Fig. 4

(a) Frequencies of Q. engelmannii-fixed alleles in the 20 scrub oaks: The frequencies of engelmannii-fixed alleles for each variant site is calculated as the number of Q. engelmannii-fixed alleles in the scrub oaks divided by the total number of alleles across all scrub oaks at that locus, usually 40 depending on missing data. The proportion of variants falling into each allele frequency bin is reported as a percentage of the total number of variants, 219,407 for all genes and 2421 for the drought genes. These variant sets are non-LD-pruned engelmannii-fixed biallelic loci with no more than 5% missing data. (b) Allele frequencies less than 0.5. Overall 8746 (4.0%) sites have a Q. engelmannii-fixed allele frequency in scrub oaks of 0.5 or less, and 137 (5.7%) drought gene variant sites have a Q. engelmannii-fixed allele frequency in scrub oaks of 0.5 or less. The difference between all tested bins of low allele frequencies mostly reversed at high frequency bins