Dissertation

Recent advances in genomic sequencing and bioinformatics now permit robust genomic studies of natural, non-model systems that were previously unfeasible. My dissertation research involves two comparative investigations of hypoxia tolerance in animals native to the Andes of South America.

Organisms inhabiting high-altitude environments experience physiological stresses due to reduced oxygen availability, low temperatures, and increased UV exposure. Despite these extreme conditions, countless species have adapted to high altitudes. Understanding the mechanisms of this adaptation will improve our overall understanding of molecular evolution and the adaptive response and may aid in the identification of the species or populations most likely to be threatened by the changing environmental conditions caused by global climate change.

We have generated a de novo assembly of the Black-breasted Hillstar (Oreotrochilus melanogaster) hummingbird, which lives at elevations between 3,500 and 4,500 meters, that I am comparing against genomic data from a second high-altitude hummingbird (Colibri coruscans), five low-elevation hummingbirds (Calypte anna, Florisuga mellivora, Glaucis hirsutus, Thalurania furcata, and Schistes geoffroyi), and two swifts (Chaetura pelagica and Chaetura vauxi) to identify positively selected genes relating to high-elevation adaptation.

Genomic sequencing also is currently underway on three sets of sister species of wild guinea pigs (Cavia tschudii and Cavia aperea, Microcavia niata and Microcavia australis, Galea comes and Galea leucoblephara), each with a high-elevation and a low-elevation member. These pairs represent three independent low-to-high divergence events in closely related species. The genome of the domestic guinea pig is already sequenced and will aid in the assembly of these six genomes. Once the genomes are mapped to the domestic reference, I will search for genes that have undergone selection in the three high-elevation species. In addition, I am generating low-coverage sequence data for a dozen domestic guinea pigs, which will be used to more accurately date the domestication events and identify the genes that have been altered by artificial selection.


Collaborative Genome Projects

In addition to the 16 genomes I am working with for my dissertation, I am involved in four additional genome projects. These include the Cinereous vulture, Amur leopard, shark, and an Actinobacterium.


Other Bioinformatics Projects

I am currently assembling a chicken transcriptome in a project with the Cancer Center at UNM, and will use it to identify the genetic basis of an avian form of leukemia. Additionally, I am analyzing ChIP-Seq data for collaborators in the Department of Neurosciences to identify the developmental consequences of prenatal arsenic exposure.


Black-breasted Hillstar
Microcavia australis
Panama