My research interests encompass exploration of the biodiversity chondrichthyan fishes, phylogenetic inference, protein folding, molecular evolution and the origin of architectural novelty. While seemingly diverse, these topics reflect different facets of an abiding interest in a single issue: understanding how changes in the genome give rise to new features over the course of evolution. If we are to understand how changes in the genome gives rise to new traits, we ideally need to look at the architectural blue-prints immediately before and after the change took place to identify the genomic elements responsible for the novelty. This is hard to do in biology as we rarely have the opportunity to catch trait evolution in action. However, arranging the organisms according to their phylogenetic relationships can tell us the likely ordering of the evolution of traits, and comparing the genomes of a range of organisms in a phylogenetic context, can give us insights into the modifications associated with the origin of new features. Clearly, accurate estimates of phylogenetic relationships are a fundamental prerequisite for understanding the genomic patterns and associated process responsible for the evolutionary origin of new traits.
My empirical work has centered around understanding evolution in sharks and rays. I study these animals because they are abundant, diverse, globally distributed and have an excellent fossil record extending back to the Triassic. This combination of attributes allows us to (a) estimate their evolutionary inter-relationships from both DNA sequence and anatomical comparisons (b) determine the order in which novel features arose and (c) tie diversification events to a temporal evolutionary framework based on fossils. I have recently been funded by NSF to pursue this work on a genomic scale using a novel deployment of next generation sequencing technologies in combination with high resolution CT and MRI data for the morphological component. We anticipate that the computational tools we develop through this project will allow for interactive exploration of skeletal and soft tissue morphology, and we hope will set the stage for a new wave of virtual comparative anatomy in the future.
I use protein coding DNA sequences to estimate evolutionary relationships. It is now well established that sequences from different genes can yield incongruent estimates of phylogeny for the same class of analyses - especially when working with distantly related groups. One reason for this is model inconsistency – the phenomenon that occurs when the models we use for estimating trees are inconsistent with the processes that gave rise to the data. Such inconsistencies have driven us to explore the constraints and context
sensitivities that affect the molecular evolution of proteins. My graduate students and I have focused on exploring phylogenetic inference methods that purport to accommodate the patterns induced by protein structural considerations in an effort to improve the accuracy of phylogenetic trees and their branch lengths. We are using our improved understanding of the mapping between sequences and their corresponding structures to explore how the vast array of proteins that exist in nature may have arisen. We anticipate that an improved understanding of the way in which proteins can traverse their evolutionary state space will provide insight into mechanisms underlying protein diversification, which may, in turn, help us understand how new traits arise at the organismal level.
While I enjoy theoretical work, I feel that it is important to be routinely exposed to empirical patterns that occur in nature. I enjoy the interplay between idealism (theory) and realism (empirical patterns). I also enjoy the exploration of well-defined mapping schemes such as the Sequence>Protein-folding>Phenotype map for the insights that they can often provide for more complex, but generally less well-defined, natural systems such as the mapping from Genome>development>morphology.
1. Faria, V.V M. T. Mcdavitt, P. Charvet, T. R. Wiley, C. A. Simpfendorfer, and G.J. P. Naylor Species Delimitation and Global Population Structure of Critically Endangered Sawfishes : Implications for Conservation and Management (Submitted)
2. Li, C., K. A. Rosana, M. Garcia, and G. J. P. Naylor (In Press) Nuclear Markers for Phylogenetics of Chondrichthyes and the Problem of Rooting Phylogenies with Distant Outgroups. Molecular Biology and Evolution XXX-XXX.
3. Aschliman, N.C ., M. Nishida, M. Miya, J. G. Inoue, K. M. Rosana and G.J.P.Naylor (In Press) Body Plan Convergence and Diversity Shaped by Mass Extinction in the Evolution of Skates and Rays (Chondrichthyes: Batoidea) Molecular Biology and Evolution.
4. Naylor, G.J.P. J.N. Caira, K. Jensen, K. Rosana, W. White And P. Last (In Press) A DNA Sequence Based Approach To The Identification of Shark and Ray Species And Its Implications For Global Elasmobranch Diversity And Parasitology. Bulletin of the American Museum of Natural History (200pp.)
5. Moore, A.B.M., W.T. White, R.D. Ward, G.J.P. Naylor, and R. Peirce. (2011). Rediscovery and redescription of the smoothtooth blacktip shark, Carcharhinus leiodon (Carcharhinidae), from Kuwait, with notes on its possible conservation status. Marine and Freshwater Research 62: 528–539.