Genetic analysis reveals a complex mosaic of admixture in Brook Trout in a historically fragmented watershed

Assess how historical fragmentation in the form of perched culverts impacts Brook Trout Salvelinus fontinalis genetic diversity and differentiation in the Beebe River watershed (central New Hampshire), the site of a major culvert removal project in 2017.We collected genetic samples from Brook Trout one year prior to (2016), and two years following (2018 and 2019) culvert removal from six tributaries in the watershed. We used two analytical approaches, STRUCTURE and discriminant analysis of principal components, to determine the degree to which admixture was occurring and the levels of genetic diversity in the sampled populations. We also compared pairwise FST values to measure the genetic differentiation between tributaries.The analysis revealed that the tributaries with impassable culverts (GR1, GR3, and GR5) exhibited a distinct genetic cluster, indicating genetic homogeneity. In contrast, the tributaries without barriers (GR2, ECR1, and GR4) showed a mixture of individuals assigned to multiple genetic clusters, indicating genetic admixture and high diversity. Culvert outlet drop heights correlated with the level of genetic differentiation and diversity. Culvert replacement did not immediately result in significant changes in the genetic composition of the Brook Trout populations. Fish in tributaries with culverts remained genetically distinct from those in other tributaries even two years after culvert removal.The study demonstrates that historical fragmentation caused by culverts has influenced the population genetic structure of Brook Trout in the Beebe River watershed. Culvert replacement did not lead to immediate changes in genetic composition, suggesting that other factors, such as prespawning behavior and geomorphological disturbances, may have limited fish movement and spawning after culvert removal. The findings highlight the importance of considering the specific characteristics of culverts and their interactions with habitat conditions in assessing their impacts on genetic connectivity.