AbstractBackgroundThe origin of species is a central topic in biology aiming at understanding mechanisms, level and rate of diversification. Ecological speciation is an important driver in adaptive radiation during post-glacial intra-lacustrine niche diversification in fishes. The Arctic charr Salvelinus alpinus L. species complex in the Northern hemisphere freshwater systems display huge morphological and life history divergence in lakes with one or several morphs present, thus offering a unique opportunity to address ongoing speciation mechanisms.We studied Arctic charr in Lake Tinnsjøen by fishing in four nominal lake habitats (pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats) down to 350 meters depth. Research topics addressed were; (1) to illuminate Holarctic phylogeography and lineages colonizing Lake Tinnsjøen, (2) to estimate reproductive isolation of morphs or fish using unbiased methods, and (3) to document eco-morphological and life history trait divergence. Also, we compared Lake Tinnsjøen with four Norwegian outgroup populations of Arctic charr.ResultsFour field-assigned morphs were identified in Lake Tinnsjøen; the planktivore morph in all habitats except deep-profundal, the dwarf morph in shallow-moderate profundal, the piscivore morph in shallow-moderate profundal (less in littoral and deep-profundal), and an undescribed new morph – the abyssal morph in the deep-profundal only. The morphs displayed extensive life history variation based on age and size patterns. A moderate to high concordance was observed between field-assigned morphs and four unbiased genetic clusters obtained from microsatellite variation. MtDNA suggested the occurrence of two minor endemic clades in Lake Tinnsjøen likely originating from one widespread colonizing clade in the Holarctic. All morphs were genetically differentiated at microsatellites (FST: 0.12-0.20; with some ongoing gene flow among morphs, and for most mtDNA comparisons (FST: 0.04-0.38). Analyses of Norwegian outgroup lakes implied colonization from a river system below Lake Tinnsjøen.ConclusionOur findings suggest post-glacial adaptive radiation of one colonizing mtDNA lineage with divergent niche specialization along a depth-temperature-productivity-pressure gradient. Concordance between reproductive isolation and the realized habitat of the morphs imply that ecological speciation may be the mechanism of divergence. Particularly novel is the extensive morph diversification with depth into the often unexplored deep-water profundal habitat, suggesting we may have systematically underestimated biodiversity present in lakes.