What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon (Salmo salar)
Abstract
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.
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BibTeX
@article{garciasouto2026what,
title = {{What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon (Salmo salar)}},
author = {Daniel García-Souto and Swapan Mallick and Elisa Barreiro-Docío and Nadin Rohland and Aisling B. Kearns and María Saura and Carlos Garcia de Leaniz and Lawrence G. Straus and Manuel R. González Morales and David Reich and Sofía Consuegra},
journal = {iScience},
year = {2026},
month = oct,
doi = {10.1016/j.isci.2026.117875},
url = {https://www.cell.com/iscience/fulltext/S2589-0042(26)03258-X},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon (Salmo salar)
AU - Daniel García-Souto
AU - Swapan Mallick
AU - Elisa Barreiro-Docío
AU - Nadin Rohland
AU - Aisling B. Kearns
AU - María Saura
AU - Carlos Garcia de Leaniz
AU - Lawrence G. Straus
AU - Manuel R. González Morales
AU - David Reich
AU - Sofía Consuegra
PY - 2026
DA - 2026/10/13
JO - iScience
DO - 10.1016/j.isci.2026.117875
UR - https://www.cell.com/iscience/fulltext/S2589-0042(26)03258-X
AB - 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.
SN - 2589-0042
ER -