Evolutionary history of the Uzon-Kronotskoe charr flock

Freshwater fishes are prone to forming polymorphisms beneficial for resource partitioning and rapid ecological adaptation. Ecomorphs that have acquired genetic differences occur in a mosaic, forming local centres of diversity. These 'hotspots' are of particular interest as they facilitate the study of speciation mechanisms. Here we examine the evolutionary patterns of the Kronotskoe-Uzon charrs, one of the most phenotypically diverse and complicated endemic assemblage of salmonids on Earth. By analyzing SNPs in SLAF sequences of 101 specimens covering all local diversity and 64 specimens from nine populations of the potential ancestor, we investigated the phylogenetic relationships, genomic structure, admixture and historical gene flow within the population system. Our findings suggest that the endemic assemblage diverged from the widespread migratory Salvelinus malma of eastern Kamchatka, which invaded the basin in several waves. Ten of the 14 genetically distinct ecomorphs diversified in Lake Kronotskoe at the centre of the hotspot. The assemblage formed in the post-LGM - Holocene time as a result of multistep adaptive radiation involving introgressive hybridization in the lake and the secondary spreading of endemic charrs into peripheral waterbodies. The steps of morph divergence coincide well with the main geological and paleoclimatic events in the area. While the diversity of Kronotskoe-Uzon charrs is unique, faunal radiation has proceeded through several archetypal ecological modes implemented by freshwater fishes in dozens of reservoirs across the Holarctic. One reason for this increased diversity is the enhanced ecological opportunities provided by the large lake-river system in the moderate marine climate.