Inferring adaptation and evolutionary change by combining data from field studies and genomics is an exciting new area in evolutionary biology but also presents challenges. These challenges are particularly acute when the focal trait has a polygenic architecture, because many long‐term field studies are sample‐size‐limited compared to studies of humans and model organisms, making the detection of loci that contribute to trait variation difficult. In a recent comment, Perrier and Charmantier (2018); hereafter P&C, highlight these issues and draw attention to several analyses described in our recent publication (Bosse et al. 2017) on the evolution of longer bill length in UK populations of the great tit (Parus major). While we support the overall message of P&C – that caution should be exercised when making inferences about long‐term evolutionary trends from shorter ecological time series – we also address some of the specific criticisms that P&C raised about the analyses described in Bosse et al. (2017).
P&C's comments can broadly be split into two sets of queries. The first considers how phenotypic variation is distributed in space and time. The second explores how signatures of selective sweeps can be sensitive to local (in the genomic sense) variation in recombination rate.