Todd Oakley

(805) 893-4715
4101 Life Sciences Building
Oakley Lab


Todd Oakley is an evolutionary biologist and professor in the EEMB Department at the University of California, Santa Barbara. Dr. Oakley earned a BS and MS from the University of Wisconsin-Milwaukee and his PhD in Biological Sciences from Duke University. He was an NIH-NRSA postdoctoral fellow at the University of Chicago. He joined the EEMB faculty in 2003. Dr. Oakley currently serves as Vice Chair of resources for EEMB, and he is a member of UCSB’s Marine Science Institute. He is the PI or Co-PI on multiple federally funded research projects in evolution, ecology, and genomics.


We currently (as of October 2012) are following four main research paths:

  1. Origins of vision and light interaction genes: Eyes and vision are often considered mind-bogglingly complex, begging the question of how evolution could have produced them. We are addressing this question by examining the components of eyes and vision in a phylogenetic context, to trace those components to their very origins. This has led to behavioral studies in Cnidaria and a chytrid fungus.
  2. Evolution of arthropod eyes. Arthropods have more types of eye design that any other phylum. How and why did this diversity arise? We are combining a variety of tools and approaches from high throughput sequencing to phylogenetics to behavioral studies in order to understand how there is so much variation in arthropod eyes. In particular we are studying ostracod crustaceans, including a group where only males have eyes.
  3. Evolutionary genomics of molluscan novelties. Evolutionary convergence provides an element of replication within the singular history of life, and can yield insight into the most general evolutionary questions. Do convergent traits utilize the same genes? We are examining these types of questions in mollusks like octopus, squid, and chitons. Cephalopods evolved convergent light organs, and chitons convergent eyes.
  4. Evolution, productivity, niche, and the genes that drive them. The world is characterized by a spectacular variety of life. But loss of biodiversity through extinction is one of the most pronounced forms of environmental change. Through collaboration, we are examining differences in gene expression when algae are grown alone, compared to in competition. Our goal is to understand the genetic basis and phylogenetic correlates of competition, and to use that information to inform algal biofuel production.

Selected Publications

  • TH Oakley JM Wolfe, AR Lindgren and AK Zaharoff (2012) Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement and Pancrustacean Phylogeny. Molecular Biology and Evolution 10.1093/molbev/mss216.
  • DC Plachetzki CR Fong and TH Oakley (2012). Cnidocyte discharge is regulated by light and opsin-mediated phototransduction. BMC Biology. 10:17.
  • AS Rivera N Ozturk B Fahey DC Plachetzki BM Degnan A Sancar and TH Oakley (2012). Blue light-receptive Cryptochrome is expressed in a sponge eye lacking neurons and opsin. Journal of Experimental Biology 215:1278-1286.
  • AE Syme and TH Oakley (2012). Dispersal between Shallow and Abyssal Seas and Evolutionary Loss and Regain of Compound Eyes in Cylindroleberidid Ostracods: Conflicting Conclusions from Different Comparative Methods. Systematic Biology. 61 (2): 314-336.
  • AR Lindgren, MS Pankey, FG Hochberg and TH Oakley (2012). A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evolutionary Biology 12:129.
  • MD Ramirez, DI Speiser, MS Pankey and TH Oakley (2011). Understanding the dermal light sense in the context of integrative photoreceptor cell biology. Visual Neuroscience 28(4):265-279.
  • Colbourne et al. (2011) The ecoresponsive genome of Daphnia pulex. Science: 331(6017): 555-561.
  • D Tong, N Rozas, TH Oakley, J Mitchell, N Colley, and MJ McFall-Ngai (2009). Light perception in a bioluminescent organ. Proceedings of the National Academy of Sciences USA. 106(24):9836-41.
  • Cadotte MW, Cardinale BJ, Oakley TH (2008). Evolutionary history explains biodiversity effects on plant productivity. Proceedings of the National Academy of Sciences USA. 105:17012-17017.

External Publication List

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