Standing genetic variation is important for population persistence in extreme environmental conditions. While some species may have the capacity to adapt to predicted average future global change conditions, the ability to survive extreme events is largely unknown. We used single-generation selection experiments on hundreds of thousands of Strongylocentrotus purpuratus sea urchin larvae generated from wild-caught adults to identify adaptive genetic variation responsive to moderate (pH 8.0) and extreme (pH 7.5) low-pH conditions. Sequencing genomic DNA from pools of larvae, we identified consistent changes in allele frequencies across replicate cultures for each pH condition and observed increased linkage disequilibrium around selected loci, revealing selection on recombined standing genetic variation. We found that loci responding uniquely to either selection regime were at low starting allele frequencies while variants that responded to both pH conditions (11.6% of selected variants) started at high frequencies. Loci under selection performed functions related to energetics, pH tolerance, cell growth and actin/cytoskeleton dynamics. These results highlight that persistence in future conditions will require two classes of genetic variation: common, pH-responsive variants maintained by balancing selection in a heterogeneous environment, and rare variants, particularly for extreme conditions, that must be maintained by large population sizes.

17Standing genetic variation is important for population persistence in extreme 18 environmental conditions. While some species may have the capacity to adapt to predicted 19 average future global change conditions, the ability to survive extreme events is largely 20 unknown. We used single generation selection experiments on hundreds of thousands of 21Strongylocentrotus purpuratus sea urchin larvae generated from wild-caught adults to identify 22 adaptive genetic variation responsive to moderate (pH 8.0) and extreme (pH 7.5) low pH 23 conditions. Sequencing genomic DNA from pools of larvae, we identified consistent changes in 24 allele frequencies across replicate cultures of both conditions and observed increased linkage 25 disequilibrium around selected loci, revealing selection on recombined standing genetic 26 variation. We found that loci responding uniquely to either selection regime were at low starting 27 allele frequencies while variants that responded to both pH conditions (11.6% of selected 28 variants) started at high frequencies. Loci under selection performed functions related to 29 energetics, pH tolerance, cell growth, and actin/cytoskeleton dynamics. These results highlight 30 that persistence in future conditions will require two classes of genetic variation: common, pH-31 responsive variants maintained by balancing selection in a heterogeneous environment, and rare 32 variants, particularly for extreme conditions, that must be maintained by large population sizes. 33

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