K-State Division of Biology



Mark C. Ungerer

Associate Professor

Ph.D. 2000, Indiana University.  Ecology and Evolutionary Biology.

Evolutionary and ecological genetics in plants; genome structure and evolution.


426 Ackert Hall
(785) 532-5845

Mark Ungerer Laboratory
Molecular Cellular Developmental Biology Web

Research Focus

Our research is broadly focused on understanding the underlying genetic basis of adaptive natural variation and evolutionary change in plants. Most of our work is conducted on species for which there are considerable and/or growing genetic and genomic resources available. Two current projects are described below:

Clinal variation in freezing tolerance in Arabidopsis thaliana.
Populations of the model plant species Arabidopsis thaliana are found over a broad geographic and latitudinal range. We have documented considerable variation in freezing tolerance among natural populations that follows a latitudinal gradient, with populations from northern latitudes expectedly more tolerant of low temperature than population from southern latitudes. This finding suggests a major role for natural selection in shaping this variation. We are currently investigating the underlying genetic and physiological basis of these natural differences by examining functional variation in important freezing tolerance candidate genes. We are additionally examining variation in global metabolite and lipid profiles, as previous work has indicated an important role of various metabolites/lipids in conveying increased freezing tolerance. These latter experiments are utilizing the Kansas Lipidomics Research Center at KSU.

Hybrid speciation, transposable elements and genome evolution in wild sunflowers.
The class I transposable elements known as long terminal repeat (LTR) retrotransposons are ubiquitous in plants and represent a significant genomic fraction in plant species with large genomes. The vast majority of LTR retrotransposons remain transcriptionally and transpositionally quiescent during normal growth and development. These periods of inactivity, however, can be interrupted by episodic bursts of transpositional activation during which massive genomic expansion and restructuring can occur. The conditions under which such events take place naturally and the consequences of such events on host species evolution are poorly understood.

We are investigating the probable causes and evolutionary consequences of massive LTR retrotransposon proliferations that have taken place independently in three diploid hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus. The evolutionary history of these hybrid taxa has been well characterized: each of the hybrid species is independently derived via hybridization between the same two parental taxa (H. annuus and H. petiolaris), and each hybrid species is adapted to an abiotically extreme environment. The evolutionary history of the hybrid sunflower species is extremely relevant because both hybridization and environmental stress have been implicated as natural agents influencing retrotransposon activation. The origin of these taxa via hybrid speciation and the ecological transitions of these hybrid species to abiotically extreme environments raise a very intriguing question: what role has LTR retrotransposon proliferation played in these evolutionary events? Have these proliferations in some way facilitated the evolutionary events that have taken place in this group? Or have these evolutionary events occurred independently of, and in fact notwithstanding the massive transposable element bombardments that have taken place in each hybrid species' genome? Support for either alternative would deeply impact our understanding of the role of transposable elements in organismic evolution.

Selected Research Publications

Ungerer, M.C., and T. Kawakami. 2013. Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. Genome Biol. Evol. 5: 329-337. 

Ungerer M.C., C.A. Weitekamp, A. Joern, E.G. Towne, J.M. Briggs.  2013. Genetic variation and mating success in managed American plains bison. Journal of Heredity 104: 182-191. 

Staton S.E., B. Hartman-Bakken, B.K. Blackman, M.A. Chapman, N.C. Kane, S. Tang, M.C. Ungerer, S.J. Knapp, L.H. Rieseberg, J.M. Burke. 2012. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant Journal 72: 142-153.

Kawakami, T., P. Dhakal, A.N. Katterhenry, C.A. Heatherington, M.C. Ungerer. 2011. Transposable element proliferation and genome expansion are rare in contemporary sunflower hybrid populations despite widespread transcriptional activity of LTR retrotransposons. Genome Biol. Evol. 3: 156-167.

Kawakami, T., T.J. Morgan, J.B. Nippert, T.W. Ocheltree, R. Keith, P. Dhakal, and M.C. Ungerer. 2011. Natural selection drives clinal life history patterns in the perennial sunflower species, Helianthus maximiliani. Molecular Ecology 20: 2318-2328.

Zhen, Y., P. Dhakal, and M.C. Ungerer. 2011. Fitness benefits and costs of cold acclimation in Arabidopsis thaliana. American Naturalist 178: 44-52.

Bryant, B., M.C. Ungerer, Q. Liu, R.M. Waterhouse, and R.J. Clem. 2010. A caspace-like decoy molecule enhances the activity of a paralogous caspace in the yellow fever mosquito, Aedes aegyptiInsect Biochemistry and Molecular Biology 40: 516-523.

Kawakami, T., S.C. Strakosh, Y. Zhen, and M.C. Ungerer. 2010. Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower speciesHeredity 104:  341-350.

Molecular Ecology Resources Primer Development Consortium, Aurelle, D., Baker, A.J., Bottin, L., Brouat, C., Caccone, A. et al. 2010. Permanent genetic resources added to the Molecular Ecology Resources Database 1 February 2010 - 31 March 2010.Molecular Ecology Resources 10(4): 751-754.

Staton, S.E., M.C. Ungerer, and R.C. Moore.  2009. The genomic organization of Ty3/gypsy retrotransposons in Helianthus homoploid hybrid species. American Journal of Botany 96: 1646-1655.

Ungerer, M.C., S.C. Strakosh, and K.M. Stimpson. 2009. Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower species inferred from phylogenetic analyses. BMC Biology 7: 40.

Miller, S.R., A.L. Strong, K.L.Jones, and M.C. Ungerer. 2009. Barcoded pyrosequencing reveals shared bacterial community properties along two alkaline hot spring temperature gradients in Yellowstone National Park. Applied and Environmental Microbiology 75(13): 4565-4572.

Olsen, K.M. and M.C. Ungerer.  2008. Freezing tolerance and cyanogenesis in white clover (Trifolium repens L. Fabaceae). International Journal of Plant Sciences 169: 1141–1147.

Zhen, Y. and M.C. Ungerer. 2008. Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing  tolerance in the southern range of Arabidopsis thaliana. Molecular Biology & Evolution 25: 2547-2555.  

Ungerer, M.C., L.C. Johnson, and M.A. Herman. 2008. Ecological genomics: understanding gene and genome function in the natural environment. Heredity 100: 178-183.

Felhberg, S.D., K.A. Ford, M.C. Ungerer, and C.J. Ferguson . 2008. Development, transferability, and application of microsatellite markers in Phlox (Polemoniaceae). Molecular Ecology Resources 8: 116-118. 

Zhen, Y. and Ungerer, M.C. 2008. Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytologist 177:419-427.

Hall M.C., I. Dworkin, M.C. Ungerer, and M. Purugganan. 2007. Genetics of micro-environmental canalization in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA  104(31): 13717-13722

Ungerer, M.C., S. Strakosh, and Y. Zhen.  2006.  Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Current Biology 16(20): r872­–r873.

Ungerer, M.C. 2005.  Priming for genetics in ecology. BioScience 55(3): 283–285. 

Ungerer, M.C. and L.H. Rieseberg.  2005.  Speciation: genetics. Encyclopedia of Life Sciences, John Wiley & Sons, Ltd.

Callahan, H.S., N. Dhanoolal, and M.C. Ungerer. 2005. Plasticity genes and plasticity costs: a new approach using an Arabidopsis recombinant inbred population. New Phytologist 166: 129–140.

Stinchcombe, J.R., C. Weinig, M.C. Ungerer, K.M. Olsen, C. Mays, S.S. Halldorsdottir, M.D. Purugganan, and A. Schmitt.  2004.  A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. Proc. Natl. Acad. Sci. USA  101(13): 4712–4717.  

Ungerer,M.C. and L.H. Rieseberg.  2003.  Genetic architecture of a selection response in Arabidopsis thaliana. Evolution 57: 2531–2539.

Ungerer,M.C., S.S. Halldorsdottir, M.D. Purugganan, and T.F.C. Mackay.  2003.  Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana. Genetics 165: 353–365.

Weinig C., L.A. Dorn, N.C. Kane, M.C. Ungerer, S.S. Halldorsdottir, Z.M. German, Y. Toyonaga, T.F.C. Mackay, M.D. Purugganan, and  J. Schmitt.  2003.  Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics 165: 321–329.

Ungerer, M.C., C.R. Linder, and L.H. Rieseberg.  2003.  Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana. Genetics 163: 277–286.

Weinig, C., M.C. Ungerer, L.A. Dorn, N.C. Kane, S.S. Halldorsdottir, Y. Toyonaga, T.F.C. Mackay, M.D. Purugganan, and J. Schmitt.  2002.  Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments. Genetics 162: 1875­–1884.  

Ungerer, M.C., S.S. Halldorsdottir, J.L. Modliszewski, T.F.C. Mackay, and M.D. Purugganan.  2002.  Quantitative trait loci for inflorescence development in Arabidopsis thaliana. Genetics 160: 1133–1151.

Remington, D.L., M.C. Ungerer, and M.D. Purugganan.  2001.  Map-based cloning of quantitative trait loci: progress and prospects. Genetical Research 78: 213–218.

  Ungerer, M.C.,  S.J.E. Baird, J. Pan, and L.H. Rieseberg.  1998.  Rapid hybrid speciation in wild sunflowers.  Proc. Natl. Acad. Sci. USA  95(20): 11757–11762.  

Gastony, G.J. and M.C. Ungerer.  1997.  Molecular systematics and a revised taxonomy of the onocleoid ferns (Dryopteridaceae:  Onocleeae).  Amer. J. Bot.  84: 840–849.    

Whitton, J., L.H. Rieseberg, and M.C. Ungerer.  1997.  Microsatellite loci are not conserved across the Asteraceae.  Mol. Biol. Evol. 14: 204–209..

Riesberg, L.H., B. Sinervo, C.R. Linder, M.C. Ungerer, and D. Arias.  1996.  Role of gene interactions in hybrid speciation: Evidence from ancient and experimental hybrids.  Science 272: 741–745.

Rieseberg, L.H., D. Arias, M.C. Ungerer, C.R. Linder, and B. Sinervo.  1996.  The effects of mating design on introgression between chromosomally divergent sunflower species. Theor. Appl. Genet. 93: 633–644..



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