Whole genome sequencing of 56 Mimulus individuals illustrates population 1 structure and local selection 2 3

10. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. ABSTRACT 11 Across western North America, Mimulus guttatus exists as many local populations adapted to site-12 specific challenges including salt spray, temperature, water availability, and soil chemistry. Gene flow 13 between locally adapted populations will effect genetic diversity in both local demes and across the larger 14 meta-population. A single population of annual M. guttatus from Iron Mountain, Oregon (IM) has been 15 extensively studied and we here building off this research by analyzing whole genome sequences from 34 16 inbred lines from IM in conjunction with sequences from 22 Mimulus individuals from across the 17 geographic range. Three striking features of these data address hypotheses about migration and selection 18 in a locally adapted population. First, we find very high intra-population polymorphism (synonymous π = 19 0.033). Variation outside genes may be even higher, but is difficult to estimate because excessive 20 divergence affects read mapping. Second, IM exhibits a significantly positive genome-wide average for 21 Tajima's D. This indicates allele frequencies are typically more intermediate than expected from 22 neutrality, opposite the pattern observed in other species. Third, IM exhibits a distinctive haplotype 23 structure. There is a genome-wide excess of positive associations between minor alleles; consistent with 24 an important effect of gene flow from nearby Mimulus populations. The combination of multiple data 25 types, including a novel, tree-based analytic method and estimates for structural polymorphism 26 (inversions) from previous genetic mapping studies, illustrates how the balance of strong local selection, 27 limited dispersal, and meta-population dynamics manifests across the genome.