1
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Aktürk Ş, Mapelli I, Güler MN, Gürün K, Katırcıoğlu B, Vural KB, Sağlıcan E, Çetin M, Yaka R, Sürer E, Atağ G, Çokoğlu SS, Sevkar A, Altınışık NE, Koptekin D, Somel M. Benchmarking kinship estimation tools for ancient genomes using pedigree simulations. Mol Ecol Resour 2024; 24:e13960. [PMID: 38676702 DOI: 10.1111/1755-0998.13960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
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Affiliation(s)
- Şevval Aktürk
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Merve N Güler
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Büşra Katırcıoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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2
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Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
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Affiliation(s)
- Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
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3
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Lammers Y, Taberlet P, Coissac E, Elliott LD, Merkel MF, Pitelkova I, Alsos IG. Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA. Mol Ecol Resour 2024; 24:e13926. [PMID: 38189170 DOI: 10.1111/1755-0998.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.
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Affiliation(s)
- Y Lammers
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - P Taberlet
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - E Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - L D Elliott
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - M F Merkel
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - I Pitelkova
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - I G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
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4
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Vallini L, Zampieri C, Shoaee MJ, Bortolini E, Marciani G, Aneli S, Pievani T, Benazzi S, Barausse A, Mezzavilla M, Petraglia MD, Pagani L. The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal. Nat Commun 2024; 15:1882. [PMID: 38528002 DOI: 10.1038/s41467-024-46161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.
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Affiliation(s)
| | - Carlo Zampieri
- Department of Biology, University of Padova, Padova, Italy
| | - Mohamed Javad Shoaee
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena, Germany
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
- Research Unit Prehistory and Anthropology, Department of Physical Sciences, Earth and Environment, University of Siena, Siena, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Telmo Pievani
- Department of Biology, University of Padova, Padova, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Alberto Barausse
- Department of Biology, University of Padova, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | | | - Michael D Petraglia
- Human Origins Program, Smithsonian Institution, Washington, DC, 20560, USA
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
| | - Luca Pagani
- Department of Biology, University of Padova, Padova, Italy.
- Institute of Genomics, University of Tartu, Tartu, Estonia.
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5
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Bergfeldt N, Kırdök E, Oskolkov N, Mirabello C, Unneberg P, Malmström H, Fraser M, Sanchez-Quinto F, Jorgensen R, Skar B, Lidén K, Jakobsson M, Storå J, Götherström A. Identification of microbial pathogens in Neolithic Scandinavian humans. Sci Rep 2024; 14:5630. [PMID: 38453993 PMCID: PMC10920878 DOI: 10.1038/s41598-024-56096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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Affiliation(s)
- Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Claudio Mirabello
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Magdalena Fraser
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jorgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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6
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Fischer A, Sjögren KG, Jensen TZT, Jørkov ML, Lysdahl P, Vimala T, Refoyo-Martínez A, Scorrano G, Price TD, Gröcke DR, Gotfredsen AB, Sørensen L, Alexandersen V, Wåhlin S, Stenderup J, Bennike O, Ingason A, Iversen R, Sikora M, Racimo F, Willerslev E, Allentoft ME, Kristiansen K. Vittrup Man-The life-history of a genetic foreigner in Neolithic Denmark. PLoS One 2024; 19:e0297032. [PMID: 38354111 PMCID: PMC10866469 DOI: 10.1371/journal.pone.0297032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024] Open
Abstract
The lethally maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features, he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a variable life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his teenage years.
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Affiliation(s)
- Anders Fischer
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Marie Louise Jørkov
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
| | - Per Lysdahl
- Vendsyssel Historical Museum, Hjørring, Denmark
| | - Tharsika Vimala
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | | | | | - T. Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Darren R. Gröcke
- Department of Earth Sciences, Durham University, Durham, England, United Kingdom
| | | | | | - Verner Alexandersen
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Stenderup
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Andrés Ingason
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rune Iversen
- The Saxo Institute—Section of Archaeology, University of Copenhagen, Copenhagen S, Denmark
| | - Martin Sikora
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Eske Willerslev
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Morten E. Allentoft
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
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7
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Antonio ML, Weiß CL, Gao Z, Sawyer S, Oberreiter V, Moots HM, Spence JP, Cheronet O, Zagorc B, Praxmarer E, Özdoğan KT, Demetz L, Gelabert P, Fernandes D, Lucci M, Alihodžić T, Amrani S, Avetisyan P, Baillif-Ducros C, Bedić Ž, Bertrand A, Bilić M, Bondioli L, Borówka P, Botte E, Burmaz J, Bužanić D, Candilio F, Cvetko M, De Angelis D, Drnić I, Elschek K, Fantar M, Gaspari A, Gasperetti G, Genchi F, Golubović S, Hukeľová Z, Jankauskas R, Vučković KJ, Jeremić G, Kaić I, Kazek K, Khachatryan H, Khudaverdyan A, Kirchengast S, Korać M, Kozlowski V, Krošláková M, Kušan Špalj D, La Pastina F, Laguardia M, Legrand S, Leleković T, Leskovar T, Lorkiewicz W, Los D, Silva AM, Masaryk R, Matijević V, Cherifi YMS, Meyer N, Mikić I, Miladinović-Radmilović N, Milošević Zakić B, Nacouzi L, Natuniewicz-Sekuła M, Nava A, Neugebauer-Maresch C, Nováček J, Osterholtz A, Paige J, Paraman L, Pieri D, Pieta K, Pop-Lazić S, Ruttkay M, Sanader M, Sołtysiak A, Sperduti A, Stankovic Pesterac T, Teschler-Nicola M, Teul I, Tončinić D, Trapp J, Vulović D, Waliszewski T, Walter D, Živanović M, Filah MEM, Čaušević-Bully M, Šlaus M, Borić D, Novak M, Coppa A, Pinhasi R, Pritchard JK. Stable population structure in Europe since the Iron Age, despite high mobility. eLife 2024; 13:e79714. [PMID: 38288729 PMCID: PMC10827293 DOI: 10.7554/elife.79714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.
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Affiliation(s)
- Margaret L Antonio
- Biomedical Informatics Program, Stanford UniversityStanfordUnited States
| | - Clemens L Weiß
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Ziyue Gao
- Department of Genetics, University of Pennsylvania, Perelman School of MedicinePhiladelphiaUnited States
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Hannah M Moots
- Stanford Archaeology Center, Stanford UniversityStanfordUnited States
- University of Chicago, Department of Human GeneticsChicagoUnited States
| | - Jeffrey P Spence
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Elisa Praxmarer
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | | | - Lea Demetz
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
- CIAS, Department of Life Sciences, University of CoimbraCoimbraPortugal
| | - Michaela Lucci
- Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza UniversityRomeItaly
| | | | - Selma Amrani
- LBEIG, Population Genetics & Conservation Unit, Department of Cellular and Molecular Biology – Faculty of Biological Sciences, University of Sciences and Technology Houari BoumedieneAlgiersAlgeria
| | - Pavel Avetisyan
- National Academy of Sciences of Armenia, Institute of Archaeology and EthnographyYerevanArmenia
| | - Christèle Baillif-Ducros
- French National Institute for Preventive Archaeological Research (INRAP)/CAGT UMR 5288ToulouseFrance
| | - Željka Bedić
- Centre for Applied Bioanthropology, Institute for Anthropological ResearchZagrebCroatia
| | | | | | - Luca Bondioli
- Dipartimento dei Beni Culturali, Archeologia, Storia dell'arte, del Cinema e della Musica, Università di PadovaPadovaItaly
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of LodzŁódźPoland
| | - Emmanuel Botte
- Aix Marseille Université, CNRS, Centre Camille JullianAix-en-ProvenceFrance
| | | | - Domagoj Bužanić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | | | - Mirna Cvetko
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Daniela De Angelis
- Museo Archeologico Nazionale di Tarquinia, Direzione Regionale Musei LazioRomeItaly
| | - Ivan Drnić
- Archaeological Museum in ZagrebZagrebCroatia
| | - Kristián Elschek
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | - Mounir Fantar
- Département des Monuments et des Sites Antiques - Institut National du Patrimoine INPTunisTunisia
| | - Andrej Gaspari
- University of Ljubljana, Faculty of Arts, Department for ArchaeologyLjubljanaSlovenia
| | - Gabriella Gasperetti
- Soprintendenza Archeologia, belle arti e paesaggio per le province di Sassari e NuoroSassariItaly
| | - Francesco Genchi
- Department of Oriental Studies, Sapienza University of RomeRomeItaly
| | | | - Zuzana Hukeľová
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | | | | | - Iva Kaić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Kevin Kazek
- Université de Lorraine, Centre de Recherche Universitaire Lorrain d' Histoire (CRULH)NancyFrance
| | - Hamazasp Khachatryan
- Department of Archaeologi, Shirak Centere of Armenological Studies, National Academy of Sciences Republic of ArmeniaGyumriArmenia
| | - Anahit Khudaverdyan
- Institute of Archaeology and Ethnography of the National Academy of Sciences of the Republic of ArmeniaYerevanArmenia
| | - Sylvia Kirchengast
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | | | | | - Mária Krošláková
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | | | - Marie Laguardia
- UMR 7041 ArScAn / French Institute of the Near EastBeirutLebanon
| | | | - Tino Leleković
- Archaeology Division, Croatian Academy of Sciences and ArtsZagrebCroatia
| | - Tamara Leskovar
- University of Ljubljana, Faculty of Arts, Department for ArchaeologyLjubljanaSlovenia
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of LodzŁódźPoland
| | | | - Ana Maria Silva
- CIAS, Department of Life Sciences, University of CoimbraCoimbraPortugal
- CEF - University of CoimbraCoimbraPortugal
- UNIARQ - University of LisbonLisbonPortugal
| | - Rene Masaryk
- Skupina STIK Zavod za preučevanje povezovalnih področij preteklosti in sedanjostiLjubljanaSlovenia
| | - Vinka Matijević
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Yahia Mehdi Seddik Cherifi
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Cardiolo-Oncology Research Collaborative Group (CORCG), Faculty of Medicine, Benyoucef Benkhedda UniversityAlgiersAlgeria
- Molecular Pathology, University Paul Sabatier Toulouse IIIToulouseFrance
| | - Nicolas Meyer
- French National Institute for Preventive Archaeological Research (INRAP)MetzFrance
| | - Ilija Mikić
- Institute of Archaeology BelgradeBelgradeSerbia
| | | | | | - Lina Nacouzi
- L’Institut français du Proche-OrientBeirutLebanon
| | - Magdalena Natuniewicz-Sekuła
- Institute of Archaeology and Ethnology Polish Academy of Sciences, Centre of Interdisciplinary Archaeological ResearchWarsawPoland
| | - Alessia Nava
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of RomeRomeItaly
| | - Christine Neugebauer-Maresch
- Austrian Archaeological Institute, Austrian Academy of SciencesViennaAustria
- Institute of Prehistory and Early History, University of ViennaViennaAustria
| | - Jan Nováček
- Thuringia State Service for Cultural Heritage and Archaeology WeimarThuringiaGermany
- Institute of Anatomy and Cell Biology, University Medical Centre, Georg-August University of GöttingenGöttingenGermany
| | | | | | | | | | - Karol Pieta
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | - Matej Ruttkay
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | - Mirjana Sanader
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | | | - Alessandra Sperduti
- Bioarchaeology Service, Museum of CivilizationsRomeItaly
- Dipartimento Asia, Africa e Mediterraneo, Università degli Studi di Napoli “L’Orientale”NaplesItaly
| | | | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Department of Anthropology, Natural History Museum ViennaViennaAustria
| | - Iwona Teul
- Chair and Department of Normal Anatomy, Faculty of Medicine and Dentistry, Pomeranian Medical UniversitySzczecinPoland
| | - Domagoj Tončinić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Julien Trapp
- Musée de La Cour d'Or, Eurométropole de MetzMetzFrance
| | | | | | - Diethard Walter
- Thuringia State Service for Cultural Heritage and Archaeology WeimarThuringiaGermany
| | - Miloš Živanović
- Department of Archeology, Center for Conservation and Archeology of MontenegroCetinjeMontenegro
| | | | | | - Mario Šlaus
- Anthropological Centre, Croatian Academy of Sciences and ArtsZagrebCroatia
| | - Dušan Borić
- Department of Environmental Biology, Sapienza University of RomeRomeItaly
- Department of Anthropology, New York UniversityNew YorkUnited States
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological ResearchZagrebCroatia
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Department of Environmental Biology, Sapienza University of RomeRomeItaly
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Jonathan K Pritchard
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
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8
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Pogorevc N, Dotsev A, Upadhyay M, Sandoval-Castellanos E, Hannemann E, Simčič M, Antoniou A, Papachristou D, Koutsouli P, Rahmatalla S, Brockmann G, Sölkner J, Burger P, Lymberakis P, Poulakakis N, Bizelis I, Zinovieva N, Horvat S, Medugorac I. Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats. Mol Ecol 2024; 33:e17190. [PMID: 37909668 DOI: 10.1111/mec.17190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Crete, Greece
| | - Dimitris Papachristou
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Siham Rahmatalla
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio, Greece
| | - Iosif Bizelis
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Natalia Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
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9
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Lucquin A, Robson HK, Oras E, Lundy J, Moretti G, González Carretero L, Dekker J, Demirci Ö, Dolbunova E, McLaughlin TR, Piezonka H, Talbot HM, Adamczak K, Czekaj-Zastawny A, Groß D, Gumiński W, Hartz S, Kabaciński J, Koivisto S, Linge TE, Meyer AK, Mökkönen T, Philippsen B, Piličiauskas G, Visocka V, Kriiska A, Raemaekers D, Meadows J, Heron C, Craig OE. The impact of farming on prehistoric culinary practices throughout Northern Europe. Proc Natl Acad Sci U S A 2023; 120:e2310138120. [PMID: 37844237 PMCID: PMC10614617 DOI: 10.1073/pnas.2310138120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.
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Affiliation(s)
- Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
| | - Ester Oras
- Institute of History and Archaeology, Institute of Chemistry, University of Tartu, Tartu50411, Estonia
- Swedish Collegium for Advanced Study, Uppsala752 38, Sweden
| | - Jasmine Lundy
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Joannes Dekker
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
- Section for Geobiology, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
| | - Özge Demirci
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
- Groningen Institute of Archaeology, University of Groningen, Groningen9712, Netherlands
| | - Ekaterina Dolbunova
- The British Museum, LondonWC1B 3DG, United Kingdom
- Department of Archaeology of Eastern Europe and Siberia, State Hermitage Museum, Saint Petersburg190000, Russia
| | | | - Henny Piezonka
- Institute of Prehistoric Archaeology, Department of History and Cultural Studies, Free University, Berlin14195, Germany
| | - Helen M. Talbot
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
| | - Kamil Adamczak
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń87-100, Poland
| | - Agnieszka Czekaj-Zastawny
- Centre for Archaeology of Hills and Uplands, Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków00-927, Poland
| | - Daniel Groß
- Museum Lolland-Falster, Nykøbing F.4800, Denmark
| | - Witold Gumiński
- Faculty of Archaeology, University of Warsaw, Warsaw00-927, Poland
| | - Sönke Hartz
- Stiftung Schleswig-Holsteinische Landesmuseen, Schloss Gottorf, Schleswig24837, Germany
| | - Jacek Kabaciński
- Centre for Archaeology of Hills and Uplands, Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków00-927, Poland
| | - Satu Koivisto
- Department of Archaeology, University of Turku, TurkuFI-20014, Finland
| | - Trond Eilev Linge
- University Museum of Bergen, Section for Cultural Heritage Management, Bergen5007, Norway
| | - Ann-Katrin Meyer
- Institute of Prehistoric and Protohistoric Archaeology, University of Hamburg, Hamburg20146, Germany
| | - Teemu Mökkönen
- Cultural Environment Services, The Finnish Heritage Agency, Helsinki913, Finland
| | - Bente Philippsen
- NTNU University Museum, Norwegian University of Science and Technology, TrondheimNO-7491, Norway
| | | | - Vanda Visocka
- Department of History and Archaeology, Faculty of History and Philosophy, University of Latvia, Rīga1050, Latvia
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu50090, Estonia
| | - Daan Raemaekers
- Groningen Institute of Archaeology, University of Groningen, Groningen9712, Netherlands
| | - John Meadows
- Centre for Baltic and Scandinavian Archaeology, Schleswig24837, Germany
| | - Carl Heron
- The British Museum, LondonWC1B 3DG, United Kingdom
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, YorkYO10 5DD, United Kingdom
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10
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Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1590-1599. [PMID: 37683613 PMCID: PMC10502851 DOI: 10.1016/j.ajhg.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Anuradha Jagadeesan
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Jazmín Ramos-Madrigal
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México
| | - Cesar A Fortes-Lima
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Judy Watson
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Erna Johannesdóttir
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Diana I Cruz-Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Shyam Gopalakrishnan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jonas Niemann
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Helena Bennett
- St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena
| | - Andrew Pearson
- Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK
| | - Agnar Helgason
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - M Thomas P Gilbert
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
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11
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Aoki K, Takahata N, Oota H, Wakano JY, Feldman MW. Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia. Proc Biol Sci 2023; 290:20231262. [PMID: 37644833 PMCID: PMC10465978 DOI: 10.1098/rspb.2023.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.
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Affiliation(s)
- Kenichi Aoki
- Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Naoyuki Takahata
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0116, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Joe Yuichiro Wakano
- School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano, Tokyo 164-8525, Japan
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12
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Moorjani P, Hellenthal G. Methods for Assessing Population Relationships and History Using Genomic Data. Annu Rev Genomics Hum Genet 2023; 24:305-332. [PMID: 37220313 PMCID: PMC11040641 DOI: 10.1146/annurev-genom-111422-025117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.
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Affiliation(s)
- Priya Moorjani
- Department of Molecular and Cell Biology and Center for Computational Biology, University of California, Berkeley, California, USA;
| | - Garrett Hellenthal
- UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom;
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13
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Mattila TM, Svensson EM, Juras A, Günther T, Kashuba N, Ala-Hulkko T, Chyleński M, McKenna J, Pospieszny Ł, Constantinescu M, Rotea M, Palincaș N, Wilk S, Czerniak L, Kruk J, Łapo J, Makarowicz P, Potekhina I, Soficaru A, Szmyt M, Szostek K, Götherström A, Storå J, Netea MG, Nikitin AG, Persson P, Malmström H, Jakobsson M. Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe. Commun Biol 2023; 6:793. [PMID: 37558731 PMCID: PMC10412644 DOI: 10.1038/s42003-023-05131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.
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Affiliation(s)
- Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Natalija Kashuba
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University, 75126, Uppsala, Sweden
| | - Terhi Ala-Hulkko
- Geography Research Unit, University of Oulu, 90014, Oulu, Finland
- Kerttu Saalasti Institute, University of Oulu, 90014, Oulu, Finland
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Mihai Constantinescu
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
- Faculty of History, University of Bucharest, 030167, Bucharest, Romania
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Nona Palincaș
- Vasile Pârvan Institute of Archaeology, Bucharest, Romania
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, 31-007, Kraków, Poland
- Karkonosze Museum, 58-500, Jelenia Góra, Poland
| | - Lech Czerniak
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, 31-016, Kraków, Poland
| | - Jerzy Łapo
- Museum of Folk Culture, 11-600, Węgorzewo, Poland
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210, Kyiv, Ukraine
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, 3008, Bern, Switzerland
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
- Archaeological Museum, 61-781, Poznań, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938, Warszawa, Poland
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University and the Swedish Museum of Natural History, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Alexey G Nikitin
- Grand Valley State University, Department of Biology, Allendale, MI, 49401, USA
| | - Per Persson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Museum of Cultural History, University of Oslo, 0130, Oslo, Norway
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
- SciLifeLab, Uppsala University, 75105, Uppsala, Sweden.
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14
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Chyleński M, Makarowicz P, Juras A, Krzewińska M, Pospieszny Ł, Ehler E, Breszka A, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Lasota-Kuś A, Wójcik I, Romaniszyn J, Szmyt M, Kośko A, Ignaczak M, Sadowski S, Matoga A, Grossman A, Ilchyshyn V, Yahodinska MO, Romańska A, Tunia K, Przybyła M, Grygiel R, Szostek K, Dabert M, Götherström A, Jakobsson M, Malmström H. Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age. Nat Commun 2023; 14:4395. [PMID: 37528090 PMCID: PMC10393988 DOI: 10.1038/s41467-023-40072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.
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Affiliation(s)
- Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology, University of Gdańsk, ul. Bielańska 5, 80-851, Gdańsk, Poland
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, Bristol, BS8 1UU, UK
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Agnieszka Breszka
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kanonicza 9, 31-002, Cracow, Poland
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Zamkowa 9, 20-117, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Irena Wójcik
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
- Archaeological Museum in Poznań, Wodna 27, 61-781, Poznań, Poland
| | - Aleksander Kośko
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marcin Ignaczak
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Sylwester Sadowski
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Andrzej Matoga
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Anna Grossman
- Muzeum Archeologiczne w Biskupinie, Biskupin 17, 88-410, Gąsawa, Poland
| | - Vasyl Ilchyshyn
- Zaliztsi Museum of Local Lore, Schevchenka 51, Zalizhtsi, 47243, Ternopil reg, Ukraine
| | - Maryna O Yahodinska
- Ternopil Regional Center for Protection and Research of Cultural Heritage Sites, Kyyivs'ka 3а, 46016, Ternopil, Ukraine
| | - Adriana Romańska
- Wojewódzki Urząd Ochrony Zabytków, Gołębia 2, 61-840, Poznań, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marcin Przybyła
- Archaeological company "Dolmen Marcin Przybyła, Michał Podsiadło s.c.", Serkowskiego Sq. 8/3, 30-512, Cracow, Poland
| | - Ryszard Grygiel
- Museum of Archaeology and Ethnography in Łódź, Plac Wolności 14, 91-415, Łódź, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-938, Warsaw, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
- SciLifeLab, Stockholm and Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
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15
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Simões LG, Günther T, Martínez-Sánchez RM, Vera-Rodríguez JC, Iriarte E, Rodríguez-Varela R, Bokbot Y, Valdiosera C, Jakobsson M. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature 2023:10.1038/s41586-023-06166-6. [PMID: 37286608 DOI: 10.1038/s41586-023-06166-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.
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Affiliation(s)
- Luciana G Simões
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Juan Carlos Vera-Rodríguez
- Área de Prehistoria, Departamento de Historia, Geografía y Antropología, Centro de Investigación en Patrimonio Histórico, Cultural y Natural, Facultad de Humanidades, Universidad de Huelva, Huelva, Spain
| | - Eneko Iriarte
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Youssef Bokbot
- Institut National des Sciences de l'Archéologie et du Patrimoine, Rabat, Morocco
| | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain.
- Department of History and Archaeology, La Trobe University, Melbourne, Victoria, Australia.
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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16
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Davy T, Ju D, Mathieson I, Skoglund P. Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Curr Biol 2023; 33:1365-1371.e3. [PMID: 36963383 PMCID: PMC10153476 DOI: 10.1016/j.cub.2023.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10-56). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.
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Affiliation(s)
- Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
| | - Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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17
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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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18
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Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe. CELL GENOMICS 2023; 3:100248. [PMID: 36819665 PMCID: PMC9932995 DOI: 10.1016/j.xgen.2022.100248] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/24/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.
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19
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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20
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Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages. PLoS One 2022; 17:e0275744. [PMID: 36223379 PMCID: PMC9555676 DOI: 10.1371/journal.pone.0275744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/22/2022] [Indexed: 11/19/2022] Open
Abstract
Questions on the timing and the center of the Indo-European language dispersal are central to debates on the formation of the European and Asian linguistic landscapes and are deeply intertwined with questions on the archaeology and population history of these continents. Recent palaeogenomic studies support scenarios in which the core Indo-European languages spread with the expansion of Early Bronze Age Yamnaya herders that originally inhabited the East European steppes. Questions on the Yamnaya and Pre-Yamnaya locations of the language community that ultimately gave rise to the Indo-European language family are heavily dependent on linguistic reconstruction of the subsistence of Proto-Indo-European speakers. A central question, therefore, is how important the role of agriculture was among the speakers of this protolanguage. In this study, we perform a qualitative etymological analysis of all previously postulated Proto-Indo-European terminology related to cereal cultivation and cereal processing. On the basis of the evolution of the subsistence strategies of consecutive stages of the protolanguage, we find that one or perhaps two cereal terms can be reconstructed for the basal Indo-European stage, also known as Indo-Anatolian, but that core Indo-European, here also including Tocharian, acquired a more elaborate set of terms. Thus, we linguistically document an important economic shift from a mostly non-agricultural to a mixed agro-pastoral economy between the basal and core Indo-European speech communities. It follows that the early, eastern Yamnaya of the Don-Volga steppe, with its lack of evidence for agricultural practices, does not offer a perfect archaeological proxy for the core Indo-European language community and that this stage of the language family more likely reflects a mixed subsistence as proposed for western Yamnaya groups around or to the west of the Dnieper River.
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21
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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 GENES|GENOMES|GENETICS 2022; 12:6647844. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University , Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV) , Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University , Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester , Leicester LE1 7RH, UK
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22
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Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022; 12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
Principal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
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Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
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23
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Scott CB, Cárdenas A, Mah M, Narasimhan VM, Rohland N, Toth LT, Voolstra CR, Reich D, Matz MV. Millennia-old coral holobiont DNA provides insight into future adaptive trajectories. Mol Ecol 2022; 31:4979-4990. [PMID: 35943423 DOI: 10.1111/mec.16642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
Abstract
Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.
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Affiliation(s)
- Carly B Scott
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA, Austin, TX, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lauren T Toth
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA, Austin, TX, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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24
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Översti S, Palo JU. Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biol Evol 2022; 14:6613373. [PMID: 35731946 PMCID: PMC9250076 DOI: 10.1093/gbe/evac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.
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Affiliation(s)
- Sanni Översti
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany Kahlaische Straße 10, 07745, Jena, Germany.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, Helsinki, Finland P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, Helsinki, Finland P.O. Box 40, FI-00014, Helsinki, Finland.,Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, Helsinki, Finland P.O. Box 30, FI-00271, Helsinki, Finland
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25
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Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 2022; 11:77625. [PMID: 35635751 PMCID: PMC9293011 DOI: 10.7554/elife.77625] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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26
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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27
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Childebayeva A, Rohrlach AB, Barquera R, Rivollat M, Aron F, Szolek A, Kohlbacher O, Nicklisch N, Alt KW, Gronenborn D, Meller H, Friederich S, Prüfer K, Deguilloux MF, Krause J, Haak W. Population Genetics and Signatures of Selection in Early Neolithic European Farmers. Mol Biol Evol 2022; 39:6586604. [PMID: 35578825 PMCID: PMC9171004 DOI: 10.1093/molbev/msac108] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.
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Affiliation(s)
- Ainash Childebayeva
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Adam Benjamin Rohrlach
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Rodrigo Barquera
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Maïté Rivollat
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615 Pessac, France
| | - Franziska Aron
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Detlef Gronenborn
- Römisch-Germanisches Zentralmuseum, Leibniz Research Institute for Archaeology, Ernst-Ludwig-Platz 2, 55116 Mainz, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kay Prüfer
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | | | - Johannes Krause
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Wolfgang Haak
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
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28
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Gelabert P, Schmidt RW, Fernandes DM, Karsten JK, Harper TK, Madden GD, Ledogar SH, Sokhatsky M, Oota H, Kennett DJ, Pinhasi R. Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine. Sci Rep 2022; 12:7242. [PMID: 35508651 PMCID: PMC9068698 DOI: 10.1038/s41598-022-11117-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000–3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935–825 cal BCE). Results reveal that the CTCC individuals’ ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980–825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Ryan W Schmidt
- University of Porto, CIBIO-InBIO, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal. .,School of Archaeology & Earth Institute, University College, Dublin, Belfield, Dublin 4, Ireland.
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jordan K Karsten
- Department of Anthropology, Global Religions, and Cultures, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI, 54901, USA
| | - Thomas K Harper
- Institute for European and Mediterranean Archaeology, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Gwyn D Madden
- Department of Anthropology, Grand Valley State University, 1 Campus Dr., Allendale, MI, 49401, USA
| | - Sarah H Ledogar
- Department of Archaeology, Classics, and History, University of New England, Armidale, NSW, 2351, Australia
| | - Mykhailo Sokhatsky
- Borschiv Regional Museum of Local Lore, Borschiv, Ternopil Oblast, Ukraine
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
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29
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Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience 2022; 25:104244. [PMID: 35494246 PMCID: PMC9051636 DOI: 10.1016/j.isci.2022.104244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 11/23/2022] Open
Abstract
Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition. Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers A near-complete genetic turnover during the Mesolithic-Neolithic transition Exchange of subsistence practices between hunter-gatherers and early farmers
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30
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Mühl DD, de Oliveira L. A bibliometric and thematic approach to agriculture 4.0. Heliyon 2022; 8:e09369. [PMID: 35600429 PMCID: PMC9118498 DOI: 10.1016/j.heliyon.2022.e09369] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/12/2021] [Accepted: 04/29/2022] [Indexed: 12/31/2022] Open
Abstract
Researchers are developing digital solutions for agriculture. Humanity has perfected agriculture throughout history because this activity is fundamental to our existence. The agricultural sector is currently incorporating new technologies from other areas. This phenomenon is agriculture 4.0. However, a challenge to research is the integration of technologies from different knowledge fields, and this has caused theoretical and practical difficulties. Thus, our purpose with this study has been to understand the core agriculture 4.0 research themes. We have used a bibliometric analysis, and guided the data collection by the PRISMA protocol. VosViewer and Bibliometrix software generated the results. We found two main research fronts, one focussed on agriculture 4.0 development, and another on the impacts of agriculture 4.0, which may be positive or negative. We found 21 main keywords or topics researched in agriculture 4.0 related to these research fronts. These themes are within five different axes. We managed to establish a good understanding of the topics around agriculture 4.0. Future studies could focus on the responsible development of digital solutions for agriculture. This is because the social, environmental, and economic impacts of these new solutions may be positive or negative. We conclude that digital agriculture is the node technologies integration for the automation of agricultural activities. There are two main research fronts. Agriculture 4.0 can have both positive and negative impacts. Agricultural development, food supply, and climate change are high centrality and density themes. Crops, remote sensing, and precision agriculture are motor themes. Agriculture, digital agriculture, and agricultural robots are basic themes.
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Affiliation(s)
- Diego Durante Mühl
- Center for Studies and Research in Agribusiness (CEPAN), Federal University of Rio Grande do Sul (UFRGS), Bento Gonçalves Avenue, 7712, Agronomy, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil
- Corresponding author.
| | - Letícia de Oliveira
- Department of Economics and International Relations (DERI), Faculty of Economics, and Interdisciplinary Center for Studies and Research in Agribusiness (CEPAN), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul 90040-060, Brazil
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31
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Török T, Maár K, Varga IG, Juhász Z. A new linear combination method of haplogroup distribution central vectors to model population admixtures. Mol Genet Genomics 2022; 297:889-901. [PMID: 35411488 PMCID: PMC9130205 DOI: 10.1007/s00438-022-01888-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/19/2022] [Indexed: 11/26/2022]
Abstract
We introduce a novel population genetic approach suitable to model the origin and relationships of populations, using new computation methods analyzing Hg frequency distributions. Hgs were selected into groups which show correlated frequencies in subsets of populations, based on the assumption that correlations were established in ancient separation, migration and admixture processes. Populations are defined with this universal Hg database, then using unsupervised artificial intelligence, central vectors (CVs) are determined from local condensations of the Hg-distribution vectors in the multidimensional point system. Populations are clustered according to their proximity to CVs. We show that CVs can be regarded as approximations of ancient populations and real populations can be modeled as weighted linear combinations of the CVs using a new linear combination algorithm based on a gradient search for the weights. The efficacy of the method is demonstrated by comparing Copper Age populations of the Carpathian Basin to Middle Age ones and modern Hungarians. Our analysis reveals significant population continuity since the Middle Ages, and the presence of a substrate component since the Copper Age.
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Affiliation(s)
- Tibor Török
- Department of Genetics, University of Szeged, Szeged, Hungary
- Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary
| | - Kitti Maár
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - István Gergely Varga
- Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Zoltán Juhász
- Institute of Technical Physics and Materials Science, Centre for Energy Research, Budapest, Hungary.
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32
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South-to-north migration preceded the advent of intensive farming in the Maya region. Nat Commun 2022; 13:1530. [PMID: 35318319 PMCID: PMC8940966 DOI: 10.1038/s41467-022-29158-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region. The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.
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Gopalan S, Berl REW, Myrick JW, Garfield ZH, Reynolds AW, Bafens BK, Belbin G, Mastoras M, Williams C, Daya M, Negash AN, Feldman MW, Hewlett BS, Henn BM. Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa. Curr Biol 2022; 32:1852-1860.e5. [PMID: 35271793 PMCID: PMC9050894 DOI: 10.1016/j.cub.2022.02.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/12/2021] [Accepted: 02/16/2022] [Indexed: 12/31/2022]
Abstract
The fate of hunting and gathering populations following the rise of agriculture and pastoralism remains a topic of debate in the study of human prehistory. Studies of ancient and modern genomes have found that autochthonous groups were largely replaced by expanding farmer populations with varying levels of gene flow, a characterization that is influenced by the almost universal focus on the European Neolithic.1-5 We sought to understand the demographic impact of an ongoing cultural transition to farming in Southwest Ethiopia, one of the last regions in Africa to experience such shifts.6 Importantly, Southwest Ethiopia is home to several of the world's remaining hunter-gatherer groups, including the Chabu people, who are currently transitioning away from their traditional mode of subsistence.7 We generated genome-wide data from the Chabu and four neighboring populations, the Majang, Shekkacho, Bench, and Sheko, to characterize their genetic ancestry and estimate their effective population sizes over the last 60 generations. We show that the Chabu are a distinct population closely related to ancient people who occupied Southwest Ethiopia >4,500 years ago. Furthermore, the Chabu are undergoing a severe population bottleneck, which began approximately 1,400 years ago. By analyzing eleven Eastern African populations, we find evidence for divergent demographic trajectories among hunter-gatherer-descendant groups. Our results illustrate that although foragers respond to encroaching agriculture and pastoralism with multiple strategies, including cultural adoption of agropastoralism, gene flow, and economic specialization, they often face population decline.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA; Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Richard E W Berl
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO 80523, USA
| | - Justin W Myrick
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Zachary H Garfield
- Department of Anthropology, Washington State University, Vancouver, WA 98686, USA; Institute for Advanced Study in Toulouse, Université Toulouse, Toulouse 31080, France
| | - Austin W Reynolds
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; Department of Anthropology, Baylor University, Waco, TX 76798, USA
| | - Barnabas K Bafens
- Diaspora and Protocol Affairs Office, Bench Sheko Zone Administration, Mizan, Ethiopia
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mira Mastoras
- UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Cole Williams
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michelle Daya
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Akmel N Negash
- Department of Anthropology, Hawassa University, Hawassa, SNNPR, Ethiopia
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Barry S Hewlett
- Department of Anthropology, Washington State University, Vancouver, WA 98686, USA.
| | - Brenna M Henn
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA.
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Rio J, Quilodrán CS, Currat M. Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations. Commun Biol 2021; 4:1163. [PMID: 34621003 PMCID: PMC8497574 DOI: 10.1038/s42003-021-02670-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.
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Affiliation(s)
- Jérémy Rio
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Claudio S Quilodrán
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
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35
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Göransson M, Sigurdardottir TH, Lillemo M, Bengtsson T, Hallsson JH. The Winter-Type Allele of HvCEN Is Associated With Earliness Without Severe Yield Penalty in Icelandic Spring Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:720238. [PMID: 34630467 PMCID: PMC8500236 DOI: 10.3389/fpls.2021.720238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Icelandic barley genotypes have shown extreme earliness both in flowering and maturity compared to other north European genotypes, whereas earliness is a key trait in adapting barley to northern latitudes. Four genes were partially re-sequenced, which are Ppd-H1, HvCEN, HvELF3, and HvFT1, to better understand the mechanisms underlying this observed earliness. These genes are all known to play a part in the photoperiod response. The objective of this study is to correlate allelic diversity with flowering time and yield data from Icelandic field trials. The resequencing identified two to three alleles at each locus which resulted in 12 haplotype combinations. One haplotype combination containing the winter-type allele of Ppd-H1 correlated with extreme earliness, however, with a severe yield penalty. A winter-type allele in HvCEN in four genotypes correlated with earliness combined with high yield. Our results open the possibility of marker-assisted pyramiding as a rapid way to develop varieties with a shortened time from sowing to flowering under the extreme Icelandic growing conditions and possibly in other arctic or sub-arctic regions.
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Affiliation(s)
- Magnus Göransson
- Faculty of Agriculture, Agricultural University of Iceland, Reykjavík, Iceland
- Department of Plant Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Morten Lillemo
- Department of Plant Science, Norwegian University of Life Sciences, Ås, Norway
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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36
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Kivisild T, Saag L, Hui R, Biagini SA, Pankratov V, D'Atanasio E, Pagani L, Saag L, Rootsi S, Mägi R, Metspalu E, Valk H, Malve M, Irdt K, Reisberg T, Solnik A, Scheib CL, Seidman DN, Williams AL, Tambets K, Metspalu M. Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population. Am J Hum Genet 2021; 108:1792-1806. [PMID: 34411538 DOI: 10.1016/j.ajhg.2021.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8th-10th centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.
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Affiliation(s)
- Toomas Kivisild
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK.
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Research Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Vasili Pankratov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eugenia D'Atanasio
- Instituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Heiki Valk
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Martin Malve
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Kadri Irdt
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Tuuli Reisberg
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; St John's College, University of Cambridge, Cambridge CB2 1TP, UK
| | - Daniel N Seidman
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Amy L Williams
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Keolu Fox
- Department of Anthropology, University of California San Diego, La Jolla, CA, USA
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abdul Salam M Sofro
- Department of Biochemistry, Faculty of Medicine, Yayasan Rumah Sakit Islam (YARSI) University, Cempaka Putih, Jakarta, Indonesia
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Translational Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
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38
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Serrano JG, Ordóñez AC, Fregel R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. Ann Hum Biol 2021; 48:179-190. [PMID: 34459342 DOI: 10.1080/03014460.2021.1942205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.
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Affiliation(s)
- Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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40
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Aneli S, Caldon M, Saupe T, Montinaro F, Pagani L. Through 40,000 years of human presence in Southern Europe: the Italian case study. Hum Genet 2021; 140:1417-1431. [PMID: 34410492 PMCID: PMC8460580 DOI: 10.1007/s00439-021-02328-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022]
Abstract
The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Matteo Caldon
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Via Edoardo Orabona 4, 70125, Bari, Italy
| | - Luca Pagani
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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41
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Schwörer C, Gobet E, van Leeuwen JFN, Bögli S, Imboden R, van der Knaap WO, Kotova N, Makhortykh S, Tinner W. Holocene vegetation, fire and land use dynamics at Lake Svityaz, an agriculturally marginal site in northwestern Ukraine. VEGETATION HISTORY AND ARCHAEOBOTANY 2021; 31:155-170. [PMID: 35273429 PMCID: PMC8897337 DOI: 10.1007/s00334-021-00844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/22/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Observing natural vegetation dynamics over the entire Holocene is difficult in Central Europe, due to pervasive and increasing human disturbance since the Neolithic. One strategy to minimize this limitation is to select a study site in an area that is marginal for agricultural activity. Here, we present a new sediment record from Lake Svityaz in northwestern Ukraine. We have reconstructed regional and local vegetation and fire dynamics since the Late Glacial using pollen, spores, macrofossils and charcoal. Boreal forest composed of Pinus sylvestris and Betula with continental Larix decidua and Pinus cembra established in the region around 13,450 cal bp, replacing an open, steppic landscape. The first temperate tree to expand was Ulmus at 11,800 cal bp, followed by Quercus, Fraxinus excelsior, Tilia and Corylus ca. 1,000 years later. Fire activity was highest during the Early Holocene, when summer solar insolation reached its maximum. Carpinus betulus and Fagus sylvatica established at ca. 6,000 cal bp, coinciding with the first indicators of agricultural activity in the region and a transient climatic shift to cooler and moister conditions. Human impact on the vegetation remained initially very low, only increasing during the Bronze Age, at ca. 3,400 cal bp. Large-scale forest openings and the establishment of the present-day cultural landscape occurred only during the past 500 years. The persistence of highly diverse mixed forest under absent or low anthropogenic disturbance until the Early Middle Ages corroborates the role of human impact in the impoverishment of temperate forests elsewhere in Central Europe. The preservation or reestablishment of such diverse forests may mitigate future climate change impacts, specifically by lowering fire risk under warmer and drier conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00334-021-00844-z.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Hochschulstraße 4, 3012 Bern, Switzerland
| | - Erika Gobet
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Hochschulstraße 4, 3012 Bern, Switzerland
| | | | - Sarah Bögli
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Rachel Imboden
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - W. O. van der Knaap
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Nadezhda Kotova
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Geroiv Stalingrada prospekt, Kyiv, 04210 Ukraine
| | - Sergej Makhortykh
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Geroiv Stalingrada prospekt, Kyiv, 04210 Ukraine
| | - Willy Tinner
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Hochschulstraße 4, 3012 Bern, Switzerland
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42
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Kristjansson D, Bohlin J, Jugessur A, Schurr TG. Matrilineal diversity and population history of Norwegians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:120-133. [PMID: 34110627 DOI: 10.1002/ajpa.24345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND While well known for its Viking past, Norway's population history and the influences that have shaped its genetic diversity are less well understood. This is particularly true with respect to its demography, migration patterns, and dialectal regions, despite there being curated historical records for the past several centuries. In this study, we undertook an analysis of mitochondrial DNA (mtDNA) diversity within the country to elaborate this history from a matrilineal genetic perspective. METHODS We aggregated 1174 partial modern Norwegian mtDNA sequences from the published literature and subjected them to detailed statistical and phylogenetic analysis by dialectal regions and localities. We further contextualized the matrilineal ancestry of modern Norwegians with data from Mesolithic, Iron Age, and historic period populations. RESULTS Modern Norwegian mtDNAs fell into eight West Eurasian (N, HV, JT, I, U, K, X, W), five East Eurasian (A, F, G, N11, Z), and one African (L2) haplogroups. Pairwise analysis of molecular variance (AMOVA) estimates for all Norwegians indicated they were differentiated from each other at 1.68% (p < 0.001). Norwegians within the same dialectal region also showed genetic similarities to each other, although differences between subpopulations within dialectal regions were also observed. In addition, certain mtDNA lineages in modern Norwegians were also found among prehistoric and historic period populations, suggesting some level of genetic continuity over hundreds to many thousands of years. CONCLUSIONS This analysis of mtDNA diversity provides a detailed picture of the genetic variation within Norway in light of its topography, settlement history, and historical migrations over the past several centuries.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Infection Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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43
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Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
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Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
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Yair S, Lee KM, Coop G. The timing of human adaptation from Neanderthal introgression. Genetics 2021; 218:iyab052. [PMID: 33787889 PMCID: PMC8128397 DOI: 10.1093/genetics/iyab052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/26/2021] [Indexed: 12/26/2022] Open
Abstract
Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.
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Affiliation(s)
- Sivan Yair
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Kristin M Lee
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Graham Coop
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
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45
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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46
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Yaka R, Mapelli I, Kaptan D, Doğu A, Chyleński M, Erdal ÖD, Koptekin D, Vural KB, Bayliss A, Mazzucato C, Fer E, Çokoğlu SS, Lagerholm VK, Krzewińska M, Karamurat C, Gemici HC, Sevkar A, Dağtaş ND, Kılınç GM, Adams D, Munters AR, Sağlıcan E, Milella M, Schotsmans EMJ, Yurtman E, Çetin M, Yorulmaz S, Altınışık NE, Ghalichi A, Juras A, Bilgin CC, Günther T, Storå J, Jakobsson M, de Kleijn M, Mustafaoğlu G, Fairbairn A, Pearson J, Togan İ, Kayacan N, Marciniak A, Larsen CS, Hodder I, Atakuman Ç, Pilloud M, Sürer E, Gerritsen F, Özbal R, Baird D, Erdal YS, Duru G, Özbaşaran M, Haddow SD, Knüsel CJ, Götherström A, Özer F, Somel M. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. Curr Biol 2021; 31:2455-2468.e18. [PMID: 33857427 PMCID: PMC8210650 DOI: 10.1016/j.cub.2021.03.050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022]
Abstract
The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3, 4, 5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development. Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia Close relatives are common among co-burials in Aşıklı and Boncuklu Many unrelated infants found buried in the same building in Çatalhöyük and Barcın Neolithic societies in Southwest Asia may have held diverse concepts of kinship
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Affiliation(s)
- Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Ayça Doğu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Ömür Dilek Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University (METU), Historic England, London, UK
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Alex Bayliss
- Scientific Dating, Historic England, London, UK; Biological & Environmental Sciences, University of Stirling, Stirling, UK
| | - Camilla Mazzucato
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Evrim Fer
- Department of Genetics, University of Arizona, 85719, Tucson, AZ, USA
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden; Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Hasan Can Gemici
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Nihan Dilşad Dağtaş
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Donovan Adams
- Department of Anthropology, University of Central Florida, Uppsala University, 751 05 Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden; SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marco Milella
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, CH-3007 Bern, Switzerland
| | - Eline M J Schotsmans
- Centre for Archaeological Science, University of Wollongong, Wollongong, Australia; UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Erinç Yurtman
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Ayshin Ghalichi
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745, Jena, Germany
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Maurice de Kleijn
- Spatial Information Laboratory (SPINlab) at the Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Gökhan Mustafaoğlu
- Department of Archaeology, Faculty of Letters, Ankara Hacı Bayram Veli University, Abant 1 Cad. No:10/2D, Yenimahalle, Ankara
| | - Andrew Fairbairn
- School of Social Science, The University of Queensland, Michie Building, St Lucia, Brisbane, QLD, Australia
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Nurcan Kayacan
- Department of Prehistory, Faculty of Letters, Istanbul University, Ordu Cad. No: 6, 34459, Laleli, Istanbul
| | | | | | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Çiğdem Atakuman
- Institute of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marin Pilloud
- Department of Anthropology, University of Nevada, Reno
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | | | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450 Istanbul, Turkey
| | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - Yılmaz Selim Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Güneş Duru
- Mimar Sinan Fine Arts University, Istanbul 34134, Turkey
| | | | - Scott D Haddow
- Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - Christopher J Knüsel
- UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden.
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey.
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
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Abstract
The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection—postdating the split from Native Americans—in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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48
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Million-year-old DNA sheds light on the genomic history of mammoths. Nature 2021; 591:265-269. [PMID: 33597750 PMCID: PMC7116897 DOI: 10.1038/s41586-021-03224-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022]
Abstract
Temporal genomic data hold great potential for studying evolutionary processes, including speciation. However, sampling across speciation events would in many cases require genomic time series that stretch well into the Early Pleistocene (>1 million years). Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far is from a 560-780 ka old horse specimen2. Here we report the recovery of genome-wide data from three Early and Middle Pleistocene mammoth specimens, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these gave rise to the woolly mammoth, whereas the other represents a previously unrecognised lineage that was ancestral to the first mammoths to colonise North America. Our analyses reveal that the North American Columbian mammoth traces its ancestry to a Middle Pleistocene hybridisation between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were present already a million years ago. These findings highlight the potential of deep time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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49
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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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50
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Schahbasi A, Huber S, Fieder M. Factors affecting attitudes toward migrants-An evolutionary approach. Am J Hum Biol 2021; 33:e23435. [PMID: 32458587 PMCID: PMC7900986 DOI: 10.1002/ajhb.23435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/14/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE To understand migration from an evolutionary perspective, this phenomenon has so far been mainly investigated in animal species. We therefore aim to investigate the potential evolutionary roots of attitudes toward migrants in humans. METHODS We used data from the European Social Survey (n = 83 734), analyzing attitudes toward migrants by performing ordinal mixed models. RESULTS We found that men have a more restrictive attitude toward migration than women, which increases with age and is stronger with a child in the household. Attitude toward migrants is also more skeptical if migrants have a different ethnicity and are from poorer countries. Increasing education and religiousness are associated with a more positive attitude toward migrants, particularly toward migrants of different ethnicity and from poorer countries. DISCUSSION Although migration flows are a hallmark of the human species, previous findings suggest that (pre-)historic migration flows were at times accompanied by conflict and violence, while at the same time, they insured survival by allowing cultural exchange and the avoidance of inbreeding. Accordingly, we assume that contemporary attitudes toward migration are rooted in our evolutionary past. We discuss the respective behavioral patterns from an evolutionary perspective, arguing that both-a negative attitude as well as openness-make sense.
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Affiliation(s)
- Alexander Schahbasi
- Department of Evolutionary AnthropologyUniversity of ViennaViennaAustria
- Erlangen Centre for Islam & Law in EuropeFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Susanne Huber
- Department of Evolutionary AnthropologyUniversity of ViennaViennaAustria
| | - Martin Fieder
- Department of Evolutionary AnthropologyUniversity of ViennaViennaAustria
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