Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management

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.