51
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Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
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52
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Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
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Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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53
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Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
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54
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Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
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Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
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55
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Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature 2021; 594:234-239. [PMID: 33981035 PMCID: PMC8189908 DOI: 10.1038/s41586-021-03532-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/12/2021] [Indexed: 12/26/2022]
Abstract
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
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Affiliation(s)
- Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Maxime Borry
- 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
| | - Kun D Huang
- CIBIO Department, University of Trento, Trento, Italy.,Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philipp Kirstahler
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tre Blohm
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Francis E Smiley
- Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Arnold
- Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA
| | - Sonia A Ballal
- Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Russ
- Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - 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 University, Jena, Germany
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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56
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Martinón-Torres M, d'Errico F, Santos E, Álvaro Gallo A, Amano N, Archer W, Armitage SJ, Arsuaga JL, Bermúdez de Castro JM, Blinkhorn J, Crowther A, Douka K, Dubernet S, Faulkner P, Fernández-Colón P, Kourampas N, González García J, Larreina D, Le Bourdonnec FX, MacLeod G, Martín-Francés L, Massilani D, Mercader J, Miller JM, Ndiema E, Notario B, Pitarch Martí A, Prendergast ME, Queffelec A, Rigaud S, Roberts P, Shoaee MJ, Shipton C, Simpson I, Boivin N, Petraglia MD. Earliest known human burial in Africa. Nature 2021; 593:95-100. [PMID: 33953416 DOI: 10.1038/s41586-021-03457-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 03/16/2021] [Indexed: 02/03/2023]
Abstract
The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.
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Affiliation(s)
- María Martinón-Torres
- CENIEH (National Research Center on Human Evolution), Burgos, Spain. .,Anthropology Department, University College London, London, UK.
| | - Francesco d'Errico
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France.,SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway
| | - Elena Santos
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Instituto de Salud Carlos III, Madrid, Spain.,Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales - Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Ana Álvaro Gallo
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - Noel Amano
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - William Archer
- Department of Archaeology and Anthropology, National Museum, Bloemfontein, South Africa.,Department of Archaeology, University of Cape Town, Cape Town, South Africa.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Simon J Armitage
- SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway.,Department of Geography, Royal Holloway, University of London, Egham, UK
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José María Bermúdez de Castro
- CENIEH (National Research Center on Human Evolution), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | - James Blinkhorn
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Geography, Royal Holloway, University of London, Egham, UK.,Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Stéphan Dubernet
- UMR 5060 CNRS-Université Bordeaux Montaigne IRAMAT-CRP2A: Institut de recherche sur les Archéomatériaux - Centre de recherche en physique appliquée à l'archéologie, Maison de l'archéologie, Pessac, France
| | - Patrick Faulkner
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Faculty of Arts and Social Sciences, Department of Archaeology, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Nikos Kourampas
- Centre for Open Learning, University of Edinburgh, Edinburgh, UK.,Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jorge González García
- 3D Applications Engineer and Heritage Specialist Digital Heritage and Humanities Collections, University of South Florida, Tampa, FL, USA
| | - David Larreina
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - François-Xavier Le Bourdonnec
- UMR 5060 CNRS-Université Bordeaux Montaigne IRAMAT-CRP2A: Institut de recherche sur les Archéomatériaux - Centre de recherche en physique appliquée à l'archéologie, Maison de l'archéologie, Pessac, France
| | - George MacLeod
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Laura Martín-Francés
- CENIEH (National Research Center on Human Evolution), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julio Mercader
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer M Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Emmanuel Ndiema
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,National Museums of Kenya, Department of Earth Sciences, Nairobi, Kenya
| | - Belén Notario
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - Africa Pitarch Martí
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France.,Seminari d'Estudis i Recerques Prehistòriques (SERP), Facultat de Geografia i Història, Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | | | - Alain Queffelec
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France
| | - Solange Rigaud
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Mohammad Javad Shoaee
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ceri Shipton
- Institute of Archaeology, University College London, London, UK.,Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ian Simpson
- Centre for Open Learning, University of Edinburgh, Edinburgh, UK
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. .,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia. .,Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada. .,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Michael D Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. .,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia. .,Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA. .,Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, Queensland, Australia.
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57
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Brandt MI, Trouche B, Quintric L, Günther B, Wincker P, Poulain J, Arnaud-Haond S. Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding. Mol Ecol Resour 2021; 21:1904-1921. [PMID: 33835712 DOI: 10.1111/1755-0998.13398] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 12/31/2020] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on read correction with DADA2 allowing analysing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster amplicon sequence variants (ASVs) into operational taxonomic units (OTUs) with swarm, a network-based clustering algorithm, and the option to curate ASVs/OTUs using LULU. Finally, taxonomic assignment was implemented via the Ribosomal Database Project Bayesian classifier (RDP) and BLAST. We validated this pipeline with ribosomal and mitochondrial markers using metazoan mock communities and 42 deep-sea sediment samples. The results show that ASVs and OTUs describe different levels of biotic diversity, the choice of which depends on the research questions. They underline the advantages and complementarity of clustering and LULU-curation for producing metazoan biodiversity inventories at a level approaching the one obtained using morphological criteria. While clustering removes intraspecific variation, LULU effectively removes spurious clusters, originating from errors or intragenomic variability. Swarm clustering affected alpha and beta diversity differently depending on genetic marker. Specifically, d-values > 1 appeared to be less appropriate with 18S for metazoans. Similarly, increasing LULU's minimum ratio level proved essential to avoid losing species in sample-poor data sets. Comparing BLAST and RDP underlined that accurate assignments of deep-sea species can be obtained with RDP, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific databases.
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Affiliation(s)
- Miriam I Brandt
- MARBEC, University of Montpellier, Ifremer, IRD, CNRS, Sète, France
| | - Blandine Trouche
- Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, Ifremer, CNRS, Plouzané, France
| | | | - Babett Günther
- MARBEC, University of Montpellier, Ifremer, IRD, CNRS, Sète, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université of Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université of Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
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58
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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59
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Vernot B, Zavala EI, Gómez-Olivencia A, Jacobs Z, Slon V, Mafessoni F, Romagné F, Pearson A, Petr M, Sala N, Pablos A, Aranburu A, de Castro JMB, Carbonell E, Li B, Krajcarz MT, Krivoshapkin AI, Kolobova KA, Kozlikin MB, Shunkov MV, Derevianko AP, Viola B, Grote S, Essel E, Herráez DL, Nagel S, Nickel B, Richter J, Schmidt A, Peter B, Kelso J, Roberts RG, Arsuaga JL, Meyer M. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science 2021; 372:science.abf1667. [PMID: 33858989 DOI: 10.1126/science.abf1667] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.
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Affiliation(s)
- Benjamin Vernot
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Asier Gómez-Olivencia
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain.,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alice Pearson
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Petr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nohemi Sala
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Adrián Pablos
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Arantza Aranburu
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | | | - Eudald Carbonell
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Universitat Rovira i Virgili, Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warszawa, Poland
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Steffi Grote
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Peter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Juan-Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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60
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Successful extraction of insect DNA from recent copal inclusions: limits and perspectives. Sci Rep 2021; 11:6851. [PMID: 33767248 PMCID: PMC7994385 DOI: 10.1038/s41598-021-86058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.
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61
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Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 2021; 9:e10947. [PMID: 33777521 PMCID: PMC7977378 DOI: 10.7717/peerj.10947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
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Affiliation(s)
- James A. Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Thiseas C. Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime U. Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany
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62
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Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proc Natl Acad Sci U S A 2021; 118:2022466118. [PMID: 33798098 DOI: 10.1073/pnas.2022466118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.
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63
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Environmental palaeogenomic reconstruction of an Ice Age algal population. Commun Biol 2021; 4:220. [PMID: 33594237 PMCID: PMC7887274 DOI: 10.1038/s42003-021-01710-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA. Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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64
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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65
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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66
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Bergström A, Stringer C, Hajdinjak M, Scerri EML, Skoglund P. Origins of modern human ancestry. Nature 2021; 590:229-237. [PMID: 33568824 DOI: 10.1038/s41586-021-03244-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK.
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Eleanor M L Scerri
- Pan-African Evolution Research Group, Max Planck Institute for Science of Human History, Jena, Germany.,Department of Classics and Archaeology, University of Malta, Msida, Malta.,Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
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67
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Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age. Genes (Basel) 2021; 12:genes12020146. [PMID: 33499220 PMCID: PMC7911526 DOI: 10.3390/genes12020146] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.
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Cuthbertson P, Ullmann T, Büdel C, Varis A, Namen A, Seltmann R, Reed D, Taimagambetov Z, Iovita R. Finding karstic caves and rockshelters in the Inner Asian mountain corridor using predictive modelling and field survey. PLoS One 2021; 16:e0245170. [PMID: 33471843 PMCID: PMC7816991 DOI: 10.1371/journal.pone.0245170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022] Open
Abstract
The area of the Inner Asian Mountain Corridor (IAMC) follows the foothills and piedmont zones around the northern limits of Asia's interior mountains, connecting two important areas for human evolution: the Fergana valley and the Siberian Altai. Prior research has suggested the IAMC may have provided an area of connected refugia from harsh climates during the Pleistocene. To date, this region contains very few secure, dateable Pleistocene sites, but its widely available carbonate units present an opportunity for discovering cave sites, which generally preserve longer sequences and organic remains. Here we present two models for predicting karstic cave and rockshelter features in the Kazakh portion of the IAMC. The 2018 model used a combination of lithological data and unsupervised landform classification, while the 2019 model used feature locations from the results of our 2017-2018 field surveys in a supervised classification using a minimum-distance classifier and morphometric features derived from the ASTER digital elevation model (DEM). We present the results of two seasons of survey using two iterations of the karstic cave models (2018 and 2019), and evaluate their performance during survey. In total, we identified 105 cave and rockshelter features from 2017-2019. We conclude that this model-led approach significantly reduces the target area for foot survey.
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Affiliation(s)
- Patrick Cuthbertson
- Department of Early Prehistory and Quaternary Ecology, Eberhard Karls University of Tübingen, Tübingen, Germany
- * E-mail: (PC); (RI)
| | - Tobias Ullmann
- Institute of Geography and Geology, University of Würzburg, Würzburg, Germany
| | - Christian Büdel
- Institute of Geography and Geology, University of Würzburg, Würzburg, Germany
| | - Aristeidis Varis
- Department of Early Prehistory and Quaternary Ecology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Institute for Archaeological Sciences (INA), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Abay Namen
- Department of Early Prehistory and Quaternary Ecology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Faculty of History, Archaeology, and Ethnology, Department of Archaeology, Ethnology, and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Reimar Seltmann
- Department of Earth Sciences, Centre for Russian and Central EurAsian Mineral Studies, Natural History Museum, London, United Kingdom
| | - Denné Reed
- Department of Anthropology, University of Texas, Austin, United States of America
| | | | - Radu Iovita
- Department of Early Prehistory and Quaternary Ecology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, United States of America
- * E-mail: (PC); (RI)
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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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Abstract
Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.
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Nowaczewska W, Binkowski M, Benazzi S, Vazzana A, Nadachowski A, Stefaniak K, Żarski M, Talamo S, Compton T, Stringer CB, Hajdinjak M, Hublin JJ. New hominin teeth from Stajnia Cave, Poland. J Hum Evol 2021; 151:102929. [PMID: 33418451 DOI: 10.1016/j.jhevol.2020.102929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Wioletta Nowaczewska
- Department of Human Biology, University of Wrocław, Przybyszewskiego 63, Wrocław 51-148, Poland.
| | - Marcin Binkowski
- X-ray Microtomography Lab, Department of Biomedical Computer Systems, Institute of Computer Science, Faculty of Computer and Materials Science, University of Silesia, Będzińska 39, Chorzów 41-200, Poland
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, Ravenna 48121, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D-04103, Germany
| | - Antonino Vazzana
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, Ravenna 48121, Italy
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, Kraków 31-016, Poland
| | - Krzysztof Stefaniak
- Department of Paleozoology, Institute of Environmental Biology, University of Wrocław, Sienkiewicza 21, Wrocław 50-335, Poland
| | - Marcin Żarski
- Polish Geological Institute-National Research Institute, Rakowiecka 4, Warsaw 00-975, Poland
| | - Sahra Talamo
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi, 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D-04103, Germany
| | - Tim Compton
- CHER, Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chris B Stringer
- CHER, Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D-04103, Germany; International Chair of Paleoanthropology, Collège de France, 11 Place Marcelin Berthelot, Paris 75231, France
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Cullen VL, Smith VC, Tushabramishvili N, Mallol C, Dee M, Wilkinson KN, Adler DS. A revised AMS and tephra chronology for the Late Middle to Early Upper Paleolithic occupations of Ortvale Klde, Republic of Georgia. J Hum Evol 2020; 151:102908. [PMID: 33370643 DOI: 10.1016/j.jhevol.2020.102908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
The nature and timing of the shift from the Late Middle Paleolithic (LMP) to the Early Upper Paleolithic (EUP) varied geographically, temporally, and substantively across the Near East and Eurasia; however, the result of this process was the archaeological disappearance of Middle Paleolithic technologies across the length and breadth of their geographic distribution. Ortvale Klde rockshelter (Republic of Georgia) contains the most detailed LMP-EUP archaeological sequence in the Caucasus, an environmentally and topographically diverse region situated between southwest Asia and Europe. Tephrochronological investigations at the site reveal volcanic ash (tephra) from various volcanic sources and provide a tephrostratigraphy for the site that will facilitate future correlations in the region. We correlate one of the cryptotephra layers to the large, caldera-forming Nemrut Formation eruption (30,000 years ago) from Nemrut volcano in Turkey. We integrate this tephrochronological constraint with new radiocarbon dates and published ages in an OxCal Bayesian age model to produce a revised chronology for the site. This model increases the ages for the end of the LMP (∼47.5-44.2 ka cal BP) and appearance of the EUP (∼46.7-43.6 ka cal BP) at Ortvale Klde, which are earlier than those currently reported for other sites in the Caucasus but similar to estimates for specific sites in southwest Asia and eastern Europe. These data, coupled with archaeological, stratigraphic, and taphonomic observations, suggest that at Ortvale Klde, (1) the appearance of EUP technologies of bone and stone has no technological roots in the preceding LMP, (2) a LMP population vacuum likely preceded the appearance of these EUP technologies, and (3) the systematic combination of tephra correlations and absolute dating chronologies promises to substantially improve our inter-regional understanding of this critical time interval of human evolution and the potential interconnectedness of hominins at different sites.
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Affiliation(s)
- Victoria L Cullen
- Department of Chemistry, University of Oxford, Oxford, United Kingdom; Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Victoria C Smith
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | | | - Carolina Mallol
- Archaeological Micromorphology and Biomarker Research Lab, Instituto Universitario de Bio-Orgánica Antonio González, Tenerife, Spain; Departamento de Geografía e Historia, Universidad de La Laguna Campus de Guajara, Tenerife, Spain
| | - Michael Dee
- Centre for Isotope Research, ESRIG, University of Groningen, Groningen, the Netherlands
| | - Keith N Wilkinson
- Department of Anthropology and Archaeology, University of Winchester, United Kingdom
| | - Daniel S Adler
- Department of Anthropology, University of Connecticut, CT, USA.
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Jensen MR, Sigsgaard EE, Liu S, Manica A, Bach SS, Hansen MM, Møller PR, Thomsen PF. Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples. Mol Ecol Resour 2020; 21:690-702. [PMID: 33179423 PMCID: PMC7983877 DOI: 10.1111/1755-0998.13293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023]
Abstract
Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA‐based population studies. The mitochondrial target capture successfully retrieved ~235× (90× − 352× per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant nontarget species, mackerel tuna (Euthynnus affinis), showing a clear relationship between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only a few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and nontarget sequences as well as presence of nontarget species at the sampling site, is crucial to consider. eDNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.
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Affiliation(s)
| | | | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
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74
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Rodríguez de Vera C, Herrera-Herrera AV, Jambrina-Enríquez M, Sossa-Ríos S, González-Urquijo J, Lazuen T, Vanlandeghem M, Alix C, Monnier G, Pajović G, Tostevin G, Mallol C. Micro-contextual identification of archaeological lipid biomarkers using resin-impregnated sediment slabs. Sci Rep 2020; 10:20574. [PMID: 33239666 PMCID: PMC7689525 DOI: 10.1038/s41598-020-77257-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022] Open
Abstract
Characterizing organic matter preserved in archaeological sediment is crucial to behavioral and paleoenvironmental investigations. This task becomes particularly challenging when considering microstratigraphic complexity. Most of the current analytical methods rely on loose sediment samples lacking spatial and temporal resolution at a microstratigraphic scale, adding uncertainty to the results. Here, we explore the potential of targeted molecular and isotopic biomarker analysis on polyester resin-impregnated sediment slabs from archaeological micromorphology, a technique that provides microstratigraphic control. We performed gas chromatography-mass spectrometry (GC-MS) and gas chromatography-isotope ratio mass spectromety (GC-IRMS) analyses on a set of samples including drill dust from resin-impregnated experimental and archaeological samples, loose samples from the same locations and resin control samples to assess the degree of interference of polyester resin in the GC-MS and Carbon-IRMS signals of different lipid fractions (n-alkanes, aromatics, n-ketones, alcohols, fatty acids and other high polarity lipids). The results show that biomarkers within the n-alkane, aromatic, n-ketone, and alcohol fractions can be identified. Further work is needed to expand the range of identifiable lipid biomarkers. This study represents the first micro-contextual approach to archaeological lipid biomarkers and contributes to the advance of archaeological science by adding a new method to obtain behavioral or paleoenvironmental proxies.
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Affiliation(s)
- Caterina Rodríguez de Vera
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica "Antonio González", Universidad de La Laguna, Tenerife, Spain.
| | - Antonio V Herrera-Herrera
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica "Antonio González", Universidad de La Laguna, Tenerife, Spain
| | - Margarita Jambrina-Enríquez
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica "Antonio González", Universidad de La Laguna, Tenerife, Spain
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Tenerife, Spain
| | - Santiago Sossa-Ríos
- Departamento de Historia e Historia del Arte, Universitat Rovira i Virgili, Avenida de Cataluña, 35, 43002, Tarragona, Spain
- Institut Català de Paleoecología Humana i Evolució Social (IPHES), Zona Educacional 4, Campus Sescelades Universitat Rovira I Virgili (Edificio W3), 43007, Tarragona, Spain
| | - Jesús González-Urquijo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, IIIPC-University of Cantabria, Edificio Interfacultativo, Universidad de Cantabria, Avenida de Los Castros, 52, 39005, Santander, Spain
| | - Talia Lazuen
- CNRS, MCC, PACEA, UMR 5199, Université de Bordeaux, 33600, Pessac Cedex, France
| | - Marine Vanlandeghem
- UMR 7041 ArScAn, Université Paris 1 Panthéon Sorbonne, 21 allée de l'université, 92023, Nanterre Cedex, France
| | - Claire Alix
- Université Paris 1 Panthéon Sorbonne, 8096 ArchAm, 21 allée de l'université, 92023, Nanterre Cedex, France
| | - Gilliane Monnier
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | - Goran Pajović
- National Museum of Montenegro, Novice Cerovića, 7, 81250, Cetinje, Montenegro
| | - Gilbert Tostevin
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | - Carolina Mallol
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica "Antonio González", Universidad de La Laguna, Tenerife, Spain
- Departamento de Geografía e Historia, UDI Prehistoria, Arqueología e Historia Antigua, Facultad de Geografía e Historia, Universidad de La Laguna, Tenerife, Spain
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75
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Researchers using environmental DNA must engage ethically with Indigenous communities. Nat Ecol Evol 2020; 5:146-148. [PMID: 33184485 DOI: 10.1038/s41559-020-01351-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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76
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Zhang D, Xia H, Chen F, Li B, Slon V, Cheng T, Yang R, Jacobs Z, Dai Q, Massilani D, Shen X, Wang J, Feng X, Cao P, Yang MA, Yao J, Yang J, Madsen DB, Han Y, Ping W, Liu F, Perreault C, Chen X, Meyer M, Kelso J, Pääbo S, Fu Q. Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science 2020; 370:584-587. [DOI: 10.1126/science.abb6320] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Dongju Zhang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Frontier Center for Eco-environment and Climate Change in Pan-third Pole Regions, Lanzhou University, Lanzhou 730000, China
| | - Huan Xia
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fahu Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Ting Cheng
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Xuke Shen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian Wang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- School of Earth Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Juanting Yao
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jishuai Yang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - David B. Madsen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Department of Anthropology, University of Nevada–Reno, Reno, NV 89557, USA
| | - Yuanyuan Han
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wanjing Ping
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Feng Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Charles Perreault
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoshan Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
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Li F, Petraglia M, Roberts P, Gao X. The northern dispersal of early modern humans in eastern Eurasia. Sci Bull (Beijing) 2020; 65:1699-1701. [PMID: 36659239 DOI: 10.1016/j.scib.2020.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Feng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena D-07745, Germany; School of Social Science, the University of Queensland, Brisbane, QLD 4072, Australia; Human Origins Program, Smithsonian Institution, Washington DC 20560-0004, USA
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena D-07745, Germany; School of Social Science, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
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78
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Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020; 10:18225. [PMID: 33106554 PMCID: PMC7588426 DOI: 10.1038/s41598-020-75163-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
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Affiliation(s)
- Cody Parker
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam B Rohrlach
- Max Planck Institute for the Science of Human History, Jena, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.
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79
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Sabin S, Yeh HY, Pluskowski A, Clamer C, Mitchell PD, Bos KI. Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190576. [PMID: 33012229 PMCID: PMC7702797 DOI: 10.1098/rstb.2019.0576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Susanna Sabin
- Max Planck Institute for the Science of Human History, Jena, Germany.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, 48 Nanyang Avenue, Singapore 639818, Singapore
| | - Aleks Pluskowski
- Department of Archaeology, University of Reading, Whiteknights, Reading RG6 6AB, UK
| | - Christa Clamer
- École Biblique de Jérusalem, PO Box 19053, IL9119001, Jerusalem
| | - Piers D Mitchell
- Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
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80
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Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat Protoc 2020; 15:2279-2300. [PMID: 32612278 DOI: 10.1038/s41596-020-0338-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023]
Abstract
It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.
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81
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Ardelean CF, Becerra-Valdivia L, Pedersen MW, Schwenninger JL, Oviatt CG, Macías-Quintero JI, Arroyo-Cabrales J, Sikora M, Ocampo-Díaz YZE, Rubio-Cisneros II, Watling JG, de Medeiros VB, De Oliveira PE, Barba-Pingarón L, Ortiz-Butrón A, Blancas-Vázquez J, Rivera-González I, Solís-Rosales C, Rodríguez-Ceja M, Gandy DA, Navarro-Gutierrez Z, De La Rosa-Díaz JJ, Huerta-Arellano V, Marroquín-Fernández MB, Martínez-Riojas LM, López-Jiménez A, Higham T, Willerslev E. Evidence of human occupation in Mexico around the Last Glacial Maximum. Nature 2020; 584:87-92. [PMID: 32699412 DOI: 10.1038/s41586-020-2509-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 06/16/2020] [Indexed: 11/09/2022]
Abstract
The initial colonization of the Americas remains a highly debated topic1, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations2. However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico3,4, the Chiapas Highlands5, Central Mexico6 and the Caribbean coast7-9 during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas10-17of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)18, and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.
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Affiliation(s)
- Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Zacatecas, Mexico. .,Department of Archaeology, University of Exeter, Exeter, UK.
| | - Lorena Becerra-Valdivia
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Chronos 14C-Cycle Facility, SSEAU, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Jean-Luc Schwenninger
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Charles G Oviatt
- Department of Geology, Kansas State University, Manhattan, KS, USA
| | - Juan I Macías-Quintero
- Escuela de Arqueología, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoología, Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia, Mexico City, Mexico
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Yam Zul E Ocampo-Díaz
- Facultad de Ingeniería, Universidad Autónoma de San Luís Potosí, San Luis Potosí, Mexico.,Grupo de Geología Exógena y del Sedimentario, San Luis Potosí, Mexico
| | | | - Jennifer G Watling
- Laboratório de Arqueologia dos Trópicos, Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil
| | - Vanda B de Medeiros
- Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo E De Oliveira
- Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil.,Botany Department, The Field Museum of Natural History, Chicago, IL, USA
| | - Luis Barba-Pingarón
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Agustín Ortiz-Butrón
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Jorge Blancas-Vázquez
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Irán Rivera-González
- Laboratorio de Palinología, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Corina Solís-Rosales
- Laboratorio de Espectrometría de Masas con Aceleradores, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - María Rodríguez-Ceja
- Laboratorio de Espectrometría de Masas con Aceleradores, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Devlin A Gandy
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Alejandro López-Jiménez
- Laboratorio de Arqueozoología, Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia, Mexico City, Mexico
| | - Thomas Higham
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark. .,Welcome Trust, Sanger Institute, Hinxton, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK.
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82
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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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83
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Zhang M, Fu Q. Human evolutionary history in Eastern Eurasia using insights from ancient DNA. Curr Opin Genet Dev 2020; 62:78-84. [PMID: 32688244 DOI: 10.1016/j.gde.2020.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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84
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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85
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Peyrégne S, Prüfer K. Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays 2020; 42:e2000081. [PMID: 32648350 DOI: 10.1002/bies.202000081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
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86
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Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes. Sci Rep 2020; 10:10502. [PMID: 32601368 PMCID: PMC7324595 DOI: 10.1038/s41598-020-67452-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/19/2020] [Indexed: 11/08/2022] Open
Abstract
eDNA refers to DNA extracted from an environmental sample with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDNA records. To investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil samples were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, samples were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the samples as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. Overall, these results illustrate the potential of eDNA analyses for identifying the recent (< 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. The capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales.
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87
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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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88
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Tsosie KS, Begay RL, Fox K, Garrison NA. Generations of genomes: advances in paleogenomics technology and engagement for Indigenous people of the Americas. Curr Opin Genet Dev 2020; 62:91-96. [PMID: 32721847 PMCID: PMC7484015 DOI: 10.1016/j.gde.2020.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
For decades, scientists have collected genomic information from Indigenous peoples and their ancestors with the goal of elucidating human migration events, understanding ancestral origins, and identifying ancestral variants contributing to disease. However, such studies may not have offered much benefit to the Indigenous groups who contributed DNA, and many have instead perpetuated stereotypes and other harms. With recent advances in genomic technology facilitating the study of both ancient and present-day DNA, researchers and Indigenous communities have new opportunities to begin collaboratively addressing important questions about human health and history. Yet, while there are increased efforts to ethically engage Indigenous communities, more work is still needed as the discipline struggles to absolve itself of the racialized science and extractive biocolonialism that defined its past.
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Affiliation(s)
- Krystal S Tsosie
- Vanderbilt University, Nashville, TN 37325, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Rene L Begay
- Centers for American Indian and Alaska Native Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Keolu Fox
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Global Health, University of California, San Diego, La Jolla, CA 92093, USA; Indigenous Futures Lab, University of California, San Diego, La Jolla, CA 92093, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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89
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Armbrecht L, Herrando-Pérez S, Eisenhofer R, Hallegraeff GM, Bolch CJS, Cooper A. An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Mol Ecol Resour 2020; 20:906-919. [PMID: 32277584 DOI: 10.1111/1755-0998.13162] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/17/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.
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Affiliation(s)
- Linda Armbrecht
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Salvador Herrando-Pérez
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Gustaaf M Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - Christopher J S Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tas., Australia
| | - Alan Cooper
- South Australian Museum, Adelaide, SA, Australia
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90
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Lang PLM, Weiß CL, Kersten S, Latorre SM, Nagel S, Nickel B, Meyer M, Burbano HA. Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Mol Ecol Resour 2020; 20:1228-1247. [PMID: 32306514 DOI: 10.1111/1755-0998.13168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.
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Affiliation(s)
- Patricia L M Lang
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, London, UK
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91
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Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 2020; 581:299-302. [DOI: 10.1038/s41586-020-2259-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
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92
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Martisius NL, Welker F, Dogandžić T, Grote MN, Rendu W, Sinet-Mathiot V, Wilcke A, McPherron SJP, Soressi M, Steele TE. Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals. Sci Rep 2020; 10:7746. [PMID: 32385291 PMCID: PMC7210944 DOI: 10.1038/s41598-020-64358-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for “smoothers”), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.
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Affiliation(s)
- Naomi L Martisius
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tamara Dogandžić
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA, 19104-6398, USA
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA
| | - William Rendu
- Centre National de la Recherche Scientifique, MCC, Préhistoire à l'Actuel, Cultures, Environnement, Anthropologie, UMR5199, Université de Bordeaux, FR-33615, Pessac, France
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04013, Leipzig, Germany
| | - Shannon J P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Marie Soressi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Faculty of Archaeology, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Teresa E Steele
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
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93
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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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94
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Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Pușcaș M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM, Coissac E. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. PLANTS (BASEL, SWITZERLAND) 2020; 9:E432. [PMID: 32244605 PMCID: PMC7238428 DOI: 10.3390/plants9040432] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Sebastien Lavergne
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | - Marti Boleda
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - Youri Lammers
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Charles Pouchon
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Iva Pitelkova
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Mihai Pușcaș
- A. Borza Botanical Garden and Faculty of Biology and Geology, Babeș-Bolyai University, 400015 Cluj-Napoca, Romania;
| | - Cristina Roquet
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Wilfried Thuiller
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | | | - Eric Coissac
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
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95
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Abstract
Mobile devices for on-field DNA analysis have been used for medical diagnostics
at the point-of-care, forensic investigations and environmental surveys, but
still have to be validated for ancient DNA studies. We report here on a mobile
laboratory that we setup using commercially available devices, including a
compact real-time PCR machine, and describe procedures to perform DNA extraction
and analysis from a variety of archeological samples within 4 hours. The process
is carried out on 50 mg samples that are identified at the species level using
custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated
the potential of this approach in museums lacking facilities for DNA studies by
analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3
deposits), and also performed experiments during an excavation campaign at the
Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples
only yielded DNA for the extinct steppe bison (Bison priscus),
whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta
crocuta spelaea) DNA together, for some of them, with DNA for the
European bison sister species/subspecies (Bison
schoetensacki/Bb1-X), thus highlighting the cave hyena diet.
Roc-en-Pail Bovinae bone and tooth samples also contained DNA
for the Bison schoetensacki/Bb1-X clade, and
Cervidae bone samples only yielded reindeer
(Rangifer tarandus) DNA. Subsequent DNA sequencing analyses
confirmed that correct species identification had been achieved using our TaqMan
assays, hence validating these assays for future studies. We conclude that our
approach enables the rapid genetic characterization of tens of millennia-old
archeological samples and is expected to be useful for the on-site screening of
museums and freshly excavated samples for DNA content. Because our mobile
laboratory is made up of commercially available instruments, this approach is
easily accessible to other investigators.
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96
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Moore G, Tessler M, Cunningham SW, Betancourt J, Harbert R. Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA. Ecol Evol 2020; 10:2530-2544. [PMID: 32184999 PMCID: PMC7069311 DOI: 10.1002/ece3.6082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.
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Affiliation(s)
- Grace Moore
- Smith CollegeNorthamptonMassachusetts
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | - Michael Tessler
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | - Seth W. Cunningham
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | | | - Robert Harbert
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
- Stonehill CollegeEastonMassachusetts
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97
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McGaughran A. Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? BMC Genomics 2020; 21:188. [PMID: 32111157 PMCID: PMC7048091 DOI: 10.1186/s12864-020-6594-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/19/2020] [Indexed: 01/04/2023] Open
Abstract
Background Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years. Results I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
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Affiliation(s)
- Angela McGaughran
- Australian National University, Research School of Biology, Division of Ecology and Evolution, Acton, Canberra, ACT, 2600, Australia. .,CSIRO Land and Water, Integrated Omics Team, Black Mountain Laboratories, Canberra, ACT, 2600, Australia.
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98
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Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
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Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
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99
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Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia. Proc Natl Acad Sci U S A 2020; 117:2879-2885. [PMID: 31988114 PMCID: PMC7022189 DOI: 10.1073/pnas.1918047117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.
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100
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Abstract
The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.
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