The genomic impact of ancient structural variants on species extinction

Introduction

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.

Challenges in Previous Research

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. This has impeded their incorporation into genomic extinction research.

Advancements in Technology

Recent advancements in long-read sequencing technologies have led to considerable improvements in accuracy and affordability. These advancements make it feasible to characterize structural variants at a population-level scale in non-model organisms.

Preliminary Results

Despite the fragmented nature of ancient DNA, our preliminary results show that millions of ancient DNA sequences exceeding 500 base pairs in length can be obtained from extraordinarily well-preserved samples.

Project Goals

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.

Focus on Megafauna

Focusing on megafauna 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 unprecedented resolution.

Pioneering Quantification

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.

Contribution to Understanding Extinction

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.