1
|
Holland-Lulewicz J, Thompson V, Thompson AR, Butler R, Chavez DJ, Franklin J, Hunt T, Williams M, Worth J. The initial spread of peaches across eastern North America was structured by Indigenous communities and ecologies. Nat Commun 2024; 15:8245. [PMID: 39304659 DOI: 10.1038/s41467-024-52597-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024] Open
Abstract
We conduct a synthetic archaeological and ethnohistoric dating program to assess the timing and tempo of the spread of peaches, the first Eurasian domesticate to be adopted across Indigenous eastern North America, into the interior American Southeast by Indigenous communities who quickly "Indigenized" the fruit. In doing so, we present what may be the earliest absolute dates for archaeological contexts containing preserved peach pits in what is today the United States in the early to mid-16th century. Along with our broader chronological modeling, these early dates suggest that peaches were likely in the interior prior to permanent Spanish settlement in the American Southeast and that peaches spread independently of interactions with Spanish colonizers. We further argue that that eventual spread of peaches was structured exclusively by Indigenous communities and the ecologies produced through long-term Indigenous land management and land use practices, highlighting and centering the agency of Indigenous societies in the socioecological process of colonization.
Collapse
Affiliation(s)
- Jacob Holland-Lulewicz
- Department of Anthropology, The Pennsylvania State University, University Park, United States of America.
| | - Victor Thompson
- Laboratory of Archaeology, University of Georgia, Athens, United States of America
- Department of Anthropology, University of Georgia, Athens, United States of America
| | | | - RaeLynn Butler
- Muscogee (Creek) Nation, Okmulgee, United States of America
| | - Dario J Chavez
- Department of Horticulture, University of Georgia, Griffin, United States of America
| | - Jay Franklin
- Logan Simpson Design, Tucson, United States of America
| | - Turner Hunt
- Muscogee (Creek) Nation, Okmulgee, United States of America
| | - Mark Williams
- Laboratory of Archaeology, University of Georgia, Athens, United States of America
| | - John Worth
- Department of Anthropology, University of West Florida, Pensacola, United States of America
| |
Collapse
|
2
|
Canesin LEC, Vilaça ST, Oliveira RRM, Al-Ajli F, Tracey A, Sims Y, Formenti G, Fedrigo O, Banhos A, Sanaiotti TM, Farias IP, Jarvis ED, Oliveira G, Hrbek T, Solferini V, Aleixo A. A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 2024; 14:19925. [PMID: 39261501 PMCID: PMC11390914 DOI: 10.1038/s41598-024-70305-w] [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: 05/14/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024] Open
Abstract
The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
Collapse
Affiliation(s)
| | - Sibelle T Vilaça
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Renato R M Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Farooq Al-Ajli
- Rockefeller University, New York, USA
- Katara Biodiversity Genomics Program, Katara Cultural Village Foundation, Doha, Qatar
| | | | - Ying Sims
- Rockefeller University, New York, USA
| | | | | | - Aureo Banhos
- Universidade Federal do Espírito Santo (UFES), Alegre, Brazil
| | | | | | - Erich D Jarvis
- Rockefeller University, New York, USA
- Howard Hughes Medical Institute (HHMI), New York, USA
| | - Guilherme Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas (UFAM), Manaus, Brazil
- Trinity University, San Antonio, USA
| | - Vera Solferini
- Universidade Estadual de Campinas (Unicamp), Campinas, Brazil
| | - Alexandre Aleixo
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil.
| |
Collapse
|
3
|
Del Papa M, De Los Reyes M, Poiré DG, Rascovan N, Jofré G, Delgado M. Anthropic cut marks in extinct megafauna bones from the Pampean region (Argentina) at the last glacial maximum. PLoS One 2024; 19:e0304956. [PMID: 39018301 PMCID: PMC11253959 DOI: 10.1371/journal.pone.0304956] [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: 06/13/2023] [Accepted: 05/21/2024] [Indexed: 07/19/2024] Open
Abstract
The initial peopling of South America is a topic of intense archaeological debate. Among the most contentious issues remain the nature of the human-megafauna interaction and the possible role of humans, along with climatic change, in the extinction of several megamammal genera at the end of the Pleistocene. In this study, we present the analysis of fossil remains with cutmarks belonging to a specimen of Neosclerocalyptus (Xenarthra, Glyptodontidae), found on the banks of the Reconquista River, northeast of the Pampean region (Argentina), whose AMS 14C dating corresponds to the Last Glacial Maximum (21,090-20,811 cal YBP). Paleoenvironmental reconstructions, stratigraphic descriptions, absolute chronological dating of bone materials, and deposits suggest a relatively rapid burial event of the bone assemblage in a semi-dry climate during a wet season. Quantitative and qualitative analyses of the cut marks, reconstruction of butchering sequences, and assessments of the possible agents involved in the observed bone surface modifications indicate anthropic activities. Our results provide new elements for discussing the earliest peopling of southern South America and specifically for the interaction between humans and local megafauna in the Pampean region during the Last Glacial Maximum.
Collapse
Affiliation(s)
- Mariano Del Papa
- Facultad de Ciencias Naturales y Museo, División Antropología, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martin De Los Reyes
- Facultad de Ciencias Naturales y Museo, División Paleontología Vertebrados, Universidad Nacional de La Plata, La Plata, Argentina
- Instituto Antártico Argentino (IAA), 25 de mayo 1143, San Martín, Provincia de Buenos Aires, Argentina
| | - Daniel G. Poiré
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Provincia de Buenos Aires, Argentina
- Centro de Investigaciones Geológicas (CIG), CONICET—UNLP, Diagonal 113 n°275, La Plata, Argentina
| | - Nicolás Rascovan
- Institut Pasteur, Université de Paris Cité, CNRS UMR 2000, Microbial Paleogenomics Unit, F-75015, Paris, France
| | - Guillermo Jofré
- Repositorio Paleontológico Ramón Segura, Merlo, Provincia de Buenos Aires, Argentina
| | - Miguel Delgado
- Facultad de Ciencias Naturales y Museo, División Antropología, Universidad Nacional de La Plata, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Provincia de Buenos Aires, Argentina
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| |
Collapse
|
4
|
Santana J, del Pino M, Morales J, Fregel R, Hagenblad J, Morquecho A, Brito-Mayor A, Henríquez P, Jiménez J, Serrano JG, Sánchez-Cañadillas E, Ordóñez AC, Gilson SP. The chronology of the human colonization of the Canary Islands. Proc Natl Acad Sci U S A 2024; 121:e2302924121. [PMID: 38950368 PMCID: PMC11252820 DOI: 10.1073/pnas.2302924121] [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: 02/20/2023] [Accepted: 05/27/2024] [Indexed: 07/03/2024] Open
Abstract
The human colonization of the Canary Islands represents the sole known expansion of Berber communities into the Atlantic Ocean and is an example of marine dispersal carried out by an African population. While this island colonization shows similarities to the populating of other islands across the world, several questions still need to be answered before this case can be included in wider debates regarding patterns of initial colonization and human settlement, human-environment interactions, and the emergence of island identities. Specifically, the chronology of the first human settlement of the Canary Islands remains disputed due to differing estimates of the timing of its first colonization. This absence of a consensus has resulted in divergent hypotheses regarding the motivations that led early settlers to migrate to the islands, e.g., ecological or demographic. Distinct motivations would imply differences in the strategies and dynamics of colonization; thus, identifying them is crucial to understanding how these populations developed in such environments. In response, the current study assembles a comprehensive dataset of the most reliable radiocarbon dates, which were used for building Bayesian models of colonization. The findings suggest that i) the Romans most likely discovered the islands around the 1st century BCE; ii) Berber groups from western North Africa first set foot on one of the islands closest to the African mainland sometime between the 1st and 3rd centuries CE; iii) Roman and Berber societies did not live simultaneously in the Canary Islands; and iv) the Berber people rapidly spread throughout the archipelago.
Collapse
Affiliation(s)
- Jonathan Santana
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Miguel del Pino
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Jacob Morales
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, La Laguna38200, Spain
| | - Jenny Hagenblad
- Department of Physics, Chemistry and Biology, Linköping University, Linköping583 30, Sweden
| | - Aarón Morquecho
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Aitor Brito-Mayor
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Pedro Henríquez
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Jared Jiménez
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Javier G. Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, La Laguna38200, Spain
| | - Elías Sánchez-Cañadillas
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Alejandra C. Ordóñez
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| | - Simon-Pierre Gilson
- G.I. Tarha, Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria35003, Spain
| |
Collapse
|
5
|
Saltré F, Chadœuf J, Higham T, Ochocki M, Block S, Bunney E, Llamas B, Bradshaw CJA. Environmental conditions associated with initial northern expansion of anatomically modern humans. Nat Commun 2024; 15:4364. [PMID: 38777837 PMCID: PMC11111671 DOI: 10.1038/s41467-024-48762-8] [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: 04/28/2022] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.
Collapse
Affiliation(s)
- Frédérik Saltré
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia.
| | - Joël Chadœuf
- UR 1052, French National Institute for Agricultural Research (INRA), Montfavet, France
| | - Thomas Higham
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Monty Ochocki
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Sebastián Block
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-1003, USA
| | - Ellyse Bunney
- Commonwealth Scientific and Industrial Research Organisation, Urrbrae, SA, 5064, Australia
| | - Bastien Llamas
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, 5000, Australia
| | - Corey J A Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
| |
Collapse
|
6
|
Bezanson M, Cortés-Ortiz L, Bicca-Marques JC, Boonratana R, Carvalho S, Cords M, de la Torre S, Hobaiter C, Humle T, Izar P, Lynch JW, Matsuzawa T, Setchell JM, Zikusoka GK, Strier KB. News and Perspectives: Words matter in primatology. Primates 2024; 65:33-39. [PMID: 38032520 PMCID: PMC10796633 DOI: 10.1007/s10329-023-01104-6] [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: 10/04/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Postings on social media on Twitter (now X), BioAnthropology News (Facebook), and other venues, as well as recent publications in prominent journals, show that primatologists, ecologists, and other researchers are questioning the terms "Old World" and "New World" due to their colonial implications and history. The terms are offensive if they result in erasing Indigenous voices and history, ignoring the fact that Indigenous peoples were in the Americas long before European colonization. Language use is not without context, but alternative terminology is not always obvious and available. In this perspective, we share opinions expressed by an international group of primatologists who considered questions about the use of these terms, whether primatologists should adjust language use, and how to move forward. The diversity of opinions provides insight into how conventional terms used in primatological research and conservation may impact our effectiveness in these domains.
Collapse
Affiliation(s)
- Michelle Bezanson
- Department of Anthropology, Santa Clara University, Santa Clara, CA, USA.
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, RS, Brazil
| | - Ramesh Boonratana
- Mahidol University International College, Nakhon Pathom 73210, Thailand
| | - Susana Carvalho
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford, UK
- Gorongosa National Park, Sofala, Mozambique
| | - Marina Cords
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | | | - Catherine Hobaiter
- Wild Minds Lab, School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Tatyana Humle
- Durrelll Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Kent, UK
| | - Patrícia Izar
- Department of Experimental Psychology, University of São Paulo, São Paulo, Brazil
| | - Jessica W Lynch
- Department of Anthropology, and Institute for Society and Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Tetsuro Matsuzawa
- Division of the Humanities and Social Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Pedagogy, Chubu Gakuin University, Gifu, 504-0837, Japan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | | | | | - Karen B Strier
- Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
7
|
Echeverry-Quiceno LM, Candelo E, Gómez E, Solís P, Ramírez D, Ortiz D, González A, Sevillano X, Cuéllar JC, Pachajoa H, Martínez-Abadías N. Population-specific facial traits and diagnosis accuracy of genetic and rare diseases in an admixed Colombian population. Sci Rep 2023; 13:6869. [PMID: 37106005 PMCID: PMC10140286 DOI: 10.1038/s41598-023-33374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Up to 40% of rare disorders (RD) present facial dysmorphologies, and visual assessment is commonly used for clinical diagnosis. Quantitative approaches are more objective, but mostly rely on European descent populations, disregarding diverse population ancestry. Here, we assessed the facial phenotypes of Down (DS), Morquio (MS), Noonan (NS) and Neurofibromatosis type 1 (NF1) syndromes in a Latino-American population, recording the coordinates of 18 landmarks in 2D images from 79 controls and 51 patients. We quantified facial differences using Euclidean Distance Matrix Analysis, and assessed the diagnostic accuracy of Face2Gene, an automatic deep-learning algorithm. Individuals diagnosed with DS and MS presented severe phenotypes, with 58.2% and 65.4% of significantly different facial traits. The phenotype was milder in NS (47.7%) and non-significant in NF1 (11.4%). Each syndrome presented a characteristic dysmorphology pattern, supporting the diagnostic potential of facial biomarkers. However, population-specific traits were detected in the Colombian population. Diagnostic accuracy was 100% in DS, moderate in NS (66.7%) but lower in comparison to a European population (100%), and below 10% in MS and NF1. Moreover, admixed individuals showed lower facial gestalt similarities. Our results underscore that incorporating populations with Amerindian, African and European ancestry is crucial to improve diagnostic methods of rare disorders.
Collapse
Affiliation(s)
- Luis M Echeverry-Quiceno
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643. Planta 2, 08028, Barcelona, Spain
| | - Estephania Candelo
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
- Servicio de Genética Clínica, Fundación Valle del Lili, Cali, Colombia
| | - Eidith Gómez
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
| | - Paula Solís
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
| | - Diana Ramírez
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
| | - Diana Ortiz
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
| | - Alejandro González
- HER - Human-Environment Research Group, La Salle - Universitat Ramon Llull, Barcelona, Spain
| | - Xavier Sevillano
- HER - Human-Environment Research Group, La Salle - Universitat Ramon Llull, Barcelona, Spain
| | | | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad ICESI, Cali, Colombia
- Servicio de Genética Clínica, Fundación Valle del Lili, Cali, Colombia
| | - Neus Martínez-Abadías
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643. Planta 2, 08028, Barcelona, Spain.
| |
Collapse
|
8
|
Liu J, Dawe RK. Large haplotypes highlight a complex age structure within the maize pan-genome. Genome Res 2023; 33:359-370. [PMID: 36854668 PMCID: PMC10078284 DOI: 10.1101/gr.276705.122] [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: 02/22/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
Collapse
Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
9
|
Davis LG, Madsen DB, Sisson DA, Becerra-Valdivia L, Higham T, Stueber D, Bean DW, Nyers AJ, Carroll A, Ryder C, Sponheimer M, Izuho M, Iizuka F, Li G, Epps CW, Halford FK. Dating of a large tool assemblage at the Cooper's Ferry site (Idaho, USA) to ~15,785 cal yr B.P. extends the age of stemmed points in the Americas. SCIENCE ADVANCES 2022; 8:eade1248. [PMID: 36563150 PMCID: PMC9788777 DOI: 10.1126/sciadv.ade1248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The timing and character of the Pleistocene peopling of the Americas are measured by the discovery of unequivocal artifacts from well-dated contexts. We report the discovery of a well-dated artifact assemblage containing 14 stemmed projectile points from the Cooper's Ferry site in western North America, dating to ~16,000 years ago. These stemmed points are several thousand years older than Clovis fluted points (~13,000 cal yr B.P.) and are ~2300 years older than stemmed points found previously at the site. These points date to the end of Marine Isotope Stage 2 when glaciers had closed off an interior land route into the Americas. This assemblage includes an array of stemmed projectile points that resemble pre-Jomon Late Upper Paleolithic tools from the northwestern Pacific Rim dating to ~20,000 to 19,000 years ago, leading us to hypothesize that some of the first technological traditions in the Americas may have originated in the region.
Collapse
Affiliation(s)
- Loren G. Davis
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
| | - David B. Madsen
- Department of Anthropology, University of Nevada-Reno, 512 Ansari, Reno, NV 89557, USA
| | - David A. Sisson
- Bureau of Land Management, Cottonwood Field Office, 2 Butte Drive, Cottonwood, ID 83522, USA
| | - Lorena Becerra-Valdivia
- Oxford Radiocarbon Accelerator Unit, School of Archaeology, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Thomas Higham
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, A-1030 Vienna, Austria
| | - Daniel Stueber
- Department of Anthropology, University of Victoria, P.O. Box 1700 STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Daniel W. Bean
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
| | - Alexander J. Nyers
- Department of Anthropology, Oregon State University, 203 Waldo Hall, Corvallis, OR 97331, USA
- Northwest Archaeometrics, 5060 SW Philomath Blvd, #331, Corvallis, OR 97333, USA
| | - Amanda Carroll
- SWCA Environmental Consultants, 1800 NW Upshur St, Ste. 100, Portland, OR 97209, USA
| | - Christina Ryder
- Department of Anthropology, University of Colorado Boulder, Hale Science Building, 1350 Pleasant St., Boulder, CO 80309, USA
| | - Matt Sponheimer
- Department of Anthropology, University of Colorado Boulder, Hale Science Building, 1350 Pleasant St., Boulder, CO 80309, USA
| | - Masami Izuho
- Tokyo Metropolitan University, Faculty of Humanities and Social Sciences, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
| | - Fumie Iizuka
- Department of Anthropology and Research Reactor Center, University of Missouri, Swallow Hall, 112 S 9th Street, Columbia, MO 65211, USA
| | - Guoqiang Li
- Research School of Arid Environment and Climate Change, MOE Key Laboratory of West China’s Environmental System, Lanzhou University, 222 Tianshuinanlu, Lanzhou, Gansu 730000, China
| | - Clinton W. Epps
- Oregon State University Department of Fisheries, Wildlife, and Conservation Sciences, 104 Nash Hall, Corvallis, OR 97331, USA
| | - F. Kirk Halford
- Department of Anthropology, Boise State University, Boise, ID 83725, USA
| |
Collapse
|
10
|
Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| |
Collapse
|
11
|
Simulations of human migration into North America are more sensitive to demography than choice of palaeoclimate model. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
12
|
Brown T, Rijal DP, Heintzman PD, Clarke CL, Blankholm HP, Høeg HI, Lammers Y, Bråthen KA, Edwards M, Alsos IG. Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway. PNAS NEXUS 2022; 1:pgac209. [PMID: 36712342 PMCID: PMC9802259 DOI: 10.1093/pnasnexus/pgac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.
Collapse
Affiliation(s)
- Tony Brown
- To whom correspondence should be addressed:
| | - Dilli P Rijal
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Charlotte L Clarke
- The Palaeolab., Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Hans Peter Blankholm
- The Institute of Archaeology, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Helge I Høeg
- Department of Geosciences, University of Oslo, 0371 Oslo, Norway
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kari Anne Bråthen
- The Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mary Edwards
- The Palaeolab., Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| |
Collapse
|
13
|
Rowe TB, Stafford TW, Fisher DC, Enghild JJ, Quigg JM, Ketcham RA, Sagebiel JC, Hanna R, Colbert MW. Human Occupation of the North American Colorado Plateau ∼37,000 Years Ago. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.903795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Calibrating human population dispersals across Earth’s surface is fundamental to assessing rates and timing of anthropogenic impacts and distinguishing ecological phenomena influenced by humans from those that were not. Here, we describe the Hartley mammoth locality, which dates to 38,900–36,250 cal BP by AMS 14C analysis of hydroxyproline from bone collagen. We accept the standard view that elaborate stone technology of the Eurasian Upper Paleolithic was introduced into the Americas by arrival of the Native American clade ∼16,000 cal BP. It follows that if older cultural sites exist in the Americas, they might only be diagnosed using nuanced taphonomic approaches. We employed computed tomography (CT and μCT) and other state-of-the-art methods that had not previously been applied to investigating ancient American sites. This revealed multiple lines of taphonomic evidence suggesting that two mammoths were butchered using expedient lithic and bone technology, along with evidence diagnostic of controlled (domestic) fire. That this may be an ancient cultural site is corroborated by independent genetic evidence of two founding populations for humans in the Americas, which has already raised the possibility of a dispersal into the Americas by people of East Asian ancestry that preceded the Native American clade by millennia. The Hartley mammoth locality thus provides a new deep point of chronologic reference for occupation of the Americas and the attainment by humans of a near-global distribution.
Collapse
|
14
|
Pelton SR, Becerra-Valdivia L, Craib A, Allaun S, Mahan C, Koenig C, Kelley E, Zeimens G, Frison GC. In situ evidence for Paleoindian hematite quarrying at the Powars II site (48PL330), Wyoming. Proc Natl Acad Sci U S A 2022; 119:e2201005119. [PMID: 35549550 PMCID: PMC9171918 DOI: 10.1073/pnas.2201005119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/04/2022] [Indexed: 12/01/2022] Open
Abstract
SignificanceRed ocher (also known as hematite) is relatively common in Paleoindian sites exceeding ca. 11,000 calibrated years B.P. in the Great Plains and Rocky Mountains of North America. Red ocher fulfilled a wide range of functions within Paleoindian societies, as indicated by its association with graves, caches, campsites, hide-working implements, and kill sites. To date, the Powars II site is the only red ocher quarry identified in the North American archaeological record north of Mesoamerica. Prior studies of Powars II were based on analyses of artifacts recovered from a redeposited context. This study presents in situ evidence for red ocher quarrying at Powars II.
Collapse
Affiliation(s)
- Spencer R. Pelton
- Office of the Wyoming State Archaeologist, University of Wyoming, Laramie, WY 82071
| | - Lorena Becerra-Valdivia
- Oxford Radiocarbon Accelerator Unit, School of Archaeology, University of Oxford, Oxford OX1 3TG, United Kingdom
| | - Alexander Craib
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Sarah Allaun
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Chase Mahan
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Charles Koenig
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Erin Kelley
- Office of the Wyoming State Archaeologist, University of Wyoming, Laramie, WY 82071
| | - George Zeimens
- Sunrise Historic and Prehistoric Preservation Society, Hartville, WY 82215
| | - George C. Frison
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| |
Collapse
|
15
|
Andreae MO, Andreae TW. Archaeometric studies on rock art at four sites in the northeastern Great Basin of North America. PLoS One 2022; 17:e0263189. [PMID: 35081173 PMCID: PMC8791535 DOI: 10.1371/journal.pone.0263189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/13/2022] [Indexed: 11/18/2022] Open
Abstract
Rock art originated some 46,000 years ago and can provide unique insights into the minds of our human ancestors. However, dating of these ancient images, especially of petroglyphs, remains a challenge. In this study, we explore the potential of deriving age estimates from measurements of the areal densities of manganese (DMn) and iron (DFe) in the rock varnish on petroglyphs, based on the concept that the amount of varnish that has regrown on a petroglyph since its creation, relative to the surrounding intact varnish, is a measure of its age. We measured DMn and DFe by portable X-ray fluorescence (pXRF) on dated Late Pleistocene and Holocene rock surfaces, from which we derived accumulation rates of Mn and Fe in the rock varnish. The observed rates were comparable to our previous findings on basalt surfaces in North America. We derived age estimates for the rock art at four sites in the northern Great Basin region of North America based on DMn measurements on the petroglyphs and intact varnish. They suggest that rock art creation in this region began around the Pleistocene/Holocene transition and continued into the Historic Period, encompassing a wide range of styles and motifs. Evidence of reworking of the rock art at various times by Indigenous people speaks of the continued agency of these images through the millennia. Our results are in good agreement with chronologies based on archeological and other archaeometric techniques. While our method remains subject to significant uncertainty with regard to the absolute ages of individual images, it provides the unique opportunity to obtain age estimates for large ensembles of images without the need for destructive sampling.
Collapse
Affiliation(s)
- Meinrat O. Andreae
- Max Planck Institute for Chemistry, Mainz, Germany
- Department of Geology and Geophysics, King Saud University, Riyadh, Saudi Arabia
- Scripps Institution of Oceanography, UCSD, La Jolla, California, United States of America
- * E-mail:
| | | |
Collapse
|
16
|
Davidson SC, Ruhs EC. Understanding the dynamics of Arctic animal migrations in a changing world. ANIMAL MIGRATION 2021. [DOI: 10.1515/ami-2020-0114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This is submitted as an introduction to the special collection on, “Arctic Migrations in a Changing World”.
Collapse
Affiliation(s)
- Sarah C. Davidson
- Department of Animal Migration , Max Plank Institute of Animal Behavior , Radolfzell , Germany ; Department of Biology , University of Konstanz , Konstanz , Germany Department of Civil, Environmental and Geodetic Engineering , The Ohio State University , Columbus , OH, USA
| | | |
Collapse
|
17
|
Bennett MR, Bustos D, Pigati JS, Springer KB, Urban TM, Holliday VT, Reynolds SC, Budka M, Honke JS, Hudson AM, Fenerty B, Connelly C, Martinez PJ, Santucci VL, Odess D. Evidence of humans in North America during the Last Glacial Maximum. Science 2021; 373:1528-1531. [PMID: 34554787 DOI: 10.1126/science.abg7586] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Matthew R Bennett
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - David Bustos
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Jeffrey S Pigati
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Kathleen B Springer
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Thomas M Urban
- Department of Classics and Cornell Tree Ring Laboratory, Cornell University, Ithaca, NY 14853, USA
| | - Vance T Holliday
- School of Anthropology, P.O. Box 210030, University of Arizona, Tucson, AZ 85721-0030, USA.,Department of Geosciences, University of Arizona, Tucson, AZ 85721-0030, USA
| | - Sally C Reynolds
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - Marcin Budka
- Institute for Studies in Landscapes and Human Evolution, Bournemouth University, Poole, BH12 5BB, UK
| | - Jeffrey S Honke
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Adam M Hudson
- US Geological Survey, Denver Federal Center, Box 25046, MS 980, Denver, CO 80225, USA
| | - Brendan Fenerty
- Department of Geosciences, University of Arizona, Tucson, AZ 85721-0030, USA
| | - Clare Connelly
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Patrick J Martinez
- National Park Service, White Sands National Park, P.O. Box 1086, Holloman AFB, NM 88330, USA
| | - Vincent L Santucci
- National Park Service, Geologic Resources Division, 1849 C Street NW, Washington, DC 20240, USA
| | - Daniel Odess
- National Park Service, Cultural Resources Directorate, Washington, DC 20240, USA
| |
Collapse
|
18
|
Domínguez-Rodrigo M, Baquedano E, Varela L, Tambusso PS, Melián MJ, Fariña RA. Deep classification of cut-marks on bones from Arroyo del Vizcaíno (Uruguay). Proc Biol Sci 2021; 288:20210711. [PMID: 34256002 PMCID: PMC8277477 DOI: 10.1098/rspb.2021.0711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
The earliest widely accepted presence of humans in America dates to approximately 17.5 cal kyr BP, at the end of the Last Glacial Maximum (LGM). Among other evidence, this presence is attested by stone tools and associated cut-marks and other bone surface modifications (BSM), interpreted as the result of the consumption of animals by humans. Claims of an older human presence in the continent have been made based on the proposed anthropogenic modification of faunal remains; however, these have been controversial due to the highly subjective nature of the interpretations. Here, we employ advanced deep learning algorithms to objectively increase the accuracy of BSM identification on bones. With several models that exhibit BSM classification accuracies greater than 94%, we use ensemble learning techniques to robustly classify a selected sample of BSM from the approximately 30 kyr BP site of Arroyo del Vizcaíno, Uruguay. Our results confidently show the presence of cut-marks imparted by stone tools on bones at the site. This result supports an earlier presence of humans in the American continent, expanding additional genetic and archaeological evidence of a human LGM and pre-LGM presence in the continent.
Collapse
Affiliation(s)
- Manuel Domínguez-Rodrigo
- Instituto de Evolución en África (IDEA), Covarrubias 36, 28010 Madrid, Spain
- Área de Prehistoria, Departamento de Historia y Filosofía, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Enrique Baquedano
- Instituto de Evolución en África (IDEA), Covarrubias 36, 28010 Madrid, Spain
- Museo Arqueológico de la Comunidad de Madrid, Plaza de las Bernardas s/n, Alcalá de Henares, Madrid, Spain
| | - Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - P. Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - María Julia Melián
- Departamento de Arqueología, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Uruguay 1695, 11200 Montevideo, Uruguay
| | - Richard A. Fariña
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| |
Collapse
|
19
|
Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
Collapse
Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
| |
Collapse
|
20
|
Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco GS, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 2021; 184:1706-1723.e24. [PMID: 33761327 PMCID: PMC8024902 DOI: 10.1016/j.cell.2021.02.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/20/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Abstract
The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
Collapse
Affiliation(s)
| | - Bethany Aram
- Department of Geography, History and Philosophy, the Pablo de Olavide University of Seville, Seville 41013, Spain
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy; Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Javier Rivera
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Tomás Mendizábal
- Patronato Panamá Viejo, Panama City 0823-05096, Panama; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Iosvany Hernández-Mora
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Hongjie Li
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alberto Gòmez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Garrett Hellenthal
- UCL Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | | | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia 27100, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padua, Padua 35121, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ronny Friedrich
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Corina Knipper
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Bari 70125, Italy
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Juan Guillermo Martín
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Ripan Singh Malhi
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy.
| |
Collapse
|
21
|
Boëda E, Ramos M, Pérez A, Hatté C, Lahaye C, Pino M, Hérisson D, Clemente-Conte I, Fontugne M, Guérin G, Villagran X, Santos JC, Costa L, Germond L, Ahmed-Delacroix NE, Da Costa A, Borges C, Hoeltz S, Felice G, Gluchy M, van Havre G, Griggo C, Lucas L, de Souza I, Viana S, Strauss A, Kerner J, Guidon N. 24.0 kyr cal BP stone artefact from Vale da Pedra Furada, Piauí, Brazil: Techno-functional analysis. PLoS One 2021; 16:e0247965. [PMID: 33690652 PMCID: PMC7946292 DOI: 10.1371/journal.pone.0247965] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/16/2021] [Indexed: 11/29/2022] Open
Abstract
Current archaeological paradigm proposes that the first peopling of the Americas does not exceed the Last Glacial Maximum period. In this context, the acceptance of the anthropogenic character of the earliest stone artefacts generally rests on the presence of projectile points considered no more as typocentric but as typognomonic, since it allows, by itself, to certify the human character of the other associated artefacts. In other words, without this presence, nothing is certain. Archaeological research at Piauí (Brazil) attests to a Pleistocene human presence between 41 and 14 cal kyr BP, without any record of lithic projectile points. Here, we report the discovery and interpretation of an unusual stone artefact in the Vale da Pedra Furada site, in a context dating back to 24 cal kyr BP. The knapping stigmata and macroscopic use-wear traces reveal a conception centred on the configuration of double bevels and the production in the same specimen of at least two successive artefacts with probably different functions. This piece unambiguously presents an anthropic character and reveals a technical novelty during the Pleistocene occupation of South America.
Collapse
Affiliation(s)
- Eric Boëda
- ArScAn-Équipe AnTET, UMR 7041, CNRS, Université Paris Nanterre (UPN), Nanterre, France
- Department of Anthropology, UFR SSA, Université Paris Nanterre (UPN), Nanterre, France
- * E-mail:
| | - Marcos Ramos
- PPGArq-Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Antonio Pérez
- ArScAn-Équipe AnTET, UMR 7041, CNRS, Université Paris Nanterre (UPN), Nanterre, France
- Institut français d’études andines (IFEA), Lima, Peru
| | - Christine Hatté
- LSCE/LAMPEA, UMR 8212, CNRS, CEA UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christelle Lahaye
- IRAMAT-CRP2A, UMR 5060, CNRS, Bordeaux Montaigne University, Pessac, France
| | - Mario Pino
- Instituto de Ciencias de la Tierra and TAQUACH, Universidad Austral de Chile, Valdivia, Chile
| | - David Hérisson
- ArScAn-Équipe AnTET, UMR 7041, CNRS, Université Paris Nanterre (UPN), Nanterre, France
| | | | - Michel Fontugne
- LSCE/LAMPEA, UMR 8212, CNRS, CEA UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Guillaume Guérin
- IRAMAT-CRP2A, UMR 5060, CNRS, Bordeaux Montaigne University, Pessac, France
| | - Ximena Villagran
- MAE–Museu de Arqueologia e Etnologia, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Janaina C. Santos
- Universidade Federal do Vale do São Francisco (UNIVASF), Petrolina, Brazil
| | - Lucas Costa
- Universidade Federal do Piauí (UFPI), Teresina, Brazil
| | - Lucie Germond
- ArScAn-Équipe AnTET, UMR 7041, CNRS, Université Paris Nanterre (UPN), Nanterre, France
| | | | - Amelie Da Costa
- ArScAn-Équipe AnTET, UMR 7041, CNRS, Université Paris Nanterre (UPN), Nanterre, France
| | - Carolina Borges
- Instituto do Patrimonio Histórico e Artístico Nacional (IPHAN), Piauí, Brazil
| | | | - Gisele Felice
- Universidade Federal do Vale do São Francisco (UNIVASF), Petrolina, Brazil
- Fundação Museu do Homem Americano (FUMDHAM), São Raimundo Nonato, Piauí, Brazil
| | - María Gluchy
- Universidade Federal do Rio Grande (FURG), Rio Grande, Brazil
| | | | - Christophe Griggo
- EDYTEM UMR 5204 CNRS, Université Savoie Mont Blanc, Le Bourget-du-Lac, France
| | - Livia Lucas
- Universidade Federal de Sergipe (UFS), Sergipe, Brazil
| | | | - Sibeli Viana
- Pontificia Universidade Católica de Goiás (PUC-GO), Instituto Goiano de Pré-História e Antropologia (IGPA), Goiânia, Brazil
| | - André Strauss
- MAE–Museu de Arqueologia e Etnologia, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Jennifer Kerner
- Department of Anthropology, UFR SSA, Université Paris Nanterre (UPN), Nanterre, France
| | - Niède Guidon
- Fundação Museu do Homem Americano (FUMDHAM), São Raimundo Nonato, Piauí, Brazil
| |
Collapse
|
22
|
Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fenwick P, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Rainsley E, Bronk Ramsey C, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R. A global environmental crisis 42,000 years ago. Science 2021; 371:811-818. [PMID: 33602851 DOI: 10.1126/science.abb8677] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Geological archives record multiple reversals of Earth's magnetic poles, but the global impacts of these events, if any, remain unclear. Uncertain radiocarbon calibration has limited investigation of the potential effects of the last major magnetic inversion, known as the Laschamps Excursion [41 to 42 thousand years ago (ka)]. We use ancient New Zealand kauri trees (Agathis australis) to develop a detailed record of atmospheric radiocarbon levels across the Laschamps Excursion. We precisely characterize the geomagnetic reversal and perform global chemistry-climate modeling and detailed radiocarbon dating of paleoenvironmental records to investigate impacts. We find that geomagnetic field minima ~42 ka, in combination with Grand Solar Minima, caused substantial changes in atmospheric ozone concentration and circulation, driving synchronous global climate shifts that caused major environmental changes, extinction events, and transformations in the archaeological record.
Collapse
Affiliation(s)
- Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia. .,BlueSky Genetics, PO Box 287, Adelaide, SA 5137, Australia
| | - Chris S M Turney
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Jonathan Palmer
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alan Hogg
- Radiocarbon Dating Laboratory, University of Waikato, Hamilton 3240, New Zealand
| | - Matt McGlone
- Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Janet Wilmshurst
- Landcare Research, PO Box 69040, Lincoln, New Zealand.,School of Environment, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Andrew M Lorrey
- National Institute of Water and Atmospheric Research Ltd, Auckland 1010, New Zealand
| | - Timothy J Heaton
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - James M Russell
- Department of Geological Sciences, Brown University, Providence, RI 02912, USA
| | - Ken McCracken
- University of New South Wales, Sydney, NSW 2052, Australia
| | - Julien G Anet
- Zurich University of Applied Sciences, Centre for Aviation, 8401 Winterthur, Switzerland
| | - Eugene Rozanov
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland.,Physikalisch-Meteorologisches Observatorium Davos and World Radiation Center, 7260 Davos, Switzerland.,Department of Physics of Earth, Faculty of Physics, St. Petersburg State University, St. Petersburg 198504, Russia
| | - Marina Friedel
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland
| | - Ivo Suter
- Swiss Federal Laboratories for Materials Science and Technology (Empa), 8600 Dübendorf, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland
| | - Raimund Muscheler
- Department of Geology, Quaternary Sciences, Lund University, 22362 Lund, Sweden
| | - Florian Adolphi
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Tyler Faith
- Natural History Museum of Utah and Department of Anthropology, University of Utah, Salt Lake City, UT 84108, USA
| | - Pavla Fenwick
- Gondwana Tree-Ring Laboratory, PO Box 14, Little River, Canterbury 7546, New Zealand
| | - Christopher J Fogwill
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire ST5 5BG, UK
| | - Konrad Hughen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Mathew Lipson
- Centre of Excellence for Climate System Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jiabo Liu
- Southern University of Science and Technology, Department of Ocean Science and Engineering, Shenzhen 518055, China
| | - Norbert Nowaczyk
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, 14473 Potsdam, Germany
| | - Eleanor Rainsley
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire ST5 5BG, UK
| | - Christopher Bronk Ramsey
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, OX1 3TG, UK
| | - Paolo Sebastianelli
- Faculty of Mathematics, Astronomy and Physics (FAMAF), National University of Cordoba, X5000HUA, Argentina
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Janelle Stevenson
- Archaeology and Natural History, School of Culture History and Language, ANU College of Asia and the Pacific, Canberra, ACT 2601, Australia.,Australia ARC Centre of Excellence for Australian Biodiversity and Heritage, Australian National University, ACT 2601, Australia
| | - Zoë Thomas
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Roland Zech
- Institute of Geography, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| |
Collapse
|
23
|
Abstract
The Neolithic Revolution narrative associates early-mid Holocene domestications with the development of agriculture that fueled the rise of late Holocene civilizations. This narrative continues to be influential, even though it has been deconstructed by archaeologists and geneticists in its homeland. To further disentangle domestication from reliance on food production systems, such as agriculture, we revisit definitions of domestication and food production systems, review the late Pleistocene–early Holocene archaeobotanical record, and quantify the use, management and domestication of Neotropical plants to provide insights about the past. Neotropical plant domestication relies on common human behaviors (selection, accumulation and caring) within agroecological systems that focus on individual plants, rather than populations—as is typical of agriculture. The early archaeobotanical record includes numerous perennial and annual species, many of which later became domesticated. Some of this evidence identifies dispersal with probable cultivation, suggesting incipient domestication by 10,000 years ago. Since the Pleistocene, more than 6500, 1206 and 6261 native plant species have been used in Mesoamerica, the Central Andes and lowland South America, respectively. At least 1555, 428 and 742 are managed outside and inside food production systems, and at least 1148, 428 and 600 are cultivated, respectively, suggesting at least incipient domestication. Full native domesticates are more numerous in Mesoamerica (251) than the Andes (124) and the lowlands (45). This synthesis reveals that domestication is more common in the Neotropics than previously recognized and started much earlier than reliance on food production systems. Hundreds of ethnic groups had, and some still have, alternative strategies that do involve domestication, although they do not rely principally on food production systems, such as agriculture.
Collapse
|
24
|
Timpson A, Barberena R, Thomas MG, Méndez C, Manning K. Directly modelling population dynamics in the South American Arid Diagonal using 14C dates. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190723. [PMID: 33250032 DOI: 10.1098/rstb.2019.0723] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Large anthropogenic 14C datasets are widely used to generate summed probability distributions (SPDs) as a proxy for past human population levels. However, SPDs are a poor proxy when datasets are small, bearing little relationship to true population dynamics. Instead, more robust inferences can be achieved by directly modelling the population and assessing the model likelihood given the data. We introduce the R package ADMUR which uses a continuous piecewise linear (CPL) model of population change, calculates the model likelihood given a 14C dataset, estimates credible intervals using Markov chain Monte Carlo, applies a goodness-of-fit test, and uses the Schwarz Criterion to compare CPL models. We demonstrate the efficacy of this method using toy data, showing that spurious dynamics are avoided when sample sizes are small, and true population dynamics are recovered as sample sizes increase. Finally, we use an improved 14C dataset for the South American Arid Diagonal to compare CPL modelling to current simulation methods, and identify three Holocene phases when population trajectory estimates changed from rapid initial growth of 4.15% per generation to a decline of 0.05% per generation between 10 821 and 7055 yr BP, then gently grew at 0.58% per generation until 2500 yr BP. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
Collapse
Affiliation(s)
- Adrian Timpson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.,Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Ramiro Barberena
- Instituto Interdisciplinario de Ciencias Básicas (ICB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Paleoecología Humana, Facultad de Ciencias Exactas y Naturales, Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, Argentina
| | - Mark G Thomas
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Moraleda 16, Coyhaique, Aisén, Chile
| | - Katie Manning
- Department of Geography, King's College London, Strand, London WC2R 2LS, UK
| |
Collapse
|
25
|
Roca-Rada X, Souilmi Y, Teixeira JC, Llamas B. Ancient DNA Studies in Pre-Columbian Mesoamerica. Genes (Basel) 2020; 11:E1346. [PMID: 33202852 PMCID: PMC7696771 DOI: 10.3390/genes11111346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.
Collapse
Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
26
|
|
27
|
Barras C. Controversial cave discoveries suggest humans reached Americas much earlier than thought. Nature 2020; 583:670-671. [PMID: 32699369 DOI: 10.1038/d41586-020-02190-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|