1
|
Meiri M, Bar-Oz G. Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. Trends Genet 2024; 40:398-409. [PMID: 38423916 PMCID: PMC11079635 DOI: 10.1016/j.tig.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.
Collapse
Affiliation(s)
- Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Haifa, 3498837 Mount Carmel, Israel
| |
Collapse
|
2
|
Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
Collapse
Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| |
Collapse
|
3
|
Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
Collapse
Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
| |
Collapse
|
4
|
Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? Am J Biol Anthropol 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
Collapse
Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
5
|
Shaw B, Foggin S, Hamilton-Stanley P, Barlow A, Pickard C, Fibiger L, Oldham N, Tighe P, Kootker LM, Schrader S, Layfield R. Antibody-based sex determination of human skeletal remains. iScience 2023; 26:108191. [PMID: 37953951 PMCID: PMC10632104 DOI: 10.1016/j.isci.2023.108191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023] Open
Abstract
Assignment of biological sex to skeletal remains is critical in the accurate reconstruction of the past. Analysis of sex-chromosome encoded AMELX and AMELY peptides from the enamel protein amelogenin underpins a minimally destructive mass spectrometry (MS) method for sex determination of human remains. However, access to such specialist approaches limits applicability. As a convenient alternative, we generated antibodies that distinguish human AMELX and AMELY. Purified antibodies demonstrated high selectivity and quantitative detection against synthetic peptides by ELISA. Using acid etches of enamel from post-medieval skeletons, antibody determinations corrected osteological uncertainties and matched parallel MS, and for Bronze Age samples where only enamel was preserved, also matched MS analyses. Toward improved throughput, automated stations were applied to analyze 19th-century teeth where sex of individuals was documented, confirming MS can be bypassed. Our immunological tools should underpin development of routine, economical, high-throughput methods for sex determination, potentially even in a field setting.
Collapse
Affiliation(s)
- Barry Shaw
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Sophie Foggin
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Andy Barlow
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK
| | - Catriona Pickard
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK
| | - Linda Fibiger
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK
| | - Neil Oldham
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Patrick Tighe
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Lisette M. Kootker
- Department of Earth Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sarah Schrader
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Rob Layfield
- School of Life Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
6
|
Bacon AM, Bourgon N, Dufour E, Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Ponche JL, Morley MW, Suzzoni E, Frangeul S, Boesch Q, Antoine PO, Boualaphane S, Sichanthongtip P, Sihanam D, Huong NTM, Tuan NA, Fiorillo D, Tombret O, Patole-Edoumba E, Zachwieja A, Luangkhoth T, Souksavatdy V, Dunn TE, Shackelford L, Hublin JJ. Palaeoenvironments and hominin evolutionary dynamics in southeast Asia. Sci Rep 2023; 13:16165. [PMID: 37758744 PMCID: PMC10533506 DOI: 10.1038/s41598-023-43011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164-131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46-43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
Collapse
Affiliation(s)
- Anne-Marie Bacon
- Université Paris Cité, CNRS, BABEL UMR 8045, 75012, Paris, France.
| | - Nicolas Bourgon
- IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
| | - Elise Dufour
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), MNHN, CNRS, Université Paris Cité, Musée de l'Homme, 75016, Paris, France
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France
| | - Kira E Westaway
- 'Traps' Luminescence Dating Facility, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Philippe Duringer
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- Laboratoire Image, Ville Environnement, UMR 7362 UdS CNRS, Université de Strasbourg, Strasbourg, France
| | - Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Sturt Road, Bedford Park, Adelaide, SA, 5042, Australia
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Quentin Boesch
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | | | - Daovee Sihanam
- Ministry of Information, Culture and Tourism, Vientiane, Lao PDR
| | | | | | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Elise Patole-Edoumba
- Muséum d'histoire naturelle de La Rochelle, UMRU 24140 Dynamiques, interactions, interculturalité asiatiques (UBM, LRUniv), La Rochelle, France
| | - Alexandra Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, USA
| | | | | | - Tyler E Dunn
- Anatomical Sciences Education Center, Oregon Health & Sciences University, Portland, OR, USA
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| |
Collapse
|
7
|
Wu X, Pei S, Cai Y, Tong H, Zhang Z, Yan Y, Xing S, Martinón-Torres M, Bermúdez de Castro JM, Liu W. Morphological and morphometric analyses of a late Middle Pleistocene hominin mandible from Hualongdong, China. J Hum Evol 2023; 182:103411. [PMID: 37531709 DOI: 10.1016/j.jhevol.2023.103411] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 08/04/2023]
Abstract
Excavations in Hualongdong (HLD), East China, have yielded abundant hominin fossils dated to 300 ka. There is a nearly complete mandible that fits well with a partial cranium, and together they compose the skull labeled as HLD 6. Thus far, detailed morphological description and comparisons of the mandible have not been conducted. Here we present a comprehensive morphological, metric, and geometric morphometric assessment of this mandible and compare it with both adult and immature specimens of Pleistocene hominins and recent modern humans. Results indicate that the HLD 6 mandible exhibits a mosaic morphological pattern characterized by a robust corpus and relatively gracile symphysis and ramus. The moderately developed mental trigone and a clear anterior mandibular incurvation of the HLD 6 mandible are reminiscent of Late Pleistocene hominin and recent modern human morphology. However, the weak expression of all these features indicates that this mandible does not possess a true chin. Moreover, a suite of archaic features that resemble those of Middle Pleistocene hominins includes pronounced alveolar planum, superior transverse torus, thick corpus, a pronounced endocondyloid crest, and a well-developed medial pterygoid tubercle. The geometric morphometric analysis further confirms the mosaic pattern of the HLD 6 mandible. The combination of both archaic and modern human features identified in the HLD 6 mandible is unexpected, given its late Middle Pleistocene age and differs from approximately contemporaneous Homo members such as Xujiayao, Penghu, and Xiahe. This mosaic pattern has never been recorded in late Middle Pleistocene hominin fossil assemblages in East Asia. The HLD 6 mandible provides further support for the high morphological diversity during late Middle Pleistocene hominin evolution. With these findings, it is possible that modern human morphologies are present as early as 300 ka and earlier than the emergence of modern humans in East Asia.
Collapse
Affiliation(s)
- Xiujie Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shuwen Pei
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Yanjun Cai
- Institute of Global Environmental Change, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Haowen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Ziliang Zhang
- Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Yi Yan
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Song Xing
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - María Martinón-Torres
- National Research Center on Human Evolution (CENIEH), Paseo Sierra de Atapuerca S/n, Burgos, 09002, Spain.
| | | | - Wu Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.
| |
Collapse
|
8
|
Bonfigli A, Cesare P, Volpe AR, Colafarina S, Forgione A, Aloisi M, Zarivi O, Poma AMG. Estimation of DNA Degradation in Archaeological Human Remains. Genes (Basel) 2023; 14:1238. [PMID: 37372418 DOI: 10.3390/genes14061238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.
Collapse
Affiliation(s)
- Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Rita Volpe
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alfonso Forgione
- Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy
| | - Massimo Aloisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | | |
Collapse
|
9
|
Zhang G, Xing S, Martinón-Torres M, Bermúdez de Castro JM, Wang S. A Late Middle Pleistocene human tooth from the Luonan Basin (Shaanxi, China). J Hum Evol 2023; 178:103343. [PMID: 36917893 DOI: 10.1016/j.jhevol.2023.103343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 03/13/2023]
|
10
|
Pop E, Hilgen S, Adhityatama S, Berghuis H, Veldkamp T, Vonhof H, Sutisna I, Alink G, Noerwidi S, Roebroeks W, Joordens J. Reconstructing the provenance of the hominin fossils from Trinil (Java, Indonesia) through an integrated analysis of the historical and recent excavations. J Hum Evol 2023; 176:103312. [PMID: 36745959 DOI: 10.1016/j.jhevol.2022.103312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 12/17/2022] [Accepted: 12/17/2022] [Indexed: 02/06/2023]
Abstract
In the early 1890s at Trinil, Eugène Dubois found a hominin skullcap (Trinil 2) and femur (Trinil 3, Femur I), situated at the same level ca. 10-15 m apart. He interpreted them as representing one species, Pithecanthropus erectus (now Homo erectus) which he inferred to be a transitional form between apes and humans. Ever since, this interpretation has been questioned-as the skullcap looked archaic and the femur surprisingly modern. From the 1950s onward, chemical and morphological analyses rekindled the debate. Concurrently, (bio)stratigraphic arguments gained importance, raising the stakes by extrapolating the consequences of potential mixing of hominin remains to the homogeneity of the complete Trinil fossil assemblage. However, conclusive evidence on the provenance and age of the hominin fossils remains absent. New Trinil fieldwork yielded unmanned aerial vehicle imagery, digital elevation models, and stratigraphic observations that have been integrated here with an analysis of the historical excavation documentation. Using a geographic information system and sightline analysis, the position of the historical excavation pits and the hominin fossils therein were reconstructed, and the historical stratigraphy was connected to that of new sections and test pits. This study documents five strata situated at low water level at the excavation site. Cutting into a lahar breccia are two similarly oriented, but asynchronous pre-terrace fluvial channels whose highly fossiliferous infills are identified as the primary targets of the historical excavations (Bone-Bearing Channel 1, 830-773 ka; Bone-Bearing Channel 2, 560-380 ka), providing evidence for a mixed faunal assemblage and yielding most of the hominin fossils. These channels were incised by younger terrace-related fluvial channels (terminal Middle or Late Pleistocene) that directly intersect the historical excavations and the reconstructed discovery location of Femur I, thereby providing an explanation for the relatively modern morphology of this 'bone of contention'. The paleoanthropological implications are discussed in light of the current framework of human evolution in Southeast Asia.
Collapse
Affiliation(s)
- Eduard Pop
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands.
| | - Sander Hilgen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Science, Vrije Universiteit, de Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Shinatria Adhityatama
- Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast Campus, 58 Parklands Drive, Southport, Qld, 4222, Australia
| | - Harold Berghuis
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Tom Veldkamp
- Faculty ITC, University of Twente, P.O. Box 217, 7500 AE, Enschede, the Netherlands
| | - Hubert Vonhof
- Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - Indra Sutisna
- Geological Museum, Jl. Diponegoro 57, Bandung, Jawa Barat, 40122, Bandung, Indonesia
| | - Gerrit Alink
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Sofwan Noerwidi
- Pusat Riset Arkeometri, Organisasi Riset Arkeologi, Bahasa, dan Sastra, Badan Riset dan Inovasi Nasional (OR ARBASTRA - BRIN), Jl. Condet Pejaten 4, Ps. Minggu, Jakarta Selatan, DKI Jakarta, 12510, Indonesia
| | - Wil Roebroeks
- Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands
| | - Josephine Joordens
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Archaeology, Leiden University, P.O. Box 9514, 2300 RA, Leiden, the Netherlands; Faculty of Science, Vrije Universiteit, de Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands; Faculty of Science and Engineering, Maastricht University, Paul-Henri Spaaklaan 1, 6229 EN, Maastricht, the Netherlands
| |
Collapse
|
11
|
Grealy A, Miller GH, Phillips MJ, Clarke SJ, Fogel M, Patalwala D, Rigby P, Hubbard A, Demarchi B, Collins M, Mackie M, Sakalauskaite J, Stiller J, Clarke JA, Legendre LJ, Douglass K, Hansford J, Haile J, Bunce M. Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird. Nat Commun 2023; 14:914. [PMID: 36854679 DOI: 10.1038/s41467-023-36405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
The systematics of Madagascar's extinct elephant birds remains controversial due to large gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, a molecular analysis of 1000-year-old fossil eggshells provides the first description of elephant bird phylogeography and offers insight into the ecology and evolution of these flightless giants. Mitochondrial genomes from across Madagascar reveal genetic variation that is correlated with eggshell morphology, stable isotope composition, and geographic distribution. The elephant bird crown is dated to ca. 30 Mya, when Madagascar is estimated to have become less arid as it moved northward. High levels of between-clade genetic variation support reclassifying Mullerornis into a separate family. Low levels of within-clade genetic variation suggest there were only two elephant bird genera existing in southern Madagascar during the Holocene. However, we find an eggshell collection from Madagascar's far north that represents a unique lineage of Aepyornis. Furthermore, divergence within Aepyornis coincides with the aridification of Madagascar during the early Pleistocene ca. 1.5 Ma, and is consistent with the fragmentation of populations in the highlands driving diversification and the evolution of extreme gigantism over shorts timescales. We advocate for a revision of their taxonomy that integrates palaeogenomic and palaeoecological perspectives.
Collapse
|
12
|
Heyer E. [The Nobel Prize in Physiology or Medicine 2021: Svante Pääbo, the precursor of palaeogenomics]. Med Sci (Paris) 2023; 39:181-183. [PMID: 36799756 DOI: 10.1051/medsci/2023009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Svante Pääbo s’est vu attribuer le prix Nobel de physiologie ou médecine en 2022 pour ses travaux en paléogénétique. Né le 20 avril 1955 à Stockholm, Svante Pääbo a soutenu sa thèse de doctorat en 1986 à l’université d’Uppsala en Suède. Après plusieurs séjours post-doctoraux en Suisse (Institute for Molecular Biology, University of Zürich), puis aux États-Unis (Department of Biochemistry, University of California at Berkeley), il a été nommé professeur de biologie à l’université de Munich en Allemagne. En 1997, il fonde un centre de recherche en paléogénétique au sein de l’Institut Max Planck d’anthropologie évolutionniste à Leipzig en Allemagne. Là, grâce à des soutiens financiers importants, il développe un tout nouveau champ disciplinaire : la paléogénomique humaine, une nouvelle science qui consiste en l’extraction, la lecture et l’analyse de l’ADN dans des restes de fossiles humains afin d’en déterminer l’histoire.
Collapse
Affiliation(s)
- Evelyne Heyer
- UMR 7206 Éco-anthropologie, Muséum national d'histoire naturelle, CNRS, Université Paris Cité, France - Musée de l'Homme, 17 place du Trocadéro et du 11 Novembre, 75116 Paris, France
| |
Collapse
|
13
|
Montag A. [The history of skin color is the history of mankind!]. Dermatologie (Heidelb) 2023; 74:75-79. [PMID: 36593352 DOI: 10.1007/s00105-022-05101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.
Collapse
Affiliation(s)
- Andreas Montag
- Praxis für Haut und Geschlechtskrankheiten, Allergologie, Phlebologie, Reisemedizin, Schweriner Str. 17, 22143, Hamburg, Deutschland.
| |
Collapse
|
14
|
Sharko FS, Zhur KV, Trifonov VA, Prokhortchouk EB. Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries. Acta Naturae 2023; 15:87-96. [PMID: 37153511 PMCID: PMC10154772 DOI: 10.32607/actanaturae.11898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/03/2023] [Indexed: 05/09/2023] Open
Abstract
Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.
Collapse
Affiliation(s)
- F. S. Sharko
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russian Federation
| | - K. V. Zhur
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russian Federation
| | - V. A. Trifonov
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russian Federation
- Institute for the History of Material Culture of the Russian Academy of Sciences, Saint Petersburg, 191186 Russian Federation
| | - E. B. Prokhortchouk
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russian Federation
| |
Collapse
|
15
|
Straiton J. Ancient DNA sequencing: telling the tale of human history and evolution. Biotechniques 2023; 74:5-7. [PMID: 36625391 DOI: 10.2144/btn-2022-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].
Collapse
|
16
|
Höglund P, Ljunggren H, Jonsson R. Nobel 2022: An extraordinary achievement relevant to immunity. Scand J Immunol 2022. [DOI: 10.1111/sji.13234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Petter Höglund
- Center for Hematology and Regenerative Medicine (HERM), Department of Medicine Huddinge Karolinska Institutet Stockholm Sweden
| | - Hans‐Gustaf Ljunggren
- Center for Infectious Medicine (CIM), Department of Medicine Huddinge Karolinska Institutet Stockholm Sweden
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, Faculty of Medicine University of Bergen Bergen Norway
| |
Collapse
|
17
|
Abstract
The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.
Collapse
Affiliation(s)
- Katerina Harvati
- Paleoanthropology, Institute for Archaeological Sciences and Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Rümelinstrasse 19-23, Tübingen 72070, Germany; DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Rümelinstrasse 19-23, Tübingen 72070, Germany.
| | - Hugo Reyes-Centeno
- Department of Anthropology, University of Kentucky, 211 Lafferty Hall, Lexington, KY 40506, USA; William S. Webb Museum of Anthropology, University of Kentucky, 1020 Export St, Lexington, KY 40504, USA
| |
Collapse
|
18
|
Ma Y, Xiang F. Discovery of genomes of Neanderthal, Denisova and its impact on modern human. Chin Sci Bull 2022. [DOI: 10.1360/tb-2022-1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
19
|
Callaway E. From Neanderthal genome to Nobel prize: meet geneticist Svante Pääbo. Nature 2022:10.1038/d41586-022-03191-9. [PMID: 36207518 DOI: 10.1038/d41586-022-03191-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
20
|
Callaway E, Ledford H. Geneticist who unmasked lives of ancient humans wins medicine Nobel. Nature 2022; 610:16-7. [PMID: 36192444 DOI: 10.1038/d41586-022-03086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
21
|
Skov L, Peyrégne S, Popli D, Iasi LNM, Devièse T, Slon V, Zavala EI, Hajdinjak M, Sümer AP, Grote S, Bossoms Mesa A, López Herráez D, Nickel B, Nagel S, Richter J, Essel E, Gansauge M, Schmidt A, Korlević P, Comeskey D, Derevianko AP, Kharevich A, Markin SV, Talamo S, Douka K, Krajcarz MT, Roberts RG, Higham T, Viola B, Krivoshapkin AI, Kolobova KA, Kelso J, Meyer M, Pääbo S, Peter BM. Genetic insights into the social organization of Neanderthals. Nature 2022; 610:519-525. [PMID: 36261548 PMCID: PMC9581778 DOI: 10.1038/s41586-022-05283-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022]
Abstract
Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1-8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.
Collapse
Affiliation(s)
- Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Divyaratan Popli
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Leonardo N M Iasi
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thibaut Devièse
- European Centre for Research and Education in Environmental Geosciences (CEREGE), Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Aix-en-Provence, France
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology Sackler, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- The Francis Crick Institute, London, UK
| | - Arev P Sümer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alba Bossoms Mesa
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Wellcome Sanger Institute, Hinxton, UK
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Aliona Kharevich
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V Markin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warsaw, Poland
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| |
Collapse
|
22
|
Andreeva TV, Manakhov AD, Gusev FE, Patrikeev AD, Golovanova LV, Doronichev VB, Shirobokov IG, Rogaev EI. Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations. Sci Rep 2022; 12:13016. [PMID: 35906446 PMCID: PMC9338269 DOI: 10.1038/s41598-022-16164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
Collapse
Affiliation(s)
- Tatiana V Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192.
| | - Andrey D Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Fedor E Gusev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Anton D Patrikeev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333
| | | | | | - Ivan G Shirobokov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg, Russia, 199034
| | - Evgeny I Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01604, USA.
| |
Collapse
|
23
|
Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Morley MW, Welker F, Rüther PL, Skinner MM, McColl H, Gaunitz C, Vinner L, Dunn TE, Olsen JV, Sikora M, Ponche JL, Suzzoni E, Frangeul S, Boesch Q, Antoine PO, Pan L, Xing S, Zhao JX, Bailey RM, Boualaphane S, Sichanthongtip P, Sihanam D, Patole-Edoumba E, Aubaile F, Crozier F, Bourgon N, Zachwieja A, Luangkhoth T, Souksavatdy V, Sayavongkhamdy T, Cappellini E, Bacon AM, Hublin JJ, Willerslev E, Shackelford L. A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos. Nat Commun 2022; 13:2557. [PMID: 35581187 DOI: 10.1038/s41467-022-29923-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan. Evidence for the presence of Homo during the Middle Pleistocene is limited in continental Southeast Asia. Here, the authors report a hominin molar from Tam Ngu Hao 2 (Cobra Cave), dated to 164–131 kyr. They use morphological and paleoproteomic analysis to show that it likely belonged to a female Denisovan.
Collapse
|
24
|
Kreier F. Ancient tooth suggests Denisovans ventured far beyond Siberia. Nature 2022; 605:602-603. [PMID: 35581413 DOI: 10.1038/d41586-022-01372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
25
|
Fujii K, Mita Y, Watahiki H, Fukagawa T, Kitayama T, Mizuno N, Nakahara H, Sekiguchi K. Poly_NumtS_430 or HSA_NumtS_587 observed in massively parallel sequencing of the mitochondrial HV1 and HV2 regions. Forensic Sci Int Genet 2022; 59:102717. [DOI: 10.1016/j.fsigen.2022.102717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/12/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022]
|
26
|
Sokol EV, Kozlikin MB, Kokh SN, Nekipelova AV, Kulik NA, Danilovsky VA, Khvorov PV, Shunkov MV. Phosphate Record in Pleistocene-Holocene Sediments from Denisova Cave: Formation Mechanisms and Archaeological Implications. Minerals 2022; 12:553. [DOI: 10.3390/min12050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The distribution of authigenic phosphates in the sedimentary sequence of prehistoric Denisova Cave (Altai, South Siberia) has important archeological implications. The sampled Late Pleistocene–Early Holocene sedimentary sequence in the East Chamber of the cave consists of argilo-sandy-phosphatic sediments intercalated with guano layers of insectivorous bats. The sediments bear partially degraded N-rich organic matter (OM); chitin fragments enriched in S, P, Zn, and Cu; and a set of phosphates. The guano layers record at least three prolonged episodes of cave occupation by colonies of insectivorous bats between 10 kyr and 5 kyr BP, after people had left the cave or visited it rarely in small groups. The formation of phosphates follows the OM biodegradation pathways, with acidic leaching and gradual neutralization of P-rich solutions. The depth profile of authigenic phosphates shows a suite of mineral assemblages that mark a trend from acidic to slightly alkaline pH conditions of guano degradation (from top to bottom): ardealite, taranakite, and leucophosphite corresponding to acidic environments; whitlockite, brushite, and hydroxylapatite, which are stable under slightly acidic and neutral conditions; and hydroxylapatite in coexistence with calcite and stable at the bottom of the leaching profile under alkaline conditions. Authigenic phosphates can be used as reliable indicators of human non-occupation (abandonment) periods of Denisova Cave. Acidic leaching is responsible for disturbance and/or elimination of archaeological and paleontological materials in Late Pleistocene–Early Holocene sediments that were exposed to at least three “acidic waves”.
Collapse
|
27
|
Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| |
Collapse
|
28
|
Büster L. From Human Remains to Powerful Objects: Ancestor Research from a Deep-Time Perspective. Genealogy 2022; 6:23. [DOI: 10.3390/genealogy6010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Family history research has seen a surge in popularity in recent years; however, is this preoccupation with who we are and where we come from new? Archaeological evidence suggests that ancestors played crucial and ubiquitous roles in the identities and cosmologies of past societies. This paper will explore how, in the absence of genealogical websites and DNA testing, kinship structures and understandings of personhood beyond genealogy may have influenced concepts of ancestry. Case studies from later prehistoric Britain will demonstrate the ways in which monuments, objects and human remains themselves created bonds between the living and the dead, prompting us to reflect on genealogy as just one aspect of our identity in the present.
Collapse
|
29
|
Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, Stoessel A, Jope-Street B, Meyer M, Kelso J, Pääbo S, Higham T, Douka K. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 2022; 6:28-35. [PMID: 34824388 PMCID: PMC7612221 DOI: 10.1038/s41559-021-01581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/23/2021] [Indexed: 11/15/2022]
Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
Collapse
Affiliation(s)
- Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.
| | - Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Maxim B. Kozlikin
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V. Shunkov
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P. Derevianko
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
| |
Collapse
|
30
|
Abstract
We review the state of paleoanthropology research in Asia. We survey the fossil record, articulate the current understanding, and delineate the points of contention. Although Asia received less attention than Europe and Africa did in the second half of the twentieth century, an increase in reliably dated fossil materials and the advances in genetics have fueled new research. The long and complex evolutionary history of humans in Asia throughout the Pleistocene can be explained by a balance of mechanisms, between gene flow among different populations and continuity of regional ancestry. This pattern is reflected in fossil morphology and paleogenomics. Critical understanding of the sociocultural forces that shaped the history of hominin fossil research in Asia is important in charting the way forward.
Collapse
Affiliation(s)
- Sang-Hee Lee
- Department of Anthropology, University of California, Riverside, California 92521, USA
| | - Autumn Hudock
- Department of Anthropology, University of North Carolina, Charlotte, North Carolina 28223, USA
- Current affiliation: Department of Anthropology, University of California, San Diego, La Jolla, California 92093, USA
| |
Collapse
|
31
|
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
32
|
Ruiz-García M, Pinilla-Beltrán D, Murillo-García OE, Pinto CM, Brito J, Shostell JM. Comparative mitogenome phylogeography of two anteater genera ( Tamandua and Myrmecophaga; Myrmecophagidae, Xenarthra): Evidence of discrepant evolutionary traits. Zool Res 2021; 42:525-547. [PMID: 34313411 PMCID: PMC8455474 DOI: 10.24272/j.issn.2095-8137.2020.365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 11/07/2022] Open
Abstract
The species within Xenarthra (sloths, anteaters, and armadillos) are quintessential South American mammals. Of the three groups, Vermilingua (anteaters) contains the fewest extant and paleontological species. Here, we sampled and sequenced the entire mitochondrial genomes (mitogenomes) of two Tamandua species (Tamandua tetradactyla and Tamandua mexicana) (n=74) from Central and South America, as well as Myrmecophaga tridactyla (n=41) from South America. Within Tamandua, we detected three different haplogroups. The oldest (THI) contained many specimens with the T. tetradactyla morphotype (but also several with the T. mexicana morphotype) and originated in southeastern South America (currently Uruguay) before moving towards northern South America, where the THII haplogroup originated. THII primarily contained specimens with the T. mexicana morphotype (but also several with the T. tetradactyla morphotype) and was distributed in Central America, Colombia, and Ecuador. THI and THII yielded a genetic distance of 4%. THII originated in either northern South America or "in situ" in Central America with haplogroup THIII, which consisted of ~50% T. mexicana and 50% T. tetradactyla phenotypes. THIII was mostly located in the same areas as THII, i.e., Central America, Ecuador, and Colombia, though mainly in the latter. The three haplogroups overlapped in Colombia and Ecuador. Thus, T. tetradactyla and T. mexicana were not reciprocally monophyletic. For this reason, we considered that a unique species of Tamandua likely exists, i.e., T. tetradactyla. In contrast to Tamandua, M. tridactyla did not show different morphotypes throughout its geographical range in the Neotropics. However, two very divergent genetic haplogroups (MHI and MHII), with a genetic distance of ~10%, were detected. The basal haplogroup, MHI, originated in northwestern South America, whereas the more geographically derived haplogroup, MHII, overlapped with MHI, but also expanded into central and southern South America. Thus, Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south. Our results also showed that temporal mitochondrial diversification for Tamandua began during the Late Pliocene and Upper Pleistocene, but for Myrmecophaga began during the Late Miocene. Furthermore, both taxa showed elevated levels of mitochondrial genetic diversity. Tamandua showed more evidence of female population expansion than Myrmecophaga. Tamandua experienced population expansion ~0.6-0.17 million years ago (Mya), whereas Myrmecophaga showed possible population expansion ~0.3-0.2 Mya. However, both taxa experienced a conspicuous female decline in the last 10 000-20 000 years. Our results also showed little spatial genetic structure for both taxa. However, several analyses revealed higher spatial structure in Tamandua than in Myrmecophaga. Therefore, Tamandua and Myrmecophaga were not subjected to the same biogeographical, geological, or climatological events in shaping their genetic structures.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC 110231, Colombia. E-mail:
| | - Daniel Pinilla-Beltrán
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC 110231, Colombia
| | - Oscar E Murillo-García
- Grupo de Investigación en Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Apartado Aéreo, Cali 25360, Colombia
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN 56716, USA
| |
Collapse
|
33
|
Abstract
CONTEXT For many years the Sardinian population has been the object of numerous studies because of its unique genetic structure. Despite the extreme abundance of papers, various aspects of the peopling and genetic structure of Sardinia still remain uncertain and sometimes controversial. OBJECTIVE We reviewed what has emerged from different studies, focussing on some still open questions, such as the origin of Sardinians, their relationship with the Corsican population, and the intra-regional genetic heterogeneity. METHODS The various issues have been addressed through the analysis of classical markers, molecular markers and, finally, genomic data through next generation sequencing. RESULTS AND CONCLUSIONS Although the most ancient human remains date back to the end of the Palaeolithic, Mesolithic populations brought founding lineages that left evident traces in the modern population. Then, with the Neolithic, the island underwent an important demographic expansion. Subsequently, isolation and genetic drift contributed to maintain a significant genetic heterogeneity, but preserving the overall homogeneity on a regional scale. At the same time, isolation and genetic drift contributed to differentiate Sardinia from Corsica, which saw an important gene flow from the mainland. However, the isolation did not prevent gene flow from the neighbouring populations whose contribution are still recognisable in the genome of Sardinians.
Collapse
Affiliation(s)
- Carla Maria Calò
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Giuseppe Vona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Francalacci
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| |
Collapse
|
34
|
Sun XF, Wen SQ, Lu CQ, Zhou BY, Curnoe D, Lu HY, Li HC, Wang W, Cheng H, Yi SW, Jia X, Du PX, Xu XH, Lu YM, Lu Y, Zheng HX, Zhang H, Sun C, Wei LH, Han F, Huang J, Edwards RL, Jin L, Li H. Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China. Proc Natl Acad Sci U S A 2021; 118:e2019158118. [PMID: 33558418 DOI: 10.1073/pnas.2019158118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.
Collapse
|
35
|
Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
Collapse
Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| |
Collapse
|
36
|
Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
Collapse
Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| |
Collapse
|
37
|
Smith R, Moots RJ, Murad M, Wallace GR. A Darwinian View of Behçet's Disease. Rheumatol Immunol Res 2021; 2:91-99. [PMID: 36465976 PMCID: PMC9524781 DOI: 10.2478/rir-2021-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/30/2021] [Indexed: 04/25/2023]
Abstract
Behçet's disease (BD) is a multisystem inflammatory disorder of unknown etiology, characterized by oral and genital ulceration, with other complications including eye, skin, joint, and central nervous system (CNS) lesions. Diagnosis is based on clinical findings, which may differ between patients. There is a strong genetic basis for BD; however, only a few genes have been associated with the disease across the geographical spread of BD. In this article, we discuss the history and combination of genes involved in this complex disease in relation to the geographical range and present our view that the disease has developed from a Darwinian perspective, with different gene polymorphisms that affect the same biological pathway. Moreover, these mutations individually are protective mechanisms against the disease relevant to each region, which affected both archaic and modern humans.
Collapse
Affiliation(s)
- Rhodri Smith
- Department of Rheumatology, Aintree Hospital, Liverpool, UK
| | | | - Mariam Murad
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Graham R. Wallace
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- E-mail:
| |
Collapse
|
38
|
Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
Collapse
Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
| |
Collapse
|
39
|
Abstract
The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.
Collapse
Affiliation(s)
- Jeffrey H Schwartz
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
40
|
Sullivan AP, Marciniak S, O'Dea A, Wake TA, Perry GH. Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama. Mol Ecol Resour 2021; 21:1517-1528. [PMID: 33595921 DOI: 10.1111/1755-0998.13361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984-1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.
Collapse
Affiliation(s)
- Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Aaron O'Dea
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Thomas A Wake
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Anthropology and the Costen Institute of Archaeology, University of California, Los Angeles, CA, USA
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
41
|
Devièse T, Abrams G, Hajdinjak M, Pirson S, De Groote I, Di Modica K, Toussaint M, Fischer V, Comeskey D, Spindler L, Meyer M, Semal P, Higham T. Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proc Natl Acad Sci U S A 2021; 118:e2022466118. [PMID: 33798098 DOI: 10.1073/pnas.2022466118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.
Collapse
|
42
|
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.
Collapse
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.
| |
Collapse
|
43
|
Taron UH, Paijmans JLA, Barlow A, Preick M, Iyengar A, Drăgușin V, Vasile Ș, Marciszak A, Roblíčková M, Hofreiter M. Ancient DNA from the Asiatic Wild Dog ( Cuon alpinus) from Europe. Genes (Basel) 2021; 12:144. [PMID: 33499169 PMCID: PMC7911384 DOI: 10.3390/genes12020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/11/2023] Open
Abstract
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.
Collapse
Affiliation(s)
- Ulrike H. Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Arati Iyengar
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Virgil Drăgușin
- Emil Racoviţă Institute of Speleology, Romanian Academy, 31 Frumoasă Street, 010986 Bucharest, Romania;
- Research Institute of the University of Bucharest, Earth, Environmental and Life Sciences Division, Panduri 90–92, 050663 Bucharest, Romania
| | - Ștefan Vasile
- Department of Geology, Faculty of Geology and Geophysics, University of Bucharest, 1 Nicolae Bălcescu Avenue, 010041 Bucharest, Romania;
| | - Adrian Marciszak
- Department of Paleozoology, Faculty of Biological Sciences, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland;
| | - Martina Roblíčková
- Moravian Museum, Anthropos Institute, Zelný trh 6, 65937 Brno, Czech Republic;
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| |
Collapse
|
44
|
Árnason Ú, Hallström B. The reversal of human phylogeny: Homo left Africa as erectus, came back as sapiens sapiens. Hereditas 2020; 157:51. [PMID: 33341120 PMCID: PMC7749984 DOI: 10.1186/s41065-020-00163-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/27/2020] [Indexed: 11/25/2022] Open
Abstract
Background The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25–30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo. The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades. Results The direction of evolution in the phylogenetic tree of modern humans (Homo sapiens sapiens, Hss) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor ≈ 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans) ≈ 800,000 YBP, an mtDNA introgression from Hss into Hsnn* ≈ 500,000 YBP and an Eurasian divergence among the ancestors of extant Hss ≈ 250,000 YBP at the exodus of Mbuti/San into Africa. Conclusions The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.
Collapse
Affiliation(s)
- Úlfur Árnason
- Department of Brain Surgery, Faculty of Medicine, University of Lund, Lund, Sweden.
| | - Björn Hallström
- Center for Translational Genomics, Faculty of Medicine, University of Lund, Lund, Sweden
| |
Collapse
|
45
|
Zhang D, Xia H, Chen F, Li B, Slon V, Cheng T, Yang R, Jacobs Z, Dai Q, Massilani D, Shen X, Wang J, Feng X, Cao P, Yang MA, Yao J, Yang J, Madsen DB, Han Y, Ping W, Liu F, Perreault C, Chen X, Meyer M, Kelso J, Pääbo S, Fu Q. Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science 2020; 370:584-587. [DOI: 10.1126/science.abb6320] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Dongju Zhang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Frontier Center for Eco-environment and Climate Change in Pan-third Pole Regions, Lanzhou University, Lanzhou 730000, China
| | - Huan Xia
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fahu Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Ting Cheng
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Xuke Shen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian Wang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- School of Earth Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Juanting Yao
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jishuai Yang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - David B. Madsen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Department of Anthropology, University of Nevada–Reno, Reno, NV 89557, USA
| | - Yuanyuan Han
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wanjing Ping
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Feng Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Charles Perreault
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoshan Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| |
Collapse
|
46
|
Affiliation(s)
- Feng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena D-07745, Germany; School of Social Science, the University of Queensland, Brisbane, QLD 4072, Australia; Human Origins Program, Smithsonian Institution, Washington DC 20560-0004, USA
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena D-07745, Germany; School of Social Science, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
47
|
Romandini M, Oxilia G, Bortolini E, Peyrégne S, Delpiano D, Nava A, Panetta D, Di Domenico G, Martini P, Arrighi S, Badino F, Figus C, Lugli F, Marciani G, Silvestrini S, Menghi Sartorio JC, Terlato G, Hublin JJ, Meyer M, Bondioli L, Higham T, Slon V, Peresani M, Benazzi S. A late Neanderthal tooth from northeastern Italy. J Hum Evol 2020; 147:102867. [DOI: 10.1016/j.jhevol.2020.102867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
|
48
|
Peeters S, Zwart H. Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness. Hist Philos Life Sci 2020; 42:33. [PMID: 32696095 PMCID: PMC7374475 DOI: 10.1007/s40656-020-00327-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.
Collapse
Affiliation(s)
- Susan Peeters
- Institute for Science in Society (ISiS), Radboud University Nijmegen, Huygens building - Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
- Erasmus School of Philosophy (ESPhil), Erasmus University Rotterdam, Bayle building - Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands.
| | - Hub Zwart
- Erasmus School of Philosophy (ESPhil), Erasmus University Rotterdam, Bayle building - Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| |
Collapse
|
49
|
Ruiz-garcía M, Jaramillo MF, Cáceres-martínez CH, Shostell JM. The phylogeographic structure of the mountain coati (Nasuella olivacea; Procyonidae, Carnivora), and its phylogenetic relationships with other coati species (Nasua nasua and Nasua narica) as inferred by mitochondrial DNA. Mamm Biol 2020; 100:521-48. [DOI: 10.1007/s42991-020-00050-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
50
|
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
Collapse
Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| |
Collapse
|