Dr. Michael Sanderson
Program Director
sanderm@email.arizona.edu

Pennie Liebig
Program Coordinator
genomics@email.arizona.edu

IGERT Program in Genomics
University of Arizona
Biosciences West. 328
1041 E. Lowell Street
Tucson, AZ 85721-0088
Tel: 520-626-0988
Fax: 520-621-9190




IGERT Recruitment Program

IGERT.org


IGERT PROGRAM IN GENOMICS FELLOWS


2013-2014 Cohort



Joseph Charboneau
Ecology and Evolutionary Biology

M.S. Botany, University of Wyoming, 2013
B.A. Biology and Environmental Studies, Oberlin College, 2008

I am interested in the nature and origin of plant diversity, namely in using genomic-scale DNA sequence data to understand phylogenetic relationships among plant taxa and the evolutionary events and processes that have formed and maintained the diversity of plants that we see today. My specific research interests are in the phylogeny and chromosome number evolution of the New World species of the legume genus Astragalus, a clade of 500+ species within the larger genus that is estimated to be only four to five million years old. While the Old World species of the genus have a base chromosome number of n=8 and multiples thereof, New World Astragalus species fascinatingly have almost exclusively aneuploid chromosome numbers ranging from a base number of n=11 to n=15, and the origin of this aneuploid series is unknown. I’m very excited about utilizing genomic-scale sequence data to elucidate the evolutionary relationships and chromosome number evolution in this recent, rapid radiation of plants.


Ivan Dimitrov
Molecular and Cellular Biology

BS/MS Biomedical Engineering, Washington University, 2008

Barley is the fourth highest produced cereal crop after rice, wheat and corn. Barley is relatively more tolerant to drought and cold stress than other cereals. The majority of barley is classified as “lowland barley” and is used as animal feed and in brewing. “Highland barley” is grown at the high elevations found in the highlands of China and on the Tibetan plateau. The harsher environments found in these regions have made highland barley more resistant to drought, cold and UV stresses. Three possibilities exist to explain the increased stress tolerance in highland barley: 1) evolution of a new stress response network that increases tolerance; 2) evolution of new genes that generate increased stress tolerance; or 3)accumulation of mutations in existing stress-responsive genes that have increased ability to respond to stress. These three possibilities could be quickly distinguished with the use of RNA-Seq. Based on my preliminary sequencing data, I have seen that highland barley genes have not diverged greatly from their lowland counterparts, therefore the first two possibilities are less likely. However, studying stress responsive genes in highland barley offers a simple system to see what changes in genes or gene regulation can result in a more stress-resistant organism. This information would be valuable in altering existing strains of lowland barley, as well as serve to guide breeding and genetic engineering in wheat.



Cole Eskridge
Entomology and Insect Science

B.S. Biology, University of Mary Washington, 2012

It’s my goal to study the genomic underpinnings directing these unique and diverse morphologies. Specifically, I will be focusing on the evolutionary development of highly-derived antennal morphs of beetles in the tribe Paussini (some of which can be seen illustrated here). I will be investigating: 1) The expression patterns of genes relevant to antennal development in Paussines using Metrius contractus, 2) The genomes of related Paussine beetles and the structure of their homeotic complexes, 3) The similarities in antennal gene structure and composition between related Paussines.



Evan Forsythe
Plant Sciences

B.A. Biology, St. John's University, 2011

I am a first year PhD student from Minnesota. My biology background is in Genetics and Evolutionary biology. I am interested in combining evolutionary, comparative genomic, and biochemical concepts to identify and characterize functionally relevant loci. The evolution of telomerase within the Brassicaceae plant family presents a scenario in which a combinatorial approach will be particularly useful. I am scouring the genomes of several Brassicaceae species in search of functional components of the telomerase enzyme that are either novel to plants, or remain uncharacterized in other taxa.



Benjamin Goldman-Huertas
Ecology and Evolutionary Biology

A.B. Biology, cum laude, Harvard University, 2005

I'm interested in the genetics of species interactions, particularly how genes linked to the behavior of insects evolve in conjunction with major changes in the ecology of these insects. My study system is a group of flies in the genus Scaptomyza that have evolved to be leaf-miners from ancestors that fed on yeast and other microbes. Using genomic tools available for the closely related Drosophila lineage, I study how the complement of genes involved in smell and taste sensation have changed in Scaptomyza during the evolution of leaf-mining and specialization on host-plants, and how these changes have modified the behavior and nervous system of these organisms.




Brian Hallmark
Statistics

B.A. Physics/Math, New College of Florida, 2001
M.S. Applied Mathematics, University of Arizona, 2006

My research interests lie at the intersection of population genomics and modern statistics. I am interested in developing novel statistical techniques for inferring demographic history and natural selection from next generation sequencing data. I am also interested in developing Bayesian nonparametric clustering methods for genomic datasets, where the number of clusters is intelligently inferred from the data. Currently, I am working with the Hammer lab looking for genetic signals of cold adaptation in indigenous Siberian populations.



Brianna McTeague
Ecology and Evolutionary Biology

B.A. Biological Sciences, Barnard College, 2009

My research focuses on the evolutionary ecology of plant invasions. I have worked on yellow starthistle (Centaurea solstitialis) a noxioius weed in the western US and am may also work on local desert invaders. I am interested in understanding the genetic changes associated with invasiveness in real invasions and experimental invasions that I will conduct in the Biosphere2, and in elucidating routes of invasion using RAD markers. Furthermore, invasive plants can alter the environment and impact native communities, and I am interested in looking at how native plants evolve in response to novel selective pressures imposed by the invader.



Jennifer Noble
Plant Sciences

B.S. Molecular & Cellular Biology and Plant Sciences, University of Arizona, 2012

I am a second year PhD student working with Dr. Ravishankar Palanivelu in the School of Plant Sciences.  My research comprises two projects whose goal is to understand the functions of LORELEI (LRE), a putative GPI-anchor membrane protein, in pollen tube reception in angiosperms.  The first project uses a comparative genomics approach to determine if LRE mediates the species-specific barrier in interspecific crosses, using species in the Brassicaceae family. The second project focuses on the regulation of LRE expression within the synergid cells of Arabidopsis.




Timothy O'Connor
Ecology and Evolutionary Biology

B.S. Integrative Biology, University of Illinois at Urbana-Champaign, 2009

My research background is divided between microbial ecology and insect evolution, and for my dissertation I hope to develop a project at the intersection of these fields. Like all multicellular life, insects harbor a staggering diversity of single-celled symbionts. By probing these symbioses with -omic and meta-omic tools to I hope to elucidate the dynamics of cross-domain interactions, document their history, and test the evolutionary consequences for the symbiotic players.



Justin Shaffer
Plant Sciences

B.A. Environmental Studies, University of California, Santa Cruz, 2010

My interests surround the ecology of plants and associated microbes. I am currently working on my Ph.D. in Plant Pathology and Microbiology at the University of Arizona with Drs. Betsy Arnold and Dave Baltrus, and am beginning to examine the relationships and interactions of endohyphal bacteria of seed-associated and foliar endophytic fungi. We are using a phylogenetics approach to understand the evolutionary relationships among these and other groups of bacteria, and a combination of classic and novel microbiological and molecular techniques to determine how endohyphal bacteria may be influencing plant-fungus symbioses in natural communities.



Erin Vaughn
Genetics

B.S. Conservation Biology, University of New Mexico, 2008

I am interested in utilizing genomic tools to answer wildlife conservation questions. I am working towards establishing a system of DNA methylation markers as indicators of pollutant exposure in fathead minnow, Pimephales promelas.  Due to the highly complex nature of an epigenetic response, the development of a robust marker system requires measuring methylation and gene expression changes on a genome-wide scale.  Concurrently, I am developing a series of microsatellite markers derived from 454 pyrosequencing data for a threatened population of Florida crested caracara.



August Woerner
Computer Science

M.S. Computer Science, University of Arizona, 2011
B.S. Biochemistry, Marlboro College, 2001

My research interests are in population genomics, bioinformatics and computational biology. In general, I am interested in computation from two opposing lines of inquiry: one is the development of novel algorithms to address questions of biological relevance, and the second is the use of such tools (plus a handful of inferential techniques) to conduct full-genome analyses on populations.




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