*Undergraduate co-authors

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: 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: 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: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: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: 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: 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:10.1111/j.1525-142X.2012.00550. PDF.

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:10.1016/j.cub.2011.03.028. PDF. Supplemental.

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. PDF.

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. PDF.

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. PDF.