Patterns of selection reveal shared molecular targets over short and long evolutionary timescales

Abstract

1Standing and de novo genetic variants can both drive adaptation to environmental changes, but 2 their relative contributions and interplay remain poorly understood. Here we investigated the 3 dynamics of drug adaptation in yeast populations with different levels of standing variation by 4 experimental evolution coupled with time-resolved sequencing and phenotyping. We found a 5 doubling of standing variation alone boost the adaptation by 64.1% and 51.5% in hydroxyuea and 6 rapamycin respectively. The causative standing and de novo variants were selected on shared 7 targets of RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. The standing and de novo TOR 8 variants map to different functional domains and act via distinct mechanisms. Interestingly, 9 standing TOR variants from two domesticated strains exhibited opposite resistance effects, 10 reflecting lineage-specific functional divergence. This study provides a dynamic view on how 11 standing and de novo variants interactively drive adaptation and deepens our understanding of 12 clonally evolving diseases.13 8 This adaptive gain was directly comparable to those of NA endpoint populations, and thus 1 capable of fully explaining their adaptive gains. (Figure S4B). 2 3 De novo mutations in TOR1, TOR2 and FPR1 drive rapamycin adaptation in heterogeneous 4 populations 5Both de novo and standing variants could contribute to adaptation in the four-parent populations. 6Given that they were derived from four parents, the frequency spectrum of each parental allele is 7 centered around a median frequency of 0.21 (WA), 0.26 (NA), 0.26 (WE) and 0.26 (SA) at T0 8 (Cubillos et al., 2013). In comparison, the initial frequency of de novo mutations is extremely low, 9 arising during the crossing or selection phases (Vázquez-García et al., 2017). We called de novo 10 driver mutations in genes that were recurrent mutation targets in the eight four-parent populations 11 and found that FPR1, TOR1 and TOR2 harbor such mutations ( Figure 3A). Identical FPR1 12 mutations occurred in all the replicated populations derived from one intercrossed population 13 F12_1 and the same TOR1 mutations were found in all the replicated population derived from the 14 other intercrossed population F12_2; thus these drivers emerged during the shared crossing phase 15 and then expanded independently during the selection phase. Validating this assumption, the 16 same haplotype blocks increased in frequency in the replicated populations derived from the same 17 intercrossed population, reflecting expansion of the same clones present at T0 ( Figure S6). 18Similar to the isogenic lines, we found recurrent mutations at the TOR1 1972 and 2038 amino 19 acid sites, further confirming that these were the primary RM selection targets and that they arise 20 independently of the genetic context. In one population (F12_2_RM_4) we also found a TOR2 21 Ser1975Ile mutation rising to high frequency ( Figure 3A). TOR2 Ser1975 is located in the RM-22