The first population scale compendium of complete mitochondrial genomes from Flanders, Belgium

Mitochondrial DNA (mtDNA) plays a crucial role in forensics and population genetics, especially for analysing highly degraded samples. Yet, most mitogenomic reference datasets are still limited to control region (CR) sequences, that have limited discriminatory power. This is particularly true for Belgium, where despite the introduction of new legislation in 2024 to increase the use of mitochondrial DNA in familial searching, comprehensive mitogenomic reference data remain scarce. To fill this gap, we present a new forensic-grade dataset comprising complete mitochondrial genomes from 264 individuals with maternal ancestry from Flanders, the northern part of Belgium. Maternal lineages were verified through validated genealogical records extending prior to 1750. Our Flemish dataset reveals 252 unique haplotypes, a mean pairwise difference of 27.3, and a random match probability of 0.0042, demonstrating forensic resolution comparable to other high-quality European datasets. Haplogroups H, U, and T predominate in Flanders, aligning with broadly observed European patterns, while clustering analyses show close genetic affinities with neighbouring Western European populations. Furthermore, comparison with ancient genomes from the Middle Ages reveals notable continuity in maternal ancestry in Flanders throughout the historical era. Our data substantially expand the mitochondrial reference for Flanders, providing a high-quality resource based on autochthonous maternal lineages, suitable for forensic applications, genetic genealogical analyses, and microgeographic population studies.