{"id":22,"date":"2012-09-05T11:22:33","date_gmt":"2012-09-05T15:22:33","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/template\/?page_id=22"},"modified":"2026-03-19T08:29:20","modified_gmt":"2026-03-19T12:29:20","slug":"research","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/ebraun\/research\/","title":{"rendered":"Research"},"content":{"rendered":"\r\n<section class=\"fullwidth-text-block\">\r\n\t<div class=\"container px-0 pt-5\">\r\n\t\t<div class=\"row align-items-start\">\r\n\t\t\t<div class=\"col-12\">\r\n\t\t\t\t\n<h1 class=\"wp-block-heading\">Research<\/h1>\n\n\n\n<p>My research foci include efforts to reconstruct the\u00a0Tree of Life\u00a0and understand patterns of\u00a0genome evolution. A small number of representative publications are listed below and a more\u00a0complete list\u00a0is provided on\u00a0the <a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/publications\/\">Publications<\/a>\u00a0page. Other recent scholarly work associated with the Braun lab include:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The\u00a0<a href=\"http:\/\/www.biology.ufl.edu\/earlybird\">&#8220;EARLY BIRD&#8221; project<\/a>:\n<ul>\n<li>Details of the publications produced by the &#8220;Early Bird&#8221; project along with links to the data matrices and trees generated by the project.<\/li>\n<li>A short description of the &#8220;Early Bird&#8221; project for the public appears in an\u00a0American Paleontologist\u00a0feature on the tree of life.<\/li>\n<\/ul>\n<\/li><li>The\u00a0<a href=\"http:\/\/genomeprojectsolutions.com\/GATOR_project.html\">&#8220;GATOR GENOME&#8221; project<\/a>:\n<ul>\n<li>The UF portion of the\u00a0Crocodialian Genome Project<\/li>\n<li>This project integrates research and genomics education.<\/li>\n<\/ul>\n<\/li><li>Also see below for links to my\u00a0<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#other\">other scholarly work<\/a>, including data matrices, computer programs, other publications, and web sites related to my work.<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Representative Publications<\/h3>\n\n\n\n<p>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:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><big>Phylogenetics and the Tree of Life<\/big><\/li><\/ul>\n\n\n\n<ol class=\"wp-block-list\"><li>Smith\u00a0et al.\u00a02013. Ratite non-monophyly: Independent evidence from 40 novel loci.\u00a0<a href=\"http:\/\/sysbio.oxfordjournals.org\/\"><i>Systematic Biology<\/i><\/a>, 62:35-49. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/%20#SBK2013\">full citation<\/a>]<\/li>\n<li>Yuri\u00a0et al.\u00a02013.\u00a0Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.\u00a0<a href=\"http:\/\/www.mdpi.com\/journal\/biology\"><i>Biology<\/i><\/a>, 2:419-444. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#YKH2013\">full citation<\/a>]<\/li>\n<li>Braun et al.\u00a02011. Homoplastic microinversions and the Avian Tree of Life.\u00a0<a href=\"http:\/\/www.biomedcentral.com\/bmcevolbiol\/\">BMC Evol Biol<\/a>, 11:141. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#BKH2011\">full citation<\/a>]<\/li>\n<li>Chojnowski\u00a0et al.\u00a02008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes.\u00a0<a href=\"http:\/\/www.elsevier.com\/locate\/gene\">Gene<\/a>, 410:89-96. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#CKB2008\">full citation<\/a>]<\/li>\n<li>Harshman\u00a0et al.\u00a02008. Phylogenomic evidence for multiple losses of flight in ratite birds.\u00a0<i><a href=\"http:\/\/www.pnas.org\/\" target=\"_blank\">PNAS<\/a><\/i>, 105:13462-13467. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#HBB2008\">full citation<\/a>]<\/li>\n<li><strong>Braun &amp; Kimball.<\/strong>\u00a02002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling and sequence length.\u00a0<i><a href=\"http:\/\/systbiol.org\/\" target=\"_blank\">Syst Biol<\/a><\/i>, 51:614-625. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#BK2002\">full citation<\/a>]<\/li><\/ol>\n\n\n\n<ul class=\"wp-block-list\"><li><big>Molecular evolution and gene families<\/big><\/li><\/ul>\n\n\n\n<ol class=\"wp-block-list\"><li>Feller\u00a0et al.\u00a02011. Evolutionary and comparative genomics of MYB and bHLH plant transcription factors.\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/journal\/10.1111\/%28ISSN%291365-313X\">Plant J<\/a>, 66:94-116. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#FMBG2011\">full citation<\/a>]<\/li>\n<li>Chojnowski\u00a0et al.\u00a02007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes.\u00a0<i>J Mol Evol<\/i>, 65: 259-266. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#CFK2007\">full citation<\/a>]<\/li>\n<li>Georgelis\u00a0et al.\u00a02007. 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.\u00a0<a href=\"http:\/\/www.plantcell.org\/\">Plant Cell<\/a>, 19: 1458-1472. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#GBSH2007\">full citation<\/a>]<\/li>\n<li><strong>Braun &amp; Grotewold.<\/strong>\u00a02001. Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains.\u00a0<i>Mol Biol Evol<\/i>, 18:1401-1412.\u00a0 [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#BG2001\">full citation<\/a>]<\/li><\/ol>\n\n\n\n<ul class=\"wp-block-list\"><li><big>Genomics and Phylogenomics<\/big><\/li><\/ul>\n\n\n\n<ol class=\"wp-block-list\"><li>Shaffer\u00a0et al.\u00a02013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.\u00a0<a href=\"http:\/\/genomebiology.com\/\">Genome Biology<\/a>,\u00a0in press. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#SMW2011\">full citation<\/a>]<\/li>\n<li>St John\u00a0et al.\u00a02012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.\u00a0<a href=\"http:\/\/genomebiology.com\/\">Genome Biology<\/a>, 13:415. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#StJB2011\">full citation<\/a>]<\/li>\n<li>Braun and Phillips.\u00a02008. Phylogenomics and secondary plastids: A look back and a look ahead.\u00a0J Phycol, 44:2-6. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#BP2008\">full citation<\/a>]<\/li>\n<li><strong>Braun.<\/strong>\u00a02003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution.\u00a0<i><a href=\"http:\/\/www.openmindjournals.com\/bioinformatics.html\" target=\"_blank\">Applied Bioinf<\/a><\/i>, 2:13-34.\u00a0 [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#B2003\">full citation<\/a>] [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/content-removed\/\">full text<\/a>]<\/li>\n<li><strong>Galagan\u00a0et al.<\/strong>\u00a02003. The genome sequence of the filamentous fungus\u00a0<i>Neurospora crassa<\/i>.\u00a0<i><a href=\"http:\/\/www.nature.com\/\" target=\"_blank\">Nature<\/a><\/i>, 422: 859-868. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#G2003\">full citation<\/a>]<\/li>\n<li><strong>Braun\u00a0et al.<\/strong>\u00a02000. Large scale comparison of fungal sequence information reveals innovation in the filamentous fungus\u00a0<i>Neurospora crassa<\/i>\u00a0and gene loss in the budding yeast\u00a0<i>Saccharomyces cerevisiae<\/i>.\u00a0<i><a href=\"http:\/\/www.genome.org\/\" target=\"_blank\">Genome Res<\/a><\/i>, 10:416-430. [<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/research\/#BHNN2000\">full citation<\/a>]<\/li><\/ol>\n\n\n\n<p>See <a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/publications\/\">publications<\/a> for a\u00a0complete list\u00a0of peer-reviewed philosophy.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><a name=\"other\"><\/a>Links and Other Scholarly Works<\/h3>\n\n\n\n<p>Other work produced by myself and other members of the Braun lab includes:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The web page for the\u00a0<a href=\"http:\/\/www.biology.ufl.edu\/earlybird\">&#8220;Early Bird&#8221; project<\/a>\u00a0to assemble the avian tree of life(supported by the NSF Assembling the Tree of Life program).<\/li>\n<li>&#8220;Borrowed Chloroplasts: Secondary Endosymbiosis and the Chromalveolates\u201d, a symposium at the\u00a02007\u00a0Botany and Plant Biology Joint Congress was organized by\u00a0Naomi Phillips, Edward Braun &amp; Debashish Bhattacharya.<\/li>\n<li>A short paper in the Maize Genetics Cooperation Newsletter (&#8220;Diversification of the R2R3 Myb gene family and the segmental allotetraploid origin of the maize genome&#8221;) that I co-wrote with Erich Grotewold.<\/li><\/ul>\n\n\n\n<p>Additional materials are forthcoming.<\/p>\n\n\n\r\n\t\t\t<\/div>\r\n\t\t<\/div>\r\n\t<\/div>\r\n<\/section>\r\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":544,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-22","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/22","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/users\/544"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/comments?post=22"}],"version-history":[{"count":10,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/22\/revisions"}],"predecessor-version":[{"id":496,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/22\/revisions\/496"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/media?parent=22"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}