The genetic prehistory of the Andean highlands 7,000 Years BP though European contact

Abstract

Main Text: The Andean highlands of South America have long been considered a natural laboratory for the study of genetic adaptation of humans (1), yet the genetics of Andean highland populations remain poorly understood. People likely entered the highlands shortly after their arrival on the continent (2, 3), and while some have argued that humans lived permanently in the Central Andean highlands by 12,000 BP (4), other research indicates that permanent occupation began between 9500-9000 BP (5-7). Regardless of when the peopling of high elevation environments began, selective pressure on the human genome was likely strong due to challenging environmental factors but also social processes such as the intensification of subsistence resources and residential sedentism (8), which in turn promoted the development of agricultural economies, social inequality, and relatively high population densities across much of the highlands. European contact initiated an array of economic, social, and pathogenic changes (9, 10). Although it is known that the peoples of the Andean highlands experienced population contraction after contact (11), its extent is debated from both archaeological and ethnohistorical perspectives, especially concerning the size of the indigenous populations at initial contact (12, 13). To address hypotheses regarding the population history of Andean highlanders and their genetic adaptations, we collected a time series of ancient whole genomes from individuals in the Lake Titicaca region of Peru (Fig. S1, Table 1). The series represents three different cultural periods, which include individuals from (A) Rio Uncallane, a series of cave crevice tombs dating to ~1,800 BP and used by fully sedentary agriculturists, (B) Kaillachuro, a ~3,800 year old site marked by the transition from mobile foraging to agropastoralism and residential sedentism, and (C) Soro Mik’aya Patjxa (SMP), an 8000-6500 year old site inhabited by residentially mobile huntergatherers (14). We then compare the genomes of these ancient individuals to 25 new genomes and 39 new genome-wide SNP datasets generated from two modern indigenous populations: the Aymara of highland Bolivia and the Huilliche-Pehuenche of coastal lowland Chile. The Aymara are an agropastoral people who have occupied the Titicaca basin for at least 2,000 years (15). The Huilliche-Pehuenche are traditionally hunter-gatherers from the southern coastal forest of Chile