Using ancient DNA to uncover historical disease dynamics in North American and British deer

Diseases can have dramatic impacts by limiting population growth rates, producing strong selection pressures, and potentially leading to adaptive responses. While not infective to humans, chronic wasting disease (CWD) is fatal in cervids (deer, elk, and moose). In some populations, greater than 40% of individuals have tested positive for CWD, and population sizes have started decreasing. Analyses of the Prnp gene suggest that particular alleles may influence susceptibility. For example, deer carrying one allele of the Prnp gene had CWD infection rates that were about four times less than other alleles.

Other Prnp variants are associated with slower disease progression. While this may allow for longer survival of infected individuals, it may also result in increased environmental contamination, facilitate transmission, and potentially yield higher infection rates. Given these dynamics, it is likely that CWD is exerting a strong selection pressure on cervid populations, which could result in changes in the frequencies of Prnp alleles related to disease susceptibility.

We will use ancient DNA techniques to examine changes in the frequencies of Prnp alleles through time in two deer species, European red deer (Cervus elaphus) and closely related North American elk (Cervus canadensis). For work on elk, the student will travel to the US and be hosted in the lab of our collaborator for three moths. We will investigate one population exhibiting evidence of CWD infection and another without. While CWD doesn’t infect humans, lab work will be conducted under strict protocols to eliminate risk to local deer. To examine baseline Prnp allele frequencies, ancient DNA will be extracted from bones of deer that lived in the past (e.g. from archaeological middens). PCR amplification and Sanger sequencing will be conducted on the well-characterized third exon. For comparison, we will also sequence neutral loci, which will allow discrimination of changes in allele frequencies due to selection vs. other processes. Population genetic analyses will be used to compare allele frequencies in each time window. Network and phylogenetic analysis of the sequences uncovered will demonstrate evolutionary relationships of the alleles within and between deer species, and with those known to differ in susceptibility.

A second aspect of the project will involve characterizing the diversity of Prnp alleles through time in British red deer populations. CWD is not currently present in Britain, but anthropological evidence suggests that similar diseases might have influenced deer populations in the past. This project will also yield insights into potential susceptibility of contemporary British deer to CWD should it spread from Europe. CWD susceptibility dynamics offer a case study in understanding the intricacies of natural selection and the evolution of disease resistance.

During the course of this project, the student will develop widely desired job skills as part of a dynamic group at Durham and a broader international collaborative network. She or he will build a strong foundation in disease ecology and evolutionary biology, and develop molecular lab skills, as well as skills in sophisticated bioinformatic and statistical analyses, problem solving, writing, and effective communication.