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Nichols J. Founder effects identify languages of the earliest Americans. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e24923. [PMID: 38554027 DOI: 10.1002/ajpa.24923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 04/01/2024]
Abstract
The known languages of the Americas comprise nearly half of the world's language families and a wide range of structural types, a level of diversity that required considerable time to develop. This paper proposes a model of settlement and expansion designed to integrate current linguistic analysis with other prehistoric research on the earliest episodes in the peopling of the Americas. Diagnostic structural features from phonology and morphology are compared across 60 North American languages chosen for coverage of geography and language families and adequacy of description. Frequency comparison and graphic cluster analysis are applied to assess the fit of linguistic types and families with late Pleistocene time windows when entry from Siberia to North America was possible. The linguistic evidence is consistent with two population strata defined by early coastal entries ~24,000 and ~15,000 years ago, then an inland entry stream beginning ~14,000 ff. and mixed coastal/inland ~12,000 ff. The dominant structural properties among the founder languages are still reflected in the modern linguistic populations. The modern linguistic geography is still shaped by the extent of glaciation during the entry windows. Structural profiles imply that two linguistically distinct and internally diverse ancient Siberian linguistic populations provided the founding American populations. OBJECTIVES Describe early North American linguistic population structure and chronology; align distribution of structural types with archeological and paleoclimatological evidence on the earliest settlements. Propose an improved model of early settlement and expansion and pose some priority research questions. MATERIALS AND METHODS Classification of languages based on a tripartite geolinguistic division based on geographical and linguistic evidence. Survey of phonological and morphological patterns of 60 languages representing the structural, geographical, and genealogical diversity of North America. Survey of 16 morphological and phonological features of known or likely high stability and family-identifying value across those languages. Frequency comparison and cluster analysis to elucidate the tripartite analysis and compare to the chronology and geolinguistics implied by paleoclimatological and archeological work. RESULTS There is enough evidence (linguistic, archeological, genetic, and geological) to indicate four glacial-age openings allowing entries to North America: coastal c. 24,000 and 15,000 years ago; inland c. 14,000 years ago and continuing; and coastal c. 12,000 years ago and continuing. Geographical distribution of modern languages reflects the geography and chronology of the openings and the two human and linguistic population strata they formed, and plausibly also the structural types of the founding languages. DISCUSSION Improved model of North American settlement (two chronological strata, four entries); comparison to other proposed models. Further questions and research issues for linguistic, genetic, and archeological research.
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Affiliation(s)
- Johanna Nichols
- University of California, Berkeley, USA
- HSE University, Moscow, Russia
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2
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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3
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [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: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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4
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Silva MACE, Ferraz T, Hünemeier T. A genomic perspective on South American human history. Genet Mol Biol 2022; 45:e20220078. [PMID: 35925590 PMCID: PMC9351327 DOI: 10.1590/1678-4685-gmb-2022-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.
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Affiliation(s)
- Marcos Araújo Castro E Silva
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tiago Ferraz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
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The age of the opening of the Ice-Free Corridor and implications for the peopling of the Americas. Proc Natl Acad Sci U S A 2022; 119:e2118558119. [PMID: 35312340 PMCID: PMC9168949 DOI: 10.1073/pnas.2118558119] [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] [Indexed: 12/02/2022] Open
Abstract
The Ice-Free Corridor (IFC) has long played a key role in hypotheses about the peopling of the Americas. Earlier assessments of its age suggested that the IFC was available for a Clovis-first migration, but subsequent developments now suggest a pre-Clovis occupation of the Americas that occurred before the opening of the IFC, thus supporting a Pacific coastal migration route instead. However, large uncertainties in existing ages from the IFC cannot preclude its availability as a route for the first migrations. Resolving this debate over migration route is important for addressing the questions of when and how the first Americans arrived. We report cosmogenic nuclide exposure ages that show that the final opening of the IFC occurred well after pre-Clovis occupation. The Clovis-first model for the peopling of the Americas by ∼13.4 ka has long invoked the Ice-Free Corridor (IFC) between the retreating margins of the Cordilleran and Laurentide ice sheets as the migration route from Alaska and the Yukon down to the Great Plains. Evidence from archaeology and ancient genomics, however, now suggests that pre-Clovis migrations occurred by at least ∼15.5 to 16.0 ka or earlier than most recent assessments of the age of IFC opening at ∼14 to 15 ka, lending support to the use of a Pacific coast migration route instead. Uncertainties in ages from the IFC used in these assessments, however, allow for an earlier IFC opening which would be consistent with the availability of the IFC as a migration route by ∼15.5 to 16.0 ka. Here, we use 64 cosmogenic (10Be) exposure ages to closely date the age of the full opening of the IFC at 13.8 ± 0.5 ka. Our results thus clearly establish that the IFC was not available for the first peopling of the Americas after the Last Glacial Maximum, whereas extensive geochronological data from the Pacific coast support its earlier availability as a coastal migration route.
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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Abstract
The peopling of Siberia and the Americas is intriguing for archaeologists, linguists, and human geneticists, but despite significant recent developments, many details remain controversial. Here, we provide insights based on genetic diversity within Helicobacter pylori, a bacterium that infects 50% of all humans. H. pylori strains were collected from across eastern Eurasia and the Americas. Sequence analyses indicated that Siberia contains both anciently diverged and recently admixed bacteria, supporting both human persistence over the last glacial maximum and more recent human recolonization. We inferred a single migration across the Bering land bridge, accompanied by a dramatic reduction in effective population size, followed by bidirectional Holocene gene flow between Asia and the Americas. The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.
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Sustainable Heritage Tourism: Native American Preservation Recommendations at Arches, Canyonlands, and Hovenweep National Parks. SUSTAINABILITY 2020. [DOI: 10.3390/su12239846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The sustainable use of Native American heritage places is viewed in this analysis as serving to preserve their traditional purposes and sustaining the cultural landscapes that give them heritage meaning. The research concerns the potential impacts of heritage tourism to selected Native American places at Arches National Park, Canyonlands National Park, and Hovenweep National Monument. The impacts of tourists on a heritage place must be understood as having both potential effects on the place itself and on an integrated cultural landscape. Impacts to one place potentially change other places. Their functions in a Native American landscape, and the integrity of the landscape itself. The analysis is based on 696 interviews with representatives from nine tribes and pueblos, who, in addition to defining the cultural meaning of places, officially made 349 heritage management recommendations. The U.S. National Park Service interprets Natives American resources and then brings millions of tourists to these through museums, brochures, outdoor displays, and ranger-guided tours. Native American ethnographic study participants argued that tourist education and regulation can increase the sustainability of Native American places in a park and can help protect related places beyond the park.
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9
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The timing and effect of the earliest human arrivals in North America. Nature 2020; 584:93-97. [PMID: 32699413 DOI: 10.1038/s41586-020-2491-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
Abstract
The peopling of the Americas marks a major expansion of humans across the planet. However, questions regarding the timing and mechanisms of this dispersal remain, and the previously accepted model (termed 'Clovis-first')-suggesting that the first inhabitants of the Americas were linked with the Clovis tradition, a complex marked by distinctive fluted lithic points1-has been effectively refuted. Here we analyse chronometric data from 42 North American and Beringian archaeological sites using a Bayesian age modelling approach, and use the resulting chronological framework to elucidate spatiotemporal patterns of human dispersal. We then integrate these patterns with the available genetic and climatic evidence. The data obtained show that humans were probably present before, during and immediately after the Last Glacial Maximum (about 26.5-19 thousand years ago)2,3 but that more widespread occupation began during a period of abrupt warming, Greenland Interstadial 1 (about 14.7-12.9 thousand years before AD 2000)4. We also identify the near-synchronous commencement of Beringian, Clovis and Western Stemmed cultural traditions, and an overlap of each with the last dates for the appearance of 18 now-extinct faunal genera. Our analysis suggests that the widespread expansion of humans through North America was a key factor in the extinction of large terrestrial mammals.
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Shillito LM, Whelton HL, Blong JC, Jenkins DL, Connolly TJ, Bull ID. Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon. SCIENCE ADVANCES 2020; 6:eaba6404. [PMID: 32743069 PMCID: PMC7363456 DOI: 10.1126/sciadv.aba6404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.
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Affiliation(s)
- Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Thomas J. Connolly
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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Díez-Del-Molino D, Dalén L. Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials. Cell 2020; 181:1200-1201. [PMID: 32497501 DOI: 10.1016/j.cell.2020.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments.
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Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
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Uchiyama J, Gillam JC, Savelyev A, Ning C. Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e16. [PMID: 37588381 PMCID: PMC10427466 DOI: 10.1017/ehs.2020.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.
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Affiliation(s)
- Junzo Uchiyama
- The Sainsbury Institute for the Study of Japanese Arts and Cultures, University of East Anglia, 64 The Close, NorwichNR1 4DH, UK
- Center for Cultural Resource Studies, Kanazawa University, Kakuma-machi, Kanazawa-shi, 920-1192, Japan
| | - J. Christopher Gillam
- Department of Sociology, Criminology and Anthropology, Winthrop University, 319 Kinard Hall, Rock Hill, SC29733, USA
| | - Alexander Savelyev
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
- Institute of Linguistics, Russian Academy of Sciences, Bolshoy Kislovsky Pereulok 1/1, 125009Moscow, Russia
| | - Chao Ning
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
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Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M, Potgieter M, Underdown SJ, Koopman JE, Cowan DA, Van de Peer Y, Willerslev E, Hansen AJ. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. MICROBIOME 2020; 8:62. [PMID: 32375874 PMCID: PMC7204047 DOI: 10.1186/s40168-020-00832-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
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Affiliation(s)
- Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Tina B Brand
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Guillaume Porraz
- CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
| | - Aurore Val
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Stephan Woodborne
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
- iThemba LABS, Braamfontein Johannesburg, South Africa
| | - Matthieu Le Bailly
- University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Yves Van de Peer
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- VIB Centre for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Eske Willerslev
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.
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14
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Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 2020; 8:e9001. [PMID: 32337106 PMCID: PMC7169968 DOI: 10.7717/peerj.9001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.
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Affiliation(s)
- Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Bryan Cordova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Angela Perri
- Department of Archaeology, Durham University, Durham, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marsha Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Tanvi Prasad Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Jada Ko
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Jie Yu
- Department of History, Wuhan University, Wuhan, China
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Robert C. Power
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Domingo C. Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria-Gasteiz, Spain
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | | | - Helene Carabin
- Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David Jacobson
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska, Lincoln, NE, USA
| | - Cecil Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Aleksandar Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
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15
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Waters MR. Late Pleistocene exploration and settlement of the Americas by modern humans. SCIENCE (NEW YORK, N.Y.) 2020; 365:365/6449/eaat5447. [PMID: 31296740 DOI: 10.1126/science.aat5447] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
North and South America were the last continents to be explored and settled by modern humans at the end of the Pleistocene. Genetic data, derived from contemporary populations and ancient individuals, show that the first Americans originated from Asia and after several population splits moved south of the continental ice sheets that covered Canada sometime between ~17.5 and ~14.6 thousand years (ka) ago. Archaeological evidence shows that geographically dispersed populations lived successfully, using biface, blade, and osseous technologies, in multiple places in North and South America between ~15.5 and ~14 ka ago. Regional archaeological complexes emerged by at least ~13 ka ago in North America and ~12.9 ka ago in South America. Current genetic and archaeological data do not support an earlier (pre-17.5 ka ago) occupation of the Americas.
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Affiliation(s)
- Michael R Waters
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
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16
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Hubbe M, Terrazas Mata A, Herrera B, Benavente Sanvicente ME, González González A, Rojas Sandoval C, Avilés Olguín J, Acevez Núñez E, Von Cramon-Taubadel N. Morphological variation of the early human remains from Quintana Roo, Yucatán Peninsula, Mexico: Contributions to the discussions about the settlement of the Americas. PLoS One 2020; 15:e0227444. [PMID: 31995578 PMCID: PMC6988924 DOI: 10.1371/journal.pone.0227444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/18/2019] [Indexed: 11/24/2022] Open
Abstract
The human settlement of the Americas has been a topic of intense debate for centuries, and there is still no consensus on the tempo and mode of early human dispersion across the continent. When trying to explain the biological diversity of early groups across North, Central and South America, studies have defended a wide range of dispersion models that tend to oversimplify the diversity observed across the continent. In this study, we aim to contribute to this debate by exploring the cranial morphological affinities of four late Pleistocene/early Holocene specimens recovered from the caves of Quintana Roo, Mexico. The four specimens are among the earliest human remains known in the continent and permit the contextualization of biological diversity present during the initial millennia of human presence in the Americas. The specimens were compared to worldwide reference series through geometric morphometric analyses of 3D anatomical landmarks. Morphological data were analyzed through exploratory visual multivariate analyses and multivariate classification based on Mahalanobis distances. The results show very different patterns of morphological association for each Quintana Roo specimen, suggesting that the early populations of the region already shared a high degree of morphological diversity. This contrasts with previous studies of South American remains and opens the possibility that the initial populations of North America already had a high level of morphological diversity, which was reduced as populations dispersed into the southern continent. As such, the study of these rare remains illustrates that we are probably still underestimating the biological diversity of early Americans.
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Affiliation(s)
- Mark Hubbe
- Department of Anthropology, Ohio State University, Columbus, OH, United States of America
- Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Chile
- * E-mail:
| | - Alejandro Terrazas Mata
- Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Brianne Herrera
- Department of Anthropology, Ohio State University, Columbus, OH, United States of America
| | - Martha E. Benavente Sanvicente
- Laboratorio de Prehistoria y Evolución del Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | | | | | | | - Noreen Von Cramon-Taubadel
- Department of Anthropology, State University of New York – Buffalo, Buffalo, NY, United States of America
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17
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Eisenberg C, Anderson CL, Collingwood A, Sissons R, Dunn CJ, Meigs GW, Hibbs DE, Murphy S, Kuiper SD, SpearChief-Morris J, Little Bear L, Johnston B, Edson CB. Out of the Ashes: Ecological Resilience to Extreme Wildfire, Prescribed Burns, and Indigenous Burning in Ecosystems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America. Parasitology 2019; 146:1284-1288. [PMID: 31196226 DOI: 10.1017/s0031182019000787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Parasitological analysis of coprolites has allowed exploring ecological relationships in ancient times. Ancient DNA analysis contributes to the identification of coprolites and their parasites. Pleistocene mammalian carnivore coprolites were recovered from paleontological and archaeological site Peñas de las Trampas 1.1 in the southern Puna of Argentina. With the aim of exploring ancient ecological relationships, parasitological analysis was performed to one of them, dated to 16 573-17 002 calibrated years BP, with 95.4% probability. Parasite eggs attributed to Toxascaris sp. by morphological characters were isolated. DNA of coprolite and eggs was extracted to molecular identification. Ancient mitochondrial DNA analysis confirmed the zoological origin of the coprolite as Puma concolor and that of parasite eggs as Toxascaris leonina. This is the oldest molecular parasite record worldwide, and it supports the presence of this parasite since the Pleistocene in America. These findings have implications for the biogeographic history of parasites and for the natural history of the region.
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19
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Kashuba N, Kırdök E, Damlien H, Manninen MA, Nordqvist B, Persson P, Götherström A. Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia. Commun Biol 2019; 2:185. [PMID: 31123709 PMCID: PMC6520363 DOI: 10.1038/s42003-019-0399-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/21/2019] [Indexed: 11/08/2022] Open
Abstract
Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.
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Affiliation(s)
- Natalija Kashuba
- Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway
- Department of Archaeology and Ancient History, Uppsala University, P.O. Box 626, SE-751 26 Uppsala, Sweden
| | - Emrah Kırdök
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Hege Damlien
- Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway
| | - Mikael A. Manninen
- Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway
| | - Bengt Nordqvist
- Foundation War-Booty Site Finnestorp, Klarinettvägen 75, SE-434 75 Kungsbacka, Sweden
| | - Per Persson
- Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden
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20
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Weyrich LS, Farrer AG, Eisenhofer R, Arriola LA, Young J, Selway CA, Handsley-Davis M, Adler CJ, Breen J, Cooper A. Laboratory contamination over time during low-biomass sample analysis. Mol Ecol Resour 2019; 19:982-996. [PMID: 30887686 PMCID: PMC6850301 DOI: 10.1111/1755-0998.13011] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/08/2019] [Indexed: 12/18/2022]
Abstract
Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high‐throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no‐template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long‐term contaminant diversity. We additionally compared the contaminant content within a home‐made silica‐based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human‐associated taxa in comparison to the home‐made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low‐biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high‐throughput metagenomic study.
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Affiliation(s)
- Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew G Farrer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Raphael Eisenhofer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Luis A Arriola
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer Young
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Caitlin A Selway
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Matilda Handsley-Davis
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Christina J Adler
- School of Dentistry, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - James Breen
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
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21
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Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
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Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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22
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Waters MR, Keene JL, Forman SL, Prewitt ER, Carlson DL, Wiederhold JE. Pre-Clovis projectile points at the Debra L. Friedkin site, Texas-Implications for the Late Pleistocene peopling of the Americas. SCIENCE ADVANCES 2018; 4:eaat4505. [PMID: 30397643 PMCID: PMC6200361 DOI: 10.1126/sciadv.aat4505] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/19/2018] [Indexed: 05/23/2023]
Abstract
Lanceolate projectile points of the Clovis complex and stemmed projectile points of the Western Stemmed Tradition first appeared in North America by ~13 thousand years (ka) ago. The origin, age, and chronological superposition of these stemmed and lanceolate traditions are unclear. At the Debra L. Friedkin site, Texas, below Folsom and Clovis horizons, we find stemmed projectile points dating from ~13.5 to ~15.5 ka ago, with a triangular lanceolate point form appearing ~14 ka ago. The sequential relationship of stemmed projectile points followed by lanceolate forms suggests that lanceolate points are derived from stemmed forms or that they originated from two separate migrations into the Americas.
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Affiliation(s)
- Michael R. Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
- Corresponding author.
| | - Joshua L. Keene
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Steven L. Forman
- Department of Geosciences and Institute of Archaeology, Baylor University, Waco, TX 76798, USA
| | - Elton R. Prewitt
- Texas Archeological Research Laboratory, University of Texas, Austin, TX 78712, USA
| | - David L. Carlson
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - James E. Wiederhold
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA
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23
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Abstract
The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
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Affiliation(s)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
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Da-Gloria P, Hubbe M, Neves WA. Lagoa Santa's contribution to the origins and life of early Americans. Evol Anthropol 2018; 27:121-133. [PMID: 29845689 DOI: 10.1002/evan.21587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/16/2018] [Accepted: 04/23/2018] [Indexed: 11/06/2022]
Abstract
The region of Lagoa Santa, Central-Eastern Brazil, provides an exceptional archeological record about Late Pleistocene/Early Holocene occupation of the Americas. Since the first interventions made by the Danish naturalist Peter Lund in the 19th century, hundreds of human skeletons have been exhumed in the region. These skeletons are complemented by a rich botanic, faunal, technological, and geomorphological archeological record. We explore here the contributions of Lagoa Santa material to the origins and lifestyle of early Americans, providing an historic background. Cranial morphology of Lagoa Santa skeletons allowed the proposition of a model of two biological components for the occupation of the Americas, in which early Americans are morphologically similar to people of African and Australo-Melanesian origin. Furthermore, the archeological record in the region has revealed an intense use of plant resources, a restricted spatial distribution, and the symbolic elaboration of local hunter-gatherers, unveiling a distinct lifestyle compared to early North American populations.
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Affiliation(s)
- Pedro Da-Gloria
- Programa de Pós-Graduação em Antropologia, Instituto de Filosofia e Ciências Humanas, Universidade Federal do Pará
| | - Mark Hubbe
- Instituto de Investigaciones Arqueológicas y Museo R. P Gustavo Le Paige, Universidad Católica del Norte, San Pedro de Atacama, Chile and Department of Anthropology, The Ohio State University, Columbus, Ohio
| | - Walter A Neves
- Laboratório de Estudos Evolutivos e Ecológicos Humanos, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo
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Gómez-Carballa A, Pardo-Seco J, Brandini S, Achilli A, Perego UA, Coble MD, Diegoli TM, Álvarez-Iglesias V, Martinón-Torres F, Olivieri A, Torroni A, Salas A. The peopling of South America and the trans-Andean gene flow of the first settlers. Genome Res 2018; 28:767-779. [PMID: 29735605 PMCID: PMC5991523 DOI: 10.1101/gr.234674.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/27/2018] [Indexed: 11/25/2022]
Abstract
Genetic and archaeological data indicate that the initial Paleoindian settlers of South America followed two entry routes separated by the Andes and the Amazon rainforest. The interactions between these paths and their impact on the peopling of South America remain unclear. Analysis of genetic variation in the Peruvian Andes and regions located south of the Amazon River might provide clues on this issue. We analyzed mitochondrial DNA variation at different Andean locations and >360,000 autosomal SNPs from 28 Native American ethnic groups to evaluate different trans-Andean demographic scenarios. Our data reveal that the Peruvian Altiplano was an important enclave for early Paleoindian expansions and point to a genetic continuity in the Andes until recent times, which was only marginally affected by gene flow from the Amazonian lowlands. Genomic variation shows a good fit with the archaeological evidence, indicating that the genetic interactions between the descendants of the settlers that followed the Pacific and Atlantic routes were extremely limited.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Michael D Coble
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Toni M Diegoli
- Office of the Chief Scientist, Defense Forensic Science Center, Ft. Gillem, Georgia 30297, USA.,Analytical Services, Incorporated, Arlington, Virginia 22201, USA
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
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26
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Hamilton-Brehm SD, Hristova LT, Edwards SR, Wedding JR, Snow M, Kruger BR, Moser DP. Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA. PLoS One 2018; 13:e0194223. [PMID: 29522562 PMCID: PMC5844571 DOI: 10.1371/journal.pone.0194223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.
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Affiliation(s)
- Scott D. Hamilton-Brehm
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States of America
| | - Lidia T. Hristova
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Department of Anthropology, University of Nevada, Las Vegas, NV, United States of America
| | - Susan R. Edwards
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Jeffrey R. Wedding
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, United States of America
| | - Brittany R. Kruger
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Duane P. Moser
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States of America
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Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
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Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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28
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Reinhard K. Reestablishing rigor in archaeological parasitology. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2017; 19:124-134. [PMID: 29198394 DOI: 10.1016/j.ijpp.2017.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/24/2017] [Indexed: 06/07/2023]
Abstract
Archaeological parasitology originated in the mid-twentieth century with interdisciplinary teams of specialists directed by archaeologists. The goals of such studies were detailed analyses of dietary, medicinal, and environmental factors that shaped the patterns of infection. By the 1970s, a cadre of unique coprolite analysts was trained to analyze macroscopic and microscopic remains for integrated reconstructions of the cultural determinants of parasitism. During these first phases of research, diagnostic rigor was maintained by direct training of specialists in parasitology and archaeology sub-disciplines including archaeobotany and archaeopalynology. Near the end of the twentieth century, however, "paleoparasitology" was defined as a separate field focusing on defining parasite distribution through time and space. Ironically, this focus resulted in an increase in misdiagnosis, especially prominent after 2000. Paleoparasitology does not explicitly include other specialized studies in it research design. Thus, dietary, environmental and medicinal inferences have been neglected or lost as samples were destroyed solely for the purpose of parasitological analysis. Without ancillary archaeological studies, paleoparasitology runs the risk of separation from archaeological context, thereby reducing its value to the archaeologists who recover samples for analysis.
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Affiliation(s)
- Karl Reinhard
- School of Natural Resources, Hardin Hall 719, University of Nebraska, Lincoln, Lincoln, NE 68583-0987, United States.
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29
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Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus) and the Scaled Quail ( Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3-GENES GENOMES GENETICS 2017; 7:3047-3058. [PMID: 28717047 PMCID: PMC5592930 DOI: 10.1534/g3.117.043083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15-20 KYA.
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30
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Hardiman M, Scott AC, Pinter N, Anderson RS, Ejarque A, Carter-Champion A, Staff RA. Fire history on the California Channel Islands spanning human arrival in the Americas. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0167. [PMID: 27216524 DOI: 10.1098/rstb.2015.0167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 11/12/2022] Open
Abstract
Recent studies have suggested that the first arrival of humans in the Americas during the end of the last Ice Age is associated with marked anthropogenic influences on landscape; in particular, with the use of fire which, would have given even small populations the ability to have broad impacts on the landscape. Understanding the impact of these early people is complicated by the dramatic changes in climate occurring with the shift from glacial to interglacial conditions. Despite these difficulties, we here attempt to test the extent of anthropogenic influence using the California Channel Islands as a smaller, landscape-scale test bed. These islands are famous for the discovery of the 'Arlington Springs Man', which are some of the earliest human remains in the Americas. A unifying sedimentary charcoal record is presented from Arlington Canyon, Santa Rosa Island, based on over 20 detailed sedimentary sections from eight key localities. Radiocarbon dating was based on thin, fragile, long fragments of charcoal in order to avoid the 'inbuilt' age problem. Radiocarbon dating of 49 such fragments has allowed inferences regarding the fire and landscape history of the Canyon ca 19-11 ka BP. A significant period of charcoal deposition is identified approximately 14-12.5 ka BP and bears remarkable closeness to an estimated age range of the first human arrival on the islands.This article is part of the themed issue 'The interaction of fire and mankind'.
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Affiliation(s)
- Mark Hardiman
- Department of Geography, University of Portsmouth, Portsmouth, Hampshire, UK
| | - Andrew C Scott
- Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Nicholas Pinter
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, USA
| | - R Scott Anderson
- School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Ana Ejarque
- UMR 6042, GEOLAB, CNRS, 4 rue Ledru, 63057 Clermont-Ferrand cedex 1, France GEOLAB, Université Clermont Auvergne, Université Blaise Pascal, BP 10448, 63000 Clermont-Ferrand, France
| | | | - Richard A Staff
- Oxford Radiocarbon Accelerator Unit (ORAU), Research Laboratory for Archaeology and the History of Art (RLAHA), University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, UK
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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Skoglund P, Reich D. A genomic view of the peopling of the Americas. Curr Opin Genet Dev 2016; 41:27-35. [PMID: 27507099 PMCID: PMC5161672 DOI: 10.1016/j.gde.2016.06.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 06/23/2016] [Accepted: 06/25/2016] [Indexed: 10/21/2022]
Abstract
Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.
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Affiliation(s)
- Pontus Skoglund
- Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Archaeology and Classical History, Stockholm, Sweden.
| | - David Reich
- Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
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33
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Muddy messages about American migration. Nature 2016; 537:43-44. [DOI: 10.1038/nature19421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.
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36
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Postglacial viability and colonization in North America's ice-free corridor. Nature 2016; 537:45-49. [PMID: 27509852 DOI: 10.1038/nature19085] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/07/2016] [Indexed: 02/07/2023]
Abstract
During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by approximately 12.6 cal. kyr bp, followed by open forest, with evidence of moose and elk at about 11.5 cal. kyr bp, and boreal forest approximately 10 cal. kyr bp. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr bp, are unlikely to have travelled by this route into the Americas. However, later groups may have used this north-south passageway.
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Ozga AT, Nieves‐Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:220-8. [PMID: 26989998 PMCID: PMC4866892 DOI: 10.1002/ajpa.22960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew T. Ozga
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | | | - Tanvi P. Honap
- School of Life SciencesArizona State UniversityTempeAZ85287
| | | | | | - George R. Milner
- Department of AnthropologyPennsylvania State University, University ParkPA16802
| | - Cecil M. Lewis
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeAZ85287
- Center for Bioarchaeological Research, Arizona State UniversityTempeAZ85287
- Institute of Human Origins, Arizona State UniversityTempeAZ85287
| | - Christina Warinner
- Department of AnthropologyUniversity of OklahomaNormanOK73019
- Institute of Evolutionary Medicine, University of Zurich8057 ZurichSwitzerland
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38
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Underwater archaeologists unearth ancient butchering site. Nature 2016. [DOI: 10.1038/nature.2016.19913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Halligan JJ, Waters MR, Perrotti A, Owens IJ, Feinberg JM, Bourne MD, Fenerty B, Winsborough B, Carlson D, Fisher DC, Stafford TW, Dunbar JS. Pre-Clovis occupation 14,550 years ago at the Page-Ladson site, Florida, and the peopling of the Americas. SCIENCE ADVANCES 2016; 2:e1600375. [PMID: 27386553 PMCID: PMC4928949 DOI: 10.1126/sciadv.1600375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/14/2016] [Indexed: 05/04/2023]
Abstract
Stone tools and mastodon bones occur in an undisturbed geological context at the Page-Ladson site, Florida. Seventy-one radiocarbon ages show that ~14,550 calendar years ago (cal yr B.P.), people butchered or scavenged a mastodon next to a pond in a bedrock sinkhole within the Aucilla River. This occupation surface was buried by ~4 m of sediment during the late Pleistocene marine transgression, which also left the site submerged. Sporormiella and other proxy evidence from the sediments indicate that hunter-gatherers along the Gulf Coastal Plain coexisted with and utilized megafauna for ~2000 years before these animals became extinct at ~12,600 cal yr B.P. Page-Ladson expands our understanding of the earliest colonizers of the Americas and human-megafauna interaction before extinction.
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Affiliation(s)
- Jessi J. Halligan
- Department of Anthropology, Florida State University, Tallahassee, FL 32306, USA
- Corresponding author. (J.J.H.); (M.R.W.)
| | - Michael R. Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843, USA
- Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
- Department of Geography, Texas A&M University, College Station, TX 77843, USA
- Corresponding author. (J.J.H.); (M.R.W.)
| | - Angelina Perrotti
- Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
| | - Ivy J. Owens
- Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
- The Charles McBurney Laboratory for Geoarchaeology, Division of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Joshua M. Feinberg
- University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Rock Magnetism, Department of Earth Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark D. Bourne
- University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Rock Magnetism, Department of Earth Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brendan Fenerty
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - David Carlson
- Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
| | - Daniel C. Fisher
- Museum of Paleontology and Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - James S. Dunbar
- Aucilla Research Institute Inc., 555 North Jefferson Street, Monticello, FL 32344, USA
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40
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Strauss BB, Yab TC, O'Connor HM, Taylor WR, Mahoney DW, Simonson JA, Christensen J, Chari ST, Ahlquist DA. Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms. Dig Dis Sci 2016; 61:117-25. [PMID: 26297132 DOI: 10.1007/s10620-015-3845-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/04/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND Stool DNA testing represents a potential noninvasive approach to detect upper gastrointestinal (UGI) neoplasms. However, little is known about fecal recovery efficiency of DNA exfoliated from UGI tumors. AIMS The purpose of this study was to establish a human ingestion model that quantitatively approximates daily cellular shedding from UGI neoplasms and to estimate fecal DNA marker recovery rates. METHODS Healthy volunteers (n = 10) ingested two scheduled doses of raw salmon, 0.3 and 30 g, simulating the mass exfoliated daily from 1 to 4.5 cm lesions. To approach a steady-state, each dose was ingested over three consecutive days in randomized order. Following defecation of an indicator dye ingested with test meals, stools were collected over 48 h. Ingested salmon DNA was captured from stools using probes targeting pathognomonic Salmonidae sequences (SlmII). Captured DNA was quantified using PCR primers to generate 178, 138, 88 and 55 bp amplicons. RESULTS SlmII sequences were recovered from all stools following salmon ingestion; recovery was proportional to amount ingested (p = 0.004). Fecal recovery of ingested salmon varied inversely with amplicon size targeted; mean recovery rates of SlmII were 0.49, 0.91, 3.63, and 7.31 copies per 100,000 copies ingested for 178, 134, 88, and 55 bp amplicons, respectively (p < 0.0001). Longer oro-anal transit was associated with reduced recovery. CONCLUSIONS While recovery efficiencies are low, ingested cellular DNA simulating daily amounts shed from UGI tumors can readily be detected in stool. Assay of shorter-fragment analyte increases recovery. This ingestion model has potential value in studying the effects of perturbations relevant to the fecal recovery of DNA exfoliated from UGI tumors.
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Affiliation(s)
- Benjamin B Strauss
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Helen M O'Connor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA.
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Douglas W Mahoney
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
| | - Julie A Simonson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - John Christensen
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA
| | - Suresh T Chari
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
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41
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Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hünemeier T, Petzl-Erler ML, Salzano FM, Patterson N, Reich D. Genetic evidence for two founding populations of the Americas. Nature 2015. [PMID: 26196601 PMCID: PMC4982469 DOI: 10.1038/nature14895] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genetic studies have been consistent with a single common origin of Native American groups from Central and South America1-4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island southeast Asia)5-8. Here we analyze genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Niru Chennagiri
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, 05508-090, SP, Brazil
| | | | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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43
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Strauss A, Hubbe M, Neves WA, Bernardo DV, Atuí JPV. The cranial morphology of the Botocudo Indians, Brazil. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:202-16. [PMID: 25663638 DOI: 10.1002/ajpa.22703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/13/2015] [Indexed: 01/25/2023]
Abstract
The Botocudo Indians were hunter-gatherer groups that occupied the East-Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia.
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Affiliation(s)
- André Strauss
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, OH.,Instituto de Investigaciones Arqueológicas y Museo, Universidad Católica del Norte, San Pedro de Atacama, Chile
| | - Walter A Neves
- Laboratório de Estudos Evolutivos Humanos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Danilo V Bernardo
- Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - João Paulo V Atuí
- Laboratório de Estudos Evolutivos Humanos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Warinner C, Speller C, Collins MJ, Lewis CM. Ancient human microbiomes. J Hum Evol 2015; 79:125-36. [PMID: 25559298 PMCID: PMC4312737 DOI: 10.1016/j.jhevol.2014.10.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/06/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
Abstract
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
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Affiliation(s)
- Christina Warinner
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA
| | - Camilla Speller
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Matthew J Collins
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA.
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McCauley DJ, Pinsky ML, Palumbi SR, Estes JA, Joyce FH, Warner RR. Marine defaunation: Animal loss in the global ocean. Science 2015; 347:1255641. [PMID: 25593191 DOI: 10.1126/science.1255641] [Citation(s) in RCA: 407] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Douglas J McCauley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
| | - Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - James A Estes
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Francis H Joyce
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Robert R Warner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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46
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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47
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Kinoshita A, Skinner AR, Guidon N, Ignacio E, Felice GD, Buco CDA, Tatumi S, Yee M, Figueiredo AMG, Baffa O. Dating human occupation at Toca do Serrote das Moendas, São Raimundo Nonato, Piauí-Brasil by electron spin resonance and optically stimulated luminescence. J Hum Evol 2014; 77:187-95. [PMID: 25456825 DOI: 10.1016/j.jhevol.2014.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
Excavation of Toca do Serrote das Moendas, in Piauí state, Brazil revealed a great quantity of fossil wild fauna associated with human remains. In particular, fossils of a cervid (Blastocerus dichotomus) were found, an animal frequently pictured in ancient rock wall paintings. In a well-defined stratum, two loose teeth of this species were found in close proximity to human bones. The teeth were independently dated by electron spin resonance (ESR) in two laboratories. The ages obtained for the teeth were 29 ± 3 ka (thousands of years) and 24 ± 1 ka. The concretion layer capping this stratum was dated by optically stimulated luminescence (OSL) of the quartz grains to 21 ± 3 ka. As these values were derived independently in three different laboratories, using different methods and equipment, these results are compelling evidence of early habitation in this area.
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Affiliation(s)
- Angela Kinoshita
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, 14040-901 Ribeirão Preto, São Paulo, Brazil; Universidade Sagrado Coração, Rua Irmã Arminda 10-50, 17011-160 Bauru, São Paulo, Brazil
| | - Anne R Skinner
- Chemistry Department, Williams College, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Niede Guidon
- FUMDHAM - Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, 64770-000 São Raimundo Nonato, Piauí, Brazil; Ecole des Hautes Etudes en Sciences Sociales (EHESS), 54, Boulevard Raspail, 75006 Paris, France
| | - Elaine Ignacio
- FUMDHAM - Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, 64770-000 São Raimundo Nonato, Piauí, Brazil; UNIVASF - Universidade do Vale do São Francisco, Av. José de Sá Maniçoba, S/N - Centro, 56304-205 Petrolina, Pernambuco, Brazil
| | - Gisele Daltrini Felice
- FUMDHAM - Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, 64770-000 São Raimundo Nonato, Piauí, Brazil; UFPi - Universidade Federal do Piauí, Campus Universitário Ministro Petrônio Portella, Bairro Ininga, 64049-550 Teresina, Piauí, Brazil
| | - Cristiane de A Buco
- FUMDHAM - Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, 64770-000 São Raimundo Nonato, Piauí, Brazil
| | - Sonia Tatumi
- Universidade Federal de São Paulo, Campus Baixada Santista, Avenida Saldanha da Gama, n 89, Ponta da Praia, 11030-400 Santos, SP, Brazil
| | - Márcio Yee
- Universidade Federal de São Paulo, Campus Baixada Santista, Avenida Saldanha da Gama, n 89, Ponta da Praia, 11030-400 Santos, SP, Brazil
| | - Ana Maria Graciano Figueiredo
- Instituto de Pesquisas Energéticas e Nucleares (IPEN), Cidade Universitária, Av. Lineu Prestes, 2242, 5422-970 São Paulo, São Paulo, Brazil
| | - Oswaldo Baffa
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, 14040-901 Ribeirão Preto, São Paulo, Brazil.
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Fiedel SJ. Did pre-Clovis people inhabit the Paisley Caves (and why does it matter)? Hum Biol 2014; 86:69-74. [PMID: 25401988 DOI: 10.3378/027.086.0104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Stuart J Fiedel
- Louis Berger Group, 801 East Main Street, Suite 500, Richmond, Virginia 23219, USA
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49
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Nigra BT, Faull KF, Barnard H. Analytical Chemistry in Archaeological Research. Anal Chem 2014; 87:3-18. [DOI: 10.1021/ac5029616] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin T. Nigra
- Cotsen
Institute of Archaeology, University of California, Los Angeles, A331 Fowler
Museum, 308 Charles Young Drive North, Box 951510, Los Angeles, California 90095-1510, United States
| | - Kym F. Faull
- Department
of Psychiatry and Biobehavioral Sciences and Pasarow Mass Spectrometry
Laboratory, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Hans Barnard
- Cotsen
Institute of Archaeology, University of California, Los Angeles, A331 Fowler
Museum, 308 Charles Young Drive North, Box 951510, Los Angeles, California 90095-1510, United States
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50
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Hubbe M, Okumura M, Bernardo DV, Neves WA. Cranial morphological diversity of early, middle, and late Holocene Brazilian groups: Implications for human dispersion in Brazil. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:546-58. [DOI: 10.1002/ajpa.22607] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/20/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Mark Hubbe
- Department of Anthropology; The Ohio State University; Columbus OH
- Instituto de Investigaciones Arqueológicas y Museo; Universidad Católica del Norte; Chile
| | - Mercedes Okumura
- Departamento de Antropologia, Museu Nacional, Universidade Federal do Rio de Janeiro; Brazil
| | - Danilo V. Bernardo
- Laboratório de Estudos Evolutivos Humanos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências; Universidade de São Paulo; Brazil
- Área de Arqueologia e Antropologia, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande; Rio Grande Brazil
| | - Walter A. Neves
- Laboratório de Estudos Evolutivos Humanos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências; Universidade de São Paulo; Brazil
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