Diversity of brown trout <Emphasis Type="Italic">Salmo</Emphasis> cf. <Emphasis Type="Italic">trutta</Emphasis> in the River Danube basin of Western Balkans as assessed from the structure of their mitochondrial Control Region haplotypes

The part of the River Danube basin in the Western Balkans region (11 sampled localities and 57 in total with using of published data) revealed the remarkable diversity of brown trout assessed using the Control Region (CR) of mitochondrial DNA (mtDNA) as a molecular marker. The greatest number of brown trout populations holds brown trout of the Da1 haplotype. Particular distinct haplotypes are limited to isolated brown trout stocks. There are haplotypes of Danubian (Da), and those of Atlantic (At), Adriatic (Ad) and marmoratus (MA) lineages introduced there. Phylogenetic relationships inferred between them implicate the plesiomorhic character of Da*Vr, Da*D? and Da-s6 haplotypes that were resolved as ancestral clades, with the intermediate position between clades holding haplotypes of the non-Danubian lineage and more advanced haplotypes of the Danubian lineage. A uniform rate of evolution was found for all clades. The recent widespread distribution and exclusivity of Da1 haplotype imply its ancestral character among advanced Danubian haplotypes. Populations in the Sava, Drava, Una and Drina revealed an expansion, whereas those in the Kupa and Zapadna Morava catchments revealed both stability in size and great differentiation. Gene flow between stocks was found to be negligible.