Figure 6. Thyroid hormone (T3) levels and associating highly differentiating candidates in lacustrine Dolly Varden morphs related to thyroid function and craniofacial morphology.

(A) Serum T3 levels were significantly less in Nosed 1, Nosed 3, and Smallmouth lineages relative to anadromous Dolly Varden; mean +/− 1 SD, with boundary values indicated (min/max). (B) Top 20 candidate regions differentiating Nosed lineages from Longhead and White lineages. Sites uniquely differentiating Longhead morphs from Nosed 1 and Nosed 3 morphs, and White morphs from Nosed 1 and Nosed 3 morphs identify loci associated with thyroid function (blue, T) or craniofacial developmental (orange, C) modulating elements. (C) Schematic of Leptin A paralogs in salmonids detailing previously unknown gene leptin a2 having a unique 66 amino acid N-terminus extension compared to its paralog. Nosed lineages contain a fixed, non-synonymous SNP in this conserved N-terminal sequence. (D) An otx2b CNE contains fixed or highly differentiating variants within a predicted Pax1 binding domain that associates with lake morphs exhibiting significantly different thyroid signaling activities; percentage of reference and alternate allele reads indicated per morph. Low level detection of variant or reference alleles noted (1 read for reference allele (asterisk), 2 reads for non-reference allele (dagger)).