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. 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

John Lindo  1   2 , Randall Haas  3 , Courtney Hofman  4   5 , Mario Apata  6 , Mauricio Moraga  6   7 , Ricardo A Verdugo  6   8 , James T Watson  9 , Carlos Viviano Llave  10 , David Witonsky  2 , Cynthia Beall  11 , Christina Warinner  4   5   12 , John Novembre  2 , Mark Aldenderfer  13 , Anna Di Rienzo  2
Affiliations

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

John Lindo et al. Sci Adv. .

Abstract

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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Figures

Fig. 1
Fig. 1. ƒ3 statistics.
(A to C) Left: Heat map represents the outgroup ƒ3 statistics estimating the amount of shared genetic drift between the ancient Andean individuals and each of 156 contemporary populations since their divergence with the African Yoruban population. Right: Ranked ƒ3 statistics showing the greatest affinity of the ancient Andeans with respect to 45 indigenous populations of the Americas.
Fig. 2
Fig. 2. Principal components analysis.
Principal components analysis projecting the ancient Andeans (IL2, IL3, IL4, IL5, IL7, K1, and SMP5), USR1 (Alaska) (19), Anzick-1 (Montana) (61), Saqqaq (Greenland) (62), and Kennewick Man (Washington) (63) onto a set of non-African populations from Raghavan et al. (16), with Native American populations masked for non-native ancestry. PC, principal component.
Fig. 3
Fig. 3. Genetic affinity of ancient Andeans to global and regional indigenous populations.
(A to C) Maximum likelihood trees generated by TreeMix (18) using whole-genome sequencing data from the Simons Genome Diversity Project (46). (D) Cluster analysis generated by ADMIXTURE (15) for a set of indigenous populations from Siberia, the Americas, Anzick-1, Kennewick, Saqqaq, USR1, and the ancient Andeans. The number of displayed clusters is K = 8, which was found to have the best predictive accuracy given the lowest cross-validation index value. Native American populations masked for non-native ancestry. SE, standard error.
Fig. 4
Fig. 4. Demographic model of the Andes.
ILA, Rio Uncallane.
Fig. 5
Fig. 5. Selection scans.
(A) PBS scans testing for differentiation along the Ancient Andean branch, with respect to the lowland population of the Huilliche-Pehuenche. (B) PBS scan testing for differentiation along the modern Aymara branch (post-European contact), with respect to the precontact ancient population of the Rio Uncallane. Selected global SNP frequencies (Frq) (64) and histone modifications (38) are shown on the right, which are relevant to the strongest selection signals. “*” indicates closest gene. GI, gastrointestinal tract; NK, natural killer.
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References

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