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


FACULTY

In addition to the faculty listed here, faculty in other units also participate in IGERT activities. All IGERT activities are open to participation from members of any department.

Participating Faculty in Evolutionary Genetics:


A. Elizabeth Arnold
IGERT Steering Committee Member
Associate Professor, School of Plant Sciences

The Arnold lab uses classic microbiological methods, the modern tools of metagenomics, and the robust framework of phylogenetic biology to understand fungal biodiversity, the ecological roles of newly discovered but cryptic microfungi, and the evolution of symbiotic lifestyles across the fungal tree of life. Their field sites range from the Canadian Arctic to lowland rainforests in Panama, and their interests range from bacterial symbionts of endophytic fungi (e.g., Hoffman and Arnold 2010) to the effects of soilborne molds on tropical forest dynamics (e.g., U'Ren et al. 2009). The lab’s diverse projects are united by a passion for organismal biology and an interdisciplinary approach to addressing biological questions. Representative publications include Arnold et al. (2007, 2009), Gallery et al. (2007), and U'Ren et al. (2010).

David Baltrus
Assistant Professor, School of Plant Sciences

The Baltrus Lab is interested in understanding microbial evolution with a focus on the mechanisms and costs of adaptation and guided by expectations from population genetics. We are specifically interested in using interdisciplinary approaches to investigate how adaptation in microbial pathogens, and in particular phytopathogens, is shaped by factors such as gene exchange and phenotypic tradeoffs. We approach such questions from multiple angles by harnessing the power of experimental evolution, genomics, molecular biology, as well as surveys of natural variation across phylogenetically diverse strains. Although many previous studies have strictly relied on phenotypic assays, recent advances in DNA and RNA sequencing technologies provide opportunities to actually identify mutations underlying differences in phenotype and allow a unique opportunity to understand the evolutionary process. By bridging the disciplines of microbiology, evolutionary biology, and genomics and by focusing on pathogens, our research seeks to provide insights into important evolutionary questions while also shedding light on the role of and interactions between both known and novel virulence factors.

Michael Barker
Assistant Professor, Ecology and Evolutionary Biology

The Barker Lab studies the evolution of genomic and biological diversity. We develop new bioinformatic tools, next-generation genomic data, and leverage growing public databases to gain fresh insights into how genomic changes contribute to the evolution of diversity. A significant focus of our current research is understanding how gene and genome duplication and loss have shaped the evolution of plants. Recent analyses indicate that genome duplication is an evolutionary gamble; plants with duplicated genomes suffer high extinction rates yet the few that are successful over the long term have contributed disproportionately to plant diversity. In related work, we are also studying why, despite many rounds of genome multiplication, most eukaryotes carry relatively few chromosomes. Finally, we use hybridization to explore genomic evolution at smaller phylogenetic scales and discover how combing divergent aspects of genomes may lead to novelty.

Mark Beilstein
Assistant Professor, School of Plant Sciences

In addition to coding proteins, genomes also transcribe non-coding RNA molecules. These molecules have dramatic effects in the genome including gene regulation, epigenetic silencing, and transposon suppression. The Beilstein lab is interested in the evolution of the telomerase RNA (TER), a non-coding RNA molecure that is an essential component of the enzyme telomerase, which maintains telomere length. Telomeres are the physical ends of linear chromosomes and consist of long stretches of repetitive DNA bound to accessory proteins that help distinguish chromosome ends from double-strand DNA breakpoints. Disruption of telomerase leads to progressive telomere shortening that is associated with genomic instability - particularly chromosome fusion. Little is currently known about the structure and identity of TER in plants. The Beilstein lab uses the plant genetic model Arabidopsis in combination with several emerging plant genomic models closely related to Arabidopsis to determine the structure of TER, and the effect that changes in TER can have at the genomic level.

Matthew Cordes
Associate Professor, Biochemistry and Molecular Biophysics

Research in the Cordes lab addresses how families of proteins evolve diversity of structure and function. The origin of new protein structures is a major unsolved problem in biology and its consequences for metabolic networks and for organismal evolution are not well understood. Current research focuses on the functional and structural diversification of bacteriophage transcription factors, which are useful models because of their rapid evolution and experimental tractability. Recent work integrates bioinformatics and biochemical analyses to investigate the remarkable structural and functional fluidity of the lambdoid bacteriophage cro gene (Newlove et al. 2004, 2006; Van Dorn et al. 2006). A collaboration with Ochman involves elucidation of the origin and function of the orphan genes that are unique to particular bacterial genomes and may underlie phenotypic differences among closely related species.

Katrina Dlugosch
Assistant Professor, Ecology and Evolutionary Biology

The Dlugosch lab studies the genetics of colonization and its evolutionary and ecological outcomes. Our research draws largely on the natural experiments provided by human-mediated species introductions and we are working to understand how the genetic variation in these populations translates into phenotypic diversity, adaptation, and changes in ecology. To do this, we employ genomic and quantitative genetic approaches in combination with field experiments and observations. Current research in lab includes studies of the genetic basis of adaptation in invasive plants, the contribution of multiple introductions and genomic admixture to population establishment and expansion, and the role of local adaptation in generating population stability during range expansion and in response to climate change.

Jeremiah Hackett
Assistant Professor, Ecology and Evolutionary Biology

Hackett’s research focuses on how eukaryotic genomes change their gene content, structure and complexity over evolutionary time. Much of eukaryotic genome diversity exists within the protists, as illustrated by the remarkable nucleosome-free genomes of dinoflagellates, the macro- and micro- nuclear system in ciliates, and the binucleate diplomonads. Many of these organisms are important in marine systems, affecting ocean health and global climate. Current work investigates plastid evolution in the dinoflagellates, which have acquired at least five different plastids from distant algal lineages. Hackett uses genomic tools to investigate how endosymbioses have affected genome evolution (Yoon et al. 2005; Hackett et al. 2006). He also studies gene expression as it relates to toxin production and nutrient use in bloom-forming dinoflagellates, a critical topic for understanding the causes of harmful algal blooms.



Michael Hammer
Research Scientist, Arizona Research Labs

With the completion of the human and chimpanzee genome sequences, there is now a concerted effort to describe patterns of polymorphism in populations of humans and our closest living relatives. The Hammer lab examines sequence variation at many loci to reconstruct the history of human populations, to detect evidence of natural selection (Hammer et al. 2004), and to address the extent to which archaic forms made a genetic contribution to the human genome (Wall & Hammer 2006). Related work focuses on demographic questions such as whether the transition to an anatomically modern form took place in a small, isolated population in Africa, or in structured, dispersed populations (Garrigan & Hammer 2006).



Richard Michod
Professor and Department Head, Ecology and Evolutionary Biology

The Michod Lab seeks to understand the diversity of life by studying the evolutionary processes which led to the familiar levels in the hierarchy of life. We seek to understand how groups of individuals evolve into new kinds of individuals. Such evolutionary transitions in individuality occurred during the transitions from prokaryotic to eukaryotic cells, from unicellular to multicellular organisms, from solitary to social species, and from asexual to sexual reproduction. The methods used in our work involve mathematical and computer models of population genetics and population dynamics, experiments with micro-organisms especially the volvocine green algae, and philosophical analysis.



Matthew Sullivan
IGERT Steering Committee Member
Assistant Professor, Ecology and Evolutionary Biology

The Sullivan lab is broadly interested in the the ecology and evolution of natural systems. Our focus is on how ocean viruses, as tiny but abundant biological entities, impact global biogeochemical cycles through interactions with their microbial hosts' core metabolic functions. To this end, we leverage an experimental model-systems approach with the application of modern techniques as phenomenologically-revealing windows into 'wild' viral populations.

Noah Whiteman
Assistant Professor, Ecology and Evolutionary Biology

The Whiteman Lab uses genomics and genetics approaches to understand the processes underlying host-parasite co-diversification, the mechanistic bases of their interactions and the genomic consequences of host specificity. We are particularly interested in plant-insect-plant pathogen interactions and rely on model systems, including the model plant Arabidopsis thaliana, the fruit fly Drosophila melaogaster and their herbivorous relatives in the lineage Scaptomyza, and plant pathogenic bacteria in the genus Pseudomonas. Four main questions driving our current research are: (1) What adaptations underpin a transition to herbivory from a microbe-feeding ancestor in the Scaptomyza lineage within the Drosophila radiation and what are the genetic bases of this transition, (2) Understanding the mechanisms underpinning the evolution of host plant specialization in Drosophila species, its genomic consequences and neurological bases, (3) Identifying and studying the genetic basis of plant resistance traits and insect counter-defenses in a tightly co-evolved system involving a relative of Arabidopsis and a leafmining Drosopihla, found throughout the inter-mountain west, and (4) Studying diversity of Pseudomonas species in the plant phyllosphere as well as functional studies on single lineages that interact with leafminers and plants; how single virulence/avirulence genes in bacteria influence ecological outcomes for host plants and leafminers.

Michael Worobey
Professor, Ecology and Evolutionary Biology

The Worobey lab uses an evolutionary genomic approach to understand the emergence (Worobey et al. 2004; Worobey et al. 2002) and control of pathogens, with a focus on fast-evolving RNA viruses and retroviruses, such as HIV and influenza virus. A major focus involves viral genomic analysis of samples recovered from wild chimpanzees to test how, when, and where AIDS originated (Worobey 2001). This provides a rare chance to study the evolutionary genomics of the closest relatives of both HIV-1 and its human host (SIVcpz and chimpanzees, respectively). The other main research area is the use of archival human and animal samples for understanding and controlling emerging viruses (Smith et al. 2009). Genomic analysis of HIV-1 and human DNA from decades-old paraffin-embedded tissue samples is helping to reveal how HIV-1 emerged (Worobey et al. 2008; Gilbert et al. 2007). This work is relevant for the design of AIDS vaccines.


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