Genetic Divergence in the Absence of Strong Ecological Differences Between Coexisting White and Common Atlantic Marine Stickleback

ABSTRACT Identifying taxa in the earliest phases of speciation is critical for understanding how reproductive isolation arises. In Nova Scotia, Canada, “white” threespine stickleback co‐occur with common marine stickleback but differ in size, nuptial coloration, nesting behavior, and parental care, raising the possibility that they represent a distinct ecotype with some degree of reproductive isolation. We combined population genomics, morphometrics, and stable isotope analysis to test whether white stickleback represent a distinct lineage and whether they have diverged along ecological axes as have freshwater stickleback populations. Genotyping‐by‐sequencing revealed that male and female white stickleback form a genetic cluster distinct from sympatric common stickleback with evidence of ongoing gene flow yet with very low overall genomic divergence (F ST ≈ 0.01). Genetic differences were distributed across many loci rather than localized to a single genomic region. Morphological and isotopic analyses revealed no differences in most classic ecological traits (body shape, armor, gill rakers, or trophic niche). Instead, whites are smaller‐bodied, paler, and exhibit shorter spines, reduced testes size, and smaller but more numerous eggs compared to common stickleback. These results indicate that white stickleback are genetically distinct from the common Atlantic threespine stickleback but have not diverged conspicuously in their ecology other than in size, suggesting that their differentiation is driven by reproductive and sexual traits rather than trophic specialization. The white stickleback thus represent a promising new system for investigating the interplay of sexual selection, reproductive strategy, and gene flow in the early stages of speciation.