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Northern freshwater fish may be suitable for the genetic dissection of ecological traits because they invaded new habitats after the last ice age (∼10.000 years ago). Arctic charr ( Salvelinus alpinus ) colonizing streams and lakes in Iceland gave rise to multiple populations of small benthic morphotypes, often in sympatry with a pelagic morphotype. Earlier studies have revealed significant, but subtle, genetic differentiation between the three most common morphs in Lake Thingvallavatn. We conducted a population genetic screen on four immunological candidate genes  Cathelicidin 2  ( Cath2 ),  Hepcidin  ( Hamp ),  Liver expressed antimicrobial peptide 2a  ( Leap-2a ), and  Major Histocompatibility Complex IIα  ( MHCIIα ) and a mitochondrial marker (D-loop) among the three most common Lake Thingvallavatn charr morphs. Significant differences in allele frequencies were found between morphs at the  Cath2  and  MHCIIα  loci. No such signal was detected in the D-loop nor in the other two immunological genes. In  Cath2  the small benthic morph deviated from the other two ( F ST   = 0.13), one of the substitutions detected constituting an amino acid replacement polymorphism in the antimicrobial peptide. A more striking difference was found in the  MHCIIα . Two haplotypes were very common in the lake, and their frequency differed greatly between the morphotypes (from 22% to 93.5%,  F ST   = 0.67). We then expanded our study by surveying the variation in  Cath2  and  MHCIIα  in 9 Arctic charr populations from around Iceland. The populations varied greatly in terms of allele frequencies at  Cath2 , but the variation did not correlate with morphotype. At the  MHCIIα  locus, the variation was nearly identical to the variation in the two benthic morphs of Lake Thingvallavatn. The results are consistent with a scenario where parts of the immune systems have diverged substantially among Arctic charr populations in Iceland, after colonizing the island ∼10.000 years ago.

Differentiation at the MHCIIα and Cath2 Loci in Sympatric Salvelinus alpinus Resource Morphs in Lake Thingvallavatn