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Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. In order to enlarge current information on genetic characterization of the first agricultural communities of the Southern Calchaquí Valleys, we present and discuss the first mitochondrial aDNA information obtained on samples dated to ca. 3600-1900 years BP from the Cajón Valley, Catamarca Province. Reproducible mtDNA HVR-1 sequences were obtained in 7 individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups D1 (57.1%), C1 (28.5%) and B2 (14.2%), with absence of A2.

Our results show that the Cajón Valley sample -with predominance of D1 and C1- differ from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the Valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomes analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco and the Amazon.