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Lanaud C, Vignes H, Utge J, Valette G, Rhoné B, Garcia Caputi M, Angarita Nieto NS, Fouet O, Gaikwad N, Zarrillo S, Powis TG, Cyphers A, Valdez F, Olivera Nunez SQ, Speller C, Blake M, Valdez FJ, Raymond S, Rowe SM, Duke GS, Romano FE, Loor Solórzano RG, Argout X. A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches. Sci Rep 2024; 14:2972. [PMID: 38453955 PMCID: PMC10920634 DOI: 10.1038/s41598-024-53010-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/25/2024] [Indexed: 03/09/2024] Open
Abstract
Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and Central America were analyzed using archaeogenomic and biochemical approaches. Here we show, for the first time, the widespread use of cacao in South America out of its native Amazonian area of origin, extending back 5000 years, likely supported by cultural interactions between the Amazon and the Pacific coast. We observed that strong genetic mixing between geographically distant cacao populations occurred as early as the middle Holocene, in South America, driven by humans, favoring the adaptation of T. cacao to new environments. This complex history of cacao domestication is the basis of today's cacao tree populations and its knowledge can help us better manage their genetic resources.
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Affiliation(s)
- Claire Lanaud
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France.
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Hélène Vignes
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - José Utge
- UMR 7206 Eco-anthropologie, Département Homme et Environnement, MNHN-CNRS-Université Paris Cité, Paris, France
| | - Gilles Valette
- Institut des Biomolécules Max Mousseron - (UMR IBMM), Université de Montpellier, Montpellier, France
| | - Bénédicte Rhoné
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Olivier Fouet
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Sonia Zarrillo
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Terry G Powis
- Department of Geography and Anthropology, Kennesaw State University, Kennesaw, USA
| | - Ann Cyphers
- Universidad Nacional Autónoma de México (UNAM), México, México
| | - Francisco Valdez
- Institut de Recherche pour le Développement (IRD), UMR 208 PALOC, MNHN-IRD, Paris, France
| | | | - Camilla Speller
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Michael Blake
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | | | - Scott Raymond
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Sarah M Rowe
- The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Guy S Duke
- The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | | | | | - Xavier Argout
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
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