Molecular Phylogeny of Sharks and Rays
We are exploring the nature of the molecular evolutionary process within the context of shark phylogeny. Elasmobranchs lend themselves well to the problem because they exhibit a tremendous range of adaptations, are well represented by modern forms (more than 900 species identified) and have an excellent and reasonably continuous fossil record. Indeed, they may represent one of very few groups for which it is possible to accurately estimate both the patterns of diversification (their evolutionary relationships) and the timing of the various cladogenic events. Neil Aschliman is leading this effort with his focus on skates and rays.

Mitogenomics of Elasmobranchs
Toni and Tim Williams, alumni of the lab, have sequenced whole mitochondrial genomes from more than 20 shark species. We are hoping to collaborate with Dr. Shigeru Shirai, Dr. Miya, and Prof. Nishida's group in Japan, and Toni and Tim to sequence of whole mitochondrial genomes from representatives of all elasmobranch families.

Phylogeny and Population Genetics of Pristis
Link to Vicente Faria web page

Protein Structure/Function Effects on DNA Substitutional Pattern
Clemens Lakner is exploring the effects of structural covariance on phylogenetic signal in Bayesian context. This involves accommodating restricted state space associated with different part of molecule.

Understanding Phylogenetic Signal in DNA Sequences
Several forces are known to affect molecular evolutionary change. Many of these leave their "fingerprints" 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 from those that are due to other influences. We are exploring the utility of filters to distinguish between patterns of character state variation at different scales.

Reconstructing Fossil Proteins
We are surveying extant variation in Myoglobin sequences in conjunction with a well-established phylogeny of vertebrates to estimate ancestral Myoglobin sequences. We will synthesize these estimated ancestral sequences, express them in vitro, determine their structures and contrast their functional properties with those of extant sequences using a series of functional biochemical assays. This will allow us to estimate the genotype: phenotype map for an ancestral protein and give us insight into both ancestral properties of the molecule and how its g:p map has evolved over time.

New Evolutionary Models for Mitochondrial Genome
Dr. Jun Inoue is developing new models of molecular evolution for phylogenetic inference of vertebrate groups. Dr. Inoue's models will accommodate protein structural constraints particular to mitochondrial protein coding regions. We anticipate these models will result in improved accuracy for groups that have proven to be phylogenetically recalcitrant.

Sequencing by Hybridization
We are exploring the possibilities of designing a gene specific sequencing by hybridization chip to facilitate high throughput sequencing for phylogenetic systematics.

Morphometry of Protein Structure
Geometric morphometric methods will be used to construct a 'protein shape space,' in which clusters of similarly-structured proteins can be identified. Because of the correlation between protein structure and function this should serve as a tool to identify the "functional phenotype" of an uncharacterized protein.