Research

Characterizing Signatures of Selection at Diet-Related Genes in Humans

This project involves the investigation of patterns of variation throughout human populations that are located near genes related to metabolism and digestion. We are looking to see whether or not there were any recent signatures of selection on these genes that could have possibly been caused by the population's diet. We analyze this population variation data using bioinformatics tools and several test statistics that can show signatures of selection compared to other populations.

Spotted Lanternfly Outreach Project

This project aims to take a closer look at an invasive insect that is commonly found in Pennsylvania, New Jersey, and New York. The team is aiming to identify DNA extraction techniques that will provide high molecular weight DNA samples from the insect, which we -- or you! -- will then sequence using a small portable sequencing device.  We plan to bring our genomics work on this species into the community and the classroom. If you are interested in working with us on this project, please contact us! 

We are collaborating with other research groups performing work on the spotted lanternfly, including investigators at Cedar Crest College and Temple University. 

Causes and Consequences of Gene Loss of Function in Marine Mammals

Mammals have adapted to life underwater three different times: the closest relatives of cetaceans (dolphins, porpoises, and whales); pinnipeds (sea lions, seals, and walruses); and sirenians (manatees and dugongs) are all terrestrial. This spectacular transition from land to water led to a variety of changes in marine mammals’ bodies and genomes, including some changes that completely inactivated proteins. Often this happened to proteins that were essential in terrestrial mammals but either unnecessary or harmful in marine mammals: one example is a shared loss of smell in marine mammals, with the brain region responsible for smell completely absent in cetaceans. In my past work, I used data from 58 mammals' genomes to find cases where proteins lost their function repeatedly in different marine mammals, to identify candidate proteins whose importance changed when mammals went into the ocean.

One protein that shows this pattern, PON1, is particularly interesting because it helps humans avoid getting sick from exposure to pesticides like chlorpyrifos. Working with collaborators who are experts in biochemistry and GPS mapping, I showed that losing this protein could be a big deal for manatees, which can be exposed to pesticides that run from farms into their canal and river habitats.

In follow-up work, my collaborators and I examined both the sequence and the expression of the gene that encodes the PON1 protein in semi-aquatic mammals, including more seals and sea lions and beavers. We found that two groups of seals and sea lions lost the function of this protein separately. We also found that several species, including beavers, appear to have lost the function of this protein through a reduction in gene expression rather than through inactivating changes in the protein sequence. Finally, we saw that seals and sea lions that were deeper divers were more likely to have lost function than those that were shallower divers. This provides a clue as to how and why aquatic mammals keep losing the function of this otherwise valuable protein.