PCG Projects
African Wild Dog De Novo Genome Assembly
We are collaborating with 10X Genomics to adapt their long-range genomic libraries to allow high-quality genome assemblies at low cost. We will assemble a reference genome for the African Wild Dog using samples provided by Peter Blinston, Director of Painted Dog Conservation. A reference genome will facilitate population genomic studies, inform comparative studies of canid evolution and perhaps uncover evidence of historic selection. A major goal of this study is to develop and validate a low-cost method for highquality de novo genome assembly, thereby allowing reference genomes for many more conservation and academic systems.
Black Rhino Population Genomics
In collaboration with Raoul du Toit, Director of the Lowveld Rhino Trust in Zimbabwe, we are using genomic tools to measure the reproductive success of over 800 rhinos in managed herds. Previous attempts with microsatellite loci were inconclusive due to low genetic diversity. We will then assess whether management actions (such as dehorning, or relocation) affect reproductive success. Using the high-density genotypes, we will also characterize genetic diversity, structure, and inbreeding within managed rhino herds. Finally, we will test for evidence of a prehistoric biogeographic barrier separating Kwazulu-Natal origin and Zambezi origin populations.
Tiger Worldwide Genomics
Tigers (Panthera tigris) are among the most charismatic of terrestrial mammals. They are also the largest cats, and among the most endangered. Globally, $50 million is spent annually on tiger conservation. Yet tiger habitats continue to shrink and individual populations become more isolated. This is true even in strongholds for tiger conservation like India, where 60% of global tiger populations exist (3000 of 4000 tigers), but median population sizes are of 19 individuals.
While on-ground monitoring can help understand how many tigers exist, the problems that will face tigers in the coming years include population isolation. Because small isolated populations are more prone to inbreeding and subsequent inbreeding depression, a better understanding of tiger genetic and genomic variation will be critical to successful management in the future.
In collaboration with Dr. Uma Ramakrishnan and the National Center for Biological Sciences, Bangalore, India. We have begun whole-genome sequencing over 170 individual wild and captive tigers representing all tiger subspecies worldwide. These genomes will allow us to characterize tiger worldwide genetic diversity in the wild and in captivity. We will study historic tiger population demography and migration, and evidence of natural selection in different environments.
Importantly, this dataset will also allow us to design a genotyping pool containing thousands of SNPs that can be used to study any tiger population, while allowing for data compatibility across studies of closely and distantly related populations.