GENOMICIDE · The genomic impact of ancient structural variants on species extinction

In this proposal, I seek to quantify the impact of structural variants on species genome diversity and extinction by sequencing ancient genomes of extinct megafauna. Structural variants are large genomic rearrangements capable of significantly affecting gene function and fitness. While in previous work I have investigated the genomes of extinct species at the single nucleotide polymorphism (SNP) level, the accurate identification of structural variants has been hampered by molecular and computational challenges, thus impeding their incorporation into genomic extinction research. Recent advancements in long-read sequencing technologies have led to considerable improvements in accuracy and affordability, making it feasible to characterize structural variants at population level scale in non-model organisms. Despite the fragmented nature of ancient DNA, our preliminary results show that millions of ancient DNA sequences exceeding 500 basepairs in length can be obtained from extraordinarily well-preserved samples. This project capitalizes on these samples, combined with state-of-the-art sequencing technologies, to recover high-quality long-read sequencing data from ancient specimens and subsequently reconstruct extinct genomes de-novo. Focussing on megafaunal that went extinct during the late Pleistocene, this project will examine the evolution of structural variants under scenarios of increased genetic drift and reduced selection at unprecedent resolution. Moreover, the project will pioneer the direct quantification of within-species structural variant changes through time, and provide new insights into genetic variants within previously unassembled genomic segments. By expanding our understanding of the genetic role of structural variants on extinction events, we will contribute valuable insights into the genetic determinants beyond SNPs that influence species diversity, adaptations, survival and eventual extinction.