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Joanna Kelley

Joanna Kelley

Field of Study: Evolutionary Genomics
Title: Associate Professor
Degrees: Ph.D., Genome Sciences, University of Washington; B.A., Mathematics and Biology, Brown University
Homepage: Homepage/Lab Web Site Link
Google Scholar:  Google Scholar
Office: 431B Heald Hall
Phone: 509-335-0037
Fax: nan
Mailing Address: School of Biological Sciences
Washington State University
PO Box 644236
Pullman,WA 99164-4236


The Kelley Lab is located at Washington State University, in Pullman, WA. Our research focuses on evolutionary genomics and adaptation to extreme environments. We are interested in understanding how populations diverge and adapt to the environments they encounter. To identify and characterize specific genes and pathways that underlie adaptive change, we combine statistical and genomic approaches with knowledge from organismal and ecological studies. Our work utilizes a range of technological and analytical methods for genomics. We also climb Mexican volcanoes and explore Caribbean Islands for exotic species that are specially adapted to their extreme environments. By correlating genetic changes to phenotypic outcomes using population genomics, we hope to link genomic changes to sources of selection.

Representative Publications:

  • Kelley J.L., Desvignes T., McGowan K.L., Perez M., Rodriguez L.A., Brown A.P., Culumber Z., Tobler M. (2020) microRNA expression variation in a natural system as a potential molecular mechanism contributing to adaptation to hydrogen sulfide. Journal of Evolutionary Biology. DOI: 10.1111/jeb.13727
  • Greenway R., Barts N., Henpita C., Brown A.P., Arias Rodriguez L., Rodríguez Peña C.M., Arndt S., Lau G.Y., Murphy M.P., Wu L., Lin D., Shaw J.H., Kelley J.L., Tobler M. (2020) Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. Proceedings of the National Academy of Sciences 117 (28), 16424-16430. DOI: 10.1073/pnas.2004223117
  • Hotaling S., Shah A.A., McGowan K.L., Tronstad L.M., Giersch J.J., Finn D.S., Woods H.A., Dillon M.E., Kelley J.L. (2020) Mountain stoneflies may tolerate warming streams: evidence from organismal physiology and gene expression. Global Change Biology. 26, 5524-5538. DOI: 10.1111/gcb.15294
  • Kelley J.L., Gilad Y. (2020) Effective study design for comparative functional genomics. Nature Reviews Genetics. 21, 385-386. DOI: 10.1038/s41576-020-0242-z
  • McGowan, K.L., Passow, C.N., Arias-Rodriguez, L., Tobler, M. Kelley, J.L. Expression analyses of cave mollies (Poecilia mexicana) reveal key genes involved in the early evolution of eye regression. Biol Lett. 15(10):1-7.
  • Jansen, H.T., Trojahn, S., Saxton, M.*, Quackenbush, C.R., Evans Hutzenbiler, B.D. Nelson, O.L., Cornejo, O.E., Robbins, C.T., Kelley, J.L.† (2019) Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. Communications Biology. 2:336.
  • Brown, A.P., McGowan, K.L., Schwarzkopf, E.J., Greenway, R., Arias-Rodriguez, L., Tobler, M., Kelley, J.L. (2019) Local ancestry analysis reveals genomic convergence in extremophile fishes. Philosophical Transactions of the Royal Society B.
  • Hotaling, S., Quackenbush, C.R., Bennett Ponsford, J., New, D.D., Tobler, M., Kelley, J.L. (2019) Bacterial diversity in replicated hydrogen sulfide-rich springs. Microbial Ecology. 77: 559–573.
  • Brown, A.P., Arias-Rodriguez, L., Yee, M.C, Tobler, M., Kelley, J.L. (2018) Concordant changes in gene expression and nucleotides underlie independent adaptation to extremely sulfidic environments. Genome Biology and Evolution. doi: 10.1093/gbe/evy198
  • Hotaling, S., Quackenbush, C.R., Bennett Ponsford, J., New, D.D., Tobler, M., Kelley, J.L. (2018) Bacterial diversity in replicated hydrogen sulfide-rich springs. Microbial Ecology.
  • Tobler, M., Kelley, J.L., Plath, M., Riesch, R. (2018) Extreme environments and the origins of biodiversity: adaptation and speciation in sulfide spring fishes. Molecular Ecology. 27:843–859.
  • Brown, A.P., Greenway, R., Morgan, S., Quackenbush, C.R., Giordani, L., Arias Rodriguez, L., Tobler, M., Kelley, J.L. (2017) Genome-scale data reveals that endemic Poecilia populations from small sulfidic springs display no evidence of inbreeding. Molecular Ecology. doi: 10.1111/mec.14249.
  • Lowry, D.B., Hoban, S., Kelley, J.L., Lotterhos, K.E., Reed, L.K., Antolin, M.F, Storfer, A. (2016) Breaking RAD: An Evaluation of The Utility Of Restriction Site Associated DNA Sequencing For Genome Scans Of Adaptation. Molecular Ecology Resources. doi: 10.1111/1755-0998.12596
  • Hoban, S.*, Kelley, J.L.*†, Lotterhos, K.E.*, Antolin, M.F., Bradburd, G., Lowry, D.B., Poss, M.L., Reed, L.K., Storfer, A., Whitlock, M.C. (2016) Finding the genetic basis of local adaptation in non-model organisms: pitfalls, practical solutions and future directions. American Naturalist. doi: 10.1086/688018. *Contributed equally. †Corresponding author.
  • Kelley, J.L., Brown, A.P., Overgaard Therkildsen, N., Foote, A. (2016) The life aquatic: advances in marine vertebrate genomics. Nature Reviews Genetics. 17: 523–534 doi:10.1038/nrg.2016.66
  • Kelley, J.L., Yee, M.C., Brown, A.P., Richardson, R., Taternkov, A., Lee, C., Harkins, T., Bustamante, C.D., Earley, R.L. (2016) The genome of the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus: a model for studying phenotypic plasticity and adaptations to extreme environments. Genome Biology and Evolution. 8 (7): 2145-2154. doi: 10.1093/gbe/evw145
  • Kelley, J.L., Passow, C.N., Arias Rodriguez, L., Patacsil Martin, D., Yee, M.C., Bustamante, C.D., Tobler, M. (2106) Mechanisms underlying adaptation to life in hydrogen sulfide rich environments. Molecular Biology and Evolution. doi:10.1093/molbev/msw020.
  • Kelley, J.L., Peyton, J.T.*, Fiston-Lavier, A.-S.*, Teets N.M., Yee M.C., Bustamante, C.D., Lee, R.E. and D.L. Denlinger. (2014) Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications. 5:4611. doi:10.1038/ncomms5611. * contributed equally