Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC bioinformatics. 15:350.. 2014.
Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity. PLoS One. 4:e5695.. 2009.
Understanding the dermal light sense in the context of integrative photoreceptor cell biology. Visual neuroscience. 28:265–279.. 2011.
Type II opsins: evolutionary origin by internal domain duplication? Journal of molecular evolution. 66:417–423.. 2008.
Two new sympatric species of Eusarsiella (Ostracoda: Myodocopida: Sarsiellidae) from the Florida Keys with a morphological phylogeny of Sarsiellinae. Zootaxa. 3802:444–458.. 2014.
A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. PloS one. 10:e0140484.. 2015.
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.
Testing Trait Evolution Models on Phylogenetic Trees. Computer Science. MS:34.. 2005.
Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proceedings of the National Academy of Sciences. :201817322.. 2019.
Support for the dimorphic niche hypothesis: Natural selection drives sexual eye dimorphism in ostracods. Ecology Evolution and Marine Biology. MA:42.. 2011.
Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies. Functional Ecology.. 2015.
Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae. Proceedings of the Royal Society B: Biological Sciences. 280. 2013.
A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evolution & Development. 9:514–516.. 2007.
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.
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics. 24:606.. 2008.
Reconstructing ancestral character states: a critical reappraisal. Trends in Ecology & Evolution. 13:361–366.. 1998.
Prolific origination of eyes in Cnidaria with co-option of non-visual opsins. Current Biology. 28:2413–2419.. 2018.
Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences.. 2014.
A post-synaptic scaffold at the origin of the animal kingdom. PLoS One. 2:e506.. 2007.
Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.). Gene. 194:9–18.. 1997.
Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Molecular biology and evolution. 30:215–233.. 2013.
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.. 1999.
Phylogenetic relationships among the Salmoninae based on nuclear and mitochondrial DNA sequences.. Molecular systematics of fishes. Academic Press, London.. 1997.