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Rivera AS and Oakley (In Revision). Ontogeny of extreme sexual dimorphism via tissue duplication in an ostracod (Crustacea).
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Rose MR and Oakley TH (In Review). Post-Modern Biology. BioEssays.
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Plachetzki DC and Oakley TH (In Review). Key transitions during animal eye evolution: Novelty, tree thinking, co-option and co-duplication. Integrative and Comparative Biology.
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Tinn O* and Oakley TH* (In Press). Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea). Molecular Biology and Evolution.
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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 to PNAS PDF]
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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.
[Link to EBO PDF]
[Software Homepage]
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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]
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Plachetzki DC Serb JM Oakley TH. (2005). New insights into photoreceptor evolution. 20:465-467. (Commentary). Trends in Ecology and Evolution.
[Download PDF].
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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]
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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]
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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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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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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].
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Oakley TH. (2003). Maximum likelihood models of trait evolution. Comments on Theoretical Biology 8:1-17.
[Download PDF].
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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].
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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].
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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]
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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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