Single-nucleotide polymorphisms (SNPs) reveal red–sika deer admixture in the absence of genetic structure in Central-Northern Italy

The red deer (Cervus elaphus) is a key component of Italian wildlife, yet its genetic structure and potential hybridisation with the invasive sika deer (C. nippon) remain poorly understood. Using double-digest Restriction-site Associated DNA sequencing (ddRADseq), 35,063 single-nucleotide polymorphisms (SNPs) from 66 deer sampled across Tuscany and Emilia Romagna. Population structure analyses revealed two main genetic clusters corresponding to Tuscany and Emilia Romagna, with evidence of gene flow between them. Signatures of introgression from C. nippon were detected in some individuals, particularly in Emilia Romagna, indicating historical or ongoing hybridisation in northern Apennine populations. These results provide the first genome-wide assessment of red deer in Central-Northern Italy and highlight the need for continued genetic monitoring and management actions to mitigate hybridisation risks and preserve the genetic integrity of native populations.