Genetic Adaptation to Brackish Water and Spawning Season in European Cisco

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.

Authors

Institutions

Publication Details

Journal
Molecular Ecology
Published
2025-09-03
DOI
https://doi.org/10.1111/mec.70094
Primary Topic
Fish Ecology and Management Studies
Type
article
Field-Weighted Citation Impact
0.00

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Genetic Adaptation to Brackish Water and Spawning Season in European Cisco

Henrik Lantz, Kerstin Lindblad‐Toh, Lucile Solér, Julia Heintz et al.
Molecular Ecology
Fish Ecology and Management Studies
article

Genetic Adaptation to Brackish Water and Spawning Season in European Cisco

Henrik Lantz, Kerstin Lindblad‐Toh, Lucile Solér, Julia Heintz, Elísabet Einarsdóttir, Jake Goodall, Stefan Palm, Mats E. Pettersson, Leif Andersson, Mikaela Bergenius, Ignas Bunikis, Bo Delling, Anti Vasemägi, Olga Vinnere Pettersson, Martin Pippel, Mai‐Britt Mosbech, Qiaoling Deng, Remi-André Olsen
article en

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.

Molecular EcologyVol. 34(20)
Broad Institute (US), Uppsala University (SE), Stockholm University (SE), Estonian University of Life Sciences (EE), Chinese Academy of Sciences (CN), Science for Life Laboratory (SE), Swedish Museum of Natural History (SE), Swedish University of Agricultural Sciences (SE), Institute of Hydrobiology (CN), KTH Royal Institute of Technology (SE), Texas A&M University (US)
Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, China Scholarship Council, Uppsala Universitet, Science for Life Laboratory, Uppsala Multidisciplinary Center for Advanced Computational Science
Openalex Percentile: Top 76%
Fish Ecology and Management Studies
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.