Publications

  • 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 (In Press).
  • 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.
  • 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, in press.
  • Colbourne et al. (2011) The ecoresponsive genome of Daphnia pulex. Science: 331(6017): 555.
  • Srivastava, M et al. [TH Oakley 17th of 33 authors] (2010). The Amphimedon queenslandica genome and the evolution of animal complexity. Nature doi:10.1038/nature09201.
  • Rivera, AS., MS. Pankey, D. Plachetzki, C. Villacorta, A. Syme, J. Serb, A. Omilian, and TH Oakley. (2010) Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology 10:123.
  • DC Plachetzki, CR Fong and TH Oakley (2010). Evidence that a cyclic nucleotide gated (CNG) ion channel functioned in the ancestral animal phototransduction cascade Proceedings of the Royal Society B. With cover.
  • O. Sakarya, C. Conaco, Ö. Egecioglu, S.A. Solla, T.H. Oakley, and K.S. Kosik (2010) Evolutionary Expansion and Specialization of the PDZ Domains. Molecular Biology and Evolution. doi:10.1093/molbev/msp311.
  • TH Oakley and DC Plachetzki (2010). Key transitions during animal phototransduction evolution: Co-duplication as a null hypothesis for the evolutionary rigins of novel traits. in B Shierwater and R. DeSalle. Key Innovations in Animal Evolution. CRC Press.
  • 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.
  • TH Oakley (2009). A critique of experimental phylogenetics. in Experimental Evolution, MR Rose and T Garland, Jr (eds). University of California Press.
  • MW Cadotte J Cavender-Bares GD Tilman and TH Oakley (2009) Using evolutionary, functional and trait diversity to understand patterns of plant community productivity. PLoS One
  • Rivera AS and Oakley TH (2009). Ontogeny of extreme sexual dimorphism via tissue duplication in an ostracod (Crustacea). Evolution and Development. 11(2):233-43.
  • TH Oakley (2008). Book Review: Jay Hosler, An Evolutionary Novelty: Optical Allusions. Evolution Education and Outreach. 1(4): 548-551.
  • TH Oakley and Rivera AS. (2008) Genomics and the evolutionary origins of nervous system complexity. Current Opinion in Genetics and Development. 18(6):479-92.
  • TH Oakley and MS Pankey (2008). Opening the "black box": The genetic and biochemical basis of eye evolution. Evolution Education and Outreach. DOI 10.1007/s12052-008-0090-3.
  • 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.
  • Tinn O* and Oakley TH* (2008). Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea). Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2008.03.001.
  • Larusso ND, Ruttenberg BE, Singh AK, Oakley TH (2008). Type II Opsins: Evolutionary origin by internal domain duplication? Journal of Molecular Evolution
  • Sakarya O, Kosik KS and Oakley TH (2008) Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics
  • Lum, K.E., Syme, A.S., Schwab, A.K. and T.H. Oakley. (2008). Euphilomedes chupacabra (Ostracoda: Myodocopida: Philomedidae), a new demersal marine species from coastal Puerto Rico with male-biased vespertine swimming activity. ZOOTAXA. 1684: 35-57.
  • Rose, M.R. and Oakley, TH (2007). The New Biology: beyond the Modern Synthesis. BIOLOGY DIRECT 2:30.
  • Oakley, TH (2007) Book Review. A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. EVOLUTION AND DEVELOPMENT 9(5):514-516.
  • Oakley, TH, Plachetzki, DC and AS Rivera. (2007) Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. ARTHROPOD STRUCTURE AND DEVELOPMENT 36:386-400.
  • Oakley TH (2007) Highlights and Comments: Today's multiple choice exam: a) Gene duplication; b) Structural mutation; c) Co-option; d) Regulatory mutation; e) All of the above. EVOLUTION AND DEVELOPMENT. 9(6):523-524.
  • Plachetzki DC and Oakley TH (2007). Key transitions during the evolution of animal phototransduction: Novelty, tree thinking, co-option and co-duplication. INTEGRATIVE AND COMPARATIVE BIOLOGY.
  • Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang I-F, Sachdu D, Tidor B, Degnan B, Oakley TH, Kosik KS (2007) A Post-synaptic Scaffold at the Origin of the Animal Kingdom. PLOS ONE.
  • Oakley TH (2007). Vision. For The Encylopedia of the Rocky Intertidal. M Denny and S Gaines, eds. University of California Press.
  • Oakley TH, Ostman B, Wilson ACV (2006). Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA . 103(31): 11673-11641.
  • Lee C, Mooers AO, Blay S, Singh A, Oakley TH (2006). CoMET: A Mesquite package for comparison of continuous models of character evolution on phylogenies. EVOLUTIONARY BIOINFORMATICS ONLINE. 2:193-196.
  • Serb JM and Oakley TH (2005). Hierarchical phylogenetics as an analytical framework for evolutionary developmental biology. BIOESSAYS. 27(11):1158-66. (With Cover)
  • Plachetzki D, Serb JM, and Oakley TH (2005). New Insights Into the Evolutionary History of Photoreceptor Cells. TRENDS IN ECOLOGY AND EVOLUTION. 20: 465-467. (Commentary).
  • Oakley TH. (2005). Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: Multiple origins of bioluminescence and extreme sexual dimorphism. HYDROBIOLOGIA. 538:179-192.
  • Oakley TH, Gu Z, Abouheif E, Patel NH , and Li W-H. (2005). Functional genomic evidence for punctuated evolution of gene expression. MOLECULAR BIOLOGY AND EVOLOLUTION. 22(1): 40-50.
  • Oakley TH and Huber DR. (2004). Eye-specific expression of multiple opsin genes in ostracod crustaceans. SUMBITTED TO JOURNAL OF MOLECULAR EVOLOLUTION 59(2):239-249.
  • Wang D-Y, Oakley TH, Honeycutt R, Tsao H, Li W-H. (2004) Molecular Evolution of Bat Color Vision Genes. MOLECULAR BIOLOGY AND EVOLUTION 21(2):295–302.
  • Oakley TH. (2003). The eye as a replicating and diverging, modular developmental unit. TRENDS IN ECOLOGY AND EVOLUTION 18(12):623-627. (With Cover).
  • Oakley TH (2003). On homology of arthropod compound eyes. INTEGRATIVE AND COMPARATIVE BIOLOGY. 43(4). (With Cover).
  • Patek SN and Oakley TH. (2003). Comparative tests of evolutionary trade-offs in a Palinurid lobster acoustic system. EVOLUTION. 57(9):2082-2100. (With Cover).
  • Oakley TH. (2003). Maximum likelihood models of trait evolution. COMMENTS ON THEORETICAL BIOLOGY 8:1-17.
  • Oakley TH and Cunningham CW. (2002). Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA 99(3):1426-1430.
  • Oakley TH and Cunningham CW. (2000). Independent contrasts succeed where ancestor reconstruction fails in a known bacteriphage phylogeny. EVOLUTION 54(2):397-405
  • Oakley TH and Phillips RB. (1999). Phylogeny of Salmonine Fish Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa. MOLECULAR PHYLOGENETICS AND EVOLUTION 11:381-393.
  • Cunningham CW, Omland KE, and Oakley TH (1998) Reconstructing ancestral character states: A critical reappraisal. TRENDS IN ECOLOGY AND EVOLUTION 13(4):361-366.
  • Domanico MJ, Phillips RP and Oakley TH. (1997) Phylogenetic analysis of Pacific Salmon (Genus Oncorhynchus) using nuclear and mitochondrial DNA. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES 54:1865-1872.
  • Phillips RB and Oakley TH (1997) Molecular systematics of the subfamily Salmoninae based on nuclear and mitochondrial markers. In: Kocher TD and Stepien CA (ed.) In: Molecular Systematics of Fishes. ACADEMIC PRESS.
  • Moran P, Reed KM, Perez J, Oakley TH, Phillps RB, Garcia-Vasquez E, Pendas AM (1997) Physical localization and characterization of the BglI element in the genome of Atlantic Salmon (Salmo salar L.) and Brown Trout (S. trutta L.). GENE 194:9-18.
  • Reed KM, Oakley TH, and Phillips, RB (1997) An AluI repetitive element isolated from lake trout (Salvelinus namaycush) maps to the intergenic spacer region of the rDNA cistron. GENE 186:7-11.
  • Setterquist RA, Smith GK, Oakley TH, Lee YH, Fox GE (1996) Sequencing and purification of the Vibrio proteolyticus 5S rRNA binding protein L18 for in vitro and in vivo binding assays. GENE 183:237-242.
  • Phillips RB, Oakley TH, and Davis EL (1995) Support for the paraphyly of Hucho (Salmonidae) based on rDNA RFLP's. JOURNAL OF FISH BIOLOGY 47: 956-961