001. Transcription factors and metabolic engineering: Novel applications for ancient tools. Recent Advances in Phytochemistry, 35:79-109. [description] [full text pdf].
  43. Braun, EL & E Grotewold. 2001. Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains. Molecular Biology and Evolution, 18:1401-1412. [abstract]
  44. Braun, EL & RT Kimball. 2001. Polytomies, the power of phylogenetic inferences, and the stochastic nature of molecular evolution: A comment on Walsh et al. (1999). Evolution, 55:1261-1263. [description]
  45. Dong X, EL Braun & E Grotewold. 2001. Functional conservation of plant secondary metabolic enzymes revealed by complementation of Arabidopsis flavonoid mutants with maize genes. Plant Physiology, 127:46-57. [abstract]
  46. Kimball RT, EL Braun, JD Ligon, V Lucchini & E Randi. 2001. A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours. Biological Journal of the Linnean Society, 73:187-198. [abstract]
  47. Randi, E, V Lucchini, A Hennache, RT Kimball, EL Braun & JD Ligon. 2001. Evolution of the mitochondrial DNA control region and cytochrome b genes, and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Molecular Phylogenetics and Evolution, 19:187-201. [abstract]
  48. Braun, EL, AL Halpern, MA Nelson & DO Natvig. 2000. Large scale comparison of fungal sequence information reveals innovation in the filamentous fungus Neurospora crassa and gene loss in the budding yeast Saccharomyces cerevisiae. Genome Research, 10:416-430. [abstract] [full text pdf].
  49. Randi, E, V Lucchini, T Armijo-Prewitt*, RT Kimball, EL Braun & JD Ligon. 2000. Mitochondrial DNA phylogeny and speciation of the Tragopans. The Auk, 117:1003-1015. [abstract] [full text pdf].
  50. Bieszke, JA, EL Braun, LE Bean*, S Kang, DO Natvig & KA Borkovich. 1999. The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix, retinal-binding protein homologous to archaeal rhodopsins. Proceedings of the National Academy of Sciences USA, 96:8034-8039. [abstract] [full text]
  51. Braun, EL & E Grotewold. 1999. Newly discovered plant c-myb-like genes rewrite the evolution of the plant myb gene family. Plant Physiology, 121:21-24. [full text]
  52. Kimball, RT, EL Braun, PW Zwartjes, TM Crowe & JD Ligon. 1999. A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Molecular Phylogenetics and Evolution, 11:38-54.[abstract] [full text pdf]
  53. Rabinowicz, PD, EL Braun, AD Wolfe, B Bowen & E Grotewold. 1999. Maize R2R3 Myb genes: Sequence analysis reveals amplification in the higher plants. Genetics, 153:427-444. [abstract] [full text]
  54. Braun, EL, S Kang, MA Nelson & DO Natvig. 1998. Identification of the first fungal annexin: Analysis of annexin gene duplications and implications for eukaryotic evolution. Journal of Molecular Evolution, 47: 531-543. [abstract] [full text pdf]
  55. Kimball, RT, EL Braun & JD Ligon. 1997. Resolution of the phylogenetic position of the Congo Peafowl, Afropavo congensis: A biogeographic and evolutionary enigma. Proceedings of the Royal Society of London, series B, 264: 1517-1523. [abstract] [full text pdf].
  56. Nelson, MA, S Kang, EL Braun, ME Crawford, PL Dolan, PM Leonard, J Mitchell*, AM Armijo*, L Bean*, E Blueyes*, T Cushing*, A Errett, M Fleharty*, M Gorman*, K Judson*, R Miller, J Ortega*, I Pavlova*, J Perea*, S Todisco*, R Trujillo*, J Valentine*, A Wells*, M Werner-Washburne, S Yazzie* & DO Natvig. 1997. Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genetics and Biology, 21:348-363. [abstract] [full text pdf].
  57. Braun, EL, EK Fuge, PA Padilla & M Werner-Washburne. 1996. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. Journal of Bacteriology, 178:6865-6872. [abstract] [full text pdf].
  58. Werner-Washburne, M, EL Braun, ME Crawford & VM Peck. 1996. Stationary phase in Saccharomyces cerevisiae. Molecular Microbiology, 19:1159-1166.
  59. Fuge, EK, EL Braun & M Werner-Washburne. 1994. Protein synthesis in long-term stationary phase cultures of Saccharomyces cerevisiae. Journal of Bacteriology, 176:5802-5813. [abstract] [full text pdf] (also see [PubMed central] for high resolution scans of the 2D PAGE images).
  60. Werner-Washburne, M, E Braun, GC Johnston & RA Singer. 1993. Stationary phase in the yeast Saccharomyces cerevisiae. Microbiological Reviews, 57:383-401. [abstract] [full text pdf].
  61. Werner-Washburne, M, D Brown & E Braun. 1991. Bcy1, the regulatory subunit of cAMP-dependent protein kinase in yeast, is differentially modified in response to the physiological status of the cell. Journal of Biological Chemistry, 266:19704-19709. [abstract] [full text pdf].


Updated 22 March 2013