I use high-throughput sequencing and novel computational methods to answer fundamental evolutionary questions. I’m working on projects ranging from the genomic architecture of recent adaptive radiations to new methods for investigating systematic questions with many hundreds of loci.
Dissertation Work: Anole Pigmentation
My PhD dissertation involves the genetics of speciation and adaptation in Anolis lizards. Anoles represent one of the largest adaptive radiations of any vertebrate taxa. In the Caribbean alone there are at least 150 different species. Anoles are unusual in that they have a specialized gular fold called a dewlap that they extend in intra and interspecific displays. Dewlaps come in many colors: red, orange, yellow, pink, purple, blue and some of these colors, yellow and orange in particular, appear to have evolved independently in multiple lineages. Thus, anoles are an ideal model to study the convergent evolution of pigmentation. As such, I am using the anole genome, from Anolis carolinensis, in combination with next generation sequencing and other methods to identify pigmentation genes.
Next Generation Systematics
As part of a broad collaboration with Travis Glenn, Robb Brumfield, Brant Faircloth, and John McCormack, I’ve helped develop a new type of molecular marker that is derived from ultraconserved genomic elements (UCEs). These markers include both the highly conserved UCE core as well as the more variable flanking sequence. We’ve designed biotinylated RNA-probes that capture these elements from virtually any amniote species. I have programmed software called CloudForest that takes alignments built from these markers and infers both gene and species trees.
Methods and protocols to develop UCEs can be found at ultraconserved.org.
In collaboration with Sean Mullen, Marcus Kronfrost, Rob Kulathinal, Jason Gallant, and Durrell Kapan I’m helping to analyze a number of heliconius butterfly genomes. This work aims to understand the genomic architecture that maintains species boundaries in the face of high rates of gene flow.