GENetic adaptations underlying population Structure IN herring, Clupea harengus

Atlantic herring is an important species in the pelagic fisheries with average annual harvest rates exceeding a million tons in the North-eastern Atlantic. Herring display a remarkable variability in phenotypes, e.g., size-at-age and timing of spawning, but at the same time a low genetic divergence between herring populations. The observed genetic difference between populations has however been suggested to be of adaptive relevance. Recent advances in genomics can now be used to document variability in genes with potentially high adaptive significance. During the project period we have for the first time produced viable second-generation offspring of herring from parents that have been raised their entire life under controlled experimental conditions. The studies have shown that the parental adaptation to salinity conditions during maturation subsequently influenced offspring fertilization success at different salinity conditions. Ongoing genetic analyses will reveal if specific genes are over-represented (selected) in the surviving offspring. Studies of mutations rates in herring from our experimental populations have shown that it is among the lowest documented so far in vertebrates. This may be a contributing factor to the relatively low genetic variability typically observed between different herring populations. An example of a mutation with adaptive significance is found in the genes coding for rhodopsin, where the Baltic herring has a variant commonly found in freshwater fishes, while the Atlantic herring has a variant commonly found in marine fishes. The efforts on collecting samples and undertaking genetic analyses from different natural herring populations have shown clear regional differences, and genetic assays have been developed that easily will clarify genetic origin of sampled material. As an example, genetic markers to distinguish spring- and autumn spawning herring have been developed, and international sampling programs are ongoing to document the utility of these genetic markers for herring stock management in collaboration with the International Council for the Exploration of the Seas (ICES). A new experiment has been initiated where herring from different populations have been crossed and raised at different temperature and seasonal light regimes. The work is two years on the way and has generated data on phenotypic variability generated by seasonal light and temperature differences. Genetic markers have been developed to identify individuals to specific parental genotypes. The rearing and genotyping of sampled material will continue until expected maturation at age three years (in 2022). The data will be part of an additional project co-funded PhD (2020-2024).

Prosjektet hadde som målsetting å bidra til å etablere genetiske markører som ville være anvendelig i forvaltning av sildebestandene i nordøstlige deler av Atlanteren. Dette ville bli gjort gjennom kontrollerte eksperimentelle forsøk, kartlegging av genetisk mangfold i ulike sildepopulasjoner samt inngående genetiske analyser av innsamlet materiale. Hovedmålet for prosjektet må sies å være oppnådd da det er utviklet et sett av genetiske markører (SNP) innen utgangen av prosjektperioden som danner grunnlaget for karakterisering av flere sildebestander. Arbeidet med disse SNP-panelene har vært presentert i flere møter og rapporter til det internasjonale havforskningsrådet (ICES), og brukes nå nasjonalt ved Havforskningsinstituttet (Berg et al. 2021 sitert i ICES 2021), og internasjonale partnere i Danmark (DTU) og Irland (Farrell et al. 2021). Som en oppfølging er det det foreslått en temasesjon til den planlagte ICES årskonferansen i Galway 2022.

We propose to undertake unique multigenerational experiments to separate genetic and environmental effects underlying phenotypic variability and survival in herring from fertilisation to maturation. Genome analyses combined with phenotypic characterization of offspring from these experiments will provide novel basic knowledge about the genetic basis for adaptation to different environmental conditions. Furthermore, a set of carefully selected populations of Atlantic herring will be used for whole genome sequencing to establish a more fundamental understanding of the biology and underlying genetic structure in these herring populations. The project will lead to improved quality of the assignment of herring individuals and populations, and provide a strengthened scientific basis for the management of harvested herring stocks. This is especially important under the current regime of climate change, where the genetic make-up of local populations may be under intensified selection and northward displacement due to changes in ambient environmental conditions. We consider the project consortium to be scientifically and timely positioned to undertake this task since we have: 1) unmatched experimental expertise working on all stages of herring and we have established world unique experimental herring populations (Fig. 1). 2) state-of the art genetic expertise on the herring genome (Barrio et al. 2015), and characterised genetic background of offspring herring available for experimentation. 3) extensive knowledge of herring biology and population structure and highly relevant samples of previously collected biological material available for further in depth genetic analyses.