John Colbourne
jcolbour@bio.indiana.edu
Indiana
University
Center for Genomics and Bioinformatics
915 East Third Street
Bloomington, IN 47405-7107 USA
Advisors:
Dr.
Michael Lynch, Ecology,
Evolution, & Behavior, IU
Dr. Justen
Andrews,
Genomics & Bioinformatics,
IU
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Research Interests
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My research interests include: Systematics and evolution of Daphnia; Rates of both local adaptation and molecular evolution; Functional genomics of sex determination in Drosophila and Daphnia; Phenotypic evolution with respect to genomic change
Current projects include:
* The systematics of Daphnia and Daphniopsis (Crustacea: Cladocera) *
With Chris Wislon (Trent University) and Paul Hebert (University of Guelph), this study aims to resolve the systematic relationships among species of Daphnia and Daphniopsis by including taxa from both Australia and North America. Our conclusions on the taxonomic status of ancestral daphniid lineages are based upon the relative placement of their component species onto phylogenetic trees derived from sequence diversity in three mitochondrial genes: 12S rDNA, 16S rDNA and cytochrome oxidase 1 (CO1)
* A preliminary characterization of Daphnia's Genome *
Three genomic resources have been developed to characterize one of the smallest crustacean genomes and for future applications in ecological studies. First, with Teresa Crease (University of Guelph) we are building a gene encyclopedia for Daphnia by sequencing a cDNA library. Our initial survey identified genes involved in cell structure and adhesion, cell signaling, disease resistance, metabolism, and transcription. These preliminary data show that sequencing additional cDNA from the current library will likely generate important candidate genes that respond to environmental stress. We aim to sequence between 7,500-10,000 unique genes (up to two-thirds of the full genome), which will be printed onto DNA microarray slides for analyzing gene expression patterns associated with known phases of environmental change. Second, from separate genomic libraries, we isolated over 800 DNA fragments containing hypervariable microsatellite loci. With Barrie Robison, two-hundred of these markers are currently being used to generate a genetic map, so to localize genes with significant phenotypic responses to environmental change. Third, with Justin Hicks (University of Washington) an arrayed library of approximately 40,000 cosmids has been developed, allowing for the efficient characterization of gene structure, including non-coding regulatory regions. This work is conducted in The Center for Genomics and Bioinformatics [http://cgb.indiana.edu].
* The identification of sex-genes in Drosophila and Daphnia *
With Justen Andrews, two approaches are used to find key regulatory genes involved in the sex-determination of Drosophila germ-line cells. First, bioinformatic tools are used to discover regulatory motifs upstream of genes, indicating possible targets of a key sex-determination gene called OVO. Second, full transcriptome microarrays are used to probe for genes differentially regulated in mutant drosophiliids with deletions of genes with known sexual functions.
Candidate genes that are known participants in the development of sexual traits within other model organisms are being isolated from Daphnia by designing degenerate primers, which are then applied to the cosmid library. A number of sequences homologous to DMRT - a key transcription factor for somatic sex-determination in humans, flies and nematodes - are currently being analyzed. Daphnia microarrays derived from cDNA sequences will also be produced, which will then be used for probing genes differentially regulated in male versus non-male producing clones.
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Publications
- Colbourne, J.K., B.D. Neff, J.M. Wright and M.R. Gross. 1996. DNA fingerprinting of bluegill sunfish (Lepomis macrochirus) using (GT)n microsatellites and its potential for assessment of mating success. Canadian Journal of Fisheries and Aquatic Sciences 53:342-349.
- Colbourne, J.K. and P.D.N. Hebert. 1996. The systematics of North American Daphnia (Crustacea: Anomopoda): a molecular phylogenetic approach. Philosophical Transactions of the Royal Society of London B 351:349-360.
- Taylor, D.J., P.D.N. Hebert and J.K. Colbourne. 1996. Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation. Molecular Phylogenetics and Evolution 5:495-510.
- Colbourne, J.K., P.D.N. Hebert and D.J. Taylor. 1997. Evolutionary origins of phenotypic diversity in Daphnia. In: Molecular Evolution and Adaptive Radiation. eds. T.J. Givnish and K.J. Sytsma. Cambridge University Press. pp. 163-188.
- Weider, L.J., W. Lampert, M. Wessels, J.K. Colbourne and P. Limburg. 1997. Long-term genetic shifts in microcrustacean egg bank associated with anthropogenic changes in Lake Constance ecosystem. Proceedings of the Royal Society of London B 264:1613-1618.
- Colbourne, J.K., T.J. Crease, L.J. Weider, P.D.N. Hebert, A. Hobaek and F. Dufresne. 1998. Phylogenetics and evolution of a circumarctic species complex (Cladocera: Daphnia pulex). Biological Journal of the Linnean Society 65:347-365.
- Crease, T.J. and J.K. Colbourne. 1998. The unusually long small subunit ribosomal RNA gene of the crustacean, Daphnia pulex: sequence and predicted secondary structure. Journal of Molecular Evolution 46:307-313.
- Boerlin, P., S. Chen, J.K. Colbourne, R. Johnson, S. DeGrandis and C. Gyles. 1998. Evolution of enterohemorrhagic Escherichia coli hemolysin plasmids and the locus for enterocyte effacement in Shiga toxin-producing E. coli. Infection and Immunity 66:2553-2561.
- Colbourne, J.K. 1999. A documentary on the evolutionary history of Daphnia. Ph.D. thesis. University of Guelph, Canada.
- Weider, L.J., A. Hobaek, J.K. Colbourne, T.J. Crease, F. Dufresne and P.D.N. Hebert. 1999. Holarctic phylogeography of an asexual species complex: mitochondrial DNA variation in arctic Daphnia. Evolution 53:777-792.
- Lynch, M., M. Pfrender, K. Spitze, N. Lehman, D. Allen, J. Hicks, L. Latta, M. Ottene, F. Bogues and J. Colbourne. 1999. The quantitative and molecular genetic architecture of a subdivided species: Daphnia pulex. Evolution 53:100-110.
- Havel, J.E., J.K. Colbourne and P.D.N. Hebert. 2001. Reconstructing the history of intercontinental dispersal in Daphnia lumholtzi by use of genetic markers. Limnology and Oceanography 45: 1414-1419.
- Cousyn, C., L. De Meester, J.K. Colbourne, L. Brendonck, D. Verschuren and F. Volckaert. 2001. Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes. Proceedings of the National Academy of Sciences 98:6256-6260.
- Hebert, P.D.N., E.A. Remigio, J.K. Colbourne, D.J. Taylor and C.C. Wilson. 2002. Accelerated molecular evolution in halophilic crustaceans. Evolution 556: 909-926.
- Pallard, H.G., J.K. Colbourne, B. Keller. 2003. Reconstruction of centuries old Daphnia communities in a lake recovering from acidification and metal-contamination. Ambio 32:214-218.
- Colbourne, J.K., C.C. Wilson and P.D.N. Hebert. 2003. The systematics of Australian Daphnia and Daphniopsis (Crustacea: Cladocera): a shared phylogenetic history obscured by habitat specific rates of evolution. In preparation.