Publications

*Undergraduate co-authors

*Orr, W.E., *J.Y. Kim, *I.K. Sánchez Márquez, *C.J. Ryan, *T. Raj, *E.K. Hom, *A.E. Person, *A. Vonada, J.A. Stratton, A.M. Cooley (2024). Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus. Evolution & Development 27(1): e12493. doi: 10.1111/ede.12493.

Simmons, E.S.G., A.M. Cooley, J.R. Puzey, G.D. Conradi-Smith. A multi-generational Turing model reproduces transgressive petal phenotypes in hybrid Mimulus (2023). Bulletin of Mathematical Biology 85(12): 1-24. doi: 10.1007/s11538-023-01223-7.

Kinser, T.J., R.D. Smith, A.H. Lawrence, A.M. Cooley, M. Vallejo-Marin, G.D. Conradi-Smith, and J.R. Puzey (2021). Mechanisms driving endosperm-based hybrid incompatibilities: insights from hybrid monkeyflowers. The Plant Cell 33(7): 2235-2257. doi.org/10.1093/plcell/koab117.

Cooley, A.M., S. Schmitz, *E. J. Cabrera, *M. Cutter, *M. Sheffield, *I. Gingerich, *G. Thomas, *C. N. M. Lincoln , *V. H. Moore, *A. E. Moore, *S. A. Davidson , *N. Lonberg, *E. B. Fournier, *S. Love, *G. Posch, *M. B. Bihrle, *S. D. Mayer, *K. Om, *L. Wilson, *C. Q. Doe, *C. E. Vincent , *E. R. T. Wong, *I. Wall, *J. Wicks, *S. Roberts (2021). Melanic pigmentation and light preference within and between two Drosophila species. Ecology & Evolution 12 August 2021. doi.org/10.1002/ece3.7998. 

*Zheng, X., *K. Om, K. Stanton, D. Thomas, *P. Cheng, *A. Eggert, E. Simmons, Y.-W. Yuan, G. Conradi Smith, J.R. Puzey, A.M. Cooley (2021). The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus.   Genetics 217(2): iyaa036. doi.org/10.1093/genetics/iyaa036

Sramkoski, L.L., *W.N. McLaughlin, A.M. Cooley, D.C. Yuan, A. John, P.J. Wittkopp (2020). Genetic architecture of a body color cline in Drosophila americana. Molecular Ecology 29(15): 2840-2854. doi.org/10.1111/mec.15531

Rundel, P.W. A.M. Cooley, K.L. Gerst, E.C. Riordan, M.R. Sharifi, J.W. Sun, and J.A. Tower (2020). Functional traits of broad-leaved monocot herbs in the understory and forest edges of a Costa Rican rainforest. PeerJ 8: e9958. doi.org/10.7717/peerj.9958.

Lowry, D., J. M. Sobel, A. L. Angert, T-L. Ashman, R. L. Baker, B. K. Blackman, Y. Brandvain, K. J.R.P. Byers, A. M. Cooley, J. M. Coughlan, M. R. Dudash, C. B. Fenster, K. G. Ferris, L. Fishman, J. Friedman, D. L. Grossenbacher, L. M. Holeski, C. T. Ivey, K. M. Kay, V. A. Koelling, N. J. Kooyers, C. J. Murren, C. D. Muir, T. C Nelson, M. L. Peterson, J. R. Puzey, M. C. Rotter, J. R. Seemann, J. P. Sexton, S. N. Sheth, M. A. Streisfeld, A. L. Sweigart, A. D. Twyford, M. Vallejo-Marín, J. H. Willis, C. A. Wu, Y-W. Yuan (2019). The case for the continued use of the genus name Mimulus for all monkeyflowers. Taxon 68: 617-623. Opinion piece, not peer-reviewed.

Edger, P.P., R.D. Smith, M.R. McKain, A.M. Cooley, M. Vallejo-Marin, Y. Yuan, A.J. Bewick, L. Ji, A.E. Platts, M.J. Bowman, K.L. Childs, R.J. Schmitz, G.D. Smith, J.C. Pires, and J.R. Puzey (2017). Sub-genome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower. The Plant Cell 29: 2150-2167. doi.org/10.1105/tpc.1

Stanton, K., P.P. Edger, J.R. Puzey, T. Kinser, *P. Cheng, D.M. Vernon, N.R. Forsthoefel, and A.M. Cooley (2017). A whole transcriptome approach to evaluating reference genes for quantitative gene expression studies: A case study in Mimulus. G3: Genes, Genomes, Genetics 7(4): 1085-1095. doi.org/10.1534/g3.116.038075.

Stanton, K., *C.M. Valentin, *M.E. Wijnen, *S. Stutsman, *J.J. Palacios, and A.M. Cooley (2016). Absence of post-mating barriers between a selfing vs. outcrossing Chilean Mimulus (Phrymaceae) species pair. American Journal of Botany, 103(6): 1030-1040. doi.org/10.3732/ajb.1600079. 

John, A.V., L.L. Sramkoski, E. Walker, A.M. Cooley, and P.J. Wittkopp (2016). Sensitivity of allelic divergence to genomic position: Lessons from the Drosophila tan gene. G3: Genes, Genomes, Genetics, 6(9): 2955-2962. doi.org/10.1534/g3.116.032029.

Vallejo-Marin, M., A.M. Cooley, *M.L.Y. Qi, *M. Folmer, M.R. Mckain, and J.R. Puzey (2016). Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. American Journal of Botany, 103(7): 1272-1288. doi.org/10.1101/030932.

Vallejo-Marin, M., R.J.A. Buggs, A.M. Cooley, and J.R. Puzey (2015). Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 69(6): 1487-1500. doi.org/10.1111/evo.12678.

Cooley, A.M., *L. Shefner, *W.N. Mclaughlin, *E.E. Stewart, and P.J. Wittkopp (2012). The ontogeny of color: Developmental origins of pigment divergence in Drosophila americana and D. novamexicana. Evolution & Development 14(4): 317-325. Featured cover article. doi.org/10.1111/j.1525-142X.2012.00550. 

Wittkopp, P.J., G. Smith-Winberry, L.L. Arnold, *E.M. Thompson, A.M. Cooley, D.C. Yuan, Q. Song, and B.F. McAllister (2011). Local adaptation for body color in Drosophila americana. Heredity 106(4): 592-602.

Cooley, A.M., J.L. Modliszewski, *M.L. Rommel, and J.H. Willis (2011). Gene duplication in Mimulus underlies parallel floral evolution via independent trans-regulatory changes. Current Biology 21(8): 700-704. Featured cover article. doi.org/10.1016/j.cub.2011.03.028.   

Cooley, A.M., and J.H. Willis (2009). Genetic divergence causes parallel evolution of flower color in Chilean Mimulus. New Phytologist 183(3): 729-739. Special Issue: Plant Adaptation: Following in Darwin's Footsteps. 

Cooley, A.M., G. Carvallo, and J.H. Willis (2008). Is floral diversification associated with pollinator divergence? Flower shape, flower colour, and pollinator preference in Chilean Mimulus. Annals of Botany 101(5): 641-650. Featured cover article.  

Wu, C. A., D. B. Lowry, A. M. Cooley, K. M. Wright, Y.-W. Lee, J. H. Willis (2007). Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity 100(2): 220-230.

Cooley, A. M., A. Reich, and P. Rundel (2004). Leaf support biomechanics of neotropical understory herbs. American Journal of Botany 91(4): 573-581.