David Haak

Assistant Professor

Program Focus

My research focuses on the integration of the disciplines necessary to dissect the biochemical variation leading to differences in secondary plant compound production and understand how abiotic and biotic factors interact to shape the evolution of these traits in populations. As with other studies of adaptation, my research focuses on identifying the genetic underpinnings, for both simple and complex secondary compound traits (e.g. from single compounds to induced cascades), that differentiate populations. These traits rarely act in isolation and are best studied as an integrated organismal response to selection. For example, the production of secondary defensive compounds in response to wounding has antagonistic effects on photosynthesis. My research program investigates the role of selection in generating genetic variation in secondary compounds including the ecological and environmental factors (and the interplay between) that are the critical selective forces producing this biodiversity.

Current Projects

In tomatoes, I currently have four (1-4) projects aimed at identifying the genetic basis for defense traits in wild tomatoes. The first two (1,2) approaches use DNA-seq methods to identify causal genetic variants underlying polymorphic defense traits. The second set (3,4), are part of an NSF funded proposal I have initiated with collaborators Leonie Moyle and Matt Hahn. These take a comparative and experimental RNA-seq approach to identify the molecular targets of evolution.

  1. Over 40 years ago Charlie Rick identified a presence/absence gradient in a marker (wt/h; fig. 3) associated with type I trichomes (tall trichomes with a small glandular tip) among natural populations of S. pimpinellifolium. I am sequencing pools of individuals (pool-seq) from 4 populations that are fixed (2 each) for wt or h alleles. This approach, which has been successful in identifying clinally varying genes in Drosophila, will identify genomic variations between types (wt/h). By sequencing 2 pools for each morph we can further isolate the causal genetic variant(s) associated with this trait.
  2.  Discrete natural populations of S. pennellii exist that differ in the density of multicellular glandular trichomes and the presence of acylsugars, sticky exudates. To map these traits I have generated a segregating population and am using next-generation sequencing of bulked samples (density-high/low, exudate-presence/absence). This is effectively a bulked segregant analysis (BSA).
  3.  We are using comparative genomics to generate transcriptomes for 32 diverse genotypes representing 25 species to provide a phylogenomic framework for understanding genetic variation in tomatoes and close relatives, and to identify candidate genes associated with ecological transitions. Specifically, we are taking a ‘reverse ecology’ approach to generate a list of functional loci that shift in parallel with molecular evolution. From these data we can evaluate patterns of correlated responses among ecological transitions and identify loci that allow organisms to respond to global climate change factors.
  4.  Using experimental transcriptomics, we are investigating gene expression responses to environmental stressors by looking at two traits,  drought and herbivory, critical to organism-environment interactions. This project will examine expression level differences under benign (unstressed, non-induced) and stressed (drought-stressed, induced) conditions, including the factorial combination of stressors. From these data we will identify common molecular responses to environmental stress, evaluate the magnitude of reciprocal genetic constraints on adaptation, and identify candidate genes underlying the response pathways.


Ph.D., Biology, University of Washington, 2010

M.S., Crop Science, North Carolina State University, 2002

B.S., Biology, North Carolina State University, 1997


  • 2014—present: Assistant Professor of Plant Genomics, Department of Plant Pathology, Physiology, & Weed Science, Virginia Polytechnic Institute and State University

  • 2010-2014:  Postdoctoral Fellow, Department of Biology, Indiana University
  • 2007-2010:  National Science Foundation graduate research fellow,  Department of Biology, University of Washington

Selected Major Awards

  • Kathryn C Hahn writing Fellow (2010)
  • Outstanding Poster Presentation (2008)
  • Howard Hughes Medical Institute Research Fellowship (2005)
  • North Carolina Governors' Outstanding Volunteer Award (2003)

Courses Taught

  • No courses currently listed.

Education Research

As an educator I am driven toward practices which democratize the learning environment, that is instructional methods which offer all students the chance to start from the same page.  Active learning has been demonstrated to be one of those strategies.  Working with collaborators at the University of Washington, we have demonstrated the role of active learning in reducing the achievement gap in Introductory Biology.  Also, we have implemented randomized trials of two different active learning strategies to determine which if either works better.  This led to the discovery that extra work in the form of assigned practice exam problems improves the performance of students at high-risk of failure in Intro Biology.  This improved performance was equal to the performance gains of high-risk students assigned to work as part of a collaborative group.  Contrary to popular belief/anecdote we found that high-performing students performed better as part of a collaborative group.

Natural History

My love of the natural world comes from a life growing up "outside". One of my favorite pastimes is working with very young school groups to foster a connection to the great outdoors. Children's natural inclinations toward science (see a New York Times piece here) makes it easy to pair teaching scientific fundamentals such as the scientific method with hands on investigations in natural history.

In these formal learning experiences I work with elementary school teachers to set up observational (life cycle) and manipulative (feeding trials) experiments.  We have the children work in collaborative teams and record their observations in their laboratory notebook.  For the youngest children (pre-K and K) this often means drawing their observations, at which point I get to tell them about the great natural historians – Humbolt, Darwin, Wallace, Aggasiz – and their dedication to the art of scientific drawing.  The most extraordinary learning comes when the pupae eclose and the butterflies mate and lay eggs.  After the cycle is complete we head outside to release the butterflies.

Haak, D.C., Ballenger, B.A., Moyle, L.C. 2014. No evidence for phylogenetic constraint on natural defense evolution among wild tomatoes. Ecology.

Haak, D.C., Kostyun, J., Moyle, L.C., 2014. Ecological Genomics of adaptation and speciation across a group rich in abiotic, biotic, and reproductive diversity. In: Aubin-Horth, N. and Landry, C. editors. Ecological And Evolutionary Genomics, Springer.

HilleRisLambers, J., Ettinger, A., Ford, K., Haak, D.C., Horwith, M., Miner, B., Rogers, H., Sheldon, K., Tewksbury, J.J., Waters, S., Yang, S. 2013. Accidental experiments: ecological and evolutionary insights and opportunities derived from global change. Oikos

Haak, D.C., McGinnis, L.A., Levey, D.J., and Tewksbury, J.J. 2012. Why aren’t all chilies hot? A tradeoff limits pungency. Proceedings of the Royal Society B: Biological Sciences 279.1735 doi:10.1098/rspb.2011.2091.

Haak, D. C., J. HilleRisLambers, E. Pitre, and S. Freeman. 2011. Increased Structure and Active Learning Reduce the Achievement Gap in Introductory Biology. Science 332:1213.

Freeman, S., Haak, D.C., and Wenderoth, M.P. 2011. Increased Course Structure Improves Performance in Introductory Biology. CBE Life Sci Educ 10:175‐186.

Deutsch,C., J. J. Tewksbury R. B. Huey, K. Sheldon, C. Ghalambor, D.C. Haak, P. R. Martin. 2008. Impacts of climate warming on terrestrial ectotherms across latitude. PNAS 105(18):6668‐72.

Tewksbury, J.J., Reagan, K.M, Caldaron, A.,Machnicki, N., Haak D.C., Levey, D.J. 2008. Evolutionary ecology of pungency in wild chilies. PNAS 105(33):11808‐11.

Tewksbury, J.J., Levey, D.J., Huizinga, M., Haak D.C., and Travaset, A. 2008. Costs and benefits of capsaicin‐mediated control of gut retention in dispersers of wild chilies. Ecology 89(1):107‐17.

Freeman, S, O'Connor, E, Parks, J.W., Cunningham, M., Hurley, D., Haak D.C., Dirks, C., Wenderoth, M.P. 2007. Prescribed Active Learning Increases Performance In Introductory Biology. CBE Life Sci Educ 6: 132‐139.

Levey, D.J., Izhaki, I., Tewksbury J.J.,Tsahar, E., and Haak D.C. 2007. The primary importance of secondary compounds in fruits: case studies with capsaicin and emodin In: A. Dennis, R. Green, E. Schupp and D.Westcott, editors. Seed dispersal: Theory and its application in a changing world Wallingford, Oxfordshire, UK: CABI international.

Tewksbury, J.J., Manchego, C., Haak D.C., Levey, D.J. 2006. Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species. Journal of Chemical Ecology 32(3):547‐564.

David Haak
  • (540) 231-1186
  • dhaak@vt.edu
  • 211 Latham Hall
    Mail code: 0390
    220 Ag Quad Lane
    Blacksburg, VA 24061