CV
James J Lewis
Department of Genetics and Biochemistry, Clemson University, Clemson, SC
EDUCATION
Ph.D. Ecology and Evolutionary Biology, Cornell University – 2017
M.A. Philosophy, Virginia Tech – 2010
B.A. Philosophy, University of Evansville – 2006
PROFESSIONAL EMPLOYMENT
2022 – present Assistant Professor, Department of Genetics and Biochemistry Clemson University, Clemson, SC
2021 – 2022 Postdoctoral Fellow, Mank Lab, University of British Columbia, Vancouver, BC
2017 – 2021 Postdoctoral Fellow, Danko Lab, Cornell University, Ithaca, NY
HONORS AND AWARDS
2017 T32 Reproductive Genomics Postdoctoral Training Fellowship, National Institutes of Health
2014 Kieckhefer Adirondack Fellowship, Kieckhefer Foundation
2013 Cornell Center for Comparative Population Genomics Fellowship, 3CPG Cornell University
2011 T32 Developmental Systems Biology Training Fellowship, National Institutes of Health
2010 First Year Fellowship, Dept. of Ecology and Evolutionary Biology, UC-Irvine
RESEARCH INTERESTS AND RESEARCH AREAS
My research uses butterflies as a model group of organisms to study the genetic architecture, molecular and developmental mechanisms, and evolutionary processes that underlie adaptations. Research areas include: evolutionary and population genomics, molecular evolution, evo-devo, and trait genetics.
PEER-REVIEWED PUBLICATIONS
Corresponding author(s)*
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).
Barshad G, Ting H, Oyesola OO, Onyekwere GO, Lewis JJ, Rice EJ, Matheson MK, Sun X, von Moltke J, Danko CG, Webb LM, Tait Wojno ED. E-protein inhibition in ILC2 development shapes the function of mature ILC2s during allergic airway inflammation. The Journal of Immunology. 208(5): 1007-1020 (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 Belleghem SM, Lewis JJ, Rivera ES, Papa R. Heliconius butterflies: A window into the evolution and development of diversity. Current Opinion in Genetics and Development. 69, 72-81 (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* and Van Belleghem SM*. Mechanisms of change: a population-based perspective on the roles of modularity and pleiotropy in diversification. Frontiers in Ecology and Evolution. 8(261) (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).
van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, Danko CG, Reed RD. Contrasting roles of spineless and EcR in the highly dynamic chromatin landscape of butterfly wing metamorphosis. Cell Reports. 27(4):1027-38 (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).
Lewis JJ*, van der Burg KRL, Mazo-Vargas A, Reed RD. ChIP-seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera. Cell Reports. 16(11):2855-63 (2016).
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).
Cai R, Lewis JJ, Yan S, Liu H, Clarke CR, Campanile F, Almeida NF, Studholme DJ, Lindeberg M, Schneider D, Zaccardelli M, Setubal JC, Morales N, Bernal A, Coaker G, Baker C, Bender C, Leman S, Vinatzer BA. (2011) The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathogens. 7(8):e1002130 (2011).
OTHER PUBLICATIONS
Corresponding author(s)*
Chivu AG, Basso BA, Abuhashem A, Leger MM, Barshad G, Rice EJ, Vill AC, Wong W, Chou S, Chovatiya G, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito1 IL, Ruiz-Trillo I, Hadjantonakis A, Lis JT*, Lewis JJ*, and Danko CG*. Evolution of promoter-proximal pausing enabled a new layer of transcription control. Revised for resubmission.
GRANTSMANSHIP
NSF CAREER Primary Investigator 2024-2029
Title: Functional genomic architecture and population differentiation of a polygenic and sexually dimorphic butterfly mimicry phenotype. $1,327,000
NIH 5P20GM146584 Primary Investigator 2023-2024
Title: The genetic architecture of covariation in transcriptional response to heat stress and infection. $50,000
NASA 17-EXO-17-2-0112 Co-Author, named as personnel 2018-2022
Title: POL II Pausing as a Milestone on the Road to Complex Animals. $791,000
NSF DEB-1546049 Primary Author, named as personnel 2016-2019
Title: Developing a High-Resolution Method for Mapping Regulatory QTLs. $300,000
NSF DEB-1354318 Co-Author, named as personnel 2014-2017
Title: cis-Regulatory Architecture of Adaptive Radiation. $740,000
INVITED RESEARCH PRESENTATIONS
Evolution of wing pattern mimicry in heliconiine butterflies. Entomology departmental seminar. University of Georgia. Athens, GA. 2024.
Adaptive trait evolution in heliconiine butterflies. Biological Sciences departmental seminar. Clemson University. Clemson, SC. 2023.
Evolutionary and molecular genetics of adaptation in butterflies. Rising Stars Symposium. Clemson University. Clemson, SC. 2022.
The genetic architecture of adaptive trait evolution in butterflies. Faculty Search Seminar. Clemson University. Clemson, SC (online). 2022.
Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. Great Lakes Evolutionary Genomics Symposium. Rochester, NY (online). 2020.
Butterfly mimicry evolved via parallel evolution of ancient, pleiotropic enhancers. Meeting of the Society for Molecular Biology and Evolution. Manchester, UK. 2019.
Epigenetic adaptation shapes population-level genomic landscapes in Heliconius. Joint Evolution Meeting. Montpellier, FR. 2018
cis-regulatory evolution drives diversification in lepidoptera. Baker Institute for Animal Health, Cornell University. Ithaca, NY. 2017.
Regulatory evolution of a butterfly wing color pattern. Evo-Day 2013: Novel Traits and Rapid Evolution. Cornell University, Ithaca, NY. 2013.
An update on Optix regulatory evolution. Heliconius Meeting. Harvard University, Cambridge, MA. 2013.
OUTREACH AND COMMUNITY SERVICE
2017 Presenter - ATAC-seq workshop. Smithsonian Tropical Research Institute, Gamboa, Panama
2018 Lead Organizer - ATAC-seq workshop. University of Puerto Rico, San Juan, PR
2012 Organizer - Cornell EvoDay (annual single day evolution conference). Cornell University, Ithaca, NY
Journal Reviews:
PNAS (2) PLOS Computational Biology
Nature Genetics BMC Biology
Molecular Biology and Evolution (3) Proceedings of the Royal Society B (2)
Genetics (2) BMC Genomics
Developmental Biology GigaScience
Current Opinions in Insect Science eLife
Insect Biochemistry and Molecular Biology PLOS Genetics (2)
Science Advances G3 (2)
Cell Reports
TEACHING
GEN 4100/4100H/6100: Introduction to Population and Quantitative Genetics 2023-2024
GEN 4930: Senior Seminar 2024
ADVISING
Postdoc Advising
Dr. Brianna Ports (2023-2024), Secured tenure track faculty appointment.
PhD Advising
Ashly Nussbaum (2023-present)
Sriya Pothapragada (2023-present)
MS Advising
Marshall Norman Hoskins (2024-present)
Thesis committee member
Leah DeLorenzo (2022-2024), Biological Sciences, PhD. Graduated.
Undergraduate Mentoring
Rachel Geltman, project: Identifying the cis-regulatory loci of butterfly wing adaptation, Cornell University, 2018-2019.
Madison Ramsey, project: Mapping nucleosome stability in butterfly wings, Cornell University, 2016 – 2017.
Christopher McAllester, project: Identification and k-means clustering of putative transcription factor binding sites from DNase I hypersensitivity data, Cornell University, 2014 – 2016.
- Graduated with Honors, Currently a PhD student at UW-Madison (Pool Lab).
PROFESSIONAL ACTIVITY
Society membership:
Society for Molecular Biology and Evolution
Society for the Study of Evolution
Pan-American Society for Evolutionary Developmental Biology