Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area

Sixty-four samples from 46 salmon populations totalling 2369 specimens were used for polymerase chain reaction-restriction fragment length polymorphis m (PCR-RFLP) analysis of the mitochondrial ND1 region. The final analyses i ncluded 3095 specimens from 60 populations in Northern Europe. A subsample was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from diff erent parts of the distribution area were sequenced and the phylogeny of Eu ropean haplotypes and their relations to the North American lineage was des cribed. The four common European haplotypes derive from the ancestral ND1-B BBA (rooting the European clade to the North American) by one-step substitu tions: AAAA < AABA < BBBA > BBBB. The Swedish west-coast populations differ from the geographically close southern Baltic, indicating absence of inwar d and limited outward gene flow through the Danish straits during the last 8000 years. Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vanern, Ladoga and Onega the haplotype AABA dominated. Proposed po stglacial colonization routes to the Baltic Sea are discussed in relation t o the haplotype distribution pattern.