My research investigates the influences of geological and climatic changes on the divergence and distribution of populations, species, and higher taxa. Specifically, I have addressed questions regarding the effects of Pleistocene glacial cycles on genetic diversity within and among western North American cyprinid fishes. I have also addressed the phylogeographic implications of ancient changes to the landscape by using molecular dating techniques to correlate divergences between species (and genera) to known geological events (e.g., stream captures and other well-documented ancient hydrological
connections). [Pictured: Distributions of five cyprinid species from three genera, along with their phylogenetic relationships and divergence time estimates. Note that the earliest divergence post-dates the formation of the Rocky Mountains by ~60 million years, so dispersal across the Continental Divide has occurred.]
Recent advances in high-throughput DNA (i.e., next-generation) sequencing technologies have revolutionized population genetics by making it relatively easy and affordable to generate large genomic data sets, even for non-model organisms for which genetic resources have not previously been available. I am currently involved in a National Science Foundation funded study investigating the role of effective population size on flowering asymmetry and parasite load in the Sonoran Desert rock fig, and how these population dynamics are expected to shift with changing global climates. My colleagues and I have sequenced transcriptomes and identified single nucleotide polymorphisms (SNPs) that we are now using to estimate effective population sizes and to assess gene flow within and among fig populations in Baja California, MX. [Pictured: Parasitic fig wasps of the genus Idarnes sit atop a fig fruit]
Taking advantage of the aforementioned advances in DNA sequencing technologies, my colleagues and I generated a library of single nucleotide polymorphisms (SNPs) that can be used to differentiate cutthroat trout subspecies (some of which are threatened or endangered), thus helping inform management decisions for a charismatic species that has several anthropogenically imposed threats. [Pictured: A NeighborNet phylogenetic network illustrating genetic distances among nine cutthroat trout subspecies based on a panel of 125 SNPs developed using 454 pyrosequencing, genomic and bioinformatic techniques.]
While numerous studies have provided robust evolutionary hypotheses regarding the phylogenetic relationships of many taxa, the increasing popularity of genetic techniques has allowed researchers to uncover an abundance of cryptic genetic diversity, sometimes resulting in necessary taxonomic changes. Much of my previous work has used mitochondrial DNA and nuclear intron sequence data to reconstruct phylogenies, but advances in next-generation sequencing technologies and analytical techniques have allowed my colleagues and I to generate thousands of loci for these purposes. As aquatic habitats become increasingly more threatened by anthropogenic activities and changing global climate, there is a greater need to evaluate the phylogenetic diversity that occurs in these habitats. Any cryptic genetic diversity that is discovered might then be the focus of conservation efforts, if necessary. Moreover, the application of these markers should prove to be useful in tracking the responses of these organisms to their changing habitats.
My colleagues and I have used next-generation sequencing to develop SNP libraries and a panel of microsatellite markers for two North American burying beetle species. We will use these markers to genotype wild breeding pairs and their offspring to assess parentage and test hypotheses about the role of extra-pair mating in the evolution of bi-parental care. [Pictured: An ethanol preserved Nicrophorus orbicollis specimen, just prior to DNA extraction.]