Abstract
The central Southern Cone of South America was one of the last regions of the globe to become inhabited by people1, and remains under-represented in studies of ancient DNA. Here we report genome-wide data from 238 ancient individuals spanning ten millennia. The oldest, from the Pampas region and dating to 10,000 years before present (bp), had distinct genetic affinity to Middle Holocene Southern Cone individuals, showing that differentiation from the central Andes and central east Brazil had begun by this time. Individuals dating to 4,600–150 bp primarily descended from a previously unsampled deep lineage of which the earliest representative is an individual dating to around 8,500 bp. This central Argentina lineage co-existed with two other lineages during the Mid-Holocene and, within central Argentina, this ancestry persisted for thousands of years with little evidence of inter-regional migration. Central Argentina ancestry was involved in three distinct gene flows: it mixed into the Pampas by 3,300 bp and seemingly became the main component there after 800 bp, with central Andes ancestry in northwest Argentina, and with tropical and subtropical forest ancestry in the Gran Chaco. In northwest Argentina, there was an increased rate of close-kin unions by 1,000 bp, paralleling the pattern in the central Andes. In the Paraná River region, a 400 bp individual with a Guaraní archaeological association clusters with Brazilian groups, consistent with Guaraní presence by this time.
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Data availability
Genotype data for newly reported individuals included in main analyses from this study can be obtained from the Harvard Dataverse repository (https://doi.org/10.7910/DVN/UQVPJQ). The aligned sequences for all individuals are available through the European Nucleotide Archive (PRJEB97713). Previously published data used in our analyses are available as follows: genetic data for modern individuals from Native American groups2 are available for non-profit research on population history under an interinstitutional data access agreement with the Universidad de Antioquia, Colombia (queries regarding data access should be sent to a.ruizlin@ucl.ac.uk); genetic data for previously published ancient individuals are available at the Allen Ancient DNA Resource (https://doi.org/10.7910/DVN/FFIDCW); 1000 Genomes haplotype reference panel (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/), human reference genome hg19 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.13/); data used for map plotting are available at Natural Earth (https://www.naturalearthdata.com), GADM (https://gadm.org) and Portal de Información Hídrica de Córdoba-APRHI (https://portal-aprhi.opendata.arcgis.com/). Other newly reported data, such as radiocarbon dates and archaeological context information, are included in this Article and its Supplementary Information.
Code availability
Custom scripts and accompanying materials for the appropriate results sections are available at GitHub (https://github.com/javiermaravall/aDNA_CSC/).
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Acknowledgements
We acknowledge the ancient individuals whose data we analysed. We thank the staff at the Consejo de Comunidades de Pueblos Indígenas de la Provincia de Córdoba for endorsing and supporting this research; the members of the local communities for their selfless collaboration during the fieldwork; the museum curators and the many individuals who were directly or indirectly involved in this work for their efforts; N. Adamski, E. Curtis, K. Stewardson and F. Zalzala for ancient DNA laboratory work; T. Wang, B. Sousa da Mota, J. Choin and K. Sirak for providing feedback on an earlier version of this manuscript; and Leonard, S. Ravishankar, G. Purnomo and R. Davidson for discussions and technical guidance. M.D. and G.G.F. were supported by Secretaría de Ciencia y Tecnología of the Universidad Nacional de Córdoba (SECyT-UNC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, PIP 2017-2019) and Proyecto de Investigación de UE CONICET (2017-2 024). G.M.S. was supported by SECyT-UNC. P.C.M.d.Z. and D.E.O. thank the Antofagasta de la Sierra Archaeological Project (ANS) and all of its members (PIP 11220200103166CO). D.C.L. was supported by Proyecto de investigación trianual (ANPCyT, PICT 2018-2947). R.A.M. was supported by Proyecto I+D UNLP (11/N928), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, PICT 2020, 1787). M.F. was supported by PICT 2020, 2701 and PIP 11220200102318CO. P.B., S.H. and L.G.G.B. acknowledge CONICET, PIP 1423, ANPCyT (PICT 3049), Universidad Nacional de Tucumán (PIUNT G/707) and The H. and T. King Grant for Archaeology of the Ancient Americas, administered by the Society for American Archaeology (grant 202003). M.B., G.G.P. and C.S. were funded by CONICET (PIP 0126), ANPCyT (PICT 0252) and UNLP (N1007). L.G.G.B. acknowledges CONICET Doctoral and Postdoctoral Research Grants. P.G.M., G.G.P. and M.E.G. were supported by National Geographic Society (grant NGS-50543R-18), CONICET (PIP11220210100004CO and PUE no. 0079). G.N.L. was supported by Dinámica cultural prehispánica en el Gran Chaco y ambientes asociados (11/N983) and CONICET; and acknowledges El Quebracho community, E. Boló Bolaño, A. Pusineri, R. Zalazar and the members of the Fundación La Piedad of the Museo Etnográfico Andrés Barbero (Asunción, Paraguay). R.N. was supported by the National Geographic Society, CONICET (PIP 2021-11220200103037CO, PUE 2016 IDACOR and BecExt 2017), ANPCyT (PICT 2020, 3937) and SECyT-UNC. The generation and analysis of ancient DNA data for this study was supported by the National Institutes of Health (R01-HG012287), the John Templeton Foundation (grant 61220), a gift from J.-F. Clin, the Allen Discovery Center programme, a Paul G. Allen Frontiers Group advised programme of the Paul G. Allen Family Foundation and the Howard Hughes Medical Institute (to D.R.). Computations were carried out on the O2 research computing platform at Harvard Medical School.
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J.M.-L., J.M.B.M., N. Pastor, D.R. and R.N. wrote the manuscript and Supplementary Information with input from all of the co-authors. J.M.-L. performed all genetic analyses under the supervision of D.R. N. Pastor generated several figures and refined all of them. J.M.-L., J.M.B.M., N. Pastor, D.R. and R.N. interpreted the results. N.R., L.F.-S., C.P., B.L., S.M., D.A.D., G.S.C., D.R. and R.N. supervised different aspects of the study. R.N. coordinated sample collection and management. J.M.B.M., M.P.T., M.F., P.B., M.B., S.E.C., G.N.L., D.C.L., P.C.M.d.Z., G.G.P., G.R.C., M.D., H.D., L.G.G.B., S.H., A.D.I., R.A.M., V.A., D.M.B., C.B., M.G.C., U.D., P.D.R., G.G.F., R.F., M.E.G., A.G.L., J.G.M., P.G.M., B.N., D.E.O., G.M.S., A.S., C.S., A.M.T., R.V., O.E. and R.N. contributed anthropological remains and/or contributed to the creation of the archaeological Supplementary Information. K.-L.K., M.M., A.M., X.R.-R., G.S., P.A.W., N. Paterson, I.L., S.M. and D.R. performed bioinformatics data processing. M.P.T., S.C.A., K.C., E.C., T.F., L.I., A.K., J.K., K.-L.K., A.M.L., N.M., I.P., L.Q., X.R.-R., P.A.W., J.N.W. and R.N. carried out wet laboratory work. D.R. and R.N. conceived and co-directed the study.
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Extended data figures and tables
Extended Data Fig. 1 Geographical origin of previously-published individuals included in co-analysis.
Each dot indicates the geographical origin, within North, Central and South America, of a previously-published ancient grouping. Dot colours indicate the original publication, and dot sizes indicate the sample size of the grouping.
Extended Data Fig. 2 Affinities of Anzick to Early/Middle Holocene South Americans quantified by f4 statistics.
Bars denote 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 3 Fst tree for selected groupings.
Complete hierarchical-clustering tree from Fst distances, restricted to populations for which at least 5000 SNPs were used for all pairwise computations. Colours represent automatically-inferred clusters.
Extended Data Fig. 4 Affinities of a representative 4200BP Central Argentina population to Early/Middle Holocene South American samples quantified by f4 statistics.
Bars are 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates. (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 5 Affinities of a representative 400BP Central Argentina population to Early/Middle Holocene South Americans quantified by f4 statistics.
Bars are 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 6 Affinities of a representative 150BP Central Argentina population to Early/Middle Holocene South Americans quantified by f4 statistics.
Bars are 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 7 Affinities of a modern Central Argentina admixed population4 to Late Holocene South Americans quantified by f4 statistics.
Bars are 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 8 Affinities of Northwest_NorthernPuna_Cochinoca_700BP to Late Holocene Bolivians quantified by f4 statistics.
Bars are 95% confidence intervals (1.96 × SE) around the mean across genomic-block jackknife pseudoreplicates (point estimate). The number of SNPs used for each test is shown above each point estimate in the figure.
Extended Data Fig. 9 Differences in the distribution of cumulative length of ROH segments greater than 20 cM for Southern Cone groupings up to 3000BP.
Horizontal red lines denote median values (log scale), with boxes showing the interquartile range (IQR) and bars showing 1.5 x IQR Pairwise group comparisons were performed using a Conover’s test (two-sided), with correction for multiple comparisons (Benjamini–Hochberg) at FDR = 0.05. Corrected p-values for a difference between Northwest Argentina and Central Argentina (p = 0.00739), and between Northwest Argentina and Argentina Pampas (p = 0.0274), were significant at α = 0.05 (see Supplementary Fig. 76 for details). The number of individuals within each grouping is shown below each X axis label in the figure.
Extended Data Fig. 10 No evidence of population size growth or decline in Central Argentina in the last two and a half millennia.
Linear regression of cumulative length of ROH between 4 and 12 cM on date (mean bp), for individuals from Argentina Central at high enough coverage to call ROH (mean bp below 2500). Error bands show 95% confidence intervals around the mean linear regression fit. There is no evidence of a significant association (p = 0.238 from a two-sided t-test on the slope coefficient being zero).
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Maravall-López, J., Motti, J.M.B., Pastor, N. et al. Eight millennia of continuity of a previously unknown lineage in Argentina. Nature 649, 647–656 (2026). https://doi.org/10.1038/s41586-025-09731-3
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DOI: https://doi.org/10.1038/s41586-025-09731-3
