Structural Variants: Population Size Shapes Jay Genome Evolution

A 100-megabase reduction in genome size defines the evolutionary divergence of North American scrub-jays. This massive architectural shift was revealed through 45 long-read de novo assemblies. By analysing structural variants across three Aphelocoma species, researchers uncovered a 55-fold range in effective population size ($N_e$).

Structural Variants and Rapid Architecture Shifts

The findings are stark. Rapid evolution is not limited to single nucleotide polymorphisms. Instead, shifts in complex satellite landscapes drove significant genome contraction. The data indicates these structural changes are often slightly deleterious. Their survival in the gene pool is modulated by two factors: the length of the variant and the size of the population. Large variants usually disappear. Small ones linger. This dynamic highlights the volatility of vertebrate genomes over relatively short evolutionary timescales.

The Power of Population Size

Demography shapes destiny. In the largest jay population, the team identified consistent evidence of adaptive fixation. Evolution works efficiently there. In contrast, gene copy number variants displayed an inverse relationship with population size. This implies that smaller populations accumulate strongly deleterious changes simply because selection is too weak to remove them. Bad genes drift. Good genes fail to fix. The pangenome analysis demonstrates that genomic complexity is inextricably linked to the number of breeding individuals.

Why This Matters

Conservation biology often ignores genomic architecture. It shouldn't. This study suggests that as species abundance declines, their genomes become vulnerable to structural decay. The accumulation of deleterious copy number variants could compromise gene expression, creating a feedback loop of decline. Understanding how population bottlenecks influence pangenome complexity provides a critical metric for assessing extinction risk in vertebrates. We must recognise that a shrinking population means a deteriorating genome.