Publications
Type II opsins: evolutionary origin by internal domain duplication? Journal of molecular evolution. 66:417–423.
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2008. 
Testing Trait Evolution Models on Phylogenetic Trees. Computer Science. MS:34.
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2005. 
CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evolutionary Bioinformatics Online. 2:183.
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2008. Occurrence of Hemocyanin in Ostracod Crustaceans. Journal of Molecular Evolution. :1–9.
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2014. .
1997. 
Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae. Journal of Ecology. 105:580–591.
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2017. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae. PloS one. 10:e0137085.
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2015. Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae. Ecology Letters. 16:1373–1381.
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2013. 
Phylogenetic distance does not predict competition in green algal communities. Ecosphere. 6:art116.
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2015. Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod structure & development. 36:386–400.
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2007. Eyes to See: The Astonishing Variety of Vision in Nature. Nature. 563:182–183.
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2018. .
2001. Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. Proceedings of the National Academy of Sciences. 103:11637.
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2006. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution. 54:397–405.
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2000. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics. 15:230.
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2014. The eye as a replicating and diverging, modular developmental unit. TRENDS in Ecology and Evolution. 18:623–627.
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2003. A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evolution & Development. 9:514–516.
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2007. How Complexity Originates: The Evolution of Animal Eyes. Annual Review of Ecology, Evolution, and Systematics. 46
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2015. 
Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular biology and evolution. 22:40–50.
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2005. Opening the “black box”: the genetic and biochemical basis of eye evolution. Evolution: Education and Outreach. 1:390–402.
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2008. 
Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences. 99:1426.
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2002. 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.
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2007. Maximum likelihood models of trait evolution. Comments on Theoretical Biology. 8:609–625.
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2003.