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Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait‐specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkey flower,  Mimulus guttatus , and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations representing annual and perennial strategies from across the native range revealed strong correlations between vegetative and reproductive traits. To determine whether these multitrait patterns arise from pleiotropic or independent loci, we mapped  QTL s using an approach combining high‐throughput sequencing with bulk segregant analysis on a cross between populations with divergent life histories. We find extensive pleiotropy for  QTL s related to flowering time and stolon production, a key feature of the perennial strategy. Candidate genes related to axillary meristem development colocalize with the  QTL s in a manner consistent with either pleiotropic or independent  QTL  effects. Further, these results are analogous to previous work showing pleiotropy‐mediated genetic correlations within a single population of  M. guttatus  experiencing heterogeneous selection. Our findings of strong multivariate trait associations and pleiotropic  QTL s suggest that patterns of genetic variation may determine the trajectory of adaptive divergence.

The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus