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Sci Adv. 2018 Nov 8;4(11):eaau4921. doi: 10.1126/sciadv.aau4921. eCollection 2018 Nov.

The genetic prehistory of the Andean highlands 7000 years BP though European contact.

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Department of Anthropology, Emory University, Atlanta, GA 30322, USA.
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Department of Anthropology, University of California, Davis, CA 95616, USA.
Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA.
Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA.
Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile.
Departamento de Antropología, Universidad de Chile, Santiago, Chile.
Departamento de Oncología Básico-Clínica, Universidad de Chile, Santiago, Chile.
Arizona State Museum and School of Anthropology, University of Arizona, Tucson, AZ 85721, USA.
Peruvian Register of Professional Archaeologists, Peru.
Department of Anthropology, Case Western University, Cleveland, OH 44106, USA.
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
School of Social Sciences, Humanities, and Arts, University of California, Merced, Merced, CA 95343, USA.


The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

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