CV

James J Lewis

Department of Zoology, University of British Columbia, Vancouver, BC

Education

Ph.D. Ecology and Evolutionary Biology – 2017

Cornell University – Ithaca, NY

M.A. Philosophy – 2010

Virginia Tech – Blacksburg, VA

B.A. Philosophy –2006

University of Evansville – Evansville, IN

Research Experience

Postdoctoral Fellow – Mank Lab, University of British Columbia – May 2021 – Present

I am working on the evolution of sex-biased gene expression, regional color pattern variation, and sexual dimorphism in the basal heliconiine butterfly Dryas iulia.

Postdoctoral Fellow – Danko Lab, Cornell University – 2017 – 2021

I investigated the evolution and molecular mechanisms of butterfly wing pattern development in heliconiine butterflies.

Research Assistant – Vinatzer Lab, Virginia Tech - 2008 – 2010

- I investigated the evolution and epidemiology of the plant pathogen Pseudomonas syringae combining bioinformatic, evolutionary, and molecular biology approaches to study the evolution of bacterial virulence mechanisms.

Research Assistant – Baudoin Lab, Virginia Tech - 2008

- I investigated occurrence and frequency of fungicide resistance in the grape pathogen powdery mildew (Erysiphe necator) to determine fungicide effectiveness in local vineyards.

Fellowship Support

National Institutes of Health – 2017-18: $48,000

- T32 Reproductive Genomics Postdoctoral Training Fellowship

Cornell University – Spring 2013: $11,450 + tuition/fees

- Cornell Center for Comparative Population Genomics Fellowship

National Institutes of Health – 2011-12: $21,600 + tuition/fees

- T32 Developmental Systems Biology Training Fellowship

UC-Irvine – 2010: $3,000

- Ecology and Evolutionary Biology: First Year fellowship

Research Grants

Co-Author (named as personnel): NASA 17-EXO-17-2-0112: 2018 – present: $791,000 (with C. Danko as PI). POL II Pausing as a Milestone on the Road to Complex Animals.

Primary Author (named as personnel): NSF DEB-1546049: 2016 - 2019: $300,000 (Submitted by R. Reed as PI). EAGER: Developing a High-Resolution Method for Mapping Regulatory QTLs.

Co-Author (named as personnel): NSF DEB-1354318: 2014 - 2016: $740,000 (with R. Reed as PI). cis-Regulatory Architecture of Adaptive Radiation.

Cornell University – Spring 2014: $5,000. Kieckhefer Adirondack Fellowship.

NIH – 2011-12: $2,700. Developmental Systems Biology Training Grant.

Sigma Xi – 2010: $750. Grant in aid of research.

Publications & Presentations

Publications:

* Equal contributions # corresponding author

1. 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. In Press. bioRxiv 2020.07.29.227660

2. 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. In Press. https://doi.org/10.1093/molbev/msab185

3. 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).

4. 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).

5. 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).

6. van der Burg KRL, Lewis JJ, Brack BJ, Fandino RA, Mazo-Vargas A, Reed RD. Genomic architecture of a genetically assimilated seasonal color pattern. In press. Science.

- Covered by 3 news outlets

7. 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).

8. 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).

- 2020 Editor’s Choice article: https://fro.ntiers.in/FrontEcolEvol_2020Highlights

9. 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).

- Highly cited

- Covered by 3 news outlets

10. 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).

11. 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).

12. 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).

13. Lewis JJ# & Reed RD. Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius. Molecular Biology and Evolution. 36(1):159-173 (2019). Published online (2018).

14. 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).

- Highly cited

15. 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).

16. 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).

17. International Heliconius Genome Consortium. A butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 487(7405):94-8 (2012).

- Highly cited

- Covered by 1 news outlet

18. 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).

- Highly cited

- Covered by 6 news outlets

Presentations:

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. Evolution meeting. Online program. 2021.

Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD. Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. Great Lakes Evolutionary Genomics Symposium. Rochester, NY (online). 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. Butterfly mimicry evolved via parallel evolution of ancient, pleiotropic enhancers. Evolution Meeting. Providence, RI. 2019.

Lewis JJ, Geltman RC, Rondham KE, Van Belleghem SM, Munn PR, Danko CG, Counterman BA, Papa R, Reed RD. Epigenetic adaptation shapes population-level genomic landscapes in Heliconius. Joint Evolution Meeting. Montpellier, FR. 2018

Lewis JJ, Edelman N, Mallet J, Danko, C, & Reed RD. Genome assembly strategies for outbred, non-model organisms. Evolution Meeting. Portland, OR. 2017.

Lewis JJ. cis-regulatory evolution drives diversification in lepidoptera. Baker Institute for Animal Health, Cornell University. Ithaca, NY. 2017.

Lewis JJ & Reed RD. Rapid cis-regulatory evolution underlies racial divergence in the mimetic butterfly Heliconius erato. SSE Spotlight Symposium: Understanding history and process in rapid diversification with genomic data. Evolution Meeting. Austin, TX. 2016.

Lewis, JJ. Regulatory evolution of a butterfly wing color pattern. Evo-Day 2013: Novel Traits and Rapid Evolution. Cornell University, Ithaca, NY. 2013.

Lewis JJ. An update on Optix regulatory evolution. Heliconius Meeting. Harvard University, Cambridge, MA. 2013.

Lewis, JJ. Integrating Development into Adaptive Landscape Models of Evolution. Darwin’s Legacy: Evolution’s Impact on Science and Culture. University of North Carolina, Wilmington. Wilmington, NC. 2009.

Posters:

Lewis JJ & Reed RD. Chromatin state evolution shapes population-level genomic landscapes in Heliconius butterflies. SMBE, Poster Session. Austin, TX. 2017.

Lewis JJ & Reed RD. Epigenetic profiling of functional loci driving wing pattern variation in phenotypically diverse races of Heliconius erato. Pan-American Society for Evolutionary Developmental Biology Inaugural Meeting, Poster Session. Berkeley, CA. 2015.

Teaching Experience

Workshops:

ATAC-seq workshop – STRI, Gamboa, Panama, 2017.

- Provided ATAC-seq protocol, designed and led bioinformatics session.

ATAC-seq workshop – University of Puerto Rico, San Juan, PR. 2018.

- Designed and led workshop for students and professors at UPR, covering the ATAC-seq protocol and an introduction to data analysis.

Undergraduate and Graduate Teaching:

BioEE 7600 – Comparative Functional Genomics Seminar (Spring 2015)

- Co-taught with R. Reed. Assisted in course design, led 20% of course days

Independent Study Group – Introduction to Python Programming (Spring 2014)

- Designed and led introduction to python programming for graduate students

BioEE 1780 – Evolution and Diversity, writing section (3 semesters, 2013-2015)

- Designed and led course modules on evolution and development:

Bio Sci E112L - Physiology Lab (3 Quarters, 2010-2012):

- Reviewed discussion material, oversaw lab exercises, proctored and graded exams

Bio Sci E106 - Ecology and Evolutionary Biology (Winter 2012):

- Held weekly discussion section, proctored and graded exams, quizzes

Bio Sci E142W - Philosophy of Biology (Winter 2011):

- Held weekly discussion section, reviewed and assisted in student writing projects

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

Journal Reviewer:

PNAS PLOS Computational Biology

Nature Genetics BMC Biology

Molecular Biology and Evolution (2) Genetics (2)

Developmental Biology GigaScience

Current Opinions in Insect Science eLife

Insect Biochemistry and Molecular Biology Proceedings of the Royal Society B

Bioinformatics and Software projects

Software Applications Developed:

Genome-wide prediction of enhancer-promoter interactions using Hi-C data

Parsing uniquely mapped reads from Bowtie2 outputs

Mapping synteny-based scaffold alignment coordinates to chromosome level assemblies

Reciprocal BLAST analysis of regulatory sequences between distantly related species

Programming Languages:

C/C++, Python, & R