University of Vermont

The College of Arts and Sciences

Department of Biology

Faculty - Melissa Pespeni


Melissa Pespeni, Assistant Professor

  • Ph.D., Stanford University, 2010
  • Stanford University 2010-2011, Postdoctoral Fellow
  • Indiana University, 2011-2014, National Science Foundation Postdoctoral Fellow
  • University of Vermont 2014-present, Assistant Professor
  • CV (PDF)
Area of expertise

Ecological genomics, population genetics, evolutionary biology, physiology

Contact Information
Email: Melissa Pespeni

Office Hours: Tue & Wed 2:00-3:00
Marsh Life Science Building, Rm 326A
Phone: (802) 656-0628

Pespeni Lab WEBSITE


The Pespeni Lab studies the processes that generate and impact the incredible biodiversity that exists on this planet, particularly in the contexts of complex natural ecosystems and rapidly changing climatic conditions. To discover connections between variation in genes and phenotypes in the context of the environment, we integrate approaches in genomics, population genetics, developmental genetics, physiology, and ecology using natural populations in both field- and lab-based investigations. Conceptually, our research addresses integrative questions in evolutionary biology, ecological genomics, and global change biology.

Our models systems to explore these mechanistic questions are sea urchins, copepods, and horned beetles. Sea urchins allow the investigation of fundamental physiological phenotypes that are particularly important in the context of climate change; copepods are fundamental to the function of ocean ecosystems and are easy to maintain in the lab across many generations; and horned beetles, the most speciose animal group on the planet, exhibit novel and elaborate morphological phenotypes amenable to developmental and gene function analyses.

Currently, our research focuses on two major lines of investigation: (1) Can populations/species adapt to rapidly changing climate conditions? Does this capacity to adapt depend upon the history of environmental variability or stability experienced by a species? And (2) What are the genetic and developmental bases for trait diversification? Do the same genes and pathways underlie trait differentiation among populations and divergence between species?


  • Lloyd, M.M., Makukhov, A.D., & Pespeni, M.H. 2016. Loss of genetic diversity as a consequence of selection in response to high pCO2. Evolutionary Applications, DOI: 10.1111/eva.12404/
  • De Wit, P., Pespeni, M.H., & Palumbi, S. R. (2015) SNP genotyping and population genomics from expressed sequences–current advances and future possibilities. Molecular ecology, 24(10), 2310-2323.
  • Evans, T. G., J. L. Padilla-Gamiño, M. W. Kelly, Pespeni, M.H., F. Chan, B. A. Menge, B. Gaylord, T. M. Hill, A. D. Russell, S. R. Palumbi, E. Sanford, G. E. Hofmann. (2015) Ocean acidification research in the ‘post-genomic’ era: roadmaps from the purple sea urchin Strongylocentrotus purpuratus. Comparative Biochemistry and Physiology, Part B., 185:33-42.
  • Kijimoto, T., E.C. Snell-Rood, Pespeni, M.H., G. Rocha, K. Kafadar, A.P. Moczek. (2014) The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus Taurus and the importance of sexual dimorphism and body region. Proceedings of the Royal Society, B., 281:1797, 2014-2084.
  • Pespeni, M. H., F. Chan, B. A. Menge, S. R. Palumbi. 2013. Signs of adaptation to local pH conditions across an environmental mosaic in the California Current Ecosystem. Integrative and Comparative Biology, 53:5, 857-870.
  • Pespeni, M. H., E. Sanford, B. Gaylord, T. M. Hill, J. D. Hosfelt, H. Jaris, M. LaVigne, E. Lenz, A. D. Russell, M. K. Young, and S. R. Palumbi. 2013. Evolutionary change during experimental ocean acidification. Proceedings of the National Academy of Sciences, 110:17, 6937-6942. [Press coverage by Nature, Scientific American, New Scientist, Mother Jones, Science News for Kids, and more.]
  • Pespeni, M. H. and S. R. Palumbi. 2013. Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic. Molecular Ecology, 22:13, 3580-3597.
  • Pespeni, M. H., B. Barney and S. R. Palumbi. 2013. Differences in the regulation of growth and biomineralization genes revealed through long-term common-garden acclimation and experimental genomics in the purple sea urchin. Evolution, 67:7, 1901-1914.
  • Kijimoto, T.,* M. H. Pespeni,* O. Beckers,* and A. P. Moczek. 2012. Beetle horns and horned beetles: emerging models in developmental evolution and ecology. WIREs Developmental Biology, 2:3, 405-418. * These authors equally contributed to the work summarized in the manuscript.
  • De Wit, P.,* M. H. Pespeni,* J. T. Ladner, D. J. Barshis, F. Seneca, H. Jaris, N. Overgaard Therkildsen, M. Morikawa, and S. R. Palumbi. 2012. The Simple Fool’s Guide to population genomics: Gene expression and SNP data analysis in the age of high-throughput sequencing. Molecular Ecology Resources, 12, 1058-1067. * These authors equally contributed to the work summarized in the manuscript.
  • Pespeni, M. H., D. A. Garfield, M. K. Manier, and S. R. Palumbi. 2012. Genome-wide polymorphisms show unexpected targets of natural selection. Proceedings of the Royal Society, B., 279:1732, 1412-1420.
  • Pespeni, M. H., T. A. Oliver, M. K. Manier, and S. R. Palumbi. 2010. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays. Genome Biology, 11:R44. [highly accessed]
  • Woodson, C. B., D. I. Eerkes-Medrano, A. Flores-Morales, M.M. Foley, S.K. Henkel, M. Hessing-Lewis, D. Jacinto, L. Needles, M.T. Nishizaki, J. O’Leary, C.E. Ostrander, M. Pespeni, K.B. Schwager, J.A. Tyburczy, K.A. Weersing, A.R. Kirincich, J.A. Barth, M.A. McManus, L. Washburn. 2007. Local diurnal upwelling driven by sea breezes in northern Monterey Bay. Continental Shelf Research, 27:18, 2289-2302.
  • Pespeni, M., M. Hodnett, K. S. Abayasiriwardana, J. Roux, M. Howard, V. C. Broaddus and J.F. Pittet. 2007. Sensitization of mesothelioma cells to tumor necrosis factor–related apoptosis–inducing ligand–induced apoptosis by heat stress via the inhibition of the 3-phosphoinositide-dependent kinase 1/Akt pathway. Cancer Research, 67, 2865-71.
  • Pespeni, M., R.C. Mackersie, H. Lee, D. Morabito, M. Hodnett, M. Howard, and J.F. Pittet. 2005. Serum levels of Hsp60 measured early after injury correlate with the development of acute lung injury following severe trauma. Journal of Surgical Research, 126, 41-7.
  • Pespeni, M., M. Hodnett, and J.F. Pittet. 2005. In vivo stress preconditioning. Methods, 35, 158-64.