Genomics of inbreeding in wild populations

Integrating high-resolution genomic data into long-term field studies offers an opportunity to understand key questions in evolutionary biology. One such question of considerable interest to conservation science is the genomics of inbreeding depression. This thesis develops and applies a high-throughput genomic toolkit for the recently bottlenecked and long-term studied Seychelles warbler (Acrocephalus sechellensis) to study inbreeding depression. I use low-coverage (2.6×) whole-genome sequencing and reference-panel-free genotype imputation to generate 18 million biallelic variants across 1,935 individuals mapped to a novel chromosome-level genome assembly. This cost-effective trade-off between sequencing coverage and sample size yielded 96.1% accuracy for regions with read depth artificially downsampled to 0.1x. This genomic toolkit facilitated an audit of the 37-year longitudinal dataset, correcting historical sample errors. Applying this toolkit to analysis of the population’s demographic history revealed a severe bottleneck following human colonization in 1780, which resulted in pervasive inbreeding depression across all major fitness proxies. A 10% increase in realized inbreeding (FROH) was found to reduce lifetime fecundity by 15.1%. Despite this cost, the absence of detectable recessive lethal haplotypes suggests that the species' long-term history of small effective population size (Ne < 300) or recent bottleneck has facilitated the purging of large-effect deleterious alleles, leaving a genetic load dominated by many weakly deleterious recessive alleles. To contextualize these findings, a global meta-analysis of 20 wild vertebrate populations confirmed a pervasive cost of inbreeding on fitness, while identifying significant male-biased sensitivity to inbreeding costs. Overall, this thesis presents a novel genomic toolkit for a long-term studied wild population that has been recently bottlenecked which is used to quantify the genomic architecture of inbreeding depression.