Confirmation of the presence of non‐native, self‐sustaining brook trout S alvelinus fontinalis and genomic distinction between populations in southwest Germany

Abstract Introduced to Europe from North America in the 19th century, Brook trout, Salvelinus fontinalis , can negatively impact native fish communities, yet self‐sustaining populations remain rare in southern Germany despite a long stocking history. Here, we report a survey of 1618 electrofishing records from Baden‐Württemberg, identifying only three small streams harbouring established, reproducing populations. Population density in upstream reaches was positively associated with greater pH variation and warmer winter water temperatures (indicative of well‐water dominance) and negatively associated with stream depth. RADseq‐derived SNPs (203,484 loci) from 34 individuals revealed strong genomic differentiation among all three populations despite their geographic proximity. The degree of differentiation is high for introduced salmonid populations and may reflect multiple stocking events from distinct breeding lineages, post‐introduction genetic drift or a combination of both. The absence of recent stocking and the long‐term spatial containment of these populations to small headwater sections suggest that the ecological threat posed by S. fontinalis to native fish fauna in the region is currently limited.