What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon (Salmo salar)

Conservation plans for declining species often rely on contemporary genetic/genomic data to infer historical population structure and evolutionary history of the species. However, modern samples alone may not accurately reflect historical genetic variation, especially after severe population declines or intensive management, and need reference baseline data prior to anthropogenic impact. We analyzed whole-genome sequences dating to 18,800–16,700 years ago from Atlantic salmon ( Salmo salar ), that experienced major declines over the past century. Comparing Paleolithic and modern genomes, we found that ancient salmon from the Iberian glacial refugium were genetically closer to present-day northern European populations than to modern Iberian salmon, consistent with southward displacement of northern lineages during glacial periods, postglacial decline of Iberian populations, and contemporary human impacts. We identified ancient SNPs linked to reproduction and age at maturation in modern salmon populations, while high ancient mitochondrial effective population size suggests greater prehistoric female lineage diversity. These genetic discontinuities between ancient and modern Iberian salmon, not evident in modern samples alone, highlight the value of ancient genomics in conservation.