Participating Faculty


Joanna Kelley

Department:School of Biological Sciences
Credentials:2008 - PhD, University of Washington; Genome Sciences
Office:Heald 431A
Mailing Address:School of Biological Sciences
PO Box 644236
Pullman, WA 99164-4236
Web Site:Click here  or Kelley Lab

Research Interests

Adaptation to extreme environments. Population genomics.

Research Summary

My research examines the genomic basis of adaptation and speciation, with the ultimate goal of understanding how organisms diverge and adapt to the wide-range of environments they encounter. Understanding the origins of biodiversity requires fundamental knowledge of the mechanisms leading to phenotypic diversification and the mechanisms underlying the evolution of reproductive isolating barriers. Diversification and reproductive isolation often evolve together and can directly affect each other, such that reproductive isolation often evolves as a by-product of adaptive trait divergence.

Considerable progress has been made in understanding the mechanisms underlying adaptation and speciation in the past decades by integrating ecological and genetic approaches. However, elucidating the genetic basis of adaptation remains difficult, especially when basic genomic resources are lacking and the genomic regions that are the targets of selection are unknown. Recent technological advances permit the rapid and affordable generation of genome-scale data, including whole genome sequencing, measurement of gene expression levels and identification of epigenetic modifications. Coupled with important advances in bioinformatics and computation, these novel approaches offer an unprecedented ability to dissect the genomic basis of population differentiation and adaptation. My work utilizes a range of computational, molecular, and analytical approaches to address questions related to the genomic basis of organismal diversity, including reproductive isolation and barriers to reproduction, both pre- and post-zygotic. My research combines genomics, evolutionary bioinformatics, and computational biology to understand the genetics of adaptation and speciation.

Research Publications

Lins, L.S.F, Trojahn, S., Sockell, A., Yee, M-C, Tatarenkov, A., Bustamante, C.D., Earley, R.L., Kelley, J.L. (2018) Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate Genome. In press. 

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

Cribbin, K., Quackenbush, C.R., Taylor, K., Arias Rodriguez, L. Kelley, J.L. (2017) Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. BMC Genomics. 18(1):283. doi: 10.1186/s12864-017-3652-3.

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. (2016) Mechanisms underlying adaptation to life in hydrogen sulfide rich environments. Molecular Biology and Evolution. doi:10.1093/molbev/msw020

McManus, K.F.*, Kelley, J.L.*, Song, S.*, Veeramah, K., Woerner, A.E., Stevison, L.S., Ryder, O.A., Great Ape Genome Project, Kidd, J.M., Wall, J.D., Bustamante, C.D, Hammer, M.F. (2015). Inference of Gorilla demographic and selective history from whole genome sequence data. Molecular Biology and Evolution. 32 (3): 600-612. doi: 10.1093/molbev/msu394. * contributed equally

Kelley, J.L., Peyton, J.T., Fiston-Lavier, A.-S., Teets N.M., Yee M.C., Johnston, J.S., 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

Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M and 1000 Genomes Project Consortium. (2011) Classic selective sweeps were rare in recent human evolution. Science 331:920-24.

Washington State University