The impacts of genomic structural variants on population viability in endangered species

Structural variants (SVs) are large rearrangements within the genome that often impact gene function and thus have large effects on fitness.

While the genomes of many threatened species have been extensively studied on a single nucleotide polymorphism (SNP) level, the molecular and computational challenges surrounding accurate identification of SVs have thus far precluded incorporating SVs into conservation genomic studies.

Thus, despite their importance for the long-term survival of species, little is known about the genetic impacts of SVs during population declines. Long-read sequencing technologies have now exponentially improved in read length, accuracy and costs.

De-novo assembly of mammalian genomes below $1000 is a reality, making it feasible to accurately characterise SVs on a population level.

In this project, we propose to study the evolution of SVs during population bottlenecks and declines, making use of the latest long-read sequencing technologies.

This project will focus on a set of endangered mammals, varying in their demographic histories, allowing us to obtain fine-scale resolution of SV evolution under different scenarios of drift and selection.

In addition to sequencing modern genomes, we propose an approach to recover long-read sequencing data from historical specimens, providing, for the first time, a direct quantification of within-species SV evolution over time.