Multiple secondary contacts and historic hybridization between glacial lineages of charr (Salvelinus, Salmonidae) in northeastern Asia

Arctic regions of northeastern Asia represent areas of secondary contact of the glacial phylogenetic lineages of charrs belonging to the genus Salvelinus (Salmoniformes: Salmonidae). However, the post‐glacial dispersion of charr across Arctic regions is poorly understood, as knowledge of populations from Chukotka and its neighbouring areas remains limited. Specifically, there is no clear understanding of which charr species inhabit significant regions of Chukotka from the sea coasts to the Kolyma drainage. In this study, we explored the affiliation of lacustrine charrs from the Chukotka area with (1) the Arctic lineage of Taranetz' charr (Salvelinus taranetzi); (2) the Bering lineage of Northern Dolly Varden (Salvelinus malma malma) and (3) the Siberia and Atlantic lineages of Arctic charr (Salvelinus alpinus). We analysed sequence variation of the mitochondrial DNA control region (mtDNA CR; 960 base pairs) and genotyped seven microsatellite loci of nuclear DNA from charr collected at 13 sampling sites. We found different consequences of secondary contact: (1) complete fixation of introgressed mtDNA (mitochondrial capture) and (2) preservation of several mtDNA lineages with the absence of contemporary gene flow between resident populations. Combining the distribution patterns, phylogenetic network topology and knowledge of the glaciation history of the region, we propose two zones of secondary contact of the glacial lineages in Chukotka–Kolima‐Chukotka River system and Paleo‐Amguema River–from where charrs with introgressed genomes spread throughout this range. However, in some cases, the process of foreign mtDNA capture likely occurs in a more localised manner.