Using comparative genomics to uncover the origins of phenotypic modularity in squamate reptiles

The genomic determinants of morphological change are of great interest to evolutionary biologists, particularly how they relate to the loss and evolution of key traits. Ultraconserved elements (UCEs) are regions of genomes that are highly conserved across distantly related organisms.

Many UCEs are located in cis-regulatory (enhancer) regions of the genome that play critical developmental roles in determining morphology; when UCEs are removed notable changes to the skulls and limbs of mammals can occur.

These UCEs are highly conserved across vertebrates and the evolutionary loss of a single UCE (Sonic hedgehog limb enhancer) has been associated with partial and complete limb loss in squamate reptiles.

However, much of what is known about the causal role UCEs play in development is derived from functional studies, which have only examined a handful of model species.

A broader phylogenetic and genomic perspective of how UCEs relate to morphological variation would offer much needed information for interpreting the results of functional studies.

Comparative genomics offers a means to dramatically increase the taxonomic sampling of UCEs, both through examination of annotated genomes and comparison of UCE loci obtained using sub-genomic sampling methodologies.

I will use UCEs to characterize the enhancer landscapes of squamate reptiles that putatively underpin cranial and limb diversity.

I will then relate the dynamics of these genomic landscapes to the modularity and integration of crania and limbs that occur across squamates using 3-dimensional (3D) scan data derived from museum specimens. This project will produce novel sub-genomic data and 3D scans that will be shared in online repositories.

I will be aided by my hosts and their world-renowned museum collections to deliver this novel and cutting-edge project which will act as a springboard for my own independent research and teaching program.