Characterisation of deleterious genetic variants in non-model organisms: from present to extinct species

Animals have always been exposed to mass extinctions, but during the last few hundred years, human activities have been one of the main reasons for dramatic decline. When a population becomes smaller, threats affecting the species’ genome become larger. It becomes more prone to inbreeding, good genetic variation will be lost and damaging variation will increase.

This leads to a worse ability to adapt to changing environments and then extinction.

Hence, there is a crucial need to characterize and quantify damaging variation and its contribution to species decline, both for conservational purposes and understanding what drove former species to extinction.

In the proposed three-year project, I will first create a bioinformatic method to score genetic variants based on their predicted deleteriousness.

I will make use of sequenced genomes of pig, and annotation methods, to annotate genomic features that can be used to predict deleteriousness. In the second part, I will translate the predicted deleteriousness per variant to genetic load per individual. I will then train it within genetic data from pig, and validate it in sequence data from wild boar.

Lastly, I will test the method in endangered pig species and in already extinct animals, like mammoths and rhinos.

As these types of scores are almost always species specific, there is a crucial need to expand beyond species borders with the long-term goal of estimating how much genetic variation is contributing to animal extinction.