Genetic insights on old riddles : the Chachapoyas from the Northeastern Peruvian cloud forests

This dissertation focusses on the genetic diversity of the Chachapoyas in the context of northeast Peruvian and South American populations. The genetic survey of indigenous human populations from the Americas is still far from being comprehensive, which is in stark contrast with other areas of the globe, such as Europe, where an in-depth understanding of the genetic variation and its use in forensic and medical genetics has been attained. This highlights the need for increasing genetic research in Peru as to continue laying the foundation for human genetics and its applications in other fields such as forensics. The montane forests of northeast Peru are one of the most biologically diverse ecosystems in the world and it is there where the ancient Chachapoyas throve and where their descendants nowadays live. Archaeological, historical and linguistic records inform of a complex region where local populations interacted with others throughout prehistory up until the time of European contact in the 16th century. Although traces of past cultural diversity persist in the Chachapoyas region, the series of demographic, environmental and cultural impacts have blurred this cultural differentiation and debilitated the local identities of present-day peoples. Among other factors, cultural diversity in the region has also been shaped by a series of population-level phenomena, which are the focus of this research. To address various questions that emanate from archaeology and ethnohistory, samples from the modern Chachapoyas and three of their neighbors were genotyped for various types of markers (mtDNA, Y-chromosome and autosomal data). These and reference data were analyzed to uncover patterns of population structure and gain insights into the demographic history of the studied populations, with particular emphasis in the Chachapoyas. The new data show exceptionally high levels of genetic diversity in the Chachapoyas region and contrasting patterns of genetic affinities for lineage markers. In clear contrast with the archaeological and ethnohistorical evidence, there was negligible population substructure within Chachapoyas. Asymmetrical European gene flow for autosomes was detected throughout the region but the pattern does not mirror Inca settlement densities at subregional level. Signatures of demographic collapse likely associated with the Spanish conquest were observed in both mtDNA and Y-chromosome, although for males the reduction appeared more drastic. In addition to these insights, the new autosomal STR and SNP datasets generated unveiled another level of variation by providing, in addition to traditional length-based genotypes, sequence-based information for several Peruvian populations which may be of utility for individual identification in the context of South America.