Van Belleghem SM, Paola A, Heriberto CG, Counterman BA, and R Papa. 2020. Perfect mimicry between Heliconius butterflies is constrained by genetics and development. Proceedings of the. Royal Society B. 287: 20201267


Fenner J, Benson C, Rodriguez-Caro LF, Ren A, Papa R, Martin A and BA Counterman. 2020. Wnt Genes in Wing Pattern Development of Coliadinae Butterflies. Frontiers in Ecology and Evolution 8, 197.


Ren A, Day CR, Hanly JJ, Counterman BA, Morehouse N and A Martin. 2020. Convergent evolution of broadband reflectors underlies metallic coloration in butterflies. Frontiers in Ecology and Evolution 8, 206.


Shelby EA, Fenner J and BA Counterman. 2020. Impact of Artificial Diet on Development and Coloration in Zerene cesonia. The Journal of the Lepidopterists' Society 74 (2), 65-72.


Rodriguez Caro LF, Fenner J, Benson C, Van Belleghem SM, and BA Counterman. 2020. Genome assembly of the dogface butterfly Zerene cesonia. Genome Biology & Evolution. 12 (1), 3580-3585.


Edelman NB, Frandsen, PB, Miyagi, M, Clavijo, B, Davey, J, Dikow, RB, García-Accinelli, G, Van Belleghem, SM, Patterson, N,  Neafsey, DE, Challis, R, Kumar, S, Moreira, GRP, Salazar, C, Chouteau, M, Counterman, BA, Papa, R, Blaxter, M, Reed, RD, Dasmahapatra, KK, Kronforst, M, Joron, M, Jiggins, CD, McMillan, WO, Di Palma, F, Blumberg, AJ, Wakeley, J, Jaffe, D, & J. Mallet. 2019. Genomic architecture and introgression shape a butterfly radiation. Science. 01 Nov: 594-599.


Lewis, JJ, Geltman, RC, Pollak, PC, Rondem, KE, Van Belleghem, SM, Hubisz, MJ, Munn, PR, Zhang, L, Benson, C, Mazo-Vargas, A,  Danko, CG, Counterman, BA, Papa, R, & RD Reed. 2019 Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proceedings of the National Academy of Sciences. Nov 2019.


Concha, C, Wallbank, RWR,  Hanly, JJ, Fenner, J, Livraghi, L, Santiago Rivera, E, Paulo, DF, Arias, C, Vargas, M, Sanjeev, M, Morrison, C, Tian, D, Aguirre, P, Ferrara, S, Foley, J, Pardo-Diaz, C, Salazar, C, Linares, M, Massardo, D, Counterman, BA,  Scott, MJ,  Jiggins, CD, Papa, R, Martin, A, & WO McMillan. Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing Patterns. Current Biology. November 14, 2019.

Fenner, J, Rodriguez Caro, LF, and BA Counterman. 2019. Plasticity and divergence in ultraviolet reflecting structures on Dogface butterfly wings. Arthropod Structure & Development. 51, 14-22. 2.


Zhang, W, Leon-Ricardo, B. X, Van Schooten, B, Van Belleghem, SM, Counterman, BA, McMillan, WO, Kronforst, MR & R. Papa,  2019. Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation. Genome Biology & Evolution. 3.    


Ray, DA, Grimshaw, JR, Halsey, MK, Korstian, JM, Osmanski, A.B., Sullivan, KAM, Wolf, KA. Reddy, H, Foley, N, Stevens, RD, Knisbacher, B, Levy, O., Counterman, BA, Edelman, NB, and J. Mallet. 2019. Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-based Genome Diversification and Multiple SINE Births and Deaths. Genome Biology & Evolution, 11(8) 2162-77


Fenner J, Schartel, T, and BA Counterman. 2018. Lessons from Butterflies of the Black Belt Prairie: The Southern Dogface as an Indicator of Prairie Remnants. Transactions of the American Entomological Society 144 (2), 295-308.

Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, and SH Martin. 2018. Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography. Molecular Ecology. doi.org/10.1111/mec.14560

Van Belleghem SM, Papa R, Ortiz-Zuazaga H, Hendrickx F, Jiggins CD, McMillan WO, and BA Counterman. 2018. patternize: An R package for quantifying color pattern variation. Methods in Ecology and Evolution 9 (2), 390-8.


Van Belleghem SM, P Rastas, A Papanicolaou, SH Martin, CF Arias, MA Supple, JJ Hanly, J Mallet, JJ Lewis, HM Hines, M Ruiz, C Salazar, M Linares, GRP Moreira, CD Jiggins, BA Counterman, WO McMillan & R Papa. 2017. Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology & Evolution 1 (2), 0052

Shaak SG, BA Counterman. 2017. High warning colour polymorphism in Heliconius hybrid zone roosts. Ecological Entomology 42 (3), 315-324

Fenner J, J Seltzer, S Peyton, H Sullivan, P Tolson, RP Walsh, JV Hill, BA Counterman. 2017. Demographic variation of Wolbachia infection in the endangered Mitchell’s satyr butterfly. Insects 8 (2), 50


Counterman BA. 2016. Hybrid speciation. In: Encyclopedia of Evolutionary Biology. Eds: Kliman, R. & Ortiz-Barrientos, D. Elsevier. Cambridge, MA.



Supple M, Papa R, Hines H, McMillan WO & BA Counterman. 2015. Divergence with gene flow across the speciation continuum in Heliconius erato. BMC Evolutionary Biology, 15 (204). doi:10.1186/s12862-015-0486-y 


Hoffman F, McGuire L, Counterman BA & DA Ray. 2015. Transposable elements and small RNAs: genomic fuel for species diversity. Mobile Genetic Elements, 5 (5). doi:10.1080/2159256X.2015.1066919


Outlaw RK, Counterman BA & DC Outlaw. 2015. Differential patterns of molecular evolution among Haemosporidian Parasite Groups. Parasitology, 142 (4). doi: 10.1017/S0031182014001668


Nadeau N, Ruiz M, Salazar P, Counterman BA, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan, WO, Jiggins CD, & R Papa. 2014. Population genomics of parallel hybrid zones in the mimetic butterflies, Heliconius erato and H. melpomene. Genome Research. doi: 10.1101/gr.169292.1138


Supple M, Papa R, Counterman BA & WO McMillan. 2014. The genomics of an adaptive radiation—insights across the Heliconius speciation continuum. In: Ecological Genomics. C. Landry and N. Aubin-Horth (Eds.) Springer, New York.ISBN 978-94-007-7346-2



Lavoie C, Platt RN, Novick PA, Counterman BA & DR Ray. 2013. Transposable element evolution in Heliconius suggests substantial genome diversity among Lepidopterans. Mobile DNA, 4 (21). doi:10.1186/1759-8753-4-21


Papa R, Kapan DD, Counterman BA, Maldonado K, Lindstrom DP, Reed RD, Nijhout HF, Hrbek T & WO McMillan. 2013. Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato. PLoS ONE. doi:10.1371/journal.pone.0057033


Supple MA, Hines HM, Lavoie C, Ray D, Nielsen DM, Salazar C, Dasmahaptara K, McMillan WO & BA Counterman. 2013. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research. doi:10.1101/gr.150615.11



Martin A, Papa R, Nadeau N, Hill RI, Counterman BA, Jiggins CD, Kronforst MR, Long AD, McMillan WO & RD Reed. 2012. Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proceedings of the National Academy of Sciences, USA, 109 (31). doi:10.1073/pnas.1204800109


The Heliconius Genome Consortium. 2012. A butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487 (7405). doi:10.1038/nature11041 (Open Access)



Hines HM, Counterman BA, Papa R, Albuquerque De Moura P, Cardoso MZ, Linares M, Mallet J, Reed R, Jiggins CD, Kronforst MR & WO McMillan. 2011. A wing patterning gene redefines the mimetic history of Heliconius butterflies. Proceedings of the National Academy of Sciences, USA, 108 (49). doi:10.1073/pnas.1110096108


Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR, Chen R, Halder G, Nijhout HF & WO McMillan. 2011. Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science, 333 (6046). doi:10.1126/science.1208227 



Quek S-P, Counterman BA, Albuquerque De Moura P, Cardoso, MZ, Marshall CR, McMillan WO & MR Kronforst. 2010. Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies. Proceedings of the National Academy of Sciences, USA, 107 (16). doi:10.1073/pnas.0911572107


Counterman BA, Arajuo-Perez F, Hine, HM, Baxter SW, Morrison CM, Lindstrom DP, Papa R, Ferguson L, Joron M, Ffrench-Constant R, Smith C, Nielsen DM, Chen R, Jiggins CD, Reed RD, Halder G, Mallet J & WO McMillan. 2010. Genomic hotspots for adaptation: population genetics of Mullerian mimicry in Heliconius erato. PLoS Genetics 6(2): e1000796. doi:10.1371/journal.pgen.1000796 


Baxter SW, Nadeau N, Maroja L, Wilkinson P, Counterman BA, Dawson A, Beltran M, Perez-Espinoza S, Chamberlain N, Ferguson L, Clark R, Davidson C, Glithero R, Mallet J, WO McMillan, Kronforst M, Joron M, Ffrench-Constant R & CD Jiggins. 2010. Genomic Hotspots for adaptation: population genetics of Mullerian mimicry in the Heliconius melpomene clade. PLoS Genetics 6 (2) e1000794. doi:10.1371/journal.pgen.1000794 



Papa R, Morrison CM, Walters JR, Counterman BA, Chen R, Halder G, Ferguson L, Chamberlain N, Ffrench-Constant R, Kapan DD, Jiggins CD, Reed RD & WO McMillan. 2008. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. BMC Genomics 9, 345. doi:10.1186/1471-2164-9-345



Ortíz-Barrientos D, Counterman BA & MA Noor. 2007. Gene expression divergence and the origin of species. Genetica 129: 71-81. doi:10.1007/s10709-006-0034-1



Counterman BA, & MA Noor. 2006. Multilocus test for introgression between the cactophilic species Drosophila mojavensis and D. arizonae. American Naturalist 168: 682-696. http://www.jstor.org/stable/10.1086/508632



Yang JY, Counterman BA, Eckert CG & SA Hodges. 2005. Microsatellite markers for evolutionary studies in Aquilegia. Molecular Ecology Notes 5: 317-320.doi:10.1111/j.1471-8286.2005.00913



Ortíz-Barrientos D, Counterman BA & MA Noor . 2004. The genetics of reinforcement in Drosophila. PLoS Biology 2(12): e416.doi:10.1371/journal.pbio.0020416


Counterman BA, Ortíz-Barrientos D & MA Noor. 2004. Using comparative genomic data to test for fast-X evolution. Evolution 58: 656-660.doi:10.1111/j.0014-3820.2004.tb01688


Stevison LS, Counterman BA & MA Noor. 2004. Molecular population genetics of X-linked accessory gland proteins in Drosophila pseudoobscura. Journal of Heredity 95: 114-118. doi:10.1093/jhered/esh027