The focus of my research is the origin and maintenance of marine biodiversity, particularly in coral reef fishes. My Ph.D. dissertation work focused on the population genetics and rates of molecular evolution of a group of small Neotropical reef fishes, the tube blenny genus Acanthemblemaria. My postdoctoral work focuses on resolving and dating the Acanthomorph tree of life. I work at different levels of biological organization ranging from molecular evolution at the level of the genome, population genetics at regional spatial scales, to higher level molecular phylogenetics and systematics. Click on images to enlarge.
Through the use of Bayesian divergence dating I have found that Acanthemblemaria blennies have a very fast mitochondrial substitution rate - over 25% sequence divergence per million years. This rapid rate is exclusive to the mitochondrion, which is evolving nearly 100 times faster than the nuclear genome. This mitochondrial rate has consequences that extend to speciation through epistasis between co-adapted mitochondrial and nuclear proteins.
Proteins encoded in the mitochondrial genome, such as those responsible for oxidative phosphorylation, directly interact with nuclear-encoded proteins. Gene products from each genome must be able to work properly with each other, or organismal breakdown will occur. Given their high rate of mitochondrial evolution, Acanthemblemaria is an ideal study group to answer whether hybrid fitness suffers due to poor interactions between mismatched mitochondrial and nuclear genomes. This will be tested by using hybrid crosses and sequence capture.
The primary focus of my population genetics research has been the tube blenny genus Acanthemblemaria, a genus of Neotropical coral reef fishes. In a comparative study of the two most widely distributed Caribbean species, I found that despite near identical life histories and distributions, one of the taxa, A. spinosa, a habitat specialist, has been able to persist through glacial cycles, while the other, A. aspera, a habitat generalist, has not. Signals of population expansions in these two species were obscured by the rapid rate of mitochodrial evolution in these fishes. However, by using both mitochondrial and nuclear sequence data, I was able to recover temporally separated population expansions.
This research is ongoing and is expanding to other fish species. The large amount of genomic data that can be collected can be used to infer multiple population size changes over time.
As part of my postdoctoral research in the lab of Tom Near at Yale, I am resolving the relationships within and between fish families with the use of genomic data. We are using genome capture and next generation sequencing technology to sequence hundreds of genes for dozens of taxa. We are using these data to build a high-resolution species phylogeny of representative taxa from some of the most species-rich families of fishes. Using multiple fossil calibrations and relaxed molecular clock methods, this tree will be used to estimate absolute ages of all major lineages as well as the timing of diversification in these groups. Future research aims to use these techniques at the genus and species level.
Coral reefs are in global decline due to disease. Understanding the causes and modes
of disease transmission are essential to protecting reefs. Florida populations of the endangered Western Atlantic coral Acropora palmata have seen steep declines due to white pox disease, caused by the microbe Serratia marcescens. Found in human wastewater and with several vectors and reservoirs, I am studying the transmission dynamics of Serratia on reefs in the Florida Keys. As part of my postdoctoral research in the labs of Erin Lipp and John Wares while at the University of Georgia, we are using thousands of SNPs derived from Illumina data from whole bacterial genomes to perform next-generation phylogeography and population genetic analyses. This is being done with the goal of understanding the spatial and temporal mode of transmission
of Serratia between human wastewater, vectors and reservoirs, and Acropora palmata itself.
In collaboration with Marshall Hayes, Margaret Miller, and my former advisor
Michael Hellberg, I have worked on the population genetics of the threatened temperate coral genus Oculina. The deepwater Oculina population located at the Oculina Banks in Florida creates a unique habitat for associated taxa, but is threatened by anthropogenic disturbance in the form of trawling. Using nuclear sequence data, we found that the Oculina Banks population is genetically isolated from shallow water congeners. This suggests that
reseeding from shallow water populations may not be possible and that further protection
for the Oculina Banks is required.