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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

Affiliations

    t
  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. t
  3. Department of Archaeology, University of Exeter, Exeter, UK

    Ciprian F. Ardelean

  4. t
  5. Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK

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

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

    Lorena Becerra-Valdivia

  8. t
  9. Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark

    Mikkel Winther Pedersen, Martin Sikora & Eske Willerslev

  10. t
  11. Department of Geology, Kansas State University, Manhattan, KS, USA

    Charles G. Oviatt

  12. t
  13. Escuela de Arqueología, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico

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

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

    Joaquin Arroyo-Cabrales & Alejandro López-Jiménez

  16. t
  17. Facultad de Ingeniería, Universidad Autónoma de San Luís Potosí, San Luis Potosí, Mexico

    Yam Zul E. Ocampo-Díaz

  18. t
  19. Grupo de Geología Exógena y del Sedimentario, San Luis Potosí, Mexico

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

  20. t
  21. Laboratório de Arqueologia dos Trópicos, Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil

    Jennifer G. Watling

  22. t
  23. Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil

    Vanda B. de Medeiros & Paulo E. De Oliveira

  24. t
  25. Botany Department, The Field Museum of Natural History, Chicago, IL, USA

    Paulo E. De Oliveira

  26. t
  27. 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

  28. t
  29. Laboratorio de Palinología, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico

    Irán Rivera-González

  30. t
  31. 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

  32. t
  33. Department of Archaeology, University of Cambridge, Cambridge, UK

    Devlin A. Gandy

  34. t
  35. Welcome Trust, Sanger Institute, Hinxton, UK

    Eske Willerslev

  36. t
  37. The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark

    Eske Willerslev

  38. t
  39. Department of Zoology, University of Cambridge, Cambridge, UK

    Eske Willerslev

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.

Ethics declarations

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

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.

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).

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.

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.

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.

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.

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
Supplementary information

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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 (2020). https://doi.org/10.1038/s41586-020-2509-0

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