The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise, and where many species synchronize their reproduction to seasonal cycles of planktonic productivity. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1,600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season we observed isolation by distance, indicating that gene flow is limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in reproductive timing when delineating management units for Pacific herring. On several chromosomes we detected linkage disequilibrium extending over millions of base pairs, suggesting the presence of chromosomal rearrangements. The frequencies of putative chromosomal rearrangements differed between populations spawning at different times of year. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2, which influences the development of retinal photoreceptors in vertebrates. SYNE2 is likely within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity likely underlies resource waves provided by spawning herring and demonstrates how population-level genetic diversity can influence ecosystem processes. Given the ecological, economic, and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.

This supplemental data set contains filtered genotypes in standard vcf file format for 1,104 herring collected from active spawning aggregations. Details on sample collection, laboratory work, and bioinformatic analyses can be found in the manuscript.

The genotype data are in standard vcf file format. Missing data are denoted by this character: ./.