Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

FPT Consortium, Morten T. Limborg*, Sarah J. Helyar, Mark de Bruyn, Martin I. Taylor, Einar E. Nielsen, Rob Ogden, Gary R. Carvalho, Dorte Bekkevold

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (512 degrees C) and two salinity clines (535 parts per thousand). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, BalticNorth Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

Original languageEnglish
Pages (from-to)3686-3703
Number of pages18
JournalMolecular Ecology
Volume21
Issue number15
DOIs
Publication statusPublished - Aug 2012
Externally publishedYes

Keywords

  • genome scan
  • haemoglobin
  • heat shock protein
  • local adaptation
  • salinity
  • single nucleotide polymorphism
  • FLOUNDER PLATICHTHYS-FLESUS
  • COD GADUS-MORHUA
  • POPULATION-STRUCTURE
  • LOCAL ADAPTATION
  • NORTH-SEA
  • ADAPTIVE DIVERGENCE
  • NATURAL-POPULATIONS
  • LANDSCAPE GENETICS
  • FISHERIES GENETICS
  • GENOME SCANS

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