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Background  In diverse taxa, photoperiodic responses that cause seasonal physiological and behavioural shifts are controlled by genes, including the vertebrate  Clock  orthologues, that encode for circadian oscillator mechanisms. While the genetic network behind circadian rhythms is well described, relatively few reports exist of the phenological consequences of and selection on  Clock  genes in the wild. Here, we investigated variation in breeding phenology in relation to  Clock  genetic diversity in a long-distance migratory bird, the barn swallow ( Hirundo rustica ).    Methodology/Principal Findings  In a sample of 922 adult barn swallows from a single population breeding in Italy we found one very common (Q 7 ) and three rare (Q 5 , Q 6 , Q 8 ) length variants of a functionally significant polyglutamine repeat. Rare (2.9%) Q 7 /Q 8  heterozygous females, but not males, bred significantly later than common (91.5%) Q 7 /Q 7  females, consistent with the expectation that ‘long’ alleles cause late breeding, as observed in a resident population of another bird species. Because breeding date depends on arrival date from migration, present results suggest that the association between breeding date and  Clock  might be mediated by migration phenology. In addition, fecundity selection appears to be operating against Q 7 /Q 8  because late migrating/breeding swallows have fewer clutches per season, and late breeding has additional negative selection effects via reduced offspring longevity. Genotype frequencies varied marginally non-significantly with age, as Q 7 /Q 8  frequency showed a 4-fold reduction in old individuals. This result suggests negative viability selection against Q 7 /Q 8 , possibly mediated by costs of late breeding.    Conclusions/Significance  This is the first study of migratory birds showing an association between breeding phenology and  Clock  genotype and suggesting that negative selection occurs on a phenologically deviant genotype. Low polymorphism at  Clock  may constrain microevolutionary phenological response to changing climate, and may thus contribute to the decline of barn swallow populations.

Clock Gene Variation Is Associated with Breeding Phenology and Maybe under Directional Selection in the Migratory Barn Swallow