Publications

Preprints

Butterfly wing iridescence is regulated by araucan, a direct target of optix and spalt.
Chatterjee, M., K. Siegel, J.M.C. McDonald, L.S. Loh, R.D. Reed.

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies.
Loh, L.S., J.J. Hanly, A. Carter, M. Chatterjee, M. Tsimba, D.N. Shodja, L. Livraghi, C.R. Day, R.D. Reed, W.O. McMillan, G.A. Wray, A. Martin.

Synchronous seasonal plasticity in colouration, behaviour, and visual gene expression in a wild butterfly population.
Hirzel, G.E., N.K. Brady, K. Farfán-Pira, R.D. Reed, E.L. Westerman.

mirror determines the far posterior domain in butterfly wings.
Chatterjee, M., X.Y. Yu, N.K. Brady, G.C. Hatto, R.D. Reed.

2024

Beyond modular enhancers: new questions in cis-regulatory evolution.
McDonald, J.M.C., R.D. Reed. 
Trends in Ecology and Evolutionary Biology. 39: 1035-1046

The ivory lncRNA regulates seasonal color patterns in buckeye butterflies.
Fandino, R.A., N.K. Brady, M. Chatterjee, J.M.C. McDonald, L. Livraghi, K.R.L. van der Burg, A. Mazo-Vargas, E. Markenscoff-Papadimitriou, R.D. Reed.
Proceedings of the National Academy of Sciences of the USA. 121: e2403426121

• Featured in Science perspective
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A long non-coding RNA at the cortex locus controls adaptive coloration in butterflies.
Livraghi, L., J.J. Hanly, E. Evans, C.J. Wright, L.S. Loh, A. Mazo-Vargas, K. Kamrava, A. Carter, E.S.M. van der Heijden, R.D. Reed, R. Papa, C.D. Jiggins, A. Martin.
Proceedings of the National Academy of Sciences of the USA. 121: e2403326121

• Cover article
• Featured in Science perspective
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• Features in PNAS perspective

Pluripotency of a founding field: rebranding developmental biology.
Rogers, C.D., C. Amemiya, S. Arur, L. Babonis, M. Barresi, M. Bartlett, R. Behringer, B. Benham-Pyle, D. Bergmann, B. Blackman, C.T. Brown, B. Browne, J. Camacho, C.Y. Chabu, I. Chow, O. Cleaver, J. Cool, M.Y. Dennis, A.J. Dickinson, S. Di Talia, M. Frank, S. Gillmor, E.S. Haag, I. Hariharan, R. Harland, A. Husbands, L. Jerome-Majewska, K. Koenig, C. Labonne, M. Layden, C. Lowe, M. Mani, M. Martik, K. McKown, C. Moens, C. Mosimann, J. Onyenedum, R. Reed, A. Rivera, D. Rokhsar, L. Royer, F. Rutaganira, R. Shahan, N. Sinha, B. Swalla, J.M. Van Norman, D.E. Wagner, A. Wikramanayake, S. Zebell, S.M. Brady.
Developmental Biology. 151: dev202342

2023

High level of novelty under the hood of convergent evolution.
Van Belleghem, S.M, A.A. Ruggieri, L. Livraghi, L.H. López, C. Concha, E.S. Rivera, J.G. Ogilvie, J.J. Hanly, I.A. Warren, S. Planas, Y. Ortiz-Ruiz, R.D. Reed, J.J. Lewis, C.D. Jiggins, B.A. Counterman, W.O. McMillan, R. Papa.
Science. 379: 1043-1049.

Patterns of selection across gene regulatory networks.
McDonald, J.M.C., R.D. Reed.
Seminars in Cell & Developmental Biology. 69: 82-87.

2022

Deep cis-regulatory homology of the butterfly wing pattern ground plan.
Mazo-Vargas, A., A.M. Langmüller, A. Wilder, K.R.L. van der Burg, J.J. Lewis, P.W. Messer, A. Martin, L. Zhang, R.D. Reed.
Science. 378: 304-308.

• Cover article
• Featured in Science perspective
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2021

The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies.
Lewis, J.J, F. Cicconardi, S.H. Martin, R.D. Reed, C.G. Danko, S.H. Montgomery.
Genome Biology and Evolution. 13: evab128.

Chromosome fusion affects genetic diversity and evolutionary turnover of functional loci, but consistently depends on chromosome size.
Cicconardi, F., J.J. Lewis, S.H. Martin, R.D. Reed, C.G. Danko, S.H. Montgomery.
Molecular Biology and Evolution. 38: 4449-4462.

High-quality genome assembly and comprehensive transcriptome of the butterfly Vanessa cardui.
Zhang, L., R.A. Steward, C.W. Wheat, R.D. Reed
Genome Biology and Evolution. 13: 7.

Seasonal plasticity: how do butterfly wing pattern traits evolve environmental responsiveness?
van der Burg, K.R.L., R.D. Reed
Current Opinion in Genetics and Development. 69: 82-87.

2020

Genomic architecture of a genetically assimilated seasonal color pattern.
van der Burg, K.R.L., J.J. Lewis, B.J. Brack, R.A. Fandino, A. Mazo-Vargas, R.D. Reed
Science. 370: 721-725.

Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone.
Lewis, J.J., S.M. Van Belleghem, R. Papa, C.G. Danko, R.D. Reed
Science Advances. 6: eabb8617.

Transcription factors underlying butterfly wing margin color patterns and pupal cuticle markings.
Reed, R.D., J.E. Selegue, L. Zhang, C.R. Brunetti
EvoDevo. 11: 10.

Multiple roles for laccase2 in butterfly wing pigmentation, scale morphology, and cuticle tanning.
Peng, C., A. Mazo-Vargas, B.J. Brack, R.D. Reed
Evolution & Development. 22: 336-341.

2019

Dichotomy of dosage compensation on the single Z chromosome of the monarch butterfly.
Gu, L., P.F. Reilly, J.J. Lewis, R.D. Reed, P. Andolfatto, J.R. Walters
Current Biology. 29: 4071-4077.

• Featured in Current Biology dispatch

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry.
Lewis, J.J., R.C. Geltman, P.C. Pollak, K.E. Rondem, S.M. Van Belleghem, M. Hubisz, P.R. Munn, L. Zhang, C. Benson, A. Mazo-Vargas, C.G. Danko, B.A. Counterman, R. Papa, R.D. Reed
Proceedings of the National Academy of Sciences of the USA. 48: 24174-24183.

• Featured in The Scientist

Genomic architecture and introgression shape a butterfly radiation.
Edelman, N.B., P.B. Frandsen, M. Miyagi, B. Clavijo, J. Davey, R. Dikow, G. Garcia-Accinelli, S. van Belleghem, N. Patterson, D.E. Neafsey, R. Challis, S. Kumar, G. Moreira, C. Salazar, M. Choteau, B. Counterman, R. Papa, M. Blaxter, R.D. Reed, K. Dasmahapatra, M. Kronforst, M. Joron, C.D. Jiggins, W.O. McMillan, F. Di Palma, A.J. Blumberg, J. Wakeley, D. Jaffe, J. Mallet
Science. 366: 594-599.

• Cover article
• Featured in The Scientist and Smithsonian Magazine

Contrasting roles of transcription factors spineless and EcR in the highly dynamic chromatin landscape of butterfly wing metamorphosis.
van der Burg, K.R.L., J.J. Lewis, N. Patel, A. Martin, H.F. Nijhout, C. Danko, R.D. Reed
Cell Reports.  27: 1027-1038.

Seasonal plasticity in Junonia coenia (Nymphalidae): Linking wing color, temperature dynamics, and behavior.
Järvi, V.V., K.R.L. van der Burg, R.D. Reed
Journal of the Lepidopterists’ Society. 73: 34-42.

Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius.
Lewis, J.J., R.D. Reed
Molecular Biology and Evolution. 36: 159-173.

2017

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence.
Zhang, L, A. Mazo-Vargas, R.D. Reed
Proceedings of the National Academy of Sciences of the USA. 114: 10707-10712.

• Cover article
• Cozzarelli Prize – National Academy of Sciences
• PNAS highlighted article
• Featured in many national and international news outlets including New York Times, The Atlantic, Nature, Science, Smithsonian Magazine, etc.

Macro-evolutionary shifts of WntA function potentiate butterfly wing pattern diversity.
Mazo-Vargas, A., C. Concha, L. Livraghi, D. Massardo, R. Wallbank, L. Zhang, J. Papador, D. Martinez-Najera, M.R. Kronforst, C.J. Breuker, R.D. Reed, N.H. Patel, W.O. McMillan, A. Martin
Proceedings of the National Academy of Sciences of the USA. 114: 10701-10706.

• PNAS highlighted article
• Featured in many national and international news outlets including New York Times, The Atlantic, Nature, Science, Smithsonian Magazine, etc.

A practical guide to CRISPR/Cas9 genome editing in Lepidoptera.
Zhang, L., R.D. Reed
In Diversity and Evolution of Butterfly Wing Patterns.

Genetic basis of melanin pigmentation in butterfly wings.
Zhang, L., A. Martin, M.W. Perry., K.R.L. van der Burg, Y. Matsuoka, A. Monteiro, R.D. Reed
Genetics. 205: 1537-1550.

• Cover article
• Genetics Society of America Editor’s Award in Molecular Genetics

 

2016

ChIP-seq-annotated Heliconius erato genome highlights cis-regulatory evolution in Lepidoptera.
Lewis, J.J., K.R.L. van der Burg, A. Mazo-Vargas, R.D. Reed
Cell Reports. 16: 2855-2863.

Genome editing in butterflies reveals that spalt promotes and Distal-less represses eyespot colour patterns.
Zhang, L., R.D. Reed
Nature Communications. 7: 11769.

• Top 10% of Nature Communications papers (>1000 downloads in first week)
• Featured on 10 news websites, including Science News

2014

Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns.
Daniels, E.V., R. Murad, A. Mortazavi, R.D. Reed
Molecular Ecology. 23: 6123-6134

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems.
Martin, A., R.D. Reed
Developmental Biology. 395: 367-378.

Warning signals are seductive: Relative contributions of color and pattern to predator avoidance and mate attraction in Heliconius butterflies.
Finkbeiner, S.D., A.D. Briscoe, R.D. Reed
Evolution. 68: 3410-3420.

Ancient homology underlies adaptive mimetic diversity across butterflies.
Gallant, J.R., V.E. Imhoff, A. Martin, W.K. Savage, N. Chamberlain, B.L. Pote, B. Evans, R.D. Reed, M.R. Kronforst, S.P. Mullen
Nature Communications. 5: 4817.

doublesex is a mimicry supergene.
Kunte, K., W. Zhang, A. Tenger-Trolander, D. Palmer, A. Martin, R.D. Reed, S.P. Mullen, M.R. Kronforst
Nature. 507: 229-232.

• Perspective in Nature by David Loehilin and Sean Carroll
• Featured in New York Times and Science NOW
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Multiple recent co-options of Optix associated with novel traits in adaptive butterfly wing radiations.
Martin, A., K.J. McCulloch, N.H. Patel, A.D. Briscoe, L.E. Gilbert, R.D. Reed
EvoDevo. 5: 7.

2013

Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato.
Papa, R., D.D. Kapan, B.A. Counterman, K. Maldonado, D. Lindstrom, R.D. Reed, H.F. Nijhout, T. Hrbek, W.O. McMillan
PLoS One. 8: e57033.

2012

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
Martin, A., R. Papa, N. Nadeau, R.I. Hill, B.A. Counterman, C.D. Jiggins, M.R. Kronforst, A.D. Long, W.O. McMillan, R.D. Reed
Proceedings of the National Academy of Sciences of the USA. 109: 12632-12637.

• Featured in New York Times

Xanthurenic acid is a pigment in Junonia coenia butterfly wings.
Daniels, E.V., R.D. Reed
Biochemical Systematics and Ecology. 44: 161-163.

Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation.
Hines, H.M, R. Papa, M. Ruiz, A. Papanicoloau, W.O. McMillan, R.D. Reed
BMC Genomics. 13: 288.

Genomic evidence for promiscuous exchange of adaptations among Heliconius butterfly species.
The Heliconius Genome Consortium
Nature. 487: 94-98.

• Faculty of 1000 selection
• Featured in New York Times

Seasonal wing colour plasticity varies dramatically between buckeye butterfly populations in different climatic zones.
Daniels, E.V., K.A. Mooney, R.D. Reed
Ecological Entomology. 37: 155-159.

The benefit of being a social butterfly: communal roosting deters predation.
Finkbeiner, S.D., A.D. Briscoe, R.D. Reed
Proceedings of the Royal Society B: Biological Sciences. 279: 2769-2776.

• One of PRSB’s most-read articles of March 2012.
• Featured in Science and National Geographic
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• Featured in Science 2012 Year in Pictures

UV photoreceptors and UV-yellow wing pigments in Heliconius butterflies allow a color signal to serve both mimicry and intraspecific communication.
Bybee, S.M., F. Yuan, M.D. Ramstetter, J.L. Bousquets, R.D. Reed, D. Osorio, A.D. Briscoe
American Naturalist. 179: 38-51.

2011

A wing patterning gene redefines the mimetic history of Heliconius butterflies.
Hines, H.M., B.A. Counterman, R. Papa, P. A. de Moura, M.A. Cardoso, M. Linares, J. Mallet, R.D. Reed, C.D. Jiggins, M. Kronforst, W.O. McMillan
Proceedings of the National Academy of Sciences of the USA. 108: 19666-19671.

• Featured in New York Times

optix drives the repeated convergent evolution of butterfly wing pattern mimicry.
Reed, R.D., R. Papa, A. Martin, H.M. Hines, B.A. Counterman, C. Pardo-Diaz, C.D. Jiggins, N.L. Chamberlain, M.R. Kronforst, R. Chen, G. Halder, H.F. Nijhout, W.O. McMillan
Science. 333: 1137-1141.

• Faculty of 1000 selection
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• Featured in This Week in Science
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The role of environmental factors in the northeastern range expansion of Papilio cresphontes Cramer (Papilionidae).
Finkbeiner, S.D., R.D. Reed, R. Dirig, J.E. Losey
Journal of the Lepidopterists’ Society. 65: 119-125.

2010

Reply to Nozawa et al.: Complementary statistical methods support positive selection of a duplicated UV opsin gene in Heliconius.
Briscoe, A.D., S.M. Bybee, G.D. Bernard, F. Yuan, M.P. Sison-Magnus, R.D. Reed, A.D. Warren, J. Llorente-Bousquets, C.-C. Chiao
Proceedings of the National Academy of Sciences of the USA. 107: E97.

wingless and aristaless2 define a developmental ground plan for moth and butterfly wing pattern evolution.
Martin, A., R.D. Reed
Molecular Biology and Evolution. 27: 2864-2878.

Butterfly wings shaped by a molecular cookie cutter: Evolutionary radiation of lepidopteran wing shapes associated with a derived Cut / wingless wing margin boundary system.
Macdonald W.P., A. Martin, R.D. Reed
Evolution & Development. 12: 296-304.

Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies.
Briscoe, A.D., S.M. Bybee, G.D. Bernard, F. Yuan, M.P. Sison-Magnus, R.D. Reed, A.D. Warren, J. Llorente-Bousquets, C.-C. Chiao
Proceedings of the National Academy of Sciences of the USA. 107: 3628-3633.

• Faculty of 1000 selection

Genomic hotspots for adaptation: The population genetics of Müllerian mimicry in Heliconius erato.
Counterman, B. A., F. Arajuo-Perez, H.M. Hines, S.W. Baxter, C.M. Morrison, D.P. Lindstrom, R. Papa, L. Ferguson, M. Joron, R. ffrench-Constant, C. Smith, D.M. Nielsen, R. Chen, C.D. Jiggins, R.D. Reed, G. Halder, J. Mallet,  W. O. McMillan
PLoS Genetics. 6: e1000796.

• Faculty of 1000 selection
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2008

Genomic hotspots of adaptation in butterfly wing pattern evolution.
Papa, R., A. Martin, R.D. Reed
Current Opinion in Genetics and Development. 18: 559-564.

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies.
Papa R., C.M. Morrison, J.R. Walters, B.A. Counterman, R. Chen, G. Halder,L. Ferguson, N. Chamberlain, R. ffrench-Constant, D.D. Kapan, C.D. Jiggins, R.D. Reed, W.O McMillan
BMC Genomics. 9: 345.

• BMC Highly Accessed article

Gene expression underlying adaptive variation in Heliconius wing patterns: non-modular regulation of overlapping cinnabar and vermilion prepatterns.
Reed, R.D., W.O. McMillan, L.M. Nagy
Proceedings of the Royal Society B: Biological Sciences. 275: 37-45.

 

2007

Cryptic variation in butterfly eyespot development: the importance of sample size in gene expression studies.
Reed, R.D., P.-H. Chen, H.F. Nijhout
Evolution & Development. 9: 2-9.

 

 

2006

Localization of Müllerian mimicry genes on a dense linkage map of Heliconius erato.
Kapan, D.D., N.S. Flanagan, A. Tobler, R. Papa, R.D. Reed, J.A. Gonzalez, M.R. Restrepo, L. Martinez, K. Maldonado, C. Ritschoff, D.G. Heckel, W.O. McMillan
Genetics. 173: 735-757.

2005

Evolutionary redeployment of a biosynthetic module: expression of eye pigment genes vermilion, cinnabar, and white in butterfly wing development.
Reed, R.D., L.M. Nagy
Evolution & Development. 7: 301-311.

 

Gregarious oviposition in butterflies.
Reed, R.D.
Journal of the Lepidopterists’ Society. 59: 40-43.

2004 

Wing venation and Distal-less expression in Heliconius butterfly wing pattern development.
Reed, R.D., L.E. Gilbert
Development Genes and Evolution. 214: 628-634.

 

 

Butterfly wing pattern evolution is associated with changes in a Notch/Distal-less temporal pattern formation process.
Reed, R.D., M.S. Serfas
Current Biology. 14: 1159-1166.
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Evidence for Notch-mediated lateral inhibition in organizing butterfly wing scales.
Reed, R.D.
Development Genes and Evolution. 214: 43-46.

 

 

1999-2003 

Gregarious oviposition and clutch size adjustment by a Heliconius butterfly.
Reed, R.D.
Biotropica. 35: 555-559.

 

A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae).
Caterino, M., R.D. Reed, M.M. Kuo, F.A.H. Sperling
Systematic Biology. 50: 106-127.

 

 

The interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus Papilio.
Reed, R.D., F.A.H. Sperling
Molecular Biology and Evolution. 16: 286-297.