SYNE2A polymorphism in Atlantic herring and its potential role in spawning-time regulation

Sammanfattning

Atlantic herring is a useful model for studying ecological adaptation since different populations show low genetic differentiation across most of the genome, while some loci under selection show large shifts in allele frequencies. One ecologically important trait is spawning time, and previous genomic studies have identified strong differentiation between spring- and autumn-spawning herring at the SYNE2A/ESR2A locus. SYNE2A encodes a protein involved in the LINC complex, while the nearby ESR2A gene is a strong candidate for reproductive regulation since it encodes an estrogen receptor, making it unclear whether the signal reflects functional variation in SYNE2A or linkage to ESR2A. To investigate whether SYNE2A contributes to adaptation associated with spawning time, SYNE2A haplotypes from spring- and autumn-spawning Atlantic herring were analyzed using dN/dS analysis, diagnostic amino acid substitutions, comparative protein alignment, and AlphaFold3 structure prediction. All mean dN/dS values were below 1, consistent with purifying selection, but spring versus autumn comparisons had a higher mean dN/dS ratio than spring within-group comparisons. This supports the idea that the genetic differentiation between spring- and autumn-spawning herring at this locus reflects selection acting on SYNE2A. Several diagnostic amino acid substitutions were identified, many of which were non-conservative. AlphaFold3 structure prediction showed that the substitutions were distributed across the predicted SYNE2A protein structure, with many located in α-helices within spectrin-like repeats and others located in disordered regions or loops. Together, these results indicate that SYNE2A is involved in adaptation associated with spawning time, although they do not show whether the gene directly regulates spawning time or is associated with another trait affected by seasonal environmental conditions.