Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic signatures of sympatric radiation

Abstract

AbstractRecent adaptive radiations provide evolutionary case studies which can be parsed to reveal the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genusSalvelinus) present a trove for comparative genomics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, stereotypical species flocks are assemblages of only two to three lineages. However, a species flock of Dolly Varden charr (Salvelinus malma) in Lake Kronotskoe contains at least seven lineages, each with defining morphological and ecological traits. This is the most extensive radiation described for the genus. Here, we perform the first genome-wide analysis of this species flock to parse the genetic foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little hybridization. We also find that specific selection on thyroid and craniofacial genes forms a shared basis for the radiation. The data also implicate thyroid signaling in subsequent lineage specification. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.