LAB GROUP

There are a variety of graduate and undergraduate students currently working in the lab group, and  others who have worked in the past. In addition, the lab has had a variety of technicians and others who have helped out. Additional lab photos (including of previous students) can be found here.

Kimball/Braun lab, Fall 2007. Top row (left to right):  Kin Han, Rebecca Kimball, Edward Braun, Carly Ferguson, Elon Fernandez. Bottom row (left to right): Natalie Wright, Jena Chonjowski, Tamaki Yuri, Jordan Smith.
Lab Members, Fall 2007

GRADUATE STUDENTS

The graduate students in the lab do a diverse range of projects. I believe graduate students (particularly PhD students) should develop their own research projects, and take the primary role in determining the specific questions and approaches they use. I see my role as that of assisting and guiding, rather than directing. In addition to their main projects, many of the students in the lab are working on side projects. While I feel strongly that these should not distract from completing degrees, students have found these projects to be useful to develop additional skills and gain additional publications during their graduate career.

CURRENT GRADUATE STUDENTS

  • Jena Chojnowski (PhD, Fall 2003; supervised by Edward Braun). Jena is looking for genes that affect sex-determination in red-eared sliders (Trachemys scripta). She has developed subtraction libraries to identify candidate genes (those likely to affect sex-determination), screened clones in a macroarray, and is now doing qPCR. In addition to this project, Jena had initially come to our lab as a technician on the EarlyBird project, and she has remained involved in that project as well as being involved in others. She has first-authored two papers on vertebrate isochores (Chojnowski et al. 2007, Journal of Molecular Evolution; 2008, Integrative and Comparative Biology) and a paper on gene evolution from the EarlyBird project (Chojnowski et al. 2008, Gene)

  • Kin Han (PhD, Fall 2007). Kin completed a MS on the phylogeny of Caprimulgidae, working with Mike Braun at the Smithsonian Institution and the University of Maryland. She is interested in conservation, and looking at alternative markers that might prove more informative in conservation genetic studies. As an MS student, and now at UF, she has been involved in the EarlyBird project.

  • Jordan Smith (MS, Fall 2007; supervised by Edward Braun). Jordan began working in the lab as an undergraduate, and has remained to continue her project. She has developed 40 novel genes to examine ratite phylogeny. In addition to her thesis work, she has been active in additional primer development, coordination and genotyping of brown-headed nuthatches (see also Sarah Haas below) to examine the mating system of this poorly studied cooperative breeder. 

  • Natalie Wright (MS, Fall 2006; supervised by David Steadman). Although Natalie is advised by David Steadman (Florida Museum of Natural History), she does some of her research in the lab. She is looking at morphological and molecular differences of bird species found on both Trinidad and Tobago. 

  • Clare Rittschoff (PhD, Fall 2006; supervised by Jane Brockmann). Clare is interested in the mating system of Nephila clavipes (golden orb-weaving spider) and has developed microsatellite markers to use in her research. 

    •     FORMER GRADUATE STUDENTS

  • Sarah Haas (MS, Spring 2007). Sarah worked on population genetics of Brown-headed Nuthatch, a species in the southeastern United States that has been experiencing population declines. She developed microsatellites for this project (Haas et al. 2008, Conservation Genetics). She looked at genetics within one well-sampled population as well as across additional populations in Florida and Georgia. In addition, she worked on phylogeography of the endangered Snail Kite, as population sizes are declining again in Florida (Haas et al. 2008, Ibis). 

  • Greg Babbitt (PhD Spring 2006). Greg is looking at fluctuating asymmetry. Some of this research involved clonal lines of aphids, raised under varying conditions to examine affects of "stress" on fluctuating asymmetry. Much of Greg's research, however, focussed on the mathematical distribution and analysis of fluctuating asymmetry. He is currently doing a post-doc with Yuseob Kim at Arizona State

  • Melissa Cousins (MS Spring 2006). Melissa examined reproductive behaviors in the Florida Flagfish. In particular, she looked at resource allocation towards reproduction by females in response to males of varying quality.

  • Jeremy Kirchman (PhD Summer 2006; Advisor David Steadman). Jeremy is examining phylogeography, phylogenetics, and evolution of flightlessness of rails in the genus Gallirallus, which is distributed in Oceania. He is incorporating paleontology, ancient DNA, and work with extant populations of rails. He is currently at the New York State Museum.

    • UNDERGRADUATE STUDENTS

    The undergraduate students in the lab work in a variety of capacities. Most new students are encouraged to work on a variety of projects, until they are comfortable with the basics (PCR, agarose gel electrophoresis, cloning, editing and contiging DNA sequences). Students that have performed well and are motivated often begin to work independently once they are familiar with the lab. The degree of independence depends upon the students interests, abilities, and the time they can devote to a project. Some students take a portion of an existing project and collect all the data associated with that portion. Still others work even more independently, and actively participate in developing the project idea, methods, analyses, and write up.
     
        CURRENT UNDERGRADUATE  STUDENTS
  • Carly Ferguson (Since Fall 2007). Carly is now working on examining how many independent barriers to recombintion have evolved among Neoaves. Previous research has suggested at least four independent barriers to recombination at the ATP5a1 locus, but only four orders were examined. Carly has been amplifying and cloning ATP5a1 from additional species throughout the Neoaves to get a better understanding of this. She is also helping to finish a dataset of non-canonical introns (see Victoria Heimer-Torres, below). Carly is currently president of the UF chapter of AMSA. 

  • Reid Green (Since Spring 2008).  Reid was working on a variety of projects last year, and will begin on an independent project this fall. 

  • Caitlin Wildes (Since Spring 2008).  Caitlin was working on a variety of projects last year, and will begin on an independent project this fall. 

  • Katie Zelle (Fall 2007, should return Fall 2008).  Katie worked on sexing nuthatches and amplifying and sequencing one intron for the EarlyBird project. She has then spent time in Australia doing research on Drosophila, and will return to UF this fall to graduate.

  • Nick Lysak (Since Summer 2008).  Nick began in the lab to help on the brown-headed nuthatch project. He has been sexing and genotyping nuthatches with great success. In addition, he has amplified and sequenced a number of different loci for the EarlyBird project.

    •     PREVIOUS UNDERGRADUATE STUDENTS

  • Elon Fernandez (Began Spring 2006, graduated Spring 2007).  Elon helped out on the EarlyBird project, collecting data from 42 species for one locus. He then developed markers for long PCR to obtain 8-10kb segments of a single locus for phylogenetics, and he amplified and sequenced several of these as well as some long mitochondrial regions.

  • Amber Bonilla (Began Spring 2005; graduated Spring 2006).  For her senior thesis, Amber examined the phylogenetic utility and molecular evolution of 3' UTR regions. She collected sequence data from 5 different loci. For each locus, we also have sequenced intron data to allow us to compare patterns of molecular evolution between the 3' UTR's and linked introns. Amber has primarily worked on galliforms, but we are exploring whether her data will allow us to develop primers usable in the EarlyBird project. She is currently writing these results into a first authored publication!

  • Padi Tester (Spring 2003-Spring 2006). Padi has worked on everything in the lab, and contributed a lot to several projects. Following her graduation, she stayed on as a technician before beginning an accelerated nursing program and is now employed as a nurse. Her primary work was been on the EarlyBird project, where she has been in charge of the aldolase B locus (one of the most difficult). In addition to this, she collected all of the data for one of the galliform introns, and collected partial data sets for other projects. She also contributed a lot of work on the alligator EST project. 

  • Natasha Elejalde (Summer 2005-Fall 2006). Natasha initially began collecting intron data for galliforms,  but then she moved on to collecting most of the mitochondrial data to address questions of hybridization in two species of paradise flycatcher, Terpsiphone viridis and Terpsiphone rufiventer. 

  • Victoria Heimer-Torres (Summer 2004-Summer 2006). Victoria used the chicken genome project to locate non-canonical introns. She then developed primers to amplify these introns. She has currently obtained data from several galliform taxa for the non-canonical introns. For her REU project, was obtaining sequences from the non-canonical introns for a set of taxa spanning all birds. She did a Fulbright in Norway and is now in graduate school in Ireland.

  • James Franklin (Spring 2004-Spring 2006). James came in to the lab working with Jeremy Kirchman working on the phylogeography of three different species distributed throughout Oceania. He subsequently worked with Jena Chojnowski and Edward Braun developing cDNA libraries of reptiles, and collected most of the data for one EarlyBird locus.

  • Syki Duong (Spring 2003 - Spring 2005). Syki has been involved in a number of projects in the lab. She assisted in the EarlyBird project, worked on a project examining novel loci in the plant genus Coreocarpus, and worked on alligator genomics. For the alligator genomics project she was funded through the University Scholars Program and the University of Florida. For this project, she developed a fosmid library of the alligator. She then sequenced random fosmids. Three of the fosmids showed high identity to the chicken genome (two to the MHC region), and she selected these to fully sequence. Syki is beginning medical school at Washington University in St. Louis in the fall of 2005.

  • Katherine Rozofsky (Summer 2004 - Spring 2005). Assisted on the EarlyBird project, working on Alpha-crystallin intron 1 in birds. Katie is in Surinam in the Peace Corps where it sounds like she is having an amazing experience..

  • Kevin Johnson (Fall 2004 - Spring 2005). Assisted on the galliform intron project. He also worked on developing a library for the fungus Allomyces.

  • W. Andrew Cox (Spring 2003 - Spring 2004; and beyond). Andrew has worked on a variety of projects in the lab (staying on for a while even once we was done with his coursework). He collected data, helped analyze, and then write a paper examining the phylogenetic position of the New World Quail (Cox et al. 2008, Auk). Andrew also provided a huge amount of assistance on the EarlyBird project. He also helped with the galliform intron project, Galapagos Hawk phylogeography, and collecting EST sequences from the alligator. Andrew is currently in graduate school in avian ecology at Univ. of Missouri, where he will be working with J. Faaborg.

  • Dieula John (Spring 2003-Spring 2004). Dee provided general assistance on all of the projects in the lab. She contributed most to the alligator EST project and to EarlyBird.

  • Dawn Yang (Spring 2004). Dawn assisted with the EarlyBird project, particularly doing PCR and prepping samples for sequencing.

  • Andrea Garcia (Fall 2002 - Spring 2003). Andrea developed her own project on the genetics of Gambusia exposed to toxins. She examined one gene (PGI) that has been suggested (using allozyme data) to be involved in resistance to pesticides. Andrea sequenced a region of this gene from fish from three different populations (two polluted, one clean) to see if the alleles segregated based on population (suggesting selection).

  • Doug Storch (Fall 2002 - Spring 2003). Doug worked on a variety of projects, but primarily collected the BFib5 data for the galliform intron project.

  • Laura Salazar (Spring 2003). Laura assisted with various aspects of the EarlyBird project.

  • Amanda Hudson (Fall 2001 - Spring 2002). Amanda developed many of the primers that were used for the galliform intron project, and made it a much better project with many more loci than would have happened otherwise. Some of these also formed the basis for the primers we use in the EarlyBird project. She found many good target genes for phylogenetic uses, and we have repeatedly gone to her notes to look up new target loci.

  • Laura Patterson (Spring 2002). Laura helped to obtain the complete mitochondrial sequence of Falco sparverius and Dryocopus pileatus.

  • Ana Galarza (Fall 2001). Ana helped with the initial lab set up, and collected some of the preliminary galliform data in the lab.