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The Atlantic herring (Clupea harengus) is a model organism for exploring the genetic basis of ecological adaptation on account of its large effective population size which greatly restrains the disturbance of genetic drift. In this project, I conducted an evolutionary conservation analysis of the Atlantic herring genome using conservation scores generated by phastCon, phyloP and GERP++ in order to study the sequence variants related to salinity or spawning-time adaptation in Atlantic herring. Results of conservation score comparisons between SNPs and randomly selected bases showed that SNPs strongly related to ecological adaptation in Atlantic herring did not tend to have high conservation scores, suggesting that sequences showing high sequence conservation among species may contribute relatively little to ecological adaptation in herring. SNPs associated with ecological adaptation in Atlantic herring might be located in fast-evolving genomic regions involved in recurring adaptive evolution in Clupeiformes. Results of the enrichment analysis indicated that nonsynonymous coding variants was the most overrepresented variant group among those associated with ecological adaptation in Atlantic herring, followed by synonymous coding variants, 5kb-upstream and 5kb-downstream variants. Taken all the results together, the conclusion is that coding SNPs under positive selection were the most strongly enriched variant group underlying ecological adaptation in Atlantic herring, while non-coding SNPs, mostly neutral or under negative selection, did not show a similar enrichment.