Demography and selection shape gene loss in freshwater sticklebacks - A pangenomic perspective

The extent of within-species variation in genome assembly size, and the relative contributions of neutral vs. adaptive processes to it, remains poorly understood. We assembled the pangenome for the nine-spined stickleback (Pungitius pungitius) from whole-genome resequencing data obtained from range-wide sampling of 1,478 individuals across 47 populations. Our analysis recovered approximately 234.15 Mb of novel sequence and identified 11,151 protein-coding genes annotated in non-reference-represented regions, which accounted for 28.8% of all annotated pangenomic genes, corresponding to a 40.6% expansion relative to the 27,450 protein-coding genes annotated in the updated v8 reference genome. The identified presence/absence variation (PAV) genes exhibited a higher incidence of deleterious and non-synonymous mutations than core genes. Freshwater populations with smaller effective population sizes had lost more genes and had smaller assembly sizes relative to larger marine populations. Larger genome sizes of marine populations were primarily associated with higher transposable element content. Across gene categories, patterns of molecular variation were consistent with weaker purifying selection in freshwater populations than in marine populations, while recurrent freshwater-biased loss of a subset of PAV genes suggested that gene loss is not entirely random. Together, these results indicate that demographic history explains the overall pattern of gene loss, whereas negative natural selection may contribute to repeated loss of a subset of genes.