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Omar Cornejo

Omar E Cornejo

Field of Study: Population and Evolutionary Genomics
Title: Associate Professor
Degrees: PhD. Biological and Biomedical, Emory University
Homepage: Homepage/Lab Web Site Link
Google Scholar:  Google Scholar
Office: 429B Heald Hall
Phone: 509-335-0179
Fax: nan
Mailing Address: School of Biological Sciences
Washington State University
PO Box 644236
Pullman,WA 99164-4236


Our ability to understand how hosts and microbes have adapted to each other requires understanding how evolutionary processes have shaped their genomes. My career is dedicated to answering fundamental questions on the evolution of microbes and humans from a population genetics and functional genomics perspective. A major area of research in my lab is the inference of the evolutionary context in which natural selection has favored the gain and loss of genetic variants responsible for the adaptation of microbes to their hosts and the evolution of disease resistance in hosts.

We investigate these questions in different systems: humans, microbiomes, malarial parasites, and plants. Some of the questions we address in our research are:

How historical changes in host populations have impacted the evolution of microbes and other species of importance?

How important is homologous recombination for the evolution of traits involved in host shifts or adaptation to new environments in microbes and hosts?

How do differences in microbiome composition modulate phenotypes in hosts?

How has the demographics impacts the accumulation of deleterious mutations, impacting the fitness of individuals?

Representative Publications:

  • Schwarzkopf, E.J. and Cornejo, O.E. (2021) PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene.
  • Nelson, J.T., Motamayor, J.C. and Cornejo, O.E. (2020) Environment and pathogens shape local and regional adaptations to global change in the chocolate tree, Theobroma cacao L. Molecular Ecology 30(3): 656-669.
  • Osorio J, Quackenbush CR, Cornejo O.E. (2018) Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLOS One 13(10): e0203973.
  • Cornejo OE, Yee M-C, Mockaitis K, Adams A, Strandberg R, Livingston D, Stack C, Umaharan P, Royaert S, Tawari NR, Ng P, Schnell R, Phillips W, Bustamante CD, Motamayor JC. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into the domestication process. Communications Biology 1. Article number: 167(2018)
  • Xia, C., Wang, M., Cornejo, O.E., Jiwan, D.A., See, D.R., Chen, X. (2017). Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Frontiers in Microbiology 2017;00-12. doi: 10.3389/fmicb.2017.02394.
  • Livingstone III, D., Stack, C., Mustiga, G., Rodezno, D., Suarez, C., Amores, F., Feltus, A., Mockaitis, K., Cornejo, O.E., Motamayor, JC. (2017). A large chocolate chip – development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps. Frontiers in Plant Science 8:2008.
  • Cornejo OE*, Hickey RJ, Suzuki H, Forney LJ*. (2017). Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes. Evolutionary Applications 2017;00:1–13.
  • McManus KF, Tavarella A, Henn B, Bustamante CD, Sikora M*, Cornejo OE*. (2017) Population genetic analysis of the DARC locus (Duffy) reveals complex evolutionary history of a malaria resistance locus. PLOS Genetics 13(3): e1006560. doi:10.1371/journal.pgen.1006560. (Highlighted in Science, Mar 2017: Dramatic evolution within human genome may have been caused by malaria parasite)
  • Cornejo OE, Fisher D, Escalante AA. (2015) Genome-wide patterns of genetic polymorphism and signatures of selection in Plasmodium vivax. Genome Biology and Evolution. 7(1): 106-119. (Highlighted in Nature Reviews Microbiology in the News and Analysis – Genome Watch section, March 2015)
  • Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T Jr, Grimes V, Renouf MA, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TV, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O’Rourke DH, Jakobsson M, Gilbert MT, Nielsen R, Willerslev E. (2014) The genetic prehistory of the New World Arctic. Science. 345 (6200) DOI: 10.1126/science.1255832
  • Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506 (7487): 225 – 229 doi:10.1038/nature13025
  • Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. (2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution. 30(4): 881-893. [Highlighted in Science: “How Sweet it is: genes show how bacteria colonized human teeth” by Ann Gibbons]