From prehistory to present-day: How isolation shaped the distinct genomic makeup of Italian Alpine valleys

This Zenodo dataset includes Human Origin genotypes generated for the study "From prehistory to present-day: How isolation shaped the distinct genomic makeup of Italian Alpine valleys", (currently under submission). Datasets Data provided in PLINK binary format (.bed, .bim, .fam). Datasets are provided raw, filtering out unmapped SNPs and individuals with over 2% of missingness and call rate less than 95% (n SNPs = 615,151). No further filtering based on genotype missingness thresholds or relatedness was applied. Same sample labels (FID and IID, SEX) as original publication. LedroRendena_Dataset.zip contains individuals with at least one grandparent (GP) from either of the two Alpine valleys (Ledro Valley, Rendena Valley) (n Individuals = 87) Italian_Dataset.zip comprises Italian individuals, divided by provenance, plus ADMIXED and Trentino_3GP individuals (n Individuals = 144) See original publication Supplementary Data for addtional metadata. See Materials and Methods for which filters on quality and kinship were implemented for final results. Brief description of the study For the first time, we analyzed the genome-wide profiles of human populations from two historically isolated valleys in the eastern Italian Alps, the Ledro and Rendena Valleys (Province of Trento), providing both a mitochondrial (maternal) history and a nuclear genome (biparental) perspective. To better contextualize this genomic variation within the Italian landscape, a new dataset of peninsular and insular Italy was also generated. The Ledro and Rendena communities are genetically distinct from all other Italian populations, but have a common Alpine background shared with ancient individuals from the region, including the Tyrolean Iceman, primarily due to isolation that differentially preserved specific ancestral components. Notably, the two valleys exhibit internal substructure correlated with topography, which may have also been influenced by longstanding socio-economic practices.