Type II opsins: evolutionary origin by internal domain duplication? Journal of molecular evolution. 66:417–423.. 2008.
Testing Trait Evolution Models on Phylogenetic Trees. Computer Science. MS:34.. 2005.
CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evolutionary Bioinformatics Online. 2:183.. 2006.
A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evolutionary Biology. 12:129.. 2012.
Occurrence of Hemocyanin in Ostracod Crustaceans. Journal of Molecular Evolution. :1–9.. 2014.
Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae. Journal of Ecology. 105:580–591.. 2017.
Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae. PloS one. 10:e0137085.. 2015.
Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae. Ecology Letters. 16:1373–1381.. 2013.
Phylogenetic distance does not predict competition in green algal communities. Ecosphere. 6:art116.. 2015.
Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod structure & development. 36:386–400.. 2007.
Eyes to See: The Astonishing Variety of Vision in Nature. Nature. 563:182–183.. 2018.
Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. Proceedings of the National Academy of Sciences. 103:11637.. 2006.
Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution. 54:397–405.. 2000.
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics. 15:230.. 2014.
The eye as a replicating and diverging, modular developmental unit. TRENDS in Ecology and Evolution. 18:623–627.. 2003.
A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evolution & Development. 9:514–516.. 2007.
How Complexity Originates: The Evolution of Animal Eyes. Annual Review of Ecology, Evolution, and Systematics. 46. 2015.
Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular biology and evolution. 22:40–50.. 2005.
Opening the “black box”: the genetic and biochemical basis of eye evolution. Evolution: Education and Outreach. 1:390–402.. 2008.
Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences. 99:1426.. 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.. 2007.
Maximum likelihood models of trait evolution. Comments on Theoretical Biology. 8:609–625.. 2003.