Genetic structure, species boundaries, and evidence of hybridization in Turkish brown trout populations

Abstract The brown trout ( Salmo trutta Linnaeus, 1758) species complex in Türkiye displays significant genetic diversity across various river basins. Despite numerous taxonomic revisions, species boundaries and the extent of hybridization remain unresolved. This study investigates the genetic structure and hybridization in 37 brown trout populations from 12 basins using mitochondrial DNA (COI, Cyt-b, D-loop), nuclear DNA (ITS), and 16 microsatellite loci. Mitochondrial haplotype networks indicate extensive haplogroup sharing among populations, even those geographically distant. Microsatellite analyses reveal structured populations, with genetic clusters corresponding to river basins, though evidence of admixture suggests ongoing gene flow. PCoA and STRUCTURE analyses support four main genetic clusters with considerable mixing, particularly in areas affected by translocations and stocking. These findings question recent species classifications based on morphological and limited genetic data, highlighting the need for an integrative taxonomic approach incorporating genomic, ecological, and morphological data. The observed genetic variation is largely attributable to intra-specific diversity and local adaptation rather than the presence of distinct species. Hybridization, likely driven by human activities, plays a major role in shaping the genetic structure of Turkish brown trout. These results provide valuable insights for conservation and management, emphasizing the importance of basin-scale population structure and mitigating anthropogenic impacts.