Shifting Balancing Selection Underlies an Inversion Cline in Eurasian Blackcap

ABSTRACT Divergent selection on chromosomal inversions associated with locally adaptive traits can generate inversion clines. Typical clines span a narrow width of the species' geographic range, with each arrangement maintained at high frequency on its respective side. While balancing selection also maintains inversion polymorphisms, it is not known whether spatial heterogeneity in its parameters, or shifting balancing selection, can generate inversion clines. Here, we study a cline of an 8 Mb‐long inversion inv_12_3 in a widespread seasonal migratory songbird, the Eurasian blackcaps ( Sylvia atricapilla ). Unlike typical inversion clines, this gradient spans the entire species range with one arrangement being the minor allele in all populations, and thus cannot be explained by divergent selection. More specifically, the inv_12_3 frequency among continental populations is decreased in populations with shorter migratory distance, with residents being the lowest; and the frequency is even lower in six island populations, which are all resident. Using demography inference, population genomic simulation under the blackcap demography, and approximate Bayesian computation, we identify the type of balancing selection and estimate its spatially varying parameters. We show that inv_12_3 is under negative frequency‐dependent selection (NFDS) with a lower optimal frequency on islands. Corroborating with biogeographic history, our results suggest that inv_12_3 was maintained at an optimal frequency in a glacial refugium, then populations diverged through post‐glacial expansion, during which the selection may have changed upon island colonisation. To our knowledge, this is the first case of NFDS suggested to underlie inversion clines, highlighting the underappreciated role of shifting balancing selection.