# Genetic Adaptation to Brackish Water and Spawning Season in European Cisco

## TL;DR

This study explores how European cisco fish adapt genetically to different water types and spawning seasons, using genome data to identify key genes and population structures.

## Contribution

The study provides a high-quality genome reference and identifies specific genes and SNPs linked to spawning timing and salinity adaptation in European cisco.

## Key findings

- A major genetic subdivision was found between populations likely originating from different glacial refugia.
- Genetic differentiation was detected between spring- and autumn-spawning populations and between freshwater and brackish water populations.
- Outlier SNPs and genes like BHLHE40, TIMELESS, and CPT1A were linked to spawning timing and salinity adaptation.

## Abstract

How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (
Coregonus albula
) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring‐ and autumn‐spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high‐quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC‐directed scaffolding. We generated low‐coverage whole‐genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring‐ and autumn‐spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome‐wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.