Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

Xavier Roca-Rada; Gustavo Politis; Pablo G Messineo; Nahuel Scheifler; Clara Scabuzzo; Mariela González; Kelly M Harkins; David Reich; Yassine Souilmi; João C Teixeira; Bastien Llamas; Lars Fehren-Schmitz

doi:10.1016/j.isci.2021.102553

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

iScience. 2021 May 19;24(6):102553. doi: 10.1016/j.isci.2021.102553. eCollection 2021 Jun 25.

Authors

Xavier Roca-Rada¹, Gustavo Politis^{2

3}, Pablo G Messineo², Nahuel Scheifler², Clara Scabuzzo⁴, Mariela González², Kelly M Harkins⁵, David Reich^{6

7

8

9}, Yassine Souilmi^{1

10

11}, João C Teixeira^{1

12}, Bastien Llamas^{1

10

11

12}, Lars Fehren-Schmitz^{5

13}

Affiliations

¹ Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
² INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina.
³ Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina.
⁴ CICYTTP-CONICET, Provincia de Entre Ríos-UADER-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata. Dr. Materi y España (3105), Diamante, Entre Ríos Argentina.
⁵ UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁷ Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
⁸ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁹ Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
¹⁰ National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia.
¹¹ Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia.
¹² Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.
¹³ UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Abstract

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

Keywords: Genetics; Genomics; Paleogenetics.