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Evidence of human occupation in Mexico around the Last Glacial Maximum - Nature

  • ️Willerslev, Eske
  • ️Wed Jul 22 2020

Data availability

The data that support the findings of this study are available in the Article and its Supplementary Information. Raw data and sequence alignments are available from the European Nucleotide Archive under accession number PRJEB37914. The exact coordinates of Chiquihuite Cave are available from C.F.A. on reasonable request. C.F.A. can also be contacted at cip_ardelean@hotmail.com.

Code availability

Code for R and OxCal is noted within the Supplementary Information. Code for environmental DNA data analysis can be found at https://github.com/miwipe/ngsLCA.

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Acknowledgements

The field explorations and part of the laboratory studies were made possible by the special sponsorship from the Government of the State of Zacatecas, through the Consejo Zacatecano de Ciencia, Tecnología e Innovación (COZCyT); we thank its consecutive directors, G. A. Mercado-Sánchez and A. Enciso-Muñoz, and the Governor of Zacatecas, A. Tello-Cristerna. Seed money for cave exploration came from the Center for American Paleolithic Research (CAPR); we thank S. Holen, K. Holen and the members of the board. Fieldwork, laboratory analyses and publication expenses were partially covered by CONACYT grant CB-2016-286130. The Concepción del Oro municipality, and A. Maldonado-Falcón, offered administrative and occasional financial assistance. Radiocarbon work at Oxford was supported by the NERC Radiocarbon Facility (NRCF), Merton College, Santander and the Clarendon Fund. We thank all colleagues at the ORAU. D. Peat contributed greatly to laboratory preparation of OSL samples. A. Ocaña and I. Alarcón participated in the identification of animal bones. The environmental DNA work was supported by the Lundbeck Foundation, the Novo Nordic Foundation, the Wellcome Trust Foundation, the Carlsberg Foundation and the Danish National Research Foundation. We thank INAH’s Archaeology Council for authorization and legal permits; the inhabitants of Guadalupe Garzarón for accepting this project in their territory and participating in the caravans; and J. Martínez-Ledezma for his constant support as an on-site administrator and liaison with the community.

Author information

Authors and Affiliations

  1. Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Zacatecas, Mexico

    Ciprian F. Ardelean, Zamara Navarro-Gutierrez, Jesús J. De La Rosa-Díaz, Vladimir Huerta-Arellano & L. Martin Martínez-Riojas

  2. Department of Archaeology, University of Exeter, Exeter, UK

    Ciprian F. Ardelean

  3. Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK

    Lorena Becerra-Valdivia, Jean-Luc Schwenninger & Thomas Higham

  4. Chronos 14C-Cycle Facility, SSEAU, University of New South Wales, Sydney, New South Wales, Australia

    Lorena Becerra-Valdivia

  5. Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark

    Mikkel Winther Pedersen, Martin Sikora & Eske Willerslev

  6. Department of Geology, Kansas State University, Manhattan, KS, USA

    Charles G. Oviatt

  7. Escuela de Arqueología, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico

    Juan I. Macías-Quintero & Marco B. Marroquín-Fernández

  8. Laboratorio de Arqueozoología, Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia, Mexico City, Mexico

    Joaquin Arroyo-Cabrales & Alejandro López-Jiménez

  9. Facultad de Ingeniería, Universidad Autónoma de San Luís Potosí, San Luis Potosí, Mexico

    Yam Zul E. Ocampo-Díaz

  10. Grupo de Geología Exógena y del Sedimentario, San Luis Potosí, Mexico

    Yam Zul E. Ocampo-Díaz & Igor I. Rubio-Cisneros

  11. Laboratório de Arqueologia dos Trópicos, Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil

    Jennifer G. Watling

  12. Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil

    Vanda B. de Medeiros & Paulo E. De Oliveira

  13. Botany Department, The Field Museum of Natural History, Chicago, IL, USA

    Paulo E. De Oliveira

  14. Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico

    Luis Barba-Pingarón, Agustín Ortiz-Butrón & Jorge Blancas-Vázquez

  15. Laboratorio de Palinología, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico

    Irán Rivera-González

  16. Laboratorio de Espectrometría de Masas con Aceleradores, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico

    Corina Solís-Rosales & María Rodríguez-Ceja

  17. Department of Archaeology, University of Cambridge, Cambridge, UK

    Devlin A. Gandy

  18. Welcome Trust, Sanger Institute, Hinxton, UK

    Eske Willerslev

  19. The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark

    Eske Willerslev

  20. Department of Zoology, University of Cambridge, Cambridge, UK

    Eske Willerslev

Authors

  1. Ciprian F. Ardelean

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  2. Lorena Becerra-Valdivia

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  3. Mikkel Winther Pedersen

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  4. Jean-Luc Schwenninger

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  5. Charles G. Oviatt

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  6. Juan I. Macías-Quintero

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  7. Joaquin Arroyo-Cabrales

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  8. Martin Sikora

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  9. Yam Zul E. Ocampo-Díaz

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  10. Igor I. Rubio-Cisneros

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  11. Jennifer G. Watling

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  12. Vanda B. de Medeiros

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  13. Paulo E. De Oliveira

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  14. Luis Barba-Pingarón

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  15. Agustín Ortiz-Butrón

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  16. Jorge Blancas-Vázquez

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  17. Irán Rivera-González

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  18. Corina Solís-Rosales

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  19. María Rodríguez-Ceja

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  20. Devlin A. Gandy

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  21. Zamara Navarro-Gutierrez

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  22. Jesús J. De La Rosa-Díaz

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  23. Vladimir Huerta-Arellano

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  24. Marco B. Marroquín-Fernández

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  25. L. Martin Martínez-Riojas

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  26. Alejandro López-Jiménez

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  27. Thomas Higham

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  28. Eske Willerslev

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Contributions

C.F.A. designed the project, directed excavations, analysed lithics, photographed artefacts and put together the research team. L.B.-V. and T.H. performed sampling, AMS radiocarbon dating and Bayesian modelling analysis. C.S.-R. and M.R.-C. performed AMS radiocarbon dating. M.W.P., M.S. and E.W. designed and conducted the DNA and bioinformatic analyses. J.-L.S. undertook the OSL dating. C.G.O. performed geological studies. J.I.M.-Q. participated in the discovery of the site, mapping, artefact plotting and GIS analyses. J.A.-C. conducted the zooarchaeological analysis. L.B.-P. and A.O.-B. conducted chemical residues analysis. J.B.-V. performed X-ray fluorescence. Y.Z.E.O.-D. and I.I.R.-C. conducted thin-section petrography and micromorphology analyses. J.G.W. performed the phytolith analysis. V.B.d.M., P.E.D.O. and I.R.-G. studied pollen samples. Z.N.-G. performed flotation and malacology analyses. D.A.G. performed photogrammetry. Z.N.-G., J.J.D.L.R.-D., V.H.-A., M.B.M.-F., L.M.M.-R., and A.L.-J. excavated. C.F.A., L.B.-V., M.W.P., J.I.M.-Q., J.J.D.L.R.-D. and D.A.G. created figures. C.F.A. wrote the paper with co-authors contributing to the draft.

Corresponding authors

Correspondence to Ciprian F. Ardelean or Eske Willerslev.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Deborah M. Pearsall, Fiona Petchey and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Additional information on the site and excavation.

a, Digital elevation model (DEM) map of Mexico with the study area (rectangle) in relationship to relevant modern and prehistoric localities. b, The study region (Concepción del Oro endorheic basin), with Chiquihuite Cave (green dot) on the Astillero Mountains. DEM mosaic generated from ortophotographs and elevation data from National Institute of Statistics and Geography (INEGI) of Mexico. c, Chiquihuite Peak, seen from the south; the arrow indicates the entrance of the cave. d, The main chamber, looking west towards the double-eyed entrance. e, Contact between the limestone lintel of the ancient entrance (25 m west of X-12), and the debris that sealed it, probably at the end of the Pleistocene epoch. f, The south profile of the central–eastern squares, as in Fig. 1b. g, Western profiles of the central sector, showing the exposed interface 1210 tilted in the centre of the photograph. h, East–west cross-section of the northern sector of the main chamber of the cave, along the southern profile of the dig. i, X-12 cross-section, showing the inclination of the cave floor and the stepped approach. The DEMs in a, b were created with ArcMap/ArcScene (by ESRI) using open-access topographical data provided by INEGI.

Extended Data Fig. 2 Three-dimensional photogrammetric model of excavation X-12 and the location of samples extracted and analysed for ancient environmental DNA.

a, North-facing profile. b, East-facing profile. Triangles indicate the respective locations of environmental DNA samples extracted in 2019, corresponding to different stratigraphic units (‘UE’, as shown in the key). The circled samples are the initial ones, from the 2016–2017 excavation. c, Complete 3D photogrammetric view of the excavation towards the southern profile. The reddish-brown layers visible along the entire southern profile represent the stratigraphic component C (SC-C), starting downwards with stratum 1212, the terminal LGM chronostratigraphic marker that defines the separation between SC-B and SC-C (Fig. 1b, Extended Data Fig. 7).

Extended Data Fig. 3 Finds plotted onto the excavation grid.

a, Horizontal (x and y axes) spatial distribution of lithic artefacts, radiocarbon and OSL samples on the excavation grid. b, Side view (from the south) of the vertical distribution (x and z axes) of finds and samples. Illustrated dating samples: (1) LEMA-635.1.1 and LEMA-635.1.2; (2) OxA-36608 and LEMA-978.1.1; (3) OxA-36610; (4) LEMA-574.1.1; (5) LEMA-640.1.1; (6) OxA-36496; (7) OxA-36613; (8) X-7227; (9) OxA-36614; (10) LEMA-636.1.1 and LEMA-636.1.2; (11) LEMA-576.1.1; (12) LEMA-577.1.1; (13) X-7228; (14) X-7231 and X-7232; (15) X-7229; (16) OxA-36530; (17) OxA-36633; (18) OxA-36609; (19) OxA-36612; (20) OxA-36360; (21) BETA-345055; (22) X-4135; (23) OxA-34965; (24) ICA-16OS/0510; (25) PRI-5414; (26) OxA-36616; (27) OxA-36620; (28) OxA-36618; (29) OxA-36615; (30) OxA-36617; (31) OxA-36621; (32) OxA-36619; (33) OxA-36753; (34) OxA-36611; (35) X-7233; (36) LEMA-573.1.1; (37) OxA-36359; (38) LEMA-892.1.2; (39) OxA-36622; (40) OxA-36623; (41) OxA-36634; (42) LEMA-893.1.1; (43) LEMA-977.1.1; (44) OxA-36624; and (45) OxA-36625.

Extended Data Fig. 4 Taxonomic profiles of animals (Amniota) and plants (Viridiplantae) identified by ancient environmental DNA.

a, b, Animals presented as the proportion of reads found of each taxa and plotted as a bar plot (b) and stratigraphic plot (a). c, d, All plants are presented as the proportion of reads found of each taxa and plotted as a bar plot (c) and stratigraphic plot (d). *Taxa also found by pollen, phytoliths or faunal remains.

Extended Data Fig. 5 Additional Chiquihuite lithic artefacts.

a–c, Cores. d, e, Bifacial preforms on ovoid nodules. f–n, Flakes. o–t, Blades. u–x, Microliths. y, w, Burins. z, a′, Scrapers. b′–l′, Points and point-like shapes. m′–p′, Geometric items made by fracturing calcite laminae. Artefacts i, n, o, b′, c′, f′, and k′ are from SC-C; all others are from SC-B. Scale bars, 1 cm.

Extended Data Fig. 6 Additional examples of lithics.

a, Core. b, Flake with isolated platform. c, Flake with lipped platform. d–i, Blades and microlith blade segments. j, Circular scraper on trimmed flake. k, Possible preform. l, Point on plaquette. m, Bifacial point preform. n, o, s–a′, d′–g′, Transversal points (obtained by slightly modifying transversal flake blanks). p–r, b′, c′, Other points. h′, A geometric, point-like shape on calcite sheet. Most artefacts were discovered in SC-B. Specimens x–z, b′, g′, h′ are from SC-C. Scale bars, 1 cm.

Extended Data Fig. 7 Stratigraphic correlations across different profiles in X-12.

a, b, Excavation grid diagram (a) and maximum-depth diagram (b) showing the position of the profiles depicted below. For correlation reasons, all profiles show the upper contact of stratum 1210 with 1212 marked with a white contour. The position of OSL samples is indicated (labels beginning with X-). c, South profile, squares K2, K3, L2 and L3. d, South profile, square H2. e, South profile, square G2. f, South profile, square F2. g, South profile, squares M3, M4, N3 and N4. h, West profile, square J4. i, West profile, squares I5 and I6. j, Eastern profile, squares M4, M5 and M6 (profile removed during the 2016–2017 winter excavations). k, Eastern profile, squares N4, N5 and N6 (new eastern profile after the excavation of the one shown in j).

Extended Data Table 1 Chronometric data ordered by strata and depth

Full size table

Supplementary information

Supplementary Information 1

This file contains the concentration of data from all the different scientific approaches included in the paper. Each proxy-related section is numbered consecutively, from 1 to 10, such as: 1.1. Geology; 1.2. Radiocarbon dating and Bayesian modelling. 1.3. Lithic artefact metrics. 1.4. Chemical residues. 1.5. Faunal remains. 1.6. Phytoliths and pollen. 1.7. Thin-section and micromorphology. 1.8. Commercial radiocarbon dating methods. 1.9. Optically stimulated luminescence (OSL) dating. 1.10. Environmental DNA. Each section number is referred as such in the manuscript.

Reporting Summary

Supplementary Information 2

This file contains plots used in the assessment of ancient DNA authentication for the animal taxa found. The first column contains the read length distribution (in Bp) of the reads aligning to the reference (see supplementary metadata file), the second columns plots the number of mismatches (edit distance) of each read to the same reference. In the third column, the fraction of C-T transitions due to DNA damage, as calculated by mapDamage2.0, is plotted. Each new row contains a new species from a specific layer.

Supplementary Information 3

This file contains plots used in the assessment of ancient DNA authentication for the plant taxa found. The first column contains the read length distribution (in Bp) of the reads aligning to the reference (see supplementary metadata file), the second columns plots the number of mismatches (edit distance) of each read to the same reference. In the third column, the fraction of C-T transitions due to DNA damage, as calculated by mapDamage2.0, is plotted. Each new row contains a new species from a specific layer.

Supplementary Information 4

A link to the 3D digital photogrammetric model of excavation X-12. This is an on-line dynamic model that shows the tridimensional photographic modelling of the excavation, same as in Fig. 1c and Extended Data Fig. 2. It includes the display of the entire spectrum of eDNA samples extracted in 2019 for aDNA reassessment, as well as the northern wall of the cave. The viewer can rotate the model around the x,y,z axis.

Supplementary Data

The eDNA metadata file contains information relating to layer in excavation, excavation coordinate, total sequences sequenced, reads after quality control, sequencing batch, extraction batch, number of replicated samples and total counts of total taxonomically classified reads and total classified reads at the different kingdoms; Bacteria, Viridiplantae, and Amniota. Including reads checked for DNA damage at different mapping qualities (MQ) and the proportion of damage found.

Supplementary Video 1

: A dynamic tridimensional view of the artefact-and-sample plot depicted in Extended Data Fig. 3. This video allows the viewer to appreciate the 3D relationship between the items without the need to run the model in an ArcScene (by ESRI) software. Motion starts at 00:08.

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Ardelean, C.F., Becerra-Valdivia, L., Pedersen, M.W. et al. Evidence of human occupation in Mexico around the Last Glacial Maximum. Nature 584, 87–92 (2020). https://doi.org/10.1038/s41586-020-2509-0

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  • Received: 31 August 2018

  • Accepted: 16 June 2020

  • Published: 22 July 2020

  • Issue Date: 06 August 2020

  • DOI: https://doi.org/10.1038/s41586-020-2509-0