Laura Gramolini, Paolo Ciucci, Ian Marc Bonapace, Paolo Franchini, Leonardo Gentile, Alexandros A. Karamanlidis, Oddmund Kleven, Jonas Kindberg, Alexander Kopatz, Diana Lobo, Livia Chavko, José Vicente López-Bao, Slaven Reljic, Lana Pađen, Emanuela Solano, Tomasz Zwijacz-Kozica, Paolo Colangelo

The brown bear (Ursus arctos) is a widespread Palearctic species represented in Europe by populations occupying diverse environments. Rapid environmental change is reshaping habitats and resource availability, exposing populations to new selective pressures. The species’ remarkable phenotypic plasticity may partly result from environmentally mediated regulation of gene expression through epigenetic mechanisms such as DNA methylation. We generated genomic data using Double Digest Restriction-site Associated DNA sequencing and genome-wide methylation profiles via Reduced Representation Bisulfite Sequencing from 35 individuals across six European populations: Scandinavian, Cantabrian, Dinaric-Pindos, Rhodope, Carpathian, and Apennine. We integrated these data to disentangle the role of genetic background and environment in shaping the methylation profiles of the populations. Our results revealed clear genomic and epigenomic population structure, identifying 7,932 SNPs and 1,259 methylation sites associated with population differentiation. Integrating methylation profiles with bioclimatic predictors uncovered epigenetic signatures linked to ecological gradients, independent of genetic relatedness. Latitude, temperature, and precipitation emerged as the main environmental drivers. Variance partitioning showed that climate explained 7% of methylation variation, genetic structure 5%, and their interaction an additional 5%. The methylation sites significantly associated to the environment were mainly located on promoter regions (78%), suggesting a role in regulating gene expression. While genetic variation underpins long-term evolutionary change, DNA methylation may enable faster functional responses, promoting phenotypic plasticity and rapid adjustment. Incorporating epigenetic approaches into conservation genomics can improve the assessment of short-term adaptive potential and support more effective conservation planning under rapid environmental change.