Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

Abstract

29 pages, 4 figures, supplementary information https://doi.org/10.1038/s41467-024-50239-7.-- Data availability: The sequence data generated in this study have been deposited in the public European Nucleotide Archive (ENA) database under accession code PRJEB61785. The processed data and results are available at the SciLifeLab Data Repository at https://doi.org/10.17044/scilifelab.c.6626216. The genome assembly is available in ENA and NCBI under accession code GCA_964058975.1 and SNP datasets are available under accession code PRJEB77093 in the European Variation Archive (EVA). Subsets of the data are provided in the Supplementary Information. Source data is provided as a Source Data file. This study made use data from the following public databases: AlphaFold Protein Structure Database https://alphafold.ebi.ac.uk/; Climate Reanalyzer https://climatereanalyzer.org/; Dfam (Dfam_3.5) https://dfam.org/home; EggNOG (v5.0) http://eggnog5.embl.de/; FlyBase database (release FB2021_01) https://flybase.org/; GOrilla https://cbl-gorilla.cs.technion.ac.il/; GyDB2 https://gydb.org; HomeoDB https://homeodb.zoo.ox.ac.uk/; KrillDB2 https://krilldb2.bio.unipd.it/; MITOS2 http://mitos.bioinf.uni-leipzig.de/; NCBI Conserved Domain Database (CDD) https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi; NCBI Genome Database https://www.ncbi.nlm.nih.gov/genome/; NCBI RefSeq database (release 204) https://www.ncbi.nlm.nih.gov/refseq/; OrthoDB (v10.1) https://www.orthodb.org/; Pfam (release 34.0) http://pfam.xfam.org/; Repbase (RepBaseRepeatMaskerEdition 20181026) https://www.girinst.org/server/RepBase/; REXdb http://repeatexplorer.org/?page_id=918; ShinyGO 0.77 http://bioinformatics.sdstate.edu/go77/; SILVA rRNA database project (release 132) https://www.arb-silva.de/; The SWISS-MODEL Repository https://swissmodel.expasy.org/; TOPCONS https://topcons.cbr.su.se/; UniProtKB/Swiss-Prot https://www.uniprot.org/. Biological tissue from the reference specimen tissue is available in the LIB Biobank at Museum Koenig Bonn under accession ZFMK-TIS-82493. Three additional specimens are deposited under accessions ZFMK-TIS-82494 through ZFMK-TIS-82496. Source data are provided with this paper.-- Code availability: Public code is available at https://github.com/NBISweden/genecovr and https://github.com/andreaswallberg/Ecological-Genomics-Northern-Krill. A copy of the Github repositories is available on Zenodo: https://zenodo.org/doi/10.5281/zenodo.10827407Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate changeOpen access funding provided by Uppsala University.With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe