naylor lab
molecular evolution

Phylogeny of Chondrichthyan fishes

Sharks and rays exhibit a tremendous range of adaptations. They are well represented by living forms (approximately 1250 species identified), and have an excellent fossil record predominantlky in the form of their teeth. They represent one of very few groups for which both the patterns of diversification (their evolutionary relationships) and the timing of the various cladogenic events may be accurately estimated.

Understanding phylogenetic signal in DNA sequences

Several forces are known to affect molecular evolutionary change. Many of them leave their "imprints" in the patterns of DNA sequence variation observed among organisms. In our lab we are interested in discriminating between the patterns of sequence variation that are due to phylogenetic history and those that are due to other influences. We are exploring the utility of filters for distinguishing between patterns of character state variation at different scales.

Development of Targeted Gene Capture for NextGen Sequencing

We have developed methods to capture and sequence about 1,000 pre-specified single copy genes across hundreds of taxa in a single Illumina Nextgen sequencing run. We are using these approaches to improve access to high quality data that are well disposed to estimating phylogenetic relationships. In the future we plan to use our targeted gene capture approaches to identify polymorphisms that are associated with physiological differences across species and use “comparative biochemical pathway analysis” to identify changes in the genotype phenotype map across species.

Population genetics of requiem sharks

We are interested in understanding the relationship between population structure, life history traits and biogeography in elasmobranchs. One group of particular interest are the requiem sharks of genus Carcharhinus (which include the well known Bull sharks, Dusky sharks, Silky sharks, Black-tip sharks, Spinner sharks and Oceanic white-tip sharks). We will use intron data associated with targeted gene capture to explore the genetic structuring within and between different species of this highly successful group of sharks.