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Oakley Lab Publications
In Press/In Review |
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50 |
AS Rivera et al (In Review). Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. For BMC Evolutionary Biology. | |
49 |
DC Plachetzki, CR Fong and TH Oakley.(In Review). Evidence that a cyclic nucleotide gated (CNG) ion channel functioned in the ancestral animal phototransduction cascade For Proceedings of the Royal Society B. | |
48 |
TH Oakley and DC Plachetzki (In Press). Key transitions during animal phototransduction evolution: Co-duplication as a null hypothesis for the evolutionary origins of novel traits. in B Shierwater and R. DeSalle. Key Innovations in Animal Evolution. | |
47 |
Cohen AC and Oakley TH (In Press). Marine Ostracoda. in Collection Techniques for Crustacea. Eds J Martin. | |
46 |
Syme AE and Oakley TH (In Revision). Evolutionary loss and re-gain of ostracod compound eyes: Conflicting conclusions from different comparative methods . For Systematic Biology. | |
2010 |
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45 |
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. | |
2009 |
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44 |
MW Cadotte, TJ Davies, J Regetz, SW Kembel, E Cleland and TH Oakley (2009). Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters. 13(1):96-105. | |
43 |
RM Gould, TH Oakley, JV Goldstone, JC. Dugasa, ST Bradya and A Gow (2009). Myelin sheaths are formed with proteins that originated in vertebrate lineages. Neuron Glia. doi:10.1017/S1740925X09990238. | |
42 |
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 . [Link] | |
41 |
MWCadotte J Cavender-Bares GD Tilman and TH Oakley (2009) Using evolutionary, functional and trait diversity to understand patterns of plant community productivity. PLoS-One | |
40 |
Rivera AS and Oakley TH (2009). Ontogeny of extreme sexual dimorphism via tissue duplication in an ostracod (Crustacea). Evolution and Development. 11(2): 233. | |
39 |
MS Pankey and TH Oakley (In Press). Eye Evolution. Grzimeks Animal Life Encyclopedia. | |
38 |
TH Oakley (2009). A critique of experimental phylogenetics. in Experimental Evolution, MR Rose and T Garland, Jr (eds). University of California Press. | |
2008 |
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37 |
TH Oakley and Rivera AS. (2008) Genomics and the evolutionary origins of nervous system complexity. Current Opinion in Genetics and Development. 18:XX-XX | |
36 |
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 [Link] [Blog]. | |
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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. [Link] [Press] [Blog]. |
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34 |
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. preprint | |
33 |
Larusso ND, Ruttenberg BE, Singh AK, Oakley TH (2008). Type II Opsins: Evolutionary origin by internal domain duplication? Journal of Molecular Evolution. In Press. [pdf]. | |
32 |
Sakarya O, Kosik KS and Oakley TH (2008) Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics. doi:10.1093/bioinformatics/btn005 [pdf] | |
31 |
Lum, KE Syme AS Schwab AK and TH 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. [Link to pdf] [Blog] | |
2007 |
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30 |
Oakley TH (2007). 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. 9:523-524 [pdf] Commentary. | |
29 |
DC Plachetzki, BM Degnan, TH Oakley (2007). The Origins of Novel Protein Interactions During Animal Opsin Evolution. PLoS-ONE [Open Access ] | |
28 |
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[pdf]. | |
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Rose MR and Oakley TH (2007). The New Biology: Beyond the Modern Synthesis. Biology Direct 2:30. [Open Access] | |
26 |
Oakley TH (2007). Book Review of Gene Sharing and Evolution. Evolution and Development. 9:514-516. [Link to Journal] | |
25 |
Plachetzki DC and Oakley TH (2007). Key transitions during animal eye evolution: Novelty, tree thinking, co-option and co-duplication. Integrative and Comparative Biology. [Link] | |
24 |
Oakley TH (2007). Vision. In The Encyclopedia of Tidepools and Rocky Shores. Univ of California Press. [Link] | |
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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. [ Open Access ] |
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2006 |
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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. [Link] | |
21 |
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. [Open Access] [Software Homepage] | |
2005 |
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Serb JM and Oakley TH (2005). Hierarchical phylogenetics as a quantitative analytical framework for Evolutionary Developmental Biology. BioEssays. 27:1158-1166. [Download PDF] | |
19 |
Plachetzki DC Serb JM Oakley TH. (2005). New insights into photoreceptor evolution. 20:465-467. (Commentary). Trends in Ecology and Evolution.[Download PDF]. | |
18 |
Oakley TH (2005). Myodocopa (Crustacea: Ostracoda) for studies of light and vision: Multiple origins of bioluminescence and extreme sexual dimorphism. Hydrobiologia 538:179-192.. [Download PDF] | |
17 |
Oakley TH, Gu Z-L, Abouheif E, Patel NH Li W-H. (2005) Comparative methods for the analysis of gene expression evolution: An example using yeast functional genomic data. Molecular Biology and Evolution. 22(1): 40-50. [Download PDF] [Data] [PowerPoint] [Software Homepage] | |
2004 |
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16 |
Oakley TH and Huber DR (2004). Eye-specific expression of multiple opsins in ostracod crustaceans. Journal of Molecular Evolution. 59(2): 239-249. [Download PDF] |
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15 |
Wang D-Y, Oakley TH, Honeycutt R, Tsao H, Li W-H. Molecular (2004). Evolution of Bat Color Vision Genes. Molecular Biology and Evolution. 21(2):295–302. [Download PDF] |
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2003 |
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Oakley TH. (2003). The eye as a replicating and diverging, modular developmental unit. Trends in Ecology and Evolution. 18(12):623-627. [Download PDF]. | |
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Oakley TH (2003). On homology of arthropod compound eyes. Integrative and Comparative Biology. 43(4):522-530.[Download PDF]. | |
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Patek SN and Oakley TH. (2003). Comparative tests of evolutionary trade-offs in a Palinurid lobster acoustic system. Evolution. 57(9):2082-2100. [Download PDF]. | |
11 |
Oakley TH. (2003). Maximum likelihood models of trait evolution. Comments on Theoretical Biology 8:1-17. [Download PDF]. | |
pre-2003 |
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10 |
Oakley TH and Cunningham CW (2002). The independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences USA. 99: 1426-1430. [Download PDF]. | |
9 |
Oakley TH and Cunningham CW (2000). Independent contrasts succeed where explicit ancestor reconstructions fail in a known bacteriophage phylogeny. Evolution 54(2):397-405. [Download PDF]. | |
8 |
Oakley TH and Phillips RB. (1999). Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa. Molecular Phylogenetics and Evolution 11(3):381-393 . [Download PDF] [GH1C data] [GH2C data] | |
7 |
Cunningham CW, Omland KE, and Oakley TH (1998) Reconstructing ancestral character states: A critical reappraisal. Trends in Ecology and Evolution. 13(9):361-366. [Download PDF] |
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6 |
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.) Molecular Systematics of Fish. Academic Press. | |
5 |
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. [Download PDF] | |
4 |
Domanico MJ, Phillips RP and Oakley TH. (1997) Phylogenetic analysis of Pacific Salmon (Oncorhynchus) using nuclear and mitochondrial DNA. Canadian Journal of Fisheries and Aquatic Sciences 54:1865-1872. [Download PDF] | |
3 |
Moran P, Reed KM, Perez J, Oakley TH, Phillps RB, Garcia-Vasquez E, Pendas AM (1997). Physical localization and characterization of the Bgl I element in the genome of Atlantic Salmon (Salmo salar L.) and Brown Trout (S. trutta L.). Gene 194:9-18. [Download PDF] |
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2 |
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. [Download PDF] | |
1 |
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. | |
[i] |
Bjorn Ostman (2005). Evolution of Spatial Gene Expression: Gene duplication, biased rates of regulatory evolution, and phenotypic complexity in Drosophila. MA Thesis. University of California-Santa Barbara. Download PDF. | |
[ii] |
Chunghau Lee (2005). Testing Trait Evolution Models on Phylogenetic Trees. MS Thesis. University of California-Santa Barbara. Download PDF . | |
[iii] |
Asa Wilson (2007). The divergence of genes in ciliary photoreceptors. MA Thesis. University of California-Santa Barbara. Download PDF. |