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Light-induced stress as a primary evolutionary driver of eye origins.

Swafford AJM, Oakley TH.

Integr Comp Biol. 2019 Oct 1;59(4):739-750. doi: 10.1093/icb/icz064.


Luciferase gene of a Caribbean fireworm (Syllidae) from Puerto Rico.

Mitani Y, Yasuno R, Futahashi R, Oakley TH, Ohmiya Y.

Sci Rep. 2019 Sep 10;9(1):13015. doi: 10.1038/s41598-019-49538-7.


Context-dependent evolution of ostracod morphology along the ecogeographical gradient of ocean depth.

Juarez BH, Speiser DI, Oakley TH.

Evolution. 2019 Jun;73(6):1213-1225. doi: 10.1111/evo.13748. Epub 2019 May 8.


Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies.

Hensley NM, Ellis EA, Gerrish GA, Torres E, Frawley JP, Oakley TH, Rivers TJ.

Proc Biol Sci. 2019 Jan 16;286(1894):20182621. doi: 10.1098/rspb.2018.2621.


Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3030-3035. doi: 10.1073/pnas.1817322116. Epub 2019 Jan 11.


Prolific Origination of Eyes in Cnidaria with Co-option of Non-visual Opsins.

Picciani N, Kerlin JR, Sierra N, Swafford AJM, Ramirez MD, Roberts NG, Cannon JT, Daly M, Oakley TH.

Curr Biol. 2018 Aug 6;28(15):2413-2419.e4. doi: 10.1016/j.cub.2018.05.055. Epub 2018 Jul 19.


Ecological Engineering Helps Maximize Function in Algal Oil Production.

Jackrel SL, Narwani A, Bentlage B, Levine RB, Hietala DC, Savage PE, Oakley TH, Denef VJ, Cardinale BJ.

Appl Environ Microbiol. 2018 Jul 17;84(15). pii: e00953-18. doi: 10.1128/AEM.00953-18. Print 2018 Aug 1.


Multimodal sensorimotor system in unicellular zoospores of a fungus.

Swafford AJM, Oakley TH.

J Exp Biol. 2018 Jan 19;221(Pt 2). pii: jeb163196. doi: 10.1242/jeb.163196.


Furcation and fusion: The phylogenetics of evolutionary novelty.

Oakley TH.

Dev Biol. 2017 Nov 1;431(1):69-76. doi: 10.1016/j.ydbio.2017.09.015. Epub 2017 Sep 18. Review.


The Genome Sizes of Ostracod Crustaceans Correlate with Body Size and Evolutionary History, but not Environment.

Jeffery NW, Ellis EA, Oakley TH, Gregory TR.

J Hered. 2017 Sep 1;108(6):701-706. doi: 10.1093/jhered/esx055.


Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution.

Tanner AR, Fuchs D, Winkelmann IE, Gilbert MT, Pankey MS, Ribeiro ÂM, Kocot KM, Halanych KM, Oakley TH, da Fonseca RR, Pisani D, Vinther J.

Proc Biol Sci. 2017 Mar 15;284(1850). pii: 20162818. doi: 10.1098/rspb.2016.2818.


The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins.

Ramirez MD, Pairett AN, Pankey MS, Serb JM, Speiser DI, Swafford AJ, Oakley TH.

Genome Biol Evol. 2016 Dec 1;8(12):3640-3652. doi: 10.1093/gbe/evw248.


High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays.

Ellis EA, Oakley TH.

Curr Biol. 2016 Jul 25;26(14):1916-21. doi: 10.1016/j.cub.2016.05.043. Epub 2016 Jun 23.


A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus.

Stahl BA, Gross JB, Speiser DI, Oakley TH, Patel NH, Gould DB, Protas ME.

PLoS One. 2015 Oct 13;10(10):e0140484. doi: 10.1371/journal.pone.0140484. eCollection 2015.


Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae.

Narwani A, Alexandrou MA, Herrin J, Vouaux A, Zhou C, Oakley TH, Cardinale BJ.

PLoS One. 2015 Sep 8;10(9):e0137085. doi: 10.1371/journal.pone.0137085. eCollection 2015.


The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins.

Henze MJ, Oakley TH.

Integr Comp Biol. 2015 Nov;55(5):830-42. doi: 10.1093/icb/icv100. Epub 2015 Aug 28. Review.


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.

Battelle BA, Kempler KE, Saraf SR, Marten CE, Dugger DR Jr, Speiser DI, Oakley TH.

J Exp Biol. 2015 Feb 1;218(Pt 3):466-79. doi: 10.1242/jeb.116087. Epub 2014 Dec 18.


Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae.

Alexandrou MA, Cardinale BJ, Hall JD, Delwiche CF, Fritschie K, Narwani A, Venail PA, Bentlage B, Pankey MS, Oakley TH.

Proc Biol Sci. 2015 Jan 22;282(1799):20141745. doi: 10.1098/rspb.2014.1745.


Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

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, Zigler KS, Crandall KA, Oakley TH.

BMC Bioinformatics. 2014 Nov 19;15:350. doi: 10.1186/s12859-014-0350-x.


Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid.

Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4736-42. doi: 10.1073/pnas.1416574111. Epub 2014 Oct 21.


Occurrence of hemocyanin in ostracod crustaceans.

Marxen JC, Pick C, Oakley TH, Burmester T.

J Mol Evol. 2014 Aug;79(1-2):3-11. doi: 10.1007/s00239-014-9636-x. Epub 2014 Aug 19.


The comb jelly opsins and the origins of animal phototransduction.

Feuda R, Rota-Stabelli O, Oakley TH, Pisani D.

Genome Biol Evol. 2014 Jul 24;6(8):1964-71. doi: 10.1093/gbe/evu154.


Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis.

Fritschie KJ, Cardinale BJ, Alexandrou MA, Oakley TH.

Ecology. 2014 May;95(5):1407-17.


Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.

Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CK, Chen W, Lopker KB.

BMC Bioinformatics. 2014 Jul 2;15:230. doi: 10.1186/1471-2105-15-230.


Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa).

Bielecki J, Zaharoff AK, Leung NY, Garm A, Oakley TH.

PLoS One. 2014 Jun 5;9(6):e98870. doi: 10.1371/journal.pone.0098870. eCollection 2014.


Two new sympatric species of Eusarsiella (Ostracoda: Myodocopida: Sarsiellidae) from the Florida Keys with a morphological phylogeny of Sarsiellinae.

Churchill CK, Ellis EA, Pique AE, Oakley TH.

Zootaxa. 2014 May 28;(3802):444-58. doi: 10.11646/zootaxa.3802.4.3. Erratum in: Zootaxa. 2014;3884(6):600.


Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues.

Peyer SM, Pankey MS, Oakley TH, McFall-Ngai MJ.

Mech Dev. 2014 Feb;131:111-26. doi: 10.1016/j.mod.2013.09.004. Epub 2013 Oct 21.


Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae.

Narwani A, Alexandrou MA, Oakley TH, Carroll IT, Cardinale BJ.

Ecol Lett. 2013 Nov;16(11):1373-81. doi: 10.1111/ele.12182. Epub 2013 Sep 23.


Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae.

Venail PA, Alexandrou MA, Oakley TH, Cardinale BJ.

Proc Biol Sci. 2013 Aug 14;280(1768):20131548. doi: 10.1098/rspb.2013.1548. Print 2013 Oct 7.


Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae.

Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH.

Mol Phylogenet Evol. 2013 Dec;69(3):514-23. doi: 10.1016/j.ympev.2013.07.026. Epub 2013 Aug 7.


The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics.

Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH.

Integr Comp Biol. 2013 Jul;53(1):39-49. doi: 10.1093/icb/ict060. Epub 2013 May 31.


Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea).

Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.

Integr Comp Biol. 2013 Jul;53(1):78-88. doi: 10.1093/icb/ict025. Epub 2013 May 7.


Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny.

Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK.

Mol Biol Evol. 2013 Jan;30(1):215-33. doi: 10.1093/molbev/mss216. Epub 2012 Sep 12.


Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin.

Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH.

J Exp Biol. 2012 Apr 15;215(Pt 8):1278-86. doi: 10.1242/jeb.067140.


Cnidocyte discharge is regulated by light and opsin-mediated phototransduction.

Plachetzki DC, Fong CR, Oakley TH.

BMC Biol. 2012 Mar 5;10:17. doi: 10.1186/1741-7007-10-17.


Understanding the dermal light sense in the context of integrative photoreceptor cell biology.

Ramirez MD, Speiser DI, Pankey MS, Oakley TH.

Vis Neurosci. 2011 Jul;28(4):265-79. doi: 10.1017/S0952523811000150. Epub 2011 Jul 8. Review.


The ecoresponsive genome of Daphnia pulex.

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, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.


The Amphimedon queenslandica genome and the evolution of animal complexity.

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, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS.

Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.


Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach.

Rivera AS, Pankey MS, Plachetzki DC, Villacorta C, Syme AE, Serb JM, Omilian AR, Oakley TH.

BMC Evol Biol. 2010 Apr 30;10:123. doi: 10.1186/1471-2148-10-123.


The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway.

Plachetzki DC, Fong CR, Oakley TH.

Proc Biol Sci. 2010 Jul 7;277(1690):1963-9. doi: 10.1098/rspb.2009.1797. Epub 2010 Mar 10.


Evolutionary expansion and specialization of the PDZ domains.

Sakarya O, Conaco C, Egecioglu O, Solla SA, Oakley TH, Kosik KS.

Mol Biol Evol. 2010 May;27(5):1058-69. doi: 10.1093/molbev/msp311. Epub 2009 Dec 21.


Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history.

Cadotte MW, Jonathan Davies T, Regetz J, Kembel SW, Cleland E, Oakley TH.

Ecol Lett. 2010 Jan;13(1):96-105. doi: 10.1111/j.1461-0248.2009.01405.x. Epub 2009 Nov 9.


Evidence for light perception in a bioluminescent organ.

Tong D, Rozas NS, Oakley TH, Mitchell J, Colley NJ, McFall-Ngai MJ.

Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9836-41. doi: 10.1073/pnas.0904571106. Epub 2009 Jun 9.


Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity.

Cadotte MW, Cavender-Bares J, Tilman D, Oakley TH.

PLoS One. 2009 May 27;4(5):e5695. doi: 10.1371/journal.pone.0005695.


Ontogeny of sexual dimorphism via tissue duplication in an ostracod (Crustacea).

Rivera AS, Oakley TH.

Evol Dev. 2009 Mar-Apr;11(2):233-43. doi: 10.1111/j.1525-142X.2009.00323.x.


Genomics and the evolutionary origins of nervous system complexity.

Oakley TH, Rivera AS.

Curr Opin Genet Dev. 2008 Dec;18(6):479-92. doi: 10.1016/j.gde.2008.12.002. Epub 2009 Jan 17. Review.


Evolutionary history and the effect of biodiversity on plant productivity.

Cadotte MW, Cardinale BJ, Oakley TH.

Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17012-7. doi: 10.1073/pnas.0805962105. Epub 2008 Oct 29.

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