Population Structure, Demographic History and Maladaptation Risk in Ponderosa Pine

The influence of demography and selection over a species’ evolutionary time can influence responses to current and future stressors. We used range-wide datasets in ponderosa pine (Pinus ponderosa) to understand the influence of demography and selection on current population structure. Samples were sequenced with 55,000 capture-seq probes, producing 1.2–1.5 million SNPs (~400 Mbp raw data per sample). We examined current population structure, changes in effective population size, evidence for selection, genome–environment associations and future maladaptation risk using genomic offset. Our results show support for four genetic clusters within the species, numerous bottleneck events that mirror glacial advances and past droughts, signatures of purifying and balancing selection, important environmental variables for climate adaptation, and many geographic areas with high amounts of genomic offset. Genetic differentiation was associated with two processes: (1) bottleneck-driven allele loss and reduced connectivity; and (2) spatially heterogeneous selection linked to moisture gradients. Many populations are predicted to be at risk of future maladaptation, and these populations coincide with geographic areas showing increased mortality events and decreased regeneration in previous studies. Large shifts in allele frequencies may be required for populations to track projected climates.