Todd Hampton Oakley, Ph.D. - Publications

Affiliations: 
Ecology Evolution Marine Biology University of California, Santa Barbara, Santa Barbara, CA, United States 
Area:
evolution, vision, invertebrate zoology, phylogenetics
Website:
http://www.lifesci.ucsb.edu/eemb/labs/oakley/

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Stahl BA, Gross JB, Speiser DI, Oakley TH, Patel NH, Gould DB, Protas ME. A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. Plos One. 10: e0140484. PMID 26462237 DOI: 10.1371/journal.pone.0140484  1
2015 Narwani A, Alexandrou MA, Herrin J, Vouaux A, Zhou C, Oakley TH, Cardinale BJ. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae. Plos One. 10: e0137085. PMID 26348482 DOI: 10.1371/journal.pone.0137085  1
2015 Henze MJ, Oakley TH. The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins. Integrative and Comparative Biology. 55: 830-42. PMID 26319405 DOI: 10.1093/icb/icv100  1
2015 Ramirez MD, Oakley TH. Eye-independent, light-activated chromatophore expansion (LACE) and expression of phototransduction genes in the skin of Octopus bimaculoides. The Journal of Experimental Biology. 218: 1513-20. PMID 25994633 DOI: 10.1242/jeb.110908  1
2015 Battelle BA, Kempler KE, Saraf SR, Marten CE, Dugger DR, Speiser DI, Oakley TH. Opsins in Limulus eyes: characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes. The Journal of Experimental Biology. 218: 466-79. PMID 25524988 DOI: 10.1242/jeb.116087  1
2015 Alexandrou MA, Cardinale BJ, Hall JD, Delwiche CF, Fritschie K, Narwani A, Venail PA, Bentlage B, Pankey MS, Oakley TH. Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae. Proceedings. Biological Sciences / the Royal Society. 282: 20141745. PMID 25473009 DOI: 10.1098/rspb.2014.1745  1
2015 Oakley TH, Speiser DI. How Complexity Originates: The Evolution of Animal Eyes Annual Review of Ecology, Evolution, and Systematics. 46: 237-260. DOI: 10.1146/annurev-ecolsys-110512-135907  1
2015 Cardinale BJ, Venail P, Gross K, Oakley TH, Narwani A, Allan E, Flombaum P, Joshi J, Reich PB, Tilman D, van Ruijven J. Further re-analyses looking for effects of phylogenetic diversity on community biomass and stability Functional Ecology. 29: 1607-1610. DOI: 10.1111/1365-2435.12540  1
2015 Venail P, Gross K, Oakley TH, Narwani A, Allan E, Flombaum P, Isbell F, Joshi J, Reich PB, Tilman D, van Ruijven J, Cardinale BJ. Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies Functional Ecology. 29: 615-626. DOI: 10.1111/1365-2435.12432  1
2014 Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, ... ... Oakley TH, et al. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. Bmc Bioinformatics. 15: 350. PMID 25407802 DOI: 10.1186/s12859-014-0350-x  1
2014 Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences of the United States of America. 111: E4736-42. PMID 25336755 DOI: 10.1073/pnas.1416574111  1
2014 Marxen JC, Pick C, Oakley TH, Burmester T. Occurrence of hemocyanin in ostracod crustaceans. Journal of Molecular Evolution. 79: 3-11. PMID 25135304 DOI: 10.1007/s00239-014-9636-x  1
2014 Fritschie KJ, Cardinale BJ, Alexandrou MA, Oakley TH. Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis. Ecology. 95: 1407-17. PMID 25000771 DOI: 10.1890/13-0986.1  1
2014 Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CK, Chen W, Lopker KB. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. Bmc Bioinformatics. 15: 230. PMID 24990571 DOI: 10.1186/1471-2105-15-230  1
2014 Bielecki J, Zaharoff AK, Leung NY, Garm A, Oakley TH. Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa). Plos One. 9: e98870. PMID 24901369 DOI: 10.1371/journal.pone.0098870  1
2014 Churchill CK, Ellis EA, Pique AE, Oakley TH. Two new sympatric species of Eusarsiella (Ostracoda: Myodocopida: Sarsiellidae) from the Florida Keys with a morphological phylogeny of Sarsiellinae. Zootaxa. 444-58. PMID 24871023 DOI: 10.11646/zootaxa.3802.4.2  1
2014 Peyer SM, Pankey MS, Oakley TH, McFall-Ngai MJ. Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues. Mechanisms of Development. 131: 111-26. PMID 24157521 DOI: 10.1016/j.mod.2013.09.004  1
2014 Venail PA, Narwani A, Fritschie K, Alexandrou MA, Oakley TH, Cardinale BJ. The influence of phylogenetic relatedness on species interactions among freshwater green algae in a mesocosm experiment Journal of Ecology. 102: 1288-1299. DOI: 10.1111/1365-2745.12271  1
2014 Speiser DI, DeMartini DG, Oakley TH. The shell-eyes of the chiton Acanthopleura granulata (Mollusca, Polyplacophora) use pheomelanin as a screening pigment Journal of Natural History. 48: 2899-2911. DOI: 10.1080/00222933.2014.959572  1
2013 Narwani A, Alexandrou MA, Oakley TH, Carroll IT, Cardinale BJ. Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae. Ecology Letters. 16: 1373-81. PMID 24112458 DOI: 10.1111/ele.12182  1
2013 Venail PA, Alexandrou MA, Oakley TH, Cardinale BJ. Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae. Proceedings. Biological Sciences / the Royal Society. 280: 20131548. PMID 23945692 DOI: 10.1098/rspb.2013.1548  1
2013 Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH. Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Molecular Phylogenetics and Evolution. 69: 514-23. PMID 23933489 DOI: 10.1016/j.ympev.2013.07.026  1
2013 Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH. The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics. Integrative and Comparative Biology. 53: 39-49. PMID 23727979 DOI: 10.1093/icb/ict060  1
2013 Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH. Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea). Integrative and Comparative Biology. 53: 78-88. PMID 23652199 DOI: 10.1093/icb/ict025  1
2013 Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny. Molecular Biology and Evolution. 30: 215-33. PMID 22977117 DOI: 10.1093/molbev/mss216  1
2012 Lindgren AR, Pankey MS, Hochberg FG, Oakley TH. 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. PMID 22839506 DOI: 10.1186/1471-2148-12-129  1
2012 Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH. Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin. The Journal of Experimental Biology. 215: 1278-86. PMID 22442365 DOI: 10.1242/jeb.067140  1
2012 Plachetzki DC, Fong CR, Oakley TH. Cnidocyte discharge is regulated by light and opsin-mediated phototransduction. Bmc Biology. 10: 17. PMID 22390726 DOI: 10.1186/1741-7007-10-17  1
2012 Syme AE, Oakley TH. 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: 314-36. PMID 21865337 DOI: 10.1093/sysbio/syr085  1
2011 Ramirez MD, Speiser DI, Pankey MS, Oakley TH. Understanding the dermal light sense in the context of integrative photoreceptor cell biology. Visual Neuroscience. 28: 265-79. PMID 21736861 DOI: 10.1017/S0952523811000150  1
2011 Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, et al. The ecoresponsive genome of Daphnia pulex. Science (New York, N.Y.). 331: 555-61. PMID 21292972 DOI: 10.1126/science.1197761  1
2010 Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, ... ... Oakley TH, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 466: 720-6. PMID 20686567 DOI: 10.1038/nature09201  1
2010 Rivera AS, Pankey MS, Plachetzki DC, Villacorta C, Syme AE, Serb JM, Omilian AR, Oakley TH. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. Bmc Evolutionary Biology. 10: 123. PMID 20433736 DOI: 10.1186/1471-2148-10-123  1
2010 Plachetzki DC, Fong CR, Oakley TH. The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway. Proceedings. Biological Sciences / the Royal Society. 277: 1963-9. PMID 20219739 DOI: 10.1098/rspb.2009.1797  1
2010 Sakarya O, Conaco C, Egecioglu O, Solla SA, Oakley TH, Kosik KS. Evolutionary expansion and specialization of the PDZ domains. Molecular Biology and Evolution. 27: 1058-69. PMID 20026484 DOI: 10.1093/molbev/msp311  1
2010 Cadotte MW, Jonathan Davies T, Regetz J, Kembel SW, Cleland E, Oakley TH. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters. 13: 96-105. PMID 19903196 DOI: 10.1111/j.1461-0248.2009.01405.x  1
2009 Tong D, Rozas NS, Oakley TH, Mitchell J, Colley NJ, McFall-Ngai MJ. Evidence for light perception in a bioluminescent organ. Proceedings of the National Academy of Sciences of the United States of America. 106: 9836-41. PMID 19509343 DOI: 10.1073/pnas.0904571106  1
2009 Cadotte MW, Cavender-Bares J, Tilman D, Oakley TH. Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity. Plos One. 4: e5695. PMID 19479086 DOI: 10.1371/journal.pone.0005695  1
2009 Rivera AS, Oakley TH. Ontogeny of sexual dimorphism via tissue duplication in an ostracod (Crustacea). Evolution & Development. 11: 233-43. PMID 19245554 DOI: 10.1111/j.1525-142X.2009.00323.x  1
2009 Oakley TH. A critique of experimental phylogenetics Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 678-688.  1
2008 Gould RM, Oakley T, Goldstone JV, Dugas JC, Brady ST, Gow A. Myelin sheaths are formed with proteins that originated in vertebrate lineages. Neuron Glia Biology. 4: 137-52. PMID 19737434 DOI: 10.1017/S1740925X09990238  1
2008 Oakley TH, Rivera AS. Genomics and the evolutionary origins of nervous system complexity. Current Opinion in Genetics & Development. 18: 479-92. PMID 19152785 DOI: 10.1016/j.gde.2008.12.002  1
2008 Cadotte MW, Cardinale BJ, Oakley TH. Evolutionary history and the effect of biodiversity on plant productivity. Proceedings of the National Academy of Sciences of the United States of America. 105: 17012-7. PMID 18971334 DOI: 10.1073/pnas.0805962105  1
2008 Tinn O, Oakley TH. Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea). Molecular Phylogenetics and Evolution. 48: 157-67. PMID 18482852 DOI: 10.1016/j.ympev.2008.03.001  1
2008 Larusso ND, Ruttenberg BE, Singh AK, Oakley TH. Type II opsins: evolutionary origin by internal domain duplication? Journal of Molecular Evolution. 66: 417-23. PMID 18392762 DOI: 10.1007/s00239-008-9076-6  1
2008 Sakarya O, Kosik KS, Oakley TH. Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics (Oxford, England). 24: 606-12. PMID 18184685 DOI: 10.1093/bioinformatics/btn005  1
2008 Lum KE, Syme AE, Schwab AK, Oakley TH. Euphilomedes chupacabra (Ostracoda: Myodocopida: Philomedidae), a new demersal marine species from coastal Puerto Rico with male-biased vespertine swimming activity Zootaxa. 35-57.  1
2007 Plachetzki DC, Oakley TH. Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication. Integrative and Comparative Biology. 47: 759-69. PMID 21669757 DOI: 10.1093/icb/icm050  1
2007 Oakley TH, Plachetzki DC, Rivera AS. Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod Structure & Development. 36: 386-400. PMID 18089117 DOI: 10.1016/j.asd.2007.08.002  1
2007 Rose MR, Oakley TH. The new biology: beyond the Modern Synthesis. Biology Direct. 2: 30. PMID 18036242 DOI: 10.1186/1745-6150-2-30  1
2007 Oakley TH. Today's multiple choice exam: (a) gene duplication; (b) structural mutation; (c) co-option; (d) regulatory mutation; (e) all of the above. Evolution & Development. 9: 523-4. PMID 17976048 DOI: 10.1111/j.1525-142X.2007.00192.x  1
2007 Plachetzki DC, Degnan BM, Oakley TH. The origins of novel protein interactions during animal opsin evolution. Plos One. 2: e1054. PMID 17940617 DOI: 10.1371/journal.pone.0001054  1
2007 Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, Kosik KS. A post-synaptic scaffold at the origin of the animal kingdom. Plos One. 2: e506. PMID 17551586 DOI: 10.1371/journal.pone.0000506  1
2006 Oakley TH, Ostman B, Wilson AC. Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. Proceedings of the National Academy of Sciences of the United States of America. 103: 11637-41. PMID 16864793 DOI: 10.1073/pnas.0600750103  1
2005 Plachetzki DC, Serb JM, Oakley TH. New insights into the evolutionary history of photoreceptor cells. Trends in Ecology & Evolution. 20: 465-7. PMID 16701418 DOI: 10.1016/j.tree.2005.07.001  1
2005 Serb JM, Oakley TH. Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 27: 1158-66. PMID 16237676 DOI: 10.1002/bies.20291  1
2005 Oakley TH, Gu Z, Abouheif E, Patel NH, Li WH. Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular Biology and Evolution. 22: 40-50. PMID 15356281 DOI: 10.1093/molbev/msh257  1
2005 Oakley TH. Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: Multiple origins of bioluminescence and extreme sexual dimorphism Hydrobiologia. 538: 179-192. DOI: 10.1007/s10750-004-4961-5  1
2004 Oakley TH, Huber DR. Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans. Journal of Molecular Evolution. 59: 239-49. PMID 15486697 DOI: 10.1007/s00239-004-2618-7  1
2004 Wang D, Oakley T, Mower J, Shimmin LC, Yim S, Honeycutt RL, Tsao H, Li WH. Molecular evolution of bat color vision genes. Molecular Biology and Evolution. 21: 295-302. PMID 14660703 DOI: 10.1093/molbev/msh015  1
2003 Oakley TH. On homology of arthropod compound eyes. Integrative and Comparative Biology. 43: 522-30. PMID 21680460 DOI: 10.1093/icb/43.4.522  1
2003 Patek SN, Oakley TH. Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. Evolution; International Journal of Organic Evolution. 57: 2082-100. PMID 14575329  1
2003 Oakley TH. The eye as a replicating and diverging, modular developmental unit Trends in Ecology and Evolution. 18: 623-627. DOI: 10.1016/j.tree.2003.09.005  1
2002 Oakley TH, Cunningham CW. Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences of the United States of America. 99: 1426-30. PMID 11818548 DOI: 10.1073/pnas.032483599  1
2000 Oakley TH, Cunningham CW. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution; International Journal of Organic Evolution. 54: 397-405. PMID 10937216  1
1999 Oakley TH, Phillips RB. Phylogeny of salmonine fishes based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa. Molecular Phylogenetics and Evolution. 11: 381-93. PMID 10196079 DOI: 10.1006/mpev.1998.0599  1
1998 Cunningham CW, Omland KE, Oakley TH. Reconstructing ancestral character states: a critical reappraisal. Trends in Ecology & Evolution. 13: 361-6. PMID 21238344 DOI: 10.1016/S0169-5347(98)01382-2  1
1997 Moran P, Reed KM, PérezJ, Oakley TH, Phillips RB, Garcia-Vazquez E, Pendas AM. Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.). Gene. 194: 9-18. PMID 9266667 DOI: 10.1016/S0378-1119(97)00093-0  1
1997 Reed KM, Oakley TH, Phillips RB. An AluI fragment isolated from lake trout (Salvelinus namaycush), maps to the intergenic spacer region of the rDNA cistron. Gene. 186: 7-11. PMID 9047338 DOI: 10.1016/S0378-1119(96)00655-5  1
1997 Domanico MJ, Phillips RB, Oakley TH. Phylogenetic analysis of Pacific salmon (genus Oncorhynchus) using nuclear and mitochondrial DNA sequences Canadian Journal of Fisheries and Aquatic Sciences. 54: 1865-1872. DOI: 10.1139/cjfas-54-8-1865  1
1996 Setterquist RA, Smith GK, Oakley TH, Lee YH, Fox GE. Sequence, overproduction and purification of Vibrio proteolyticus ribosomal protein L18 for in vitro and in vivo studies. Gene. 183: 237-42. PMID 8996113 DOI: 10.1016/S0378-1119(96)00402-7  1
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