Background

The focus of my research is the origin and maintenance of marine biodiversity, particularly in coral reef fishes, using genomic and computational methods. My Ph.D. dissertation work was 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 focused on resolving and dating the Acanthomorph tree of life. At this point, my lab's primary focus is on the group of fishes called blennies. Why blennies? Near et al. (2013) found that blennies are one of the most exceptionally diverse groups of fishes living on reefs. My lab aims to understand this diversity at multiple levels of biological organization, ranging from molecular evolution at the level of the genome, cryptic speciation and local endemism, population genetics at regional spatial scales, to higher level molecular phylogenetics and systematics. We have a holistic approach to our research, combining genomic, computational, and classical genetic methods, with a healthy dose of field work. Click on images to enlarge.

 

 

Molecular Evolution

Substitution Rate Ratios

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.

 

Hybrid Breakdown

Acanthemblemaria EggsProteins 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.

 

Population Genomics

Acanthemblemaria spinosaThe primary focus of my population genetics research has been the tube blenny genus Acanthemblemaria, a clade 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 mitochondrial evolution in these fishes. However, by using both mitochondrial and nuclear sequence data, I was able to recover temporally separated population expansions.

 

Acanthemblemaria spinosaThis research is ongoing and is expanding to other fish species. The large amount of genomic data that can now be collected can be used to infer multiple population size changes over time.

 

 

 

Cryptic Speciation

While we already know that blennies are one of exceptionally speciose groups of reef fishes, it has become clear that this diversity is most likely vastly underestimated. Recent work has shown that nominal species are in fact members of larger species complexes, often with limited distributions. My own work with Acanthemblemaria has found there to be fine-scale endemism in the Caribbean, with some lineages restricted to localities less than 250 km apart from one another. We are following up this work using RAD-Seq, as well as sequence capture, to discover species boundaries. However, we are not only interested in finding these lineages, but are also interested in inferring their mode and mechanism of speciation. A central goal of my lab is to expand this work throughout the Caribbean and Gulf of Mexico.

 

Phylogenomics

Our interests are not limited to species discovery. In addition to this, we want to infer the interrelationships within and among cryptic species complexes. With the advent of phylogenomics we are no longer limited in the amount of phylogenetic data we can collect (although analysis of these data is another matter). We are fortunate to have whole genome sequences of species which span the blenny Tree of Life. We are currently planning to use this resource to develop a probe set which can be used to build species phylogenies at both shallow and deep time scales.

 

Previous Research

Acanthomorph Time Tree

As part of my postdoctoral research in the lab of Tom Near at Yale, I worked to resolve and measure the fish Tree of Life. Using genetic data from a large suite of nuclear genes, we built high-resolution phylogenies of all major groups in the fish Tree of Life. Through the use of dozens of fossil calibrations and relaxed molecular clock methods, these trees were used to estimate absolute ages of all major lineages, the timing of diversification in these groups, and identification of exceptionally species-rich clades of fishes. I also focused my efforts on resolving the relationships within and between families in a clade of fishes called Ovalentaria. Ovalentaria contains some of the most diverse and species-rich groups of fishes, such as cichlids, silversides, and blennies. I used genome capture and next generation sequencing technology to sequence hundreds of genes for dozens of taxa. I used these data to build a species phylogeny of representative Ovalentaria taxa. I found that even with a large amount of genomic data, the interrelationships of the major Ovalentaria lineages remain unknown, possibly because of a rapid radiation event at the base of the tree.

 

Coral reefs are in global decline due to disease. Understanding the causes and modes Transmission pathways
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.

 

OculinaIn 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.