South-to-north migration preceded the advent of intensive farming in the Maya region

Douglas J Kennett¹, Mark Lipson^{2

3}, Keith M Prufer^{4

5}, David Mora-Marín⁶, Richard J George⁷, Nadin Rohland⁸, Mark Robinson⁹, Willa R Trask¹⁰, Heather H J Edgar¹¹, Ethan C Hill¹¹, Erin E Ray¹¹, Paige Lynch¹¹, Emily Moes¹¹, Lexi O'Donnell¹², Thomas K Harper¹³, Emily J Kate¹⁴, Josue Ramos¹⁵, John Morris¹⁵, Said M Gutierrez¹⁶, Timothy M Ryan¹³, Brendan J Culleton¹⁷, Jaime J Awe^{15

18}, David Reich^{19

20

21

22}

Affiliations

¹ Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. kennett@anth.ucsb.edu.
² Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. mlipson@genetics.med.harvard.edu.
³ Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. mlipson@genetics.med.harvard.edu.
⁴ Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. kmp@unm.edu.
⁵ Center for Stable Isotopes, University of New Mexico, Albuquerque, NM, 87106, USA. kmp@unm.edu.
⁶ Department of Linguistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA.
⁷ Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA.
⁸ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
⁹ Department of Archaeology, Exeter University, Exeter, UK.
¹⁰ Central Identification Laboratory, Defense POW/ MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, Honolulu, HI, 96853, USA.
¹¹ Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA.
¹² Department of Sociology and Anthropology, University of Mississippi, University, Oxford, MS, 38677, USA.
¹³ Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
¹⁴ Vienna Institute for Archaeological Science, University of Vienna, Vienna, Austria.
¹⁵ Belize Institute of Archaeology, Belmopan, Belize.
¹⁶ Ya'axché Conservation Trust, Punta Gorda Town, Belize.
¹⁷ Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA.
¹⁸ Department of Anthropology, Northern Arizona University, Flagstaff, AZ, 86001, USA.
¹⁹ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu.
²⁰ Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu.
²¹ Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. reich@genetics.med.harvard.edu.
²² Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu.

PMID: 35318319
PMCID: PMC8940966
DOI: 10.1038/s41467-022-29158-y

South-to-north migration preceded the advent of intensive farming in the Maya region

Douglas J Kennett et al. Nat Commun. 2022.

. 2022 Mar 22;13(1):1530.

doi: 10.1038/s41467-022-29158-y.

Authors

Affiliations

¹ Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. kennett@anth.ucsb.edu.
² Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. mlipson@genetics.med.harvard.edu.
³ Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. mlipson@genetics.med.harvard.edu.
⁴ Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. kmp@unm.edu.
⁵ Center for Stable Isotopes, University of New Mexico, Albuquerque, NM, 87106, USA. kmp@unm.edu.
⁶ Department of Linguistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA.
⁷ Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA.
⁸ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
⁹ Department of Archaeology, Exeter University, Exeter, UK.
¹⁰ Central Identification Laboratory, Defense POW/ MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, Honolulu, HI, 96853, USA.
¹¹ Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA.
¹² Department of Sociology and Anthropology, University of Mississippi, University, Oxford, MS, 38677, USA.
¹³ Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
¹⁴ Vienna Institute for Archaeological Science, University of Vienna, Vienna, Austria.
¹⁵ Belize Institute of Archaeology, Belmopan, Belize.
¹⁶ Ya'axché Conservation Trust, Punta Gorda Town, Belize.
¹⁷ Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA.
¹⁸ Department of Anthropology, Northern Arizona University, Flagstaff, AZ, 86001, USA.
¹⁹ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu.
²⁰ Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu.
²¹ Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. reich@genetics.med.harvard.edu.
²² Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu.

PMID: 35318319
PMCID: PMC8940966
DOI: 10.1038/s41467-022-29158-y

Abstract

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1. Extent of Mayan and Chibchan languages, paleobotanical records showing early horticulture, and present-day populations with genome-wide data analyzed in this study.**
a Location of MHCP and ST is shown relative to the historical distributions of people speaking Mayan (purple) and Chibchan (red) languages. Paleo-botanical records from the southeastern Yucatan and adjacent areas with evidence of maize, manioc, and chili pepper between 6500 and 4000 cal. BP are shown in black as: 1) Lake Puerto Arturo; 2) Cob Swamp; 3) Rio Hondo Delta; 4) Caye Coco; 5) Lake Yojoa; and 6) El Gigante rock-shelter. The arrow shows the proposed movement of Isthmo-Colombian horticultural populations into the southeastern Yucatan by at least 5600 cal. BP. b Distribution of present-day groups with genome-wide comparative data (also see Supplementary Fig. 20).

**Fig. 2. Genome-wide analyses of MHCP and ST individuals compared to present-day populations.**
a PCA. Axes were computed using Maleku and Teribe (Chibchan), Zapotec (highland Mexican), and Aymara (Andean), and all individuals shown were projected (MHCP.14.2.4c was omitted due to low coverage). Alternative PCA plots can be found in Supplementary Fig. 23. b Allele-sharing statistics of the form f₄(9600–7300 cal. BP, 5600–3700 cal. BP; Outgroup, X) (multiplied by 1000) for present-day geographic/linguistic groupings X (Chibchan: Guaymi, Maleku, and Bribri; Chocoan: Embera and Waunana; Brazil: Karitiana and Surui; Mexico: Mixe, Mixtec, and Zapotec; Andes: Aymara and Quechua). c Allele-sharing statistics of the form f₄(Aymara, Chibchan; Outgroup, X) (multiplied by 1000) for the ancient Belize individuals X (Chibchan as in b). Values were computed on 305,133 SNPs. Bars show one standard error in each direction around the mean (b and c).

**Fig. 3. Radiocarbon dates and evidence for farming in the Maya region.**
Top: dates of individuals with genetic data (individual 95.4% confidence intervals and total summed probability density; MHCP.19.12.17 [low-coverage] omitted for scale). *Date based on association with familial relative. Bottom: earliest radiocarbon dates associated with microbotanical evidence for maize, manioc, and chili peppers in the Maya region and adjacent areas at Lake Puerto Arturo, Guatemala (GT); Cob Swamp, Belize (BZ); Rio Hondo Delta; Caye Coco, BZ; and Lake Yojoa, Honduras (HN), together with summed probability distribution of the earliest maize cobs (n = 11) in southeastern Mesoamerica from El Gigante rock-shelter, HN. Also shown in yellow is the known transition to staple maize agriculture based on dietary stable isotope dietary data from MHCP and ST.

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References

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South-to-north migration preceded the advent of intensive farming in the Maya region

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South-to-north migration preceded the advent of intensive farming in the Maya region

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