Genomic Erosion by Structural Variation in Island and Mainland Birds : From short-reads to comparative pangenomics
Year: 2025
Type: dissertation
Abstract: Only recently has the field of conservation genomics begun to turn its focus to the interaction of deleterious variation and demographic history in contributing to genomic erosion, especially with regards to the response of larger deleterious mutations beyond single base-pair changes; e.g. structural variants (SVs). By improving protocols to rapidly curate short-read discovered SVs in the House Sparrow (Passer domesticus), I find that even a single lenient curator can substantially reduce the incidence of putative false positive SVs. High-confidence SVs recapture population structure inferred with single nucleotide polymorphisms (SNPs), but those rejected by quality filtering and/or manual curation do not. Next, I apply this protocol to examine the role of distinct demographic histories in the accumulation of deleterious SVs relative to SNPs by manually curating > 35,000 SVs in 12 island and continental populations of the Rock / Willow Ptarmigan superspecies (Lagopus spp.) from across the North Atlantic and Arctic Ocean. Both diversity ratios for non-neutral to neutral SNPs and SVs suggest that slightly deleterious SVs (<30 Kb) detectable with short-reads accumulate nearly-neutrally as a function of decreasing effective population size (Ne). Many pre-existing reference assemblies and linkage maps lack the full set of chromosomes, particularly for e.g. avian and reptilian genomes partially comprised of microchromosomes. I assemble a highly contiguous, chromosomally-complete reference genome for the House Sparrow (Passer domesticus; Passeridae) enriched for previously unresolved repeat-rich regions, such as segmental duplications (SDs) covering 11% of the autosomal genome. By leveraging this new reference and 26 contig-level assemblies, I apply a comparative pangenomic approach to contrast relative densities of distinct variant classes between two deeply diverged human-commensal songbirds (Passeriformes); the House Sparrow and House Finch (Haemorhous mexicanus; Fringillidae). Microchromosomes were enriched for highly and mildly deleterious SVs in both species, likely reflecting a unique genomic background such as higher gene densities, recombination rates, segmental duplication and satellite densities conducive to SV formation. Finally, I assess differences in genetic load imposed by pangenome-inferred SVs versus SNPs in two parallel founder events ca. 1940, with distinct outcomes in sparrows versus finches. Notwithstanding the recent timing of the bottlenecks, genetic drift and inbreeding may inform consistent shifts in relative proportions of SV-associated realised load and masked load in post-founder populations. Underscoring their promise for the field of conservation genomics, chromosomally-complete reference assemblies and population pangenomes reveal that deleterious SVs are overrepresented on avian microchromosomes and may contribute disproportionately to genomic erosion.
Author: David, Gabriel
Institution: Uppsala University
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7112137763