Afkhami, M. (2023) Neurobiology of Egg-laying Behavior in Drosophila: Neural Control of the Female Reproductive System. Preprints.org. doi: 10.20944/preprints202306.1191.v1.

Masly, J.P. and Md Golam Azom (2022) Molecular divergence with major morphological consequences: development and evolution of organ size and shape. Essays in Biochemistry EBC20220118. doi: 10.1042/EBC20220118.  PMID: 36373649

McQueen, E.W., M. Afkhami, J. Atallah, J.M. Belote, N. Gompel, Y. Heifetz, Y. Kamimura, S.C. Kornhauser, J.P. Masly, P. O’Grady, J. Peláez, M. Rebeiz, G. Rice, E. Sánchez-Herrero, M.D. Santos      Nunes, A. Santos Rampasso, S.L. Schnakenberg, M.L. Siegal, A. Takahashi, K.M. Tanaka, N. Turetzek, E. Zelinger, V. Courtier-Orgogozo, M.J. Toda, M.F. Wolfner and A. Yassin. (2022) A standardized nomenclature and atlas of the female terminalia of Drosophila melanogaster. Fly 16: 128-151. doi: 10.1080/19336934.2022.2058309.  PMID: 35575031

Frazee, S.R., A.R. Harper, M. Afkhami, M.L. Wood, J.C. McCrory‡ and J.P. Masly. (2021) Introgression reveals a role of male genital morphology during the evolution of reproductive isolation in Drosophila. Evolution 75: 989-1002. doi: 10.1111/evo.14169.  PMID: 33433903

Rice, G., J. David, Y. Kamimura, J.P. Masly, A. McGregor, O. Nagy, S. Noselli, M.D.S. Nunes, P. O’Grady, E. Sánchez-Herrero, M. Siegal, M. Toda, M. Rebeiz, V. Courtier-Orgogozo, A. Yassin (2019) A Standardized Nomenclature and Atlas of the Male Terminalia of Drosophila melanogaster. Fly 13: 51-64. doi: 10.1080/19336934.2019.1653733.  PMID: 31401934

Barnard, A.A. and J.P. Masly. (2018) Divergence in female damselfly sensory structures is consistent with a species recognition function but shows no evidence of reproductive character displacement. Ecology and Evolution 8: 12101-12114. doi:10.1002/ece3.4669. PMID: 30598803

Barnard, A.A., O.M. Fincke, M.A. McPeek, and J.P. Masly. (2017) Mechanical and tactile incompatibilities cause reproductive isolation between two young damselfly species. Evolution 71 (10): 2410-2427. doi: 10.1111/evo.13315/full. PMID: 28744900

Frazee, S.R. and J.P. Masly. (2015) Multiple sexual selection pressures drive the rapid evolution of complex morphology in a male secondary genital structure. Ecology and Evolution 5 (19): 4437-4450. doi:10.1002/ece3.1721. PMID: 26664690

Smith B.N., A.M. Ghazhanfari, R.A. Bohm, W.P. Welch, B. Zhang, and J.P. Masly. (2015) A Flippase-mediated GAL80/GAL4 Intersectional Resource for Dissecting Appendage Development in Drosophila. G3: Genes|Genomes|Genetics 5 (10): 2105-2112. doi:10.1534/g3.115.019810.  PMID: 26276385

Tanaka, K.M., C. Hopfen, M. Herbert, C. Schlötterer, D.L. Stern, J.P. Masly, A.P. McGregor, and M.D.S. Nunes. (2015) Genetic Architecture and Functional Characterization of Genes Underlying the Rapid Diversification of Male External Genitalia Between Drosophila simulans and Drosophila mauritiana. Genetics 200 (1): 357-369. doi:10.1534/genetics.114.174045. PMID: 25783699

Masly, J.P. and Y. Kamimura. (2014) Asymmetric mismatch in strain-specific genital morphology causes increased harm to Drosophila females. Evolution 68: 2401-2411. PMID: 24758304

Cooper, J.T. and J.P. Masly. (2013) Speciation in Diatoms: Patterns, Mechanisms, and Environmental Change. In, Speciation: Natural Processes, Genetics and Biodiversity. Pawel Michalak, ed. Nova Science Publishers, NY, p. 1-36.

Masly, J.P. (2012) 170 years of "Lock-and-Key": Genital Morphology and Reproductive Isolation. International Journal of Evolutionary Biology. vol. 2012, Article ID 247352, 10 pages, doi:10.1155/2012/247352. PMID: 22263116

Masly, J.P., J.E. Dalton, S. Srivastava, L. Chen, and M.N. Arbeitman. (2011) The genetic basis of rapidly evolving male genital morphology in Drosophila. Genetics 189 (1): 357-374. PMID: 21750260

Tao, Y., J.P. Masly, L. Araripe, Y. Ke, and D.L. Hartl. (2007) A new sex-ratio meiotic drive system in Drosophila simulans. I. Characterization of an autosomal suppressor. PLoS Biology 5 (11): e292. doi: 10.1371/journal.pbio.0050292.  PMID: 17988172

Masly, J.P. and D.C. Presgraves. (2007) High-resolution genome-wide dissection of the two rules of speciation in Drosophila. PLoS Biology 5 (9): e243. doi:10.1371/journal.pbio.0050243.  PMID: 17850182

Orr, H.A., J.P. Masly, and N. Phadnis. (2007) Speciation in Drosophila: From phenotypes to molecules. Journal of Heredity 98: 103-110. PMID: 17194791

Masly, J.P., C.D. Jones, M.A.F. Noor, J. Locke and H.A. Orr. (2006) Gene transposition as a cause of hybrid sterility in Drosophila. Science 313: 1448-1450. PMID: 16960009

Orr, H.A., J.P. Masly, and D.C. Presgraves. (2004) Speciation genes. Current Opinions in Genetics and Development 14: 675-679. PMID: 15531163

Huelsenbeck, J.P., B. Rannala, and J.P. Masly. (2000) Accommodating phylogenetic uncertainty in evolutionary studies. Science 288: 2349-2350. PMID: 10875916

Dermitzakis, E.T., J.P. Masly, H.M. Waldrip, and A.G. Clark. (2000) Non-mendelian segregation of sex chromosomes in heterospecific Drosophila males. Genetics 154: 687-694. PMID: 10655222