Dr. Michael Sanderson
IGERT Program in Genomics
University of Arizona
Biosciences West. 328
1041 E. Lowell Street
Tucson, AZ 85721-0088
B.A. Neuroscience and Biology, Oberlin College, 2004
I'm interested in the evolution of nervous systems, in particular how adaptation and environmental forces have shaped neural systems and how nervous systems have contributed to the success of various taxa. I use arthropods as my study system as they provide a wealth of anatomical, behavioral, ecological, and taxonomic diversity unparalleled in the animal kingdom. I approach the topic of neural evolution via two avenues: molecular phylogenetics and comparative morphological studies. It is imperative, when comparing taxa on morphological ground, to have robust phylogenies on which to map anatomical characters. I have therefore built a computational pipeline for phylogenetics that utilizes publicly available expressed sequence tags (ESTs). I compare the results of these extensive analyses to phylogenies derived from neuromorphological data in order to infer principles of nervous system evolution in arthropods.
Research Associate, Biochemistry, Univ. of Wisconsin Madison, 2009-Present
Ph.D. Biochemistry, University of Arizona, 2009
M.S. Biochemistry, University of Arizona, 2006
B.S. Biochemistry & Molecular and Cellular Biology, University of Arizona, 2005
Zachary graduated in May 2009 and is currently a post-doc at the University of Wisconsin - Madison.
M.A. Secondary Education, City College of New York, 2006
M.S. Biochemistry, University of Arizona, 2004
B.S. Biochemistry, University of Arizona, 2002
Robert (Bob) Fitak
B.S. Molecular Genetics, Ohio State University, 2006
I am applying genomic tools and next-generation sequencing to the field of conservation genetics. Conservation geneticists can benefit from genomics to better manage the accrued detrimental variation and lost adaptive variation associated with endangered wildlife. I am currently working on two projects. First, in pumas, I am using 454 pyrosequencing of expressed genes to identify SNPs. I will use the SNP genotypes to address several conservation and ecological concerns. Initially, I will use the SNPs to identify suspected adaptive loci associated with their population expansion in North America, then we will identify the origin and migration pattern of puma populations to improve corridor design in the Southwest. Second, I am examining the genetic effects of the Mexican wolf's unique history (extirpated in 1980, reintroduced in 1998) using a 22k SNP chip developed for the domestic dog. I will quantify the ancestry of Mexican wolves from different captive lineages, dogs, and coyotes, in addition to identifying genes fixed by inbreeding which has plagued the population.
Ecology and Evolutionary Biology
B.S. Biochemistry & Molecular Bio., University of California Santa Cruz, 1996
Viruses are ubiquitous in nature and play an integral role in the lifecycle, development and evolution of their diverse hosts. In the ocean, viruses can harm and help their hosts in numerous ways. For example, phage, viruses that infect bacteria, can limit the population size of their hosts and as a result influence carbon and nutrient cycles, or alternatively can transmit genes to the host that confer new function thereby accelerating the host’s evolution and adaptation in a given environment. My interdisciplinary research on ocean viruses incorporates ecology and evolutionary biology, statistics, and bioinformatics to better understand their (i) distribution, diversity and function; (ii) interaction with host species; and (iii) affect on ecosystem function. I am particularly interested in applying large-scale informatics to problems in metagenomics and developing new methodologies to analyze these massive and highly contextualized datasets.
M.S. Microbiology, Middle Tennessee State University, 2005
B.S. Biology, Cumberland University, 2003
My research is focused on molecular systematics of Alternaria and related fungi. We are using a high-level phylogenetic approach (5 gene phylogeny) for the genus level and a low-level phylogenetic approach by sequencing 26 different Alternaria genomes and identifying phylogenetically informative loci focusing on Sections alternata and porri.
B.S. Biotechnology: Microbial Systems, Montana State University, 2005
I am interested in bioprospecting, the search for novel genes that have applications in industry, agriculture, or pharmaceuticals. The microbial symbionts of insects are, specifically, where my bioprospecting interests lie. The high diversity and shear number of both insects and microbes in the world leads me to believe there are useful genes to be found. Using modern techniques to search the wide variety of insects for symbionts will unlock a relatively unexplored region of discovery. This area of science is constantly searching for bacteria and other organisms that contain unique genes/genomes. The search for novel organisms widens our view of the biodiversity on earth by expanding the database of genomes, another exciting side of bioprospecting research.
B.A. Biology, University of Missouri Columbia, 2001
Jana is currently a fifth-year Ph.D. student studying with Dr. Betsy Arnold at University of Arizona. Her dissertation research investigates the evolutionary relationships, biodiversity, and metabolic profiles of fungal endophytes, saprotrophic fungi, and endolichenic fungi associated with diverse plant- and lichen hosts. Her studies also examine the scale of fungal biodiversity and the broad geographical patterns of fungal symbioses.
M.S. Biology, Northern Arizona University, 2001
B.S. Physics, Arizona State University, 1995
I'm interested in complex traits and their diseased states. For my dissertation research, I've helped to develop prediction models for normal human pigmentation variation for the skin, hair, and eye.
Ecology and Evolutionary Biology
Postdoctoral Researcher, Viral Evolution Group, UC San Diego, 2009-Present
Ph.D. Ecology & Evolutionary Biology, University of Arizona, 2009
B.A. Biology, Wesleyan University, 2004
My dissertation was entitled "Reconstructing the evolutionary history of RNA viruses using relaxed molecular clocks." My research was primarily concerned with determining the age of RNA viruses (e.g., HIV, simian immunodeficiency virus, Taura syndrome virus) and investigating the properties of the phylogenetic methods used to make these inferences.
Postdoctoral Associate, HHMI Janelia Farm Research Campus, 2009-Present
Ph.D. Computer Science, University of Arizona, 2009
M.S. Computer Science, University of Arizona, 2006
B.A. Ecology and Evolutionary Biology, University of Arizona, 1995
Primary focus is developing algorithms to allow the homology search tool HMMER to be applied to DNA search, with specific emphasis on increasing speed without sacrificing accuracy.
While at the U of A, I developed software for multiple sequence alignment (http://opal.cs.arizona.edu) and phylogeny inference (http://nimbletwist.com/software/ninja/).
Ecology and Evolutionary Biology
B.S. Biological Sciences,Humboldt State University, 2007
My research interests are in the areas of plastid evolution and algal genomics. As part of my dissertation, I am using a comparative phylogenomics approach to quantify the genetic contribution of Plantae to the chromalveolate algae and evaluate different hypotheses regarding secondary plastid evolution in these algae. I am also evaluating kleptoplastidy (sequestration of temporary plastids stolen from prey) as a model for understanding the early events in plastid acquisition.