Publications
* Equal contributions # corresponding author
2021
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).
2020
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.
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).
2019
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).
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).
2018
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).
2011-2017
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).
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).
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).