The Program for Conservation Genomics focuses on utilizing genomics tools to address conservation questions and gain insights into the basic evolutionary ecology questions.
Over the last 5+ years, this work has involved three different kinds of projects:

1. Characterization of the geographic distribution of genomics diversity of species of conservation concern in order to gain insights into population and species history as well as to lay the groundwork for development of conservation tools. We have conducted or are currently conducting this kind of study on tigers (papers here and here), Snow Leopards, African Lions, African Wild Dogs, and Plains Zebras. Note that these studies require blood or tissue samples from across a species range and are thus only possible due to expansive collaborations with countless partners.

2. Development of genomic tools that can be immediately used to help ongoing conservation work being done by conservation organizations. Specifically, we use the whole genome sequencing information generated in type 1 projects to develop SNP (single nucleotide polymorphism) panels that can be used to capture meaningful information (individual ID, geographic assignment, relatedness) from non-invasive samples (feces, saliva, confiscated materials). We have developed or are currently developing this kind of tool for tigers, snow leopards, African lions, and African wild dogs.

3. Utilization of fecal metabarcoding techniques and hormone analyses to gain insights into the ecology and health of species of conservation concern. Specifically, we use fecal metabarcoding to assess diet, intestinal parasite diversity, and microbiome, and we use hormone analyses (conducted in a service-providing lab) to assess stress and sex hormones. We are currently conducting these analyses on black rhinos and African wild dogs.

4. We intend to combine these approaches with the use of eDNA to carry out global assessment of biodiversity through time.

Gorongosa:

Over the last year, we have begun to apply these techniques to address more eco-evolutionary questions focused on Gorongosa National Park (GNP), Mozambique, as part of a collaborative NSF funded project with the Pringle Lab at Princeton University. Defaunation and rewilding, perturbations that have come to define the Anthropocene, can reveal potent insights into fundamental ecological and evolutionary processes that structure populations, communities, and ecosystems. Yet a major obstacle to inference in both intact and degraded systems is the difficulty of measuring fitness and its correlates—the common currency that links ecology and evolution and is the bedrock of theory in both fields. As part of this NSF project, we will develop the capacity to conduct comprehensive, noninvasive, real-time analysis of fitness components (reproduction, survival) and ecological correlates (diet, microbiome, parasites, hormones) from fecal samples in GNP, where wildlife is recovering from devastation by civil war. As we begin this work, we are focusing on 3 functionally important species (African wild dog, zebra, bushbuck) that exhibit diverse responses to perturbation. To accomplish this work, we will be utilizing the three research techniques outlined above and hope that our results will help to guide restoration and rewilding both locally and globally.