Profile
James Lewis
Genetics and Biochemistry
Assistant Professor
864-656-1507
AG Biotech/Biosystems Research Complex / BRC GH210 [Greenhouse]
AG Biotech/Biosystems Research Complex / BRC 316 [Office]
AG Biotech/Biosystems Research Complex / BRC 317 [Lab]
Educational Background
M.A., Philosophy, Virginia Tech, 2010
Ph.D., Evolutionary Biology, Cornell University, 2017
Research Interests
My research aims to discover the molecular mechanisms that facilitate evolution of the genotype-to-phenotype map and to connect these mechanisms to the evolutionary processes that drive adaptation. Our research strategy leverages large-scale functional and population genomic datasets, computational genomics, and CRISPR to map the genetic basis of complex traits and characterize the adaptive process. The long-term goal of our research program is to integrate functional genomic data with population and quantitative genetic models to understand the molecular mechanisms and evolutionary processes through which complex and mendelian traits evolve and differentiate among and between populations. We use several lepidopteran species groups as models for investigating the adaptive process, with a heavy focus on wing pattern mimicry.
Courses Taught
GEN 4100/4100H/6100 Population and Quantitative Genetics - Classical and computational genetics topics, including Mendelian vs. non-Mendelian inheritance, genetic variation, neutral evolution, coalescent theory, molecular evolution, quantitative trait models, phenotypic response to selection, population genetic models of selection, and the impact of linked selection on genomes.
GEN 4930 Senior Seminar - Senior undergraduate students learn to read and critically evaluate scientific literature, prepare and present a scientific presentation, and engage in scientific discussion and critique.
Selected Publications
Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ, Ma Y, Wang Z, Rando OJ, Hadjantonakis A, Danko CG. RNA polymerase II dynamics shape enhancer–promoter interactions. Nature Genetics. 55: 1370–1380 (2023).
Van Belleghem SM, Ruggieri AA, Concha C, Livraghi L, Hebberecht L, Rivera ES, Ogilvie JG, Hanly JJ, Warren IA, Planas S, Ortiz-Ruiz Y, Reed RD, Lewis JJ, Jiggins CD, Counterman BA, McMillan WO, Papa R. High level of novelty under the hood of convergent evolution. Science. 379(6636): 1043-1049 (2023).
Mazo-Vargas A, van der Burg KRL, Lewis JJ, Martin A, Zhang L, Reed RD. Deep regulatory homology and bifunctional architecture of the butterfly wing pattern groundplan. Science. 378(6617): 304-308 (2022).
Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Montgomery SH, Ghezzi A, Rodriguez-Martinez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM. A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility. Genome Research. 32(10): 1862-1875 (2022).
Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ*, Danko CG*. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nature Communications. 12(1): 1-12 (2021).
Cicconardi F*, Lewis JJ*, Martin SH, Reed RD, Danko CG, Montgomery SH*. The effects of parallel chromosome fusion on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size. Molecular Biology and Evolution. 38(10): 4449-4462 (2021).
Livraghi L, Hanly JJ, Van Belleghem SM, Montejo-Kovacevich G, van der Heijden ESM, Loh LS, Ren A, Warren IA, Lewis JJ, Concha C, Hebberecht L, Wright C, Walker JM, Foley J, Goldberg ZH, Arenas-Castro H, Salazar C, Perry MW, Papa R, Martin A, McMillan WO, Jiggins CD. Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius. eLife. 10, 68549 (2021).
Lewis JJ*, Cicconardi F*, Martin SH, Reed RD, Danko CG, Montgomery SH*. The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies. Genome Biology and Evolution. 13 (7), evab128 (2021).
van der Burg KRL, Lewis JJ, Brack BJ, Fandino RA, Mazo-Vargas A, Reed RD. Genomic architecture of a genetically assimilated seasonal color pattern. Science. 370(6517): 721-725. (2020).
Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD. Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. Science Advances. 6(39):eabb8617 (2020).
Lewis JJ, Geltman RC, Pollak PC Rondham KE, Van Belleghem SM, Hubisz MJ, Munn PR, Zhang L, Benson C, Mazo-Vargas A, Danko CG, Counterman BA, Papa R, Reed RD. Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proceedings of the National Academy of Sciences. 116(48):24174-24183 (2019).
Gu L, Reilly PF, Lewis JJ, Reed RD, Andolfatto P, Walter JR. Dichotomy of dosage compensation along the neo Z chromosome of the monarch butterfly. Current Biology. 29(23):4071-4077 (2019).
Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT. Chromatin conformation remains stable upon extensive transcriptional changes driven by heatshock. Proceedings of the National Academy of Sciences. 116(39):19431-19439 (2019).
Lewis JJ & Reed RD. Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius. Molecular Biology and Evolution. 36(1):159-173 (2019).
Van Belleghem SM, Rasta P, Papanicolaou A, Martin SH, Arias CF, Hanley JJ, Mallet J, Lewis JJ, Hines HM, Ruiz M, Salazar C, Linares M, Moreira GRP, Jiggins CD, Counterman BA, McMillan WO, Papa R. Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology & Evolution. 1(3):52 (2017).
Supple MA, Hines HM, Lavoie C, Ray D, Lewis JJ, Nielsen DM, Salazar C, Dasmahaptara K, McMillan WO, Counterman BA. 2013. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research. 23(8):1248-57 (2013).
International Heliconius Genome Consortium. A butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 487(7405):94-8 (2012).
