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Oakley TH, Cunningham CW.  2000.  Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution. 54:397–405.
Oakley TH, 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. 11:381–393.
Oakley TH, Cunningham CW.  2002.  Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences. 99:1426.
Oakley TH, Gu Z, 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. 22:40–50.
Oakley TH.  2003.  On homology of arthropod compound eyes. Integrative and comparative biology. 43:522–530.
Oakley TH.  2003.  The eye as a replicating and diverging, modular developmental unit. TRENDS in Ecology and Evolution. 18:623–627.
Oakley TH.  2003.  Maximum likelihood models of trait evolution. Comments on Theoretical Biology. 8:609–625.
Oakley TH, Østman 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. 103:11637.
Oakley TH, Huber DR.  2004.  Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans. Journal of molecular evolution. 59:239–249.
Oakley TH, Plachetzki DC, Rivera AS.  2007.  Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod structure & development. 36:386–400.
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, M Pankey S.  2008.  Opening the “black box”: the genetic and biochemical basis of eye evolution. Evolution: Education and Outreach. 1:390–402. (342.38 KB)
Oakley TH, Rivera AS.  2008.  Genomics and the evolutionary origins of nervous system complexity. Current opinion in genetics & development. 18:479–492.
Oakley TH.  1996.  Duplicated growth hormone genes from a tetraploid family of fishes: DNA sequence evolution and implications for salmonid systematics.
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 & Development. 9:523–524.
Oakley TH.  2007.  A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evolution & Development. 9:514–516.
Oakley TH.  2001.  Phylogenetic reconstruction of ancestral character states.
Oakley TH.  2008.  Jay Hosler, An Evolutionary Novelty: Optical Allusions. Evolution: Education and Outreach. 1:548–551. (212.35 KB)
Oakley TH.  2009.  A Critique of Experimental Phylogenetics.
Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK.  2013.  Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Molecular biology and evolution. 30:215–233. (1.19 MB)
Oakley TH, Speiser DI.  2015.  How Complexity Originates: The Evolution of Animal Eyes. Annual Review of Ecology, Evolution, and Systematics. 46 (351.15 KB)