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Végh EI, Douka K. SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinformatics 2024; 40:btae054. [PMID: 38337062 PMCID: PMC10918634 DOI: 10.1093/bioinformatics/btae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/08/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).
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Affiliation(s)
- Emese I Végh
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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2
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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] [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.
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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.
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3
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Taniguchi K, Miyaguchi H. COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics. J Proteome Res 2024; 23:377-385. [PMID: 38091499 DOI: 10.1021/acs.jproteome.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.
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Affiliation(s)
- Kei Taniguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
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4
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Morley MW, Moffat I, Kotarba-Morley AM, Hernandez VC, Zerboni A, Herries AIR, Joannes-Boyau R, Westaway K. Why the geosciences are becoming increasingly vital to the interpretation of the human evolutionary record. Nat Ecol Evol 2023; 7:1971-1977. [PMID: 38036632 DOI: 10.1038/s41559-023-02215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/08/2023] [Indexed: 12/02/2023]
Abstract
Advanced geoscience techniques are essential to contextualize fossils, artefacts and other archaeologically important material accurately and effectively. Their appropriate use will increase confidence in new interpretations of the fossil and archaeological record, providing important information about the life and depositional history of these materials and so should form an integral component of all human evolutionary studies. Many of the most remarkable recent finds that have transformed the field of human evolution are small and scarce, ranging in size from teeth to strands of DNA, recovered from complex sedimentary environments. Nevertheless, if properly analysed, they hold immense potential to rewrite what we know about the evolution of our species and our closest hominin ancestors.
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Affiliation(s)
- Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia.
| | - Ian Moffat
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Anna M Kotarba-Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
- School of Humanities, University of Adelaide, Adelaide, South Australia, Australia
| | - Vito C Hernandez
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra 'A. Desio', Università degli Studi di Milano, Milano, Italy
| | - Andy I R Herries
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, New South Wales, Australia
| | - Kira Westaway
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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5
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Mylopotamitaki D, Harking FS, Taurozzi AJ, Fagernäs Z, Godinho RM, Smith GM, Weiss M, Schüler T, McPherron SP, Meller H, Cascalheira J, Bicho N, Olsen JV, Hublin JJ, Welker F. Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification. Sci Rep 2023; 13:18345. [PMID: 37884544 PMCID: PMC10603084 DOI: 10.1038/s41598-023-44885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo M Godinho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Kent, UK
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Ur- und Frühgeschichte, Friedrich-Alexander-Universität, Erlangen, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology, Saxony-Anhalt-State Museum of Prehistory, Halle (Saale), Germany
| | - João Cascalheira
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Nuno Bicho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Jacques Hublin
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Wang N, Xu Y, Tang Z, He C, Hu X, Cui Y, Douka K. Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China. Proc Biol Sci 2023; 290:20231129. [PMID: 37876197 PMCID: PMC10598447 DOI: 10.1098/rspb.2023.1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
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Affiliation(s)
- Naihui Wang
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, 72070 Tübingen, Germany
| | - Yang Xu
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Zhuowei Tang
- School of Archaeology, Jilin University, 130012 Changchun, People's Republic of China
| | - Cunding He
- China-Central Asia ‘the Belt and Road’ Joint Laboratory on Human and Environment Research, 710127 Xi'an, People's Republic of China
- School of Cultural Heritage, Northwest University, 710127 Xi'an, People's Republic of China
| | - Xin Hu
- Chongqing China Three Gorges Museum, 400013 Chongqing, People's Republic of China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Katerina Douka
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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7
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Zhao D, Chen Y, Xie G, Ma P, Wen Y, Zhang F, Wang Y, Cui Y, Gao S. A multidisciplinary study on the social customs of the Tang Empire in the Medieval Ages. PLoS One 2023; 18:e0288128. [PMID: 37494335 PMCID: PMC10370703 DOI: 10.1371/journal.pone.0288128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
Multidisciplinary research on human remains can provide important information about population dynamics, culture diffusion, as well as social organization and customs in history. In this study, multidisciplinary analyses were undertaken on a joint burial (M56) in the Shuangzhao cemetery of the Tang Dynasty (618-907 AD), one of the most prosperous dynasties in Chinese history, to shed light on the genetic profile and sociocultural aspects of this dynasty. The archaeological investigation suggested that this burial belonged to the Mid-Tang period and was used by common civilians. The osteological analysis identified the sex, age, and health status of the three individuals excavated from M56, who shared a similar diet inferred from the stable isotopic data. Genomic evidence revealed that these co-buried individuals had no genetic kinship but all belonged to the gene pool of the ancient populations in the Central Plains, represented by Yangshao and Longshan individuals, etc. Multiple lines of evidence, including archaeology, historic records, as well as chemical and genetic analyses, have indicated a very probable familial joint burial of husband and wives. Our study provides insights into the burial customs and social organization of the Tang Dynasty and reconstructs a scenario of civilian life in historic China.
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Affiliation(s)
- Dongyue Zhao
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Yang Chen
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Gaowen Xie
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Yafei Wang
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
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8
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Johnston E, Buckley M. Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements. Molecules 2023; 28:4899. [PMID: 37446562 DOI: 10.3390/molecules28134899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.
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Affiliation(s)
- Elizabeth Johnston
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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9
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Bray F, Fabrizi I, Flament S, Locht JL, Antoine P, Auguste P, Rolando C. Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2023; 95:7422-7432. [PMID: 37130053 DOI: 10.1021/acs.analchem.2c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In the archaeological or paleontological field, PMF is known as zooarchaeology mass spectrometry (ZooMS) and is widely implemented to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to 10-fold the required bone sample amount (down to the milligram scale) and achieves robust deamidation value calculation in a high-throughput manner. These improvements rely on a 96-well plate samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious post-translational modification production, and PMF at high resolution using matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance (MALDI-FTICR) analysis. This method was applied to the identification of a hundred bones of herbivores from the Middle Paleolithic site of Caours (Somme, France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their osteomorphology, as well as to more challenging samples consisting of small or burned bone fragments. Deamidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.
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Affiliation(s)
- Fabrice Bray
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Isabelle Fabrizi
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Stéphanie Flament
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Jean-Luc Locht
- Inrap Hauts-de-France, 32, avenue de l'Étoile-du-Sud, Glisy 80440, France
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Pierre Antoine
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Patrick Auguste
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, Lille F-59000, France
| | - Christian Rolando
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
- Shrieking Sixties, 1-3 Allée Lavoisier, Villeneuve-d'Ascq F-59650, France
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10
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Xu Y, Wang N, Gao S, Li C, Ma P, Yang S, Jiang H, Shi S, Wu Y, Zhang Q, Cui Y. Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches. Int J Legal Med 2023; 137:319-327. [PMID: 36625884 PMCID: PMC9902420 DOI: 10.1007/s00414-022-02944-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023]
Abstract
Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.
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Affiliation(s)
- Yang Xu
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Naihui Wang
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021 China
| | - Chunxiang Li
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Shasha Yang
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Hai Jiang
- Criminal Police Detachment, Qingdao Municipal Public Security Bureau, Qingdao, 266034 China
| | - Shoujin Shi
- Criminal Investigation Team, Jimo Branch, Qingdao Municipal Public Security Bureau, Qingdao, 266205 China
| | - Yanhua Wu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, 130021 China
| | - Quanchao Zhang
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012 China ,School of Archaeology, Jilin University, Changchun, 130012 China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, 130012, China. .,Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
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11
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Bonicelli A, Mickleburgh HL, Chighine A, Locci E, Wescott DJ, Procopio N. The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics. eLife 2022; 11:e83658. [PMID: 36583441 PMCID: PMC9803353 DOI: 10.7554/elife.83658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
| | - Hayley L Mickleburgh
- Amsterdam Centre for Ancient Studies and Archaeology (ACASA) – Department of Archaeology, Faculty of Humanities, University of AmsterdamAmsterdamNetherlands
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Alberto Chighine
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Emanuela Locci
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
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12
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Silvestrini S, Lugli F, Romandini M, Real C, Sommella E, Salviati E, Arrighi S, Bortolini E, Figus C, Higgins OA, Marciani G, Oxilia G, Delpiano D, Vazzana A, Piperno M, Crescenzi C, Campiglia P, Collina C, Peresani M, Spinapolice EE, Benazzi S. Integrating ZooMS and zooarchaeology: New data from the Uluzzian levels of Uluzzo C Rock Shelter, Roccia San Sebastiano cave and Riparo del Broion. PLoS One 2022; 17:e0275614. [PMID: 36227961 PMCID: PMC9560625 DOI: 10.1371/journal.pone.0275614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
In this study we explore the potential of combining traditional zooarchaeological determination and proteomic identification of morphologically non-diagnostic bone fragments (ZooMS) collected from the Uluzzian levels of three Italian sites: Uluzzo C Rock Shelter, Roccia San Sebastiano cave, and Riparo del Broion. Moreover, we obtained glutamine deamidation ratios for all the contexts analysed during routine ZooMS screening of faunal samples, giving information on collagen preservation. We designed a selection protocol that maximizes the efficiency of the proteomics analyses by excluding particularly compromised fragments (e.g. from taphonomic processes), and that aims to identify new human fragments by favouring bones showing morphological traits more similar to Homo. ZooMS consistently provided taxonomic information in agreement with the faunal spectra outlined by traditional zooarchaeology. Our approach allows us to delineate and appreciate differences between the analysed contexts, particularly between the northern and southern sites, related to faunal, environmental, and climate composition, although no human remains were identified. We reconstructed the faunal assemblage of the different sites, giving voice to morphologically undiagnostic bone fragments. Thus, the combination of these analyses provides a more complete picture of the faunal assemblage and of the paleoenvironment during the Middle-Upper Palaeolithic transition in Italy.
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Affiliation(s)
- Sara Silvestrini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Federico Lugli
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Matteo Romandini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Cristina Real
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Eduardo Sommella
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Emanuela Salviati
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Simona Arrighi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Eugenio Bortolini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Carla Figus
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | | | - Giulia Marciani
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Gregorio Oxilia
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Davide Delpiano
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Antonino Vazzana
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Marcello Piperno
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Carlo Crescenzi
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Carmine Collina
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Marco Peresani
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
- Istituto di Geologia Ambientale e Geoingegneria, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Enza Elena Spinapolice
- Dipartimento di Scienze dell’Antichità, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Stefano Benazzi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
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13
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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] [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.
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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.
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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15
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Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils. BIOLOGY 2022; 11:biology11081184. [PMID: 36009810 PMCID: PMC9404968 DOI: 10.3390/biology11081184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Two independent research groups led by Olivares (Spain) and Lowenstein (USA) investigated the immunological reactions of proteins extracted from the controversial Orce skull (VM-0), a 1.3-million-year-old fossil found at the Venta Micena site in Orce, Granada (Spain) and initially believed to come from an unidentified hominin. Work by both groups with polyclonal and monoclonal antibodies showed that proteins from this fossil reacted most strongly to antibodies against modern human proteins. Other hominin and mammal fossils from Venta Micena were also studied. Abstract Proteomics methods can identify amino acid sequences in fossil proteins, thus making it possible to determine the ascription or proximity of a fossil to other species. Before mass spectrometry was used to study fossil proteins, earlier studies used antibodies to recognize their sequences. Lowenstein and colleagues, at the University of San Francisco, pioneered the identification of fossil proteins with immunological methods. His group, together with Olivares’s group at the University of Granada, studied the immunological reactions of proteins from the controversial Orce skull fragment (VM-0), a 1.3-million-year-old fossil found at the Venta Micena site in Orce (Granada province, southern Spain) and initially assigned to a hominin. However, discrepancies regarding the morphological features of the internal face of the fossil raised doubts about this ascription. In this article, we review the immunological analysis of the proteins extracted from VM-0 and other Venta Micena fossils assigned to hominins and to other mammals, and explain how these methods helped to determine the species specificity of these fossils and resolve paleontological controversies.
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16
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Dierickx K, Presslee S, Hagan R, Oueslati T, Harland J, Hendy J, Orton D, Alexander M, Harvey VL. Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220149. [PMID: 35911190 PMCID: PMC9326269 DOI: 10.1098/rsos.220149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples (n = 202) from three archaeological sites in the UK and France dating to the medieval period (ca seventh-sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.
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Affiliation(s)
- Katrien Dierickx
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Samantha Presslee
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Richard Hagan
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Tarek Oueslati
- Centre National de la Recherche Scientifique, University of Lille, Lille, France
| | - Jennifer Harland
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
- Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jessica Hendy
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - David Orton
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Michelle Alexander
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Virginia L. Harvey
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
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17
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Abstract
Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited.
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18
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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19
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From Human Remains to Powerful Objects: Ancestor Research from a Deep-Time Perspective. GENEALOGY 2022. [DOI: 10.3390/genealogy6010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
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20
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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] [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.
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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.
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21
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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.
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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
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22
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Peters C, Richter KK, Manne T, Dortch J, Paterson A, Travouillon K, Louys J, Price GJ, Petraglia M, Crowther A, Boivin N. Species identification of Australian marsupials using collagen fingerprinting. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211229. [PMID: 34729210 PMCID: PMC8548793 DOI: 10.1098/rsos.211229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.
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Affiliation(s)
- Carli Peters
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Tiina Manne
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
| | - Joe Dortch
- School of Social Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Alistair Paterson
- School of Social Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Kenny Travouillon
- Western Australian Museum, Collections and Research, 49 Kew Street, Welshpool, WA 6106, Australia
| | - Julien Louys
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Qld 4111, Australia
| | - Gilbert J. Price
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Qld 4111, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
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23
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Brown S, Wang N, Oertle A, Kozlikin MB, Shunkov MV, Derevianko AP, Comeskey D, Jope-Street B, Harvey VL, Chowdhury MP, Buckley M, Higham T, Douka K. Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave. Sci Rep 2021; 11:15457. [PMID: 34326389 PMCID: PMC8322063 DOI: 10.1038/s41598-021-94731-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.
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Affiliation(s)
- Samantha Brown
- Institute for Scientific Archaeology, Eberhard Karls University of Tübingen, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Naihui Wang
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Annette Oertle
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxim B Kozlikin
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Virginia L Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Manasij Pal Chowdhury
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK.,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 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.
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24
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Wang F, Du Z, Han B, Cao S, Fu F, Luo Z, Mu Z, Chen J, Qiu P, Fan H. Genetic diversity, forensic characteristics and phylogenetic analysis of the Qiongzhong aborigines residing in the tropical rainforests of Hainan Island via 19 autosomal STRs. Ann Hum Biol 2021; 48:335-342. [PMID: 34223783 DOI: 10.1080/03014460.2021.1951352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND The genetic landscape of the Qiongzhong aborigines, who reside in "the Heart of Hainan," is still unclear. The Goldeneye™ DNA ID System 20 A is available for forensic and population genetics applications. AIM To obtain genetic polymorphisms of 19 autosomal STR loci in the Qiongzhong aborigines, and to explore the genetic relationships with a total of 69,132 people from forty-five populations. SUBJECTS AND METHODS Genotype data on 19 autosomal STRs were collected from 724 Qiongzhong aborigines and phylogenetic relationships were conducted by multidimensional scaling analysis (MDS), principal component analysis (PCA) and neighbor-joining (N-J) phylogenetic tree construction. RESULTS No evidence of deviation from Hardy-Weinberg equilibrium was identified. A total of 233 distinct alleles were observed with allele frequencies ranging from 0.0007 to 0.5375. The combined power of discrimination (CPD) and combined power of exclusion (CPE) for the 19 autosomal STR loci were 1-8.28 × 10-34 and 0.999999987, respectively. CONCLUSION Our phylogenetic results demonstrated that (a) the populations of Southeast Asian countries have thorough integrations with southern China in terms of ethnicity and genetics due to long-term cultural and trade exchanges, and (b) based on genetic and linguistic analysis, the Qiongzhong aborigines have a close relationship with Fujian Han Chinese.HighlightsThe STR landscape of Qiongzhong aborigines inhabited in Hainan tropical rainforests was depicted by 19 autosomal STRs.A total of 69,132 people from forty-five populations were selected for a more extensive examination of genetic similarities and differences by multivariate statistical methods (MDS, PCA and N-J tree construction).The genetic analyses indicated that the populations of Southeast Asian countries are very genetically close to southern Chinese populations.From the genetic and linguistic perspective, the Qiongzhong aborigines have a close relationship with Han Chinese from Fujian Province.
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Affiliation(s)
- Fenfen Wang
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Zhengming Du
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Bingbing Han
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou, China
| | - Shengping Cao
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Fangshu Fu
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Zhenming Luo
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Ziqing Mu
- School of Management, Hainan Medical University, Haikou, China
| | - Jirui Chen
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- First Clinical Medical College, Hainan Medical University, Haikou, China.,School of Forensic Medicine, Southern Medical University, Guangzhou, China.,School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
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25
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Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis. BIOLOGY 2021; 10:biology10060460. [PMID: 34071025 PMCID: PMC8224596 DOI: 10.3390/biology10060460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
The evaluation of bone diagenetic phenomena in archaeological timescales has a long history; however, little is known about the origins of the microbes driving bone diagenesis, nor about the extent of bone diagenesis in short timeframes-such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful in estimating the post-mortem interval (PMI). However, there is still a great need for enhancing the understanding of the diagenetic processes taking place in forensic timeframes, and to clarify whether proteomic analyses can help to develop better models for estimating PMI reliably. To address these knowledge gaps, we designed an experiment based on whole rat carcasses, defleshed long rat bones, and excised but still-fleshed rat limbs, which were either buried in soil or exposed on a clean plastic surface, left to decompose for 28 weeks, and retrieved at different time intervals. This study aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autolysis, and gut and soil bacteria had on bone diagenesis via bottom-up proteomics. Results showed six proteins whose abundance was significantly different between samples subjected to either microbial decomposition (gut or soil bacteria) or to environmental factors. In particular, muscle- and calcium-binding proteins were found to be more prone to degradation by bacterial attack, whereas plasma and bone marrow proteins were more susceptible to exposure to extrinsic agents. Our results suggest that both gut and soil bacteria play key roles in bone diagenesis and protein decay in relatively short timescales, and that bone proteomics is a proficient resource with which to identify microbially-driven versus extrinsically-driven diagenesis.
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26
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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] [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.
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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
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27
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Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proc Natl Acad Sci U S A 2021; 118:2022466118. [PMID: 33798098 DOI: 10.1073/pnas.2022466118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.
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28
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Procopio N, Hopkins RJ, Harvey VL, Buckley M. Proteome Variation with Collagen Yield in Ancient Bone. J Proteome Res 2021; 20:1754-1769. [PMID: 33529527 PMCID: PMC7944572 DOI: 10.1021/acs.jproteome.0c01014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 11/30/2022]
Abstract
Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of "collagen yield" (as defined in radiocarbon dating and stable isotope research) is a routine step that allows for the selection of specimens that are deemed adequate for subsequent analyses, with samples containing less than ∼1% "collagen yield" normally being used for isotopic analysis but discounted for radiocarbon dating. The aims of this study were to use proteomic methods of MALDI-TOF (matrix assisted laser desorption ionization time-of-fligh mass spectrometry) and LC-ESI-MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) to investigate the endogeneity of the dominant proteinaceous biomolecules within samples that are typically considered to contain poorly preserved protein. Taking 29 archaeological samples, we evaluated the proteome variability between different acid-soluble fractions removed prior to protein gelatinization and considered waste as part of the radiocarbon dating process. We then correlated these proteomes against the commonly used "collagen yield" proxy for preservation. We found that these waste fractions contained a significant amount of both collagenous and noncollagenous proteins (NCPs) but that the abundance of these was not correlated with the acquired "collagen yield". Rather than a depleted protein load as would be expected from a low "collagen yield", the variety of the extracted NCPs was comparable with that commonly obtained from ancient samples and included informative proteins useful for species identification, phylogenetic studies, and potentially even for isotopic analyses, given further method developments. Additionally, we did not observe any correlation between "collagen yield" and peptide mass fingerprint success or between the different fractions taken from the same sample but at different radiocarbon pretreatment stages. Overall, these findings highlight the value in retaining and analyzing sample fractions that are otherwise discarded as waste during the radiocarbon dating process but more importantly, that low "collagen yield" specimens that are often misinterpreted by archaeologists as being devoid of protein can still yield useful molecular sequence-based information.
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Affiliation(s)
- Noemi Procopio
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Northumbria University Newcastle, Ellison Building, Newcastle Upon Tyne NE1 8ST, U.K.
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rachel J.A. Hopkins
- Department
of Anthropology, University of New Mexico, MSC01-1040, 1 University of New
Mexico, Albuquerque, New
Mexico 87131-0001, United States
- Research
Laboratory for Archaeology and the History of Art (RLAHA), School
of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K.
| | - Virginia L. Harvey
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Interdisciplinary
Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, U.K.
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Interdisciplinary
Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, U.K.
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29
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Sharafi A, Medina K, Zibetti MWV, Rao S, Cloos MA, Brown R, Regatte RR. Simultaneous T 1 , T 2 , and T 1ρ relaxation mapping of the lower leg muscle with MR fingerprinting. Magn Reson Med 2021; 86:372-381. [PMID: 33554369 DOI: 10.1002/mrm.28704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/31/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022]
Abstract
PURPOSE To develop a novel MR-fingerprinting (MRF) pulse sequence that is insensitive to B 1 + and B0 imperfections for simultaneous T1 , T2 , and T1ρ relaxation mapping. METHODS We implemented a totally balanced spin-lock (TB-SL) module to encode T1ρ relaxation into an existing MRF framework that encoded T1 and T2 . The spin-lock module used two 180° pulses with compensatory phases to reduce T1ρ sensitivity to B1 and B0 inhomogeneities. We compared T1ρ measured using TB-SL MRF in Bloch simulations, model agar phantoms, and in vivo experiments to those with a self-compensated spin-lock preparation module (SC-SL). The TB-SL MRF repeatability was evaluated in maps acquired in the lower leg skeletal muscle of 12 diabetic peripheral neuropathy patients, scanned two times each during visits separated by about 30 days. RESULTS The phantom relaxation times measured with TB-SL and SC-SL MRF were in good agreement with reference values in regions with low B1 inhomogeneities. Compared with SC-SL, TB-SL MRF showed in experiments greater robustness against severe B1 inhomogeneities and in Bloch simulations greater robustness against B1 and B0 . We measured with TB-SL MRF an average T1 = 950.1 ± 28.7 ms, T2 = 26.0 ± 1.2 ms, and T1ρ = 31.7 ± 3.2 ms in skeletal muscle across patients. Bland-Altman analysis demonstrated low bias between TB-SL and SC-SL MRF and between TB-SL MRF maps acquired in two visits. The coefficient of variation was less than 3% for all measurements. CONCLUSION The proposed TB-SL MRF sequence is fast and insensitive to B 1 + and B0 imperfections. It can simultaneously map T1 , T2 , T1ρ , and B 1 + in a single scan and can potentially be used to study muscle composition.
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Affiliation(s)
- Azadeh Sharafi
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Katherine Medina
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Marcelo W V Zibetti
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Smita Rao
- Department of Physical Therapy, New York University, New York, New York, USA
| | - Martijn A Cloos
- Center of Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Ryan Brown
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.,Center for Advanced Imaging Innovation and Research, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.,Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York, USA
| | - Ravinder R Regatte
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.,Center for Advanced Imaging Innovation and Research, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.,Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York, USA
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30
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Bergström A, Stringer C, Hajdinjak M, Scerri EML, Skoglund P. Origins of modern human ancestry. Nature 2021; 590:229-237. [PMID: 33568824 DOI: 10.1038/s41586-021-03244-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK.
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Eleanor M L Scerri
- Pan-African Evolution Research Group, Max Planck Institute for Science of Human History, Jena, Germany.,Department of Classics and Archaeology, University of Malta, Msida, Malta.,Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
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31
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Lugli F, Sciutto G, Oliveri P, Malegori C, Prati S, Gatti L, Silvestrini S, Romandini M, Catelli E, Casale M, Talamo S, Iacumin P, Benazzi S, Mazzeo R. Near-infrared hyperspectral imaging (NIR-HSI) and normalized difference image (NDI) data processing: An advanced method to map collagen in archaeological bones. Talanta 2021; 226:122126. [PMID: 33676680 DOI: 10.1016/j.talanta.2021.122126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/28/2022]
Abstract
In the present study, an innovative and highly efficient near-infrared hyperspectral imaging (NIR-HSI) method is proposed to provide spectral maps able to reveal collagen distribution in large-size bones, also offering semi-quantitative estimations. A recently introduced method for the construction of chemical maps, based on Normalized Difference Images (NDI), is declined in an innovative approach, through the exploitation of the NDI values computed for each pixel of the hyperspectral image to localize collagen and to extract information on its content by a direct comparison with known reference samples. The developed approach addresses an urgent issue of the analytical chemistry applied to bioarcheology researches, which rely on well-preserved collagen in bones to obtain key information on chronology, paleoecology and taxonomy. Indeed, the high demand for large-sample datasets and the consequent application of a wide variety of destructive analytical methods led to the considerable destruction of precious bone samples. NIR-HSI pre-screening allows researchers to properly select the sampling points for subsequent specific analyses, to minimize costs and time and to preserve integrity of archaeological bones (which are available in a very limited amount), providing further opportunities to understand our past.
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Affiliation(s)
- F Lugli
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - G Sciutto
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy.
| | - P Oliveri
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy.
| | - C Malegori
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy
| | - S Prati
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - L Gatti
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - S Silvestrini
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - M Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - E Catelli
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - M Casale
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy
| | - S Talamo
- University of Bologna, Department of Chemistry "G. Ciamician", Via Selmi, 2, 40126, Bologna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - P Iacumin
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area Delle Scienze, 11/a, Parma, Italy
| | - S Benazzi
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R Mazzeo
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
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32
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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33
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Naihui W, Samantha B, Peter D, Sandra H, Maxim K, Sindy L, Oshan W, Stefano G, Michael C, Liora HK, Matthew S, Glenn S, Michael S, Kristine RK, Katerina D. Testing the efficacy and comparability of ZooMS protocols on archaeological bone. J Proteomics 2020; 233:104078. [PMID: 33338688 DOI: 10.1016/j.jprot.2020.104078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/03/2020] [Accepted: 12/12/2020] [Indexed: 12/27/2022]
Abstract
Collagen peptide mass fingerprinting, best known as Zooarchaeology by Mass Spectrometry (or ZooMS) when applied to archaeology, has become invaluable for the taxonomic identification of archaeological collagenous materials, in particular fragmentary and modified bone remains. Prior to MALDI-based spectrometric analysis, collagen needs to be extracted from the bone's inorganic matrix, isolated and purified. Several protocols are currently employed for ZooMS analysis, however their efficacy and comparability has not been directly tested. Here, we use four different ZooMS protocols to analyze 400 bone samples from seven archaeological sites, dating to between ~500,000-2000 years ago. One of them, single-pot solid-phase-enhance sample preparation (SP3), is used for the first time as a ZooMS protocol. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation. Since preservation of biomolecules in archaeological bones is highly variable due to age and environmental conditions, we use the percent nitrogen by weight (%N) value as an independent semi-quantitative proxy for assessing collagen content and for predicting which bones will likely result in a successful ZooMS-based identification. We find that 0.26%N as a threshold for screening material could optimize the number of spectra which produce identifications using ZooMS. SIGNIFICANCE STATEMENT: We present a direct comparison of three previously published ZooMS protocols for the analyses of archaeological bones, and the first use of an SP3-based approach to ZooMS analysis. Our results show that the acid-based ZooMS protocols increase the success rate for bones with low-medium collagen preservation. We identify 0.26%N as a threshold for optimizing the number of samples with enough collagen for successful peptide mass fingerprinting.
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Affiliation(s)
- Wang Naihui
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Brown Samantha
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Ditchfield Peter
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK.
| | - Hebestreit Sandra
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Kozilikin Maxim
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva, 17, Novosibirsk 630090, Russia
| | - Luu Sindy
- Department of Anatomy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Wedage Oshan
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany; Department of History and Archaeology, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
| | - Grimaldi Stefano
- LaBAAF -Laboratorio Bagolini Archeologia, Archeometria, Fotografia, CeASUm - Centro di Alti Studi Umanistici, Dipartimento di Lettere e Filosofia, Università di Trento, via T.Gar14, I-38122 Trento, Italy; IsIPU - Istituto Italiano di Paleontologia Umana, Anagni, Italy.
| | - Chazan Michael
- Department of Anthropology, Canada Institute of Evolutionary Studies, University of Toronto, 19 Russell Street, Toronto, Canada; University of the Witwatersrand, Johannesburg, South Africa.
| | - Horwitz Kolska Liora
- National Natural History Collections, The Hebrew University, Berman Building, E. Safra-Givat Ram Campus, 91904 Jerusalem, Israel
| | - Spriggs Matthew
- School of Archaeology and Anthropology, Sir Roland Wilson Bldg 120, The Australian National University, Canberra, ACT 2600, Australia.
| | | | - Shunkov Michael
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva, 17, Novosibirsk 630090, Russia
| | - Richter Korzow Kristine
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Douka Katerina
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
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Froment C, Zanolli C, Hourset M, Mouton-Barbosa E, Moreira A, Burlet-Schiltz O, Mollereau C. Protein sequence comparison of human and non-human primate tooth proteomes. J Proteomics 2020; 231:104045. [PMID: 33189847 DOI: 10.1016/j.jprot.2020.104045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.
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Affiliation(s)
- Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Clément Zanolli
- Laboratoire PACEA, UMR 5199 CNRS, Université de Bordeaux, Pessac, France
| | - Mathilde Hourset
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Andreia Moreira
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Catherine Mollereau
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France.
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On the standardization of ZooMS nomenclature. J Proteomics 2020; 235:104041. [PMID: 33160104 DOI: 10.1016/j.jprot.2020.104041] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/14/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region. SIGNIFICANCE STATEMENT: We propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.
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Narakusumo RP, Riedel A, Pons J. Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils. PeerJ 2020; 8:e10017. [PMID: 33083123 PMCID: PMC7566755 DOI: 10.7717/peerj.10017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/01/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.
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Affiliation(s)
- Raden Pramesa Narakusumo
- State Museum of Natural History Karlsruhe, Karlsruhe, Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
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Le Meillour L, Zirah S, Zazzo A, Cersoy S, Détroit F, Imalwa E, Lebon M, Nankela A, Tombret O, Pleurdeau D, Lesur J. Palaeoproteomics gives new insight into early southern African pastoralism. Sci Rep 2020; 10:14427. [PMID: 32879376 PMCID: PMC7468255 DOI: 10.1038/s41598-020-71374-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/03/2020] [Indexed: 01/22/2023] Open
Abstract
The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the north-eastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments.
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Affiliation(s)
- Louise Le Meillour
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France.
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, 63 rue Buffon, 75005, Paris, France.
| | - Séverine Zirah
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, 63 rue Buffon, 75005, Paris, France
| | - Antoine Zazzo
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France
| | - Sophie Cersoy
- USR 3224 Centre de Recherche sur la Conservation (CRCC), Muséum national d'Histoire naturelle, CNRS, Ministère de la Culture, 36 rue Geoffroy Saint Hilaire, 75005, Paris, France
| | - Florent Détroit
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | | | - Matthieu Lebon
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - Alma Nankela
- National Heritage Council of Namibia, 153 Dr. AB May and Rev. Michael Scott streets, Ausspannplatz, Windhoek, Namibia
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - David Pleurdeau
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - Joséphine Lesur
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France.
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Lanigan LT, Mackie M, Feine S, Hublin JJ, Schmitz RW, Wilcke A, Collins MJ, Cappellini E, Olsen JV, Taurozzi AJ, Welker F. Multi-protease analysis of Pleistocene bone proteomes. J Proteomics 2020; 228:103889. [DOI: 10.1016/j.jprot.2020.103889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
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Martisius NL, Welker F, Dogandžić T, Grote MN, Rendu W, Sinet-Mathiot V, Wilcke A, McPherron SJP, Soressi M, Steele TE. Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals. Sci Rep 2020; 10:7746. [PMID: 32385291 PMCID: PMC7210944 DOI: 10.1038/s41598-020-64358-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for “smoothers”), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.
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Affiliation(s)
- Naomi L Martisius
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tamara Dogandžić
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA, 19104-6398, USA
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA
| | - William Rendu
- Centre National de la Recherche Scientifique, MCC, Préhistoire à l'Actuel, Cultures, Environnement, Anthropologie, UMR5199, Université de Bordeaux, FR-33615, Pessac, France
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04013, Leipzig, Germany
| | - Shannon J P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Marie Soressi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Faculty of Archaeology, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Teresa E Steele
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
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42
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Vershinina AO, Kapp JD, Baryshnikov GF, Shapiro B. The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections. Mol Ecol Resour 2020; 20:1182-1190. [DOI: 10.1111/1755-0998.13130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alisa O. Vershinina
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Joshua D. Kapp
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Gennady F. Baryshnikov
- Laboratory of Theriology Zoological Institute of the Russian Academy of Sciences St. Petersburg Russia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
- Howard Hughes Medical InstituteUniversity of California Santa Cruz Santa Cruz CA USA
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Koolstra K, Webb AG, Veeger TTJ, Kan HE, Koken P, Börnert P. Water-fat separation in spiral magnetic resonance fingerprinting for high temporal resolution tissue relaxation time quantification in muscle. Magn Reson Med 2020; 84:646-662. [PMID: 31898834 PMCID: PMC7217066 DOI: 10.1002/mrm.28143] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022]
Abstract
Purpose To minimize the known biases introduced by fat in rapid T1 and T2 quantification in muscle using a single‐run magnetic resonance fingerprinting (MRF) water–fat separation sequence. Methods The single‐run MRF acquisition uses an alternating in‐phase/out‐of‐phase TE pattern to achieve water–fat separation based on a 2‐point DIXON method. Conjugate phase reconstruction and fat deblurring were applied to correct for B0 inhomogeneities and chemical shift blurring. Water and fat signals were matched to the on‐resonance MRF dictionary. The method was first tested in a multicompartment phantom. To test whether the approach is capable of measuring small in vivo dynamic changes in relaxation times, experiments were run in 9 healthy volunteers; parameter values were compared with and without water–fat separation during muscle recovery after plantar flexion exercise. Results Phantom results show the robustness of the water–fat resolving MRF approach to undersampling. Parameter maps in volunteers show a significant (P < .01) increase in T1 (105 ± 94 ms) and decrease in T2 (14 ± 6 ms) when using water–fat‐separated MRF, suggesting improved parameter quantification by reducing the well‐known biases introduced by fat. Exercise results showed smooth T1 and T2 recovery curves. Conclusion Water–fat separation using conjugate phase reconstruction is possible within a single‐run MRF scan. This technique can be used to rapidly map relaxation times in studies requiring dynamic scanning, in which the presence of fat is problematic.
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Affiliation(s)
- Kirsten Koolstra
- C.J. Gorter Center for High Field MRI, Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Andrew G Webb
- C.J. Gorter Center for High Field MRI, Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Thom T J Veeger
- C.J. Gorter Center for High Field MRI, Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Hermien E Kan
- C.J. Gorter Center for High Field MRI, Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Peter Börnert
- C.J. Gorter Center for High Field MRI, Radiology, Leiden University Medical Center, Leiden, Netherlands.,Philips Research, Hamburg, Germany
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Swift JA, Bunce M, Dortch J, Douglass K, Faith JT, Fellows Yates JA, Field J, Haberle SG, Jacob E, Johnson CN, Lindsey E, Lorenzen ED, Louys J, Miller G, Mychajliw AM, Slon V, Villavicencio NA, Waters MR, Welker F, Wood R, Petraglia M, Boivin N, Roberts P. Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. Bioscience 2019; 69:877-887. [PMID: 31719710 PMCID: PMC6829010 DOI: 10.1093/biosci/biz105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.
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Affiliation(s)
- Jillian A Swift
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Anthropology Department of Bernice Pauahi Bishop Museum, Honolulu, Hawai’i
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Joe Dortch
- Centre for Rock Art Research and Management, University of Western Australia, Perth, Australia
| | - Kristina Douglass
- Department of Anthropology and with the Institutes for Energy and the Environment, The Pennsylvania State University, State College, Pennsylvania
| | - J Tyler Faith
- Natural History Museum of Utah and with the Department of Anthropology, University of Utah, Salt Lake City, Utah
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Judith Field
- School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, Australia
| | - Simon G Haberle
- College of Asia and the Pacific and the School of Culture, History, and Language, Australian National University, Canberra, Australia
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
| | - Eileen Jacob
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, England
| | - Chris N Johnson
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Emily Lindsey
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Louys
- Australian Research Center for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Gifford Miller
- INSTAAR and Department of Geological Sciences, University of Colorado, Boulder
| | - Alexis M Mychajliw
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Natalia A Villavicencio
- Departamento de Ecología, in the Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ecología and Biodiversidad, Santiago, Chile
| | - Michael R Waters
- Center for the Study of the First Americans, the Department of Anthropology, Texas A&M University, College Station, Texas
| | - Frido Welker
- Evolutionary Genomics Section of the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark, and with the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rachel Wood
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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45
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Sinet-Mathiot V, Smith GM, Romandini M, Wilcke A, Peresani M, Hublin JJ, Welker F. Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci Rep 2019; 9:12350. [PMID: 31451791 PMCID: PMC6710433 DOI: 10.1038/s41598-019-48706-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.
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Affiliation(s)
- Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matteo Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna, Italy.,University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Marco Peresani
- University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy.
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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46
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McGrath K, Rowsell K, Gates St-Pierre C, Tedder A, Foody G, Roberts C, Speller C, Collins M. Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points. Sci Rep 2019; 9:11027. [PMID: 31363122 PMCID: PMC6667708 DOI: 10.1038/s41598-019-47299-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.
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Affiliation(s)
- Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK.
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, York, UK.,London School of Economics and Political Science, London, UK
| | | | - Andrew Tedder
- School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - George Foody
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, York, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
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47
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Peyrégne S, Slon V, Mafessoni F, de Filippo C, Hajdinjak M, Nagel S, Nickel B, Essel E, Le Cabec A, Wehrberger K, Conard NJ, Kind CJ, Posth C, Krause J, Abrams G, Bonjean D, Di Modica K, Toussaint M, Kelso J, Meyer M, Pääbo S, Prüfer K. Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. SCIENCE ADVANCES 2019; 5:eaaw5873. [PMID: 31249872 PMCID: PMC6594762 DOI: 10.1126/sciadv.aaw5873] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Adeline Le Cabec
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | | | - Nicholas J. Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, Tübingen72070, Germany
| | - Claus Joachim Kind
- State Office for Cultural Heritage Baden-Württemberg Berliner Strasse 12, Esslingen 73728 Germany
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
| | | | | | | | | | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
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48
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Maity PP, Dutta D, Ganguly S, Kapat K, Dixit K, Chowdhury AR, Samanta R, Das NC, Datta P, Das AK, Dhara S. Isolation and mass spectrometry based hydroxyproline mapping of type II collagen derived from Capra hircus ear cartilage. Commun Biol 2019; 2:146. [PMID: 31044171 PMCID: PMC6488623 DOI: 10.1038/s42003-019-0394-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/18/2019] [Indexed: 11/19/2022] Open
Abstract
Collagen II (COLII), the most abundant protein in vertebrates, helps maintain the structural and functional integrity of cartilage. Delivery of COLII from animal sources could improve cartilage regeneration therapies. Here we show that COLII can be purified from the Capra ear cartilage, a commonly available bio-waste product, with a high yield. MALDI-MS/MS analysis evidenced post-translational modifications of the signature triplet, Glycine-Proline-Hydroxyproline (G-P-Hyp), in alpha chain of isolated COLII (COLIIA1). Additionally, thirty-two peptides containing 59 Hyp residues and a few G-X-Y triplets with positional alterations of Hyp in COLIIA1 are also identified. Furthermore, we show that an injectable hydrogel formulation containing the isolated COLII facilitates chondrogenic differentiation towards cartilage regeneration. These findings show that COLII can be isolated from Capra ear cartilage and that positional alteration of Hyp in its structural motif, as detected by newly developed mass spectrometric method, might be an early marker of cartilage disorder.
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Affiliation(s)
- Priti Prasanna Maity
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Debabrata Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Sayan Ganguly
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Kausik Kapat
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Krishna Dixit
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Amit Roy Chowdhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Ramapati Samanta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Narayan Chandra Das
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Pallab Datta
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Santanu Dhara
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
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49
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Wasinger VC, Curnoe D, Bustamante S, Mendoza R, Shoocongdej R, Adler L, Baker A, Chintakanon K, Boel C, Tacon PS. Analysis of the Preserved Amino Acid Bias in Peptide Profiles of Iron Age Teeth from a Tropical Environment Enable Sexing of Individuals Using Amelogenin MRM. Proteomics 2019; 19:e1800341. [DOI: 10.1002/pmic.201800341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/18/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Valerie C. Wasinger
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Darren Curnoe
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Raynold Mendoza
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Rasmi Shoocongdej
- Department of Archaeology Silpakorn University Bangkok 10200 Thailand
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
| | - Lewis Adler
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Andy Baker
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Kanoknart Chintakanon
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
- Advanced Dental Technology Center Thailand Science Park Amphoe Khlong Luang, Chang Wat Pathum Thani 12120 Thailand
| | - Ceridwen Boel
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Paul S.C. Tacon
- PERAHU Griffith Centre for Social and Cultural Research & School of Humanities Languages and Social Science Griffith University Gold Coast campus QLD 4222 Australia
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50
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Jacobs Z, Li B, Shunkov MV, Kozlikin MB, Bolikhovskaya NS, Agadjanian AK, Uliyanov VA, Vasiliev SK, O’Gorman K, Derevianko AP, Roberts RG. Timing of archaic hominin occupation of Denisova Cave in southern Siberia. Nature 2019; 565:594-599. [DOI: 10.1038/s41586-018-0843-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/30/2018] [Indexed: 11/09/2022]
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