Publications

*Undergraduate co-authors

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 (in press). Bulletin of Mathematical Biology. bioRxiv: doi.org/10.1101/2023.08.10.552669.

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.

E&DVallejo-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.

Mimulus cupreus cover photoCooley, 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. 

Bee pollinating a Mimulus - Cover photoCooley, 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.