Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations

Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We extend the popular restriction site-associated DNA sequencing (RAD-seq) method to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by dXY, reaches ten-fold higher than background levels and structures genomic variation into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback (Pungitius pungitius), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local adaptation in stickleback has actually been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on ecological timescales is a result of genome evolution over geological timescales, and vice versa. IMPACT STATEMENT Adaptation to changing environments requires a source of genetic variation. When environments change quickly, species often rely on variation that is already present – so-called standing genetic variation – because new adaptive mutations are just too rare. The threespine stickleback, a small fish species living throughout the Northern Hemisphere, is well-known for its ability to rapidly adapt to new environments. Populations living in coastal oceans are heavily armored with bony plates and spines that protect them from predators. These marine populations have repeatedly invaded and adapted to freshwater environments, losing much of their armor and changing in shape, size, color, and behavior. Adaptation to freshwater environments can occur in mere decades and probably involves lots of standing genetic variation. Indeed, one of the clearest examples we have of adaptation from standing genetic variation comes from a gene, eda, that controls the shifts in armor plating. This discovery involved two surprises that continue to shape our understanding of the genetics of adaptation. First, freshwater stickleback from across the Northern Hemisphere share the same version, or allele, of this gene. Second, the ‘marine’ and ‘freshwater’ alleles arose millions of years ago, even though the freshwater populations studied arose much more recently. While it has been hypothesized that other genes in the stickleback genome may share these patterns, large-scale surveys of genomic variation have been unable to test this prediction directly. Here, we use new sequencing technologies to survey DNA sequence variation across the stickleback genome for patterns like those at the eda gene. We find that every region of the genome associated with marine-freshwater genetic differences shares this pattern to some degree. Moreover, many of these regions are as old or older than eda, stretching back over 10 million years in the past and perhaps even predating the species we now call the threespine stickleback. We conclude that natural selection has maintained this variation over geological timescales and that the same alleles we observe in freshwater stickleback today are the same as those under selection in ancient, now-extinct freshwater habitats. Our findings highlight the need to understand evolution on macroevolutionary timescales to understand and predict adaptation happening in the present day.