1
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Li F, Gates DJ, Buckler ES, Hufford MB, Janzen GM, Rellán-Álvarez R, Rodríguez-Zapata F, Romero Navarro JA, Sawers RJH, Snodgrass SJ, Sonder K, Willcox MC, Hearne SJ, Ross-Ibarra J, Runcie DE. Environmental data provide marginal benefit for predicting climate adaptation. PLoS Genet 2025; 21:e1011714. [PMID: 40489511 DOI: 10.1371/journal.pgen.1011714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 05/07/2025] [Indexed: 06/11/2025] Open
Abstract
Climate change poses a major challenge for both natural and cultivated species. Genomic tools are increasingly used in both conservation and breeding to identify adaptive loci that can be used to guide management in future climates. Here, we study the utility of climate and genomic data for identifying promising alleles using common gardens of a large, geographically diverse sample of traditional maize varieties to evaluate multiple approaches. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be pre-adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify loci associated with historical divergence along climatic gradients. Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genome-wide relatedness and population structure, and that incorporating envGWAS-identified variants or environment-of-origin provide little additional predictive information. While our results suggest that environmental data provide limited benefit in predicting fitness-related phenotypes, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci associated with adaptation, especially when coupled with high density genotyping.
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Affiliation(s)
- Forrest Li
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Daniel J Gates
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Center for Population Biology, University of California Davis, Davis, California, United States of America
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Garrett M Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry and Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Fausto Rodríguez-Zapata
- Department of Molecular and Structural Biochemistry and Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, United States of America
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Cinvestav, Irapuato, México
| | | | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Samantha J Snodgrass
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Kai Sonder
- CIMMYT, El Batan, Texcoco, Estado de Mexico, Mexico
| | | | | | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Center for Population Biology, University of California Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Daniel E Runcie
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
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2
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Krettek KL, Casas-Vargas A, Mas-Sandoval A, Alvis LA, Reiter E, Madero JM, Urban M, Vargas JCN, Usaquén W, Cuenca JVR, Posth C. A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia. SCIENCE ADVANCES 2025; 11:eads6284. [PMID: 40435234 PMCID: PMC12118548 DOI: 10.1126/sciadv.ads6284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 04/18/2025] [Indexed: 06/01/2025]
Abstract
Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.
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Affiliation(s)
- Kim-Louise Krettek
- Senckenberg Centre for Human Evolution and Paleoenvironment at the University of Tübingen, Tübingen, Germany
| | - Andrea Casas-Vargas
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Alex Mas-Sandoval
- Dipartimento di Scienze Statistiche “Paolo Fortunati,” Universitá di Bologna, Bologna, Italy
| | - Leonardo Arias Alvis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Leiden University Centre for Linguistics, Leiden, Netherlands
| | - Ella Reiter
- Archeo- and Paleogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Julie Moncada Madero
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Matthias Urban
- Centre National de la Recherche Scientifique “Dynamique du Langage” (UMR5596) and Université Lumière Lyon 2, Lyon, France
| | - Juan Camilo Niño Vargas
- Department of Anthropology, Faculty of Social Sciences, Universidad de los Andes, Bogotá, Colombia
| | - William Usaquén
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jose Vicente Rodríguez Cuenca
- Grupo de Investigación en Antropología Biológica, Departamento de Antropología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Cosimo Posth
- Senckenberg Centre for Human Evolution and Paleoenvironment at the University of Tübingen, Tübingen, Germany
- Archeo- and Paleogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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3
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Beneker O, Molinaro L, Guellil M, Sasso S, Kabral H, Bonucci B, Gaens N, D'Atanasio E, Mezzavilla M, Delbrassine H, Braet L, Lambert B, Deckers P, Biagini SA, Hui R, Becelaere S, Geypen J, Hoebreckx M, Berk B, Driesen P, Pijpelink A, van Damme P, Vanhoutte S, De Winter N, Saag L, Pagani L, Tambets K, Scheib CL, Larmuseau MHD, Kivisild T. Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden. Genome Biol 2025; 26:127. [PMID: 40390081 PMCID: PMC12090598 DOI: 10.1186/s13059-025-03580-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/16/2025] [Indexed: 05/21/2025] Open
Abstract
BACKGROUND Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes. RESULTS We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes. CONCLUSIONS This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.
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Affiliation(s)
- Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | | | - Meriam Guellil
- Department for Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Stefania Sasso
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Kabral
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Noah Gaens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | | | - Linde Braet
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Bart Lambert
- SHOC Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Simone Andrea Biagini
- Department of Archaeology and Museology, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Sara Becelaere
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Birgit Berk
- Birgit Berk Fysische Anthropologie, Meerssen, Netherlands
| | | | - April Pijpelink
- Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 's-Hertogenbosch, Netherlands
| | - Philip van Damme
- Department of Neurology, University Hospitals Leuven and Department of Neuroscience, KU Leuven, Leuven, Belgium
| | | | | | - Lehti Saag
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Institute of Genomics, University of Tartu, Tartu, Estonia.
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4
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Pinotti T, Adler MA, Mermejo R, Bitz-Thorsen J, McColl H, Scorrano G, Feizabadifarahani M, Gandy D, Boulanger M, Gaunitz C, Stenderup J, Ramsøe A, Korneliussen T, Demeter F, Santos FR, Vinner L, Sikora M, Meltzer DJ, Moreno-Mayar JV, Quanchello C, Willerslev E. Picuris Pueblo oral history and genomics reveal continuity in US Southwest. Nature 2025:10.1038/s41586-025-08791-9. [PMID: 40307544 DOI: 10.1038/s41586-025-08791-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 02/14/2025] [Indexed: 05/02/2025]
Abstract
Indigenous groups often encounter significant challenges when asserting ancestral claims and cultural affiliations based on oral histories, particularly in the USA where such narratives have historically been undervalued. Although ancient DNA offers a tool to complement traditional knowledge and address gaps in oral history, longstanding disregard for Indigenous sovereignty and beliefs has understandably led many Indigenous communities to distrust DNA studies1-4. Earlier research often focused on repatriation claims5-7, whereas more recent work has increasingly moved towards enhancing Tribal histories8,9. Here we present a collaborative study initiated by a federally recognized Native American tribe, the sovereign nation of Picuris Pueblo in the Northern Rio Grande region of New Mexico, USA, to address gaps in traditional knowledge and further their understanding of their population history and ancestry. We generated genomes from 16 ancient Picuris individuals and 13 present-day members of Picuris Pueblo, providing genomic data spanning the last millennium. We show genetic continuity between ancient and present-day Picuris, and more broadly with Ancestral Puebloans from Pueblo Bonito in Chaco Canyon10, 275 km to the west. This suggests a firm spatiotemporal link among these Puebloan populations of the North American Southwest. Furthermore, we see no evidence of population decline before European arrival11-13, and no Athabascan ancestry in individuals predating 1500 CE, challenging earlier migration hypotheses14-16. This work prioritizes Indigenous control of genetic data and brings together oral tradition, archaeology, ethnography and genetics.
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Affiliation(s)
- Thomaz Pinotti
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michael A Adler
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | | | - Julie Bitz-Thorsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Molecular Anthropology for the Study of Ancient DNA, Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Motahareh Feizabadifarahani
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Devlin Gandy
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Matthew Boulanger
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), Departement ABBA, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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5
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Lopez L, Lang PLM, Marciniak S, Kistler L, Latorre SM, Haile A, Cerda EV, Gamba D, Xu Y, Woods P, Yifru M, Kerby J, McKay JK, Oakley CG, Ågren J, Wondimu T, Bulafu C, Perry GH, Burbano HA, Lasky JR. Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.06.636844. [PMID: 39975324 PMCID: PMC11839143 DOI: 10.1101/2025.02.06.636844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.
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Affiliation(s)
- Lua Lopez
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biology, California State University, San Bernardino, San Bernardino, CA, USA
| | - Patricia L. M. Lang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | | | - Sergio M. Latorre
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, England, UK
| | - Asnake Haile
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Yuxing Xu
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Patrick Woods
- Department of Soil and Crop Sciences, Colorado State University, Ft. Collins, CO, USA
| | - Mistire Yifru
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jeffrey Kerby
- Aarhus Institute of Advanced Studies, Aarhus, Denmark
| | - John K. McKay
- Department of Soil and Crop Sciences, Colorado State University, Ft. Collins, CO, USA
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology, and The Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jon Ågren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Tigist Wondimu
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Collins Bulafu
- Department of Plant Sciences, Microbiology, and Biotechnology, Makarere University, Kampala, Uganda
| | - George H. Perry
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Hernán A. Burbano
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, England, UK
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- PAC Herbarium, Pennsylvania State University, University Park, PA, USA
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6
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Yu Y, Wu H, Zhang W, Boivin N, Yu J, Zhang J, Zhou X, Luo W, Deng C, Ge J, Guo Z. Climate and cultural evolution drove Holocene cropland change in the Huai River Valley, China. iScience 2024; 27:110841. [PMID: 39319274 PMCID: PMC11421277 DOI: 10.1016/j.isci.2024.110841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/20/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
As an important way of maximizing land productivity by growing more than one crop type in the same field, mixed cropping has been an effective option for sustaining population growth under different climatic conditions since prehistoric period. We used a combination of archaeological data and an improved prehistoric land use model (PLUM) to quantitatively reconstruct spatiotemporal changes in cropland types and areas in the Huai River Valley of China, a core region of mixed cropping during the Holocene. The total cropland area increased more than 25 times during 8-2 ka BP, with northward expansion of rice-dominated cultivation during 5-4 ka BP and southward expansion of dry-dominated cultivation after 4 ka BP. Temperature and precipitation determined cropland types distribution, while that of cropland area was controlled by cultural development. The interplay between past climate, culture, and cultivation potentially provides useful insights into mitigating future population pressures with climate change.
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Affiliation(s)
- Yanyan Yu
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Haibin Wu
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenchao Zhang
- School of Earth Sciences and Resources, China University of Geosciences (Beijing), Beijing 100083, China
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena 07745, Germany
- School of Social Science, University of Queensland, Brisbane, QLD 4072, Australia
- School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia
| | - Jie Yu
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Juzhong Zhang
- School of Humanities and Social Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xin Zhou
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Wuhong Luo
- School of Humanities and Social Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Chenglong Deng
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Junyi Ge
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Zhengtang Guo
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
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7
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Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024; 630:912-919. [PMID: 38867041 PMCID: PMC11208145 DOI: 10.1038/s41586-024-07509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Oana Del Castillo-Chávez
- Centro INAH Yucatán, Instituto Nacional de Antropología e Historia (INAH), Mérida, Yucatán, Mexico.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- University of the Basque Country (EHU), San Sebastián-Donostia, Spain
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology and Cultural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Diana Iraíz Hernández-Zaragoza
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Pablo Librado
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Raffaela Angelina Bianco
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Bridget S Penman
- The Zeeman Institute and the School of Life Sciences, University of Warwick, Coventry, UK
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mary Lucas
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | | | | | | | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
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8
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Ebert CE, Hixon SW, Buckley GM, George RJ, Pacheco-Fores SI, Palomo JM, Sharpe AE, Solís-Torres ÓR, Davis JB, Fernandes R, Kennett DJ. The Caribbean and Mesoamerica Biogeochemical Isotope Overview (CAMBIO). Sci Data 2024; 11:349. [PMID: 38589396 PMCID: PMC11001905 DOI: 10.1038/s41597-024-03167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
The Caribbean & Mesoamerica Biogeochemical Isotope Overview (CAMBIO) is an archaeological data community designed to integrate published biogeochemical data from the Caribbean, Mesoamerica, and southern Central America to address questions about dynamic interactions among humans, animals, and the environment in the region over the past 10,000 years. Here we present the CAMBIO human dataset, which consists of more than 16,000 isotopic measurements from human skeletal tissue samples (δ13C, δ15N, δ34S, δ18O, 87Sr/86Sr, 206/204Pb, 207/204Pb, 208/204Pb, 207/206Pb) from 290 archaeological sites dating between 7000 BC to modern times. The open-access dataset also includes detailed chronological, contextual, and laboratory/sample preparation information for each measurement. The collated data are deposited on the open-access CAMBIO data community via the Pandora Initiative data platform ( https://pandoradata.earth/organization/cambio ).
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Affiliation(s)
- Claire E Ebert
- Department of Anthropology, University of Pittsburgh, 3302 WWPH, Pittsburgh, PA, 15260, USA.
| | - Sean W Hixon
- Department of Integrative Biology, Oregon State University, 4575 SW Research Way, Corvallis, OR, 97331, USA
- Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, D-07745, Jena, Germany
| | - Gina M Buckley
- Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Richard J George
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sofía I Pacheco-Fores
- Anthropology Department, Hamline University, 1536 Hewitt Avenue, Saint Paul, MN, 55104, USA
| | - Juan Manuel Palomo
- Department of Anthropology, University of Arizona, 1009 E South Campus Dr, Tucson, AZ, 85721, USA
| | - Ashley E Sharpe
- Center for Tropical Paleoecology and Archaeology, Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper, Ancon, Panama, Republic of Panama
| | - Óscar R Solís-Torres
- Department of Integrative Biology, Oregon State University, 4575 SW Research Way, Corvallis, OR, 97331, USA
- Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, D-07745, Jena, Germany
- Instituto Nacional de Antropología e Historia (INAH), Moneda 16, Col. Centro, Alcaldía Cuauhtémoc, 06060, Ciudad de México, México
| | - J Britt Davis
- School of Human Evolution and Social Change, Arizona State University, 900 S. Cady Mall, Tempe, AZ, 85281, USA
| | - Ricardo Fernandes
- Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, D-07745, Jena, Germany
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
- Climate Change and History Research Initiative, Princeton University, 129 Dickinson Hall, Princeton, NJ, 08544-1017, USA
- Arne Faculty of Arts, Masaryk University, Nováka 1, 602 00, Brno, Czech Republic
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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9
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Caduff M, Eckel R, Leuenberger C, Wegmann D. Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol Ecol Resour 2024; 24:e13913. [PMID: 38173222 DOI: 10.1111/1755-0998.13913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.
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Affiliation(s)
- Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Raphael Eckel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Christoph Leuenberger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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10
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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11
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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: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [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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12
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Nakatsuka N, Holguin B, Sedig J, Langenwalter PE, Carpenter J, Culleton BJ, García-Moreno C, Harper TK, Martin D, Martínez-Ramírez J, Porcayo-Michelini A, Tiesler V, Villapando-Canchola ME, Valdes Herrera A, Callan K, Curtis E, Kearns A, Iliev L, Lawson AM, Mah M, Mallick S, Micco A, Michel M, Workman JN, Oppenheimer J, Qiu L, Zalzala F, Rohland N, Punzo Diaz JL, Johnson JR, Reich D. Genetic continuity and change among the Indigenous peoples of California. Nature 2023; 624:122-129. [PMID: 37993721 PMCID: PMC10872549 DOI: 10.1038/s41586-023-06771-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA.
| | - Brian Holguin
- Department of Anthropology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - John Carpenter
- Instituto Nacional de Antropología e Historia, Sonora, Hermosillo, México
| | - Brendan J Culleton
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | | | - Thomas K Harper
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Debra Martin
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | | | | | - Vera Tiesler
- Universidad Autónoma de Yucatán, Facultad de Ciencias Antropológicas, Mérida, México
| | | | | | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - John R Johnson
- Santa Barbara Museum of Natural History, Santa Barbara, CA, USA.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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13
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Kennett DJ, Harper TK, VanDerwarker A, Thakar HB, Domic A, Blake M, Benz BF, George RJ, Scheffler TE, Culleton BJ, Kistler L, Hirth KG. Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras. PLoS One 2023; 18:e0287195. [PMID: 37352287 PMCID: PMC10289419 DOI: 10.1371/journal.pone.0287195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/01/2023] [Indexed: 06/25/2023] Open
Abstract
El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.
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Affiliation(s)
- Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Thomas K. Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Amber VanDerwarker
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Heather B. Thakar
- Department of Anthropology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alejandra Domic
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael Blake
- Department of Biology, Texas Wesleyan University, Forth Worth, Texas, United States of America
| | - Bruce F. Benz
- Department of Anthropology, Texas A & M University, College Station, Texas, United States of America
| | - Richard J. George
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Timothy E. Scheffler
- Department of Anthropology, University of Hawaii at Hilo, Hilo, Hawaii, United States of America
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, Washington, DC, United States of America
| | - Kenneth G. Hirth
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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14
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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15
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Mizuno F, Tokanai F, Kumagai M, Ishiya K, Sugiyama S, Hayashi M, Kurosaki K, Ueda S. Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes. Ann Hum Biol 2023; 50:390-398. [PMID: 37812249 DOI: 10.1080/03014460.2023.2261844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND The Teotihuacan civilisation was the largest one in ancient Mesoamerica. The Teotihuacan city was born in the north-eastern Basin of Mexico around the second century BC, reached its peak in the fourth century AD, and had cultural influence throughout Mesoamerica. At its peak, the size of the city reached more than 20 km2, and the total population is estimated to have increased from 100,000 to 200,000. However, knowledge of the genetic background of the Teotihuacan people is still limited. AIM We aimed to determine the mitogenome sequences of the Teotihuacan human remains and compare the ancient and present Mesoamericans. In addition, we aimed to identify the food habits of ancient Teotihuacans. SUBJECTS AND METHODS We determined the mitogenome sequences of human remains dated to 250-636 cal AD using target enrichment-coupled next generation sequencing. We also performed stable isotope analysis. RESULTS We successfully obtained nearly full-length sequences newly unearthed from a civilian dwelling in the Teotihuacan site. Teotihuacan mitochondrial DNA was classified into the haplogroups in present and ancient Mesoamericans. In addition, Teotihuacan individuals had a diet dependent on C4 plants such as maize. CONCLUSION Genetic diversity varied among the Teotihuacans.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Fuyuki Tokanai
- Center for Accelerator Mass Spectrometry, Yamagata University Advanced Analysis Center, Yamagata, Japan
| | - Masahiko Kumagai
- National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Chiyoda, Japan
| | - Saburo Sugiyama
- Research Institute for the Dynamics of Civilizations, Okayama University, Okayama, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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16
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Ford A. Scrutinizing the paleoecological record of the Maya forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human expansion into and occupation of the New World coincided with the great transition from the Pleistocene to the Holocene epoch, yet questions remain about how we detect human presence in the paleoecological record. In the Maya area of southern Mesoamerica, archeological evidence of the human imprint is largely invisible until ∼4,000 years ago. How do environmental changes after that time correspond and relate to human impacts? Are the archeological signatures of initial settlements in the Early Preclassic detected? Later, by ∼2,000 years ago when the Maya had fully settled the landscape, how does the evidence of forest compositional changes relate to human intervention? This paper evaluates published paleoecological data in light of the rise of the Maya civilization and reflects on interpretations of how swidden agriculture and the milpa cycle impacted the environment. Evaluating the contrast between the long archeological sequence of successful Maya development and paleoecological interpretations of destructive human-induced environmental impacts requires a concordance among pollen data, archeological evidence, ethnohistoric observations, ethnological studies of traditional Maya land use, and the historical ecology of the Maya forest today.
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
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