Population genetics and phylogeography of resident forms of arctic charr Salvelinus alpinus (L.): from neutral markers to landscape genomics

The review covers world and Russian studies of the population genetic structure and phylogeography of resident (landlocked) Arctic charr Salvelinus alpinus (L.) , from allozyme analysis and mitochondrial DNA sequencing to microsatellite loci and whole-genome resequencing. Landlocked lake populations consistently show high inter-population differentiation, restricted gene flow, small effective population sizes and reduced neutral diversity. A clarification is made regarding Brunner et al. (2001): the Beringian mtDNA lineage in that classification consists entirely of S. malma , so four lineages should be recognised for S. alpinus sensu stricto. The frequently simplified statement that Ne below 50 causes loss of heterozygosity within two or three generations is corrected: at Ne = 50 the inbreeding rate is about 1 % per generation and the consequences accumulate over five to ten generations. Russian data for European Russia, Siberia and North-East Asia are summarised. The potential of landscape genomics, isolation-by-environment analysis and demographic reconstruction by PSMC is discussed. The results are directly relevant to the definition of conservation units and to stocking practice.