Man with dark hair and beard wearing glasses and grey button up shirt standing in front of Old Centre

Kelly O'Quin

Elizabeth Molloy Dowling Associate Professor of Biology

Offices & Programs


PhD - University of Maryland
BS - Louisiana State University


Kelly O'Quin started working at Centre in 2014. Dr. O'Quin's research focuses on the use of statistical and bioinformatic techniques to study microevolution. His main research focuses on identifying genes and cell signaling pathways responsible for changes in eye development, structure, and function in Mexican blind cavefishes.  

In addition to this work, students in Dr. O'Quin's classes have also worked on projects to identify novel viruses and monitor coral reef health -- and have even published their results! Dr. O'Quin has published his research with undergraduate co-authors in the journals PLOS ONE, BMC Evolutionary Biology, Evolution & Development, and the Journal of Anatomy. He enjoys mentoring research students interested in evolutionary biology, genetics, statistics, and genomics. 


  • KY INBR Excellence IDeA Next Gen Award (2021)


  • Evolution, Diversity, and Ecology
  • Principles of Genetics
  • Biostatistics
  • Developmental Biology
  • Bioinformatics & Functional Genomics


  • Gudlavalleti BS, Phung T, Barton CL, Graul BL, Griffin JT, Hays CJ, Liang DR, Rutledge LM, Szalanczy AM, Becker A, Horn B, Gaffney R, King R, Rinehart C, Staples A, Nydam M, O'Quin KE. 2020. Whole genome sequencing reveals an allele responsible for clear vs. turbid plaque morphology in a Mycobacteriophage. BMC Microbiology 20(1):1-8.
  • Kindl G, O'Quin KE. 2019. On intra- and inter-specific variation in teleost scleral ossification. The Anatomical Record 302:1238-1249.
  • Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandzija H, Borowsky R, Espinasa L, O'Quin KE, Ornelas-Garcia CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. 2018. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Molecular Ecology 27:4397-4416.
  • Lyon A, Powers A, Gross JB, O'Quin KE. 2017. Two three genes control scleral ossicle formation via epistasis in the cavefish Astyanax mexicanus. PLoS ONE 12:e0171061.
  • Gregory AL, Sears BR, Wooten JA, Camp CD, Falk A, O'Quin KE, Pauley TK. 2016. Evolution of dentition in salamanders: relative roles of phylogeny and diet. Biological Journal of the Linnean Society. DOI: 10.1111/bij.12831.
  • O'Quin KE, McGaugh SE. 2014. The genetic bases of troglomorphy in Astyanax: How far have we come and where do we go from here?  In: Keen AD, Yoshizawa M, McGaugh SE (Eds.) The Biology and Evolution of the Mexican Cavefish. Elsevier: Waltham, MA. 412 pg.
  • O'Quin KE, Doshi P, Lyon A, Hoenemeyer E, Yoshizawa M, Jeffery WR. 2015. Complex evolutionary and genetic patterns characterize the loss of scleral ossification in the blind cavefish Astyanax mexicanus. PLoS ONE 10:e0142207. 
  • Yoshizawa M, Quin KE, Jeffery WR, Keen AD. 2014. Distinct genetic architectures underlie the convergence of foraging-related traits in the Mexican cavefish. BMC Biology 13:15.
  • McGaugh S, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery W, Keene A, Ma L, Murphy D, Quin KE, et al. 2014. The cavefish genome reveals candidate genes for eye loss. Nature Communications 5:5307.
  • Schulte J, O'Brien CS, Conte M, O'Quin KE, Carleton KL. Interspecific variation in Rx1 expression controls opsin expression and causes visual system diversity in African cichlid fishes. 2013. Molecular Biology and Evolution. doi: 10.1093/molbev/msu172.
  • Yoshizawa M, O'Quin KE, Jeffery WR. 2013. Evolution of adaptive behavior and its sensory receptors can promote eye regression in blind cavefish: A Reply to Borowsky (2013). BMC Biology 11:82.
  • Yoshizawa M, O'Quin KE, Jeffery WR. 2013. QTL clustering as a mechanism for rapid multi-trait evolution. Communicative and Integrative Biology 6:e24548.
  • O'Quin KE, Yoshizawa M, Doshi P, Jeffery WR. 2012. Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus. PLoS ONE 8:e57281 F1000.
  • Yoshizawa M, Yamamoto Y, O'Quin KE, Jeffery WR. The evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish. BMC Biology 10:108.
  • O'Quin KE, Schulte J, Patel Z, Kahn N, Naseer Z, Wang H, Hofmann CM, Ser J, Conte M, Carleton KL. 2012. Evolution of cichlid vision via trans-regulatory divergence. BMC Evolutionary Biology 12:251.
  • O'Quin KE, Smith AR, Sharma A, Carleton KL. 2011. New evidence for the role of heterochrony in the repeated evolution of cichlid opsin expression. Evolution & Development 13:192-203.
  • O'Quin KE, Smith D, Naseer Z, Schulte J, Engle SD, Loh Y-HE, Streelman JT, Boore JL, Carleton KL. 2011. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. BMC Evolutionary Biology 11:120. 
  • Hofmann CM, O'Quin KE, Marshall NJ, Carleton KL. 2010. The relationship between lens transmittance and opsin gene expression in cichlids from Lake Malawi. Vision Research 50: 357-363.
  • Derryberry E, Claramunt S, O'Quin KE, Aleixo A, Chesser RT, Remsen Jr. JV, Brumfield RT. 2010. Pseud-asthenes, a new genus of ovenbird (Aves: Passeriformes: Furnariidae). Zootaxa 2416:61-68.
  • Hofmann CM, O'Quin KE, Smith AR, Carleton KL. 2010. Plasticity of opsin gene expression in cichlids from Lake Malawi. Molecular Ecology 19:2064-2074.
  • O'Quin KE, Hofmann CM, Hofmann HA, Carleton KL. 2010. Parallel evolution of opsin gene expression in African cichlid fishes. Molecular Biology and Evolution 27:2839-2854.
  • Hofmann CM*, O'Quin KE*, Marshall NJ, Cronin TW, Seehausen O, Carleton KL. 2009. The eyes have it: regulatory and structural changes both underlie cichlid visual pigment diversity. PLoS Biology 7:e1000266.

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