Recent adaptive radiations provide experimental opportunities to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetic analyses as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, charr species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotskoe represent the most extensive radiation described for the genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages within the clade. We find that changes in genes associated with thyroid signaling and craniofacial development provided a foundational shift in evolution to the lake. The thyroid axis is further implicated in subsequent lineage partitioning events. These results delineate a genetic scenario for the diversification of specialized lineages and highlight a common axis of change biasing the generation of specific forms during adaptive radiation.

Author contributions

Conceptualization: K.C.W., C.S.M., S.K.M., J.M.D., M.P.H., F.N.S.; Methodology: K.C.W., J.M.D., F.N.S.; Validation: K.C.W., C.S.M.; Formal analysis: K.C.W., C.S.M., F.N.S.; Investigation: K.C.W.; Resources: E.V.E., G.N.M., C.S.M., J.M.D., F.N.S.; Data curation: K.C.W.; Writing - original draft: K.C.W.; Writing - review & editing: E.V.E., G.N.M., C.S.M., S.K.M., J.M.D., M.P.H., F.N.S.; Visualization: K.C.W., F.N.S.; Supervision: S.K.M., M.P.H., F.N.S.; Funding acquisition: K.C.W., S.K.M.

Funding

This work was supported by the National Institutes of Health [R35GM146467 to S.K.M., 5F32DE029362 to K.C.W.] and the National Science Foundation [NSF 1845513 to S.K.M.]. Deposited in PMC for release after 12 months.

Data availability

All targeted sequencing reads are available at NCBI Sequence Read Archive under BioProject PRJNA1155113.

Special Issue

This article is part of the Special Issue 'Uncovering developmental diversity', edited by Cassandra Extavour, Liam Dolan and Karen Sears. See related articles at https://journals.biologists.com/dev/issue/151/20.

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