1
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Anderson LA. Nanoscopic imaging of ancient protein and vasculature offers insight into soft tissue and biomolecule fossilization. iScience 2024; 27:110538. [PMID: 39286513 PMCID: PMC11404208 DOI: 10.1016/j.isci.2024.110538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/18/2024] [Accepted: 07/16/2024] [Indexed: 09/19/2024] Open
Abstract
Fossil bones have been studied by paleontologists for centuries. Despite this, empirical knowledge regarding the progression of biomolecular (soft) tissue diagenesis within ancient bone is limited; this is particularly the case for specimens spanning Pleistocene directly into pre-Ice Age strata. A nanoscopic approach is reported herein that facilitates direct imaging, and thus empirical observation, of soft tissue preservation state. Presented data include the first extensive nanoscopic (up to 150,000× magnification), three-dimensional (3D) images of ancient bone protein and vasculature; chemical signals consistent with collagen protein and membrane lipids, respectively, are also localized to these structures. These findings support the analyzed permafrost bones are not fully fossilized but rather represent subfossil bone tissue as they preserve an underlying collagen framework. Extension of these methods to specimens spanning the geologic record will help reveal changes biomolecular tissues undergo during fossilization and is a potential proxy approach for screening specimen suitability for molecular sequencing.
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Affiliation(s)
- Landon A Anderson
- Department of Biology, North Carolina State University, Raleigh, NC, USA
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2
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Li J, Ulloa GM, Mayor P, Santolalla Robles ML, Greenwood AD. Nucleic acid degradation after long-term dried blood spot storage. Mol Ecol Resour 2024; 24:e13979. [PMID: 38780145 DOI: 10.1111/1755-0998.13979] [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: 10/25/2023] [Revised: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.
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Affiliation(s)
- Juan Li
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Gabriela M Ulloa
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- Grupo de Enfermedades Infecciosas Re-emergentes, Universidad Científica del Sur (UCSUR), Lima, Peru
| | - Pedro Mayor
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- ComFauna, Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica, Iquitos, Peru
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Meddly L Santolalla Robles
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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3
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Zupanič Pajnič I, Kovačič N. DNA preservation in compact and trabecular bone. Forensic Sci Int Genet 2024; 71:103067. [PMID: 38833778 DOI: 10.1016/j.fsigen.2024.103067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
Significant variation exists in the molecular structure of compact and trabecular bone. In compact bone full dissolution of the bone powder is required to efficiently release the DNA from hydroxyapatite. In trabecular bone where soft tissues are preserved, we assume that full dissolution of the bone powder is not required to release the DNA from collagen. To investigate this issue, research was performed on 45 Second World War diaphysis (compact bone)-epiphysis (trabecular bone) femur pairs, each processed with a full dissolution (FD) and partial dissolution (PD) extraction method. DNA quality and quantity were assessed using qPCR PowerQuant analyses, and autosomal STRs were typed to confirm the authenticity of isolated DNA. Our results support different mechanisms of DNA preservation in compact and trabecular bone because FD method was more efficient than PD method only in compact bone, and no difference in DNA yield was observed in trabecular bone, showing no need for full dissolution of the bone powder when trabecular bone tissue is processed. In addition, a significant difference in DNA yield was observed between compact and trabecular bone when PD was applied, with more DNA extracted from trabecular bone than compact bone. High suitability of trabecular bone processed with PD method is also supported by the similar quantities of DNA isolated by FD method when applied to both compact and trabecular bone. Additionally similar quantities of DNA were isolated when compact bone was extracted with FD method and trabecular bone was extracted with PD method. Processing trabecular bone with PD method in routine identification of skeletonized human remains shortens the extraction procedure and simplifies the grinding process.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia.
| | - Nika Kovačič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia
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4
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Leskovar T, Jerman I, Zupanič Pajnič I. The mysteries of DNA preservation in bone: A comparative study of petrous bones and metacarpal epiphyses using ATR-FTIR spectroscopy. Forensic Sci Int 2024; 360:112076. [PMID: 38821024 DOI: 10.1016/j.forsciint.2024.112076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
A comparative analysis of 26 petrous bones and epiphyses of metacarpals from the Second World War era revealed no significant differences in DNA yield or success in STR typing. This unexpected parity in DNA preservation between the petrous bone, a renowned source of endogenous DNA in skeletal remains, and the epiphyses of metacarpals, which are porous and susceptible to taphonomic changes, is surprising. In this study, we introduced ATR-FTIR spectroscopy as an approach to unravel the correlation between bone molecular structure and DNA preservation. Metacarpals and petrous bones with same taphonomic history were sampled and prepared for DNA analyses. While one portion of the sample was used for DNA analysis, the other underwent ATR-FTIR spectroscopic examination. The normalized spectra and FTIR indices between the epiphyses of metacarpals and petrous bones were compared. Because the taphonomic history of the remains used is relatively short and stable, the ATR-FTIR spectroscopy unveiled subtle structural differences between the two bone types. Petrous bones exhibited higher mineralization, whereas epiphyses contained more organic matter. The unexpected preservation of DNA in the epiphyses of metacarpals can likely be attributed to the presence of soft tissue remnants within the trabeculae. Here observed differences in the molecular structure of bones indicate there are different mechanisms enabling DNA preservation in skeletal tissues.
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Affiliation(s)
- Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, Ljubljana 1000, Slovenia
| | - Ivan Jerman
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia.
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5
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Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024; 19:e0302646. [PMID: 38709766 PMCID: PMC11073703 DOI: 10.1371/journal.pone.0302646] [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: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
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Affiliation(s)
- Raphaël Martin-Roy
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Jakob Thyrring
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Xavier Mata
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Pernille Bangsgaard
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | | | - Svend Funder
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Carsten Ilsøe
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Frédéric Marin
- Biogéosciences, UMR6282, CNRS-EPHE-uB, University of Burgundy, EPHE, Dijon, France
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
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6
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Scaggion C, Marinato M, Dal Sasso G, Nodari L, Saupe T, Aneli S, Pagani L, Scheib CL, Rigo M, Artioli G. A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones. Sci Rep 2024; 14:1028. [PMID: 38200208 PMCID: PMC10781948 DOI: 10.1038/s41598-024-51518-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024] Open
Abstract
Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.
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Affiliation(s)
- Cinzia Scaggion
- Department of Geosciences, University of Padova, 35131, Padova, Italy.
- INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy.
| | - Maurizio Marinato
- Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padova, 35139, Padova, Italy
| | - Gregorio Dal Sasso
- Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy
| | - Luca Nodari
- Institute of Condensed Matter Chemistry and Technologies for Energy, Italian National Research Council-CNR, 35127, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Serena Aneli
- Department of Biology, University of Padova, 35122, Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Torino, 10126, Torino, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Biology, University of Padova, 35122, Padova, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Manuel Rigo
- Department of Geosciences, University of Padova, 35131, Padova, Italy
- Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy
| | - Gilberto Artioli
- Department of Geosciences, University of Padova, 35131, Padova, Italy
- INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy
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7
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Naue J, Xavier C, Hörer S, Parson W, Lutz-Bonengel S. Assessment of mitochondrial DNA copy number variation relative to nuclear DNA quantity between different tissues. Mitochondrion 2024; 74:101823. [PMID: 38040171 DOI: 10.1016/j.mito.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/23/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mitochondrial DNA is a widely tested genetic marker in various fields of research and diagnostics. Nonetheless, there is still little understanding on its abundance and quality within different tissues. Aiming to obtain deeper knowledge about the content and quality of mtDNA, we investigated nine tissues including blood, bone, brain, hair (root and shaft), cardiac muscle, liver, lung, skeletal muscle, and buccal mucosa of 32 deceased individuals using two real-time quantitative PCR-based assays with differently sized mtDNA and nDNA targets. The results revealed that the quantity of nDNA is a weak surrogate to estimate mtDNA quantities among tissues of an individual, as well as tissues across individuals. Especially hair showed extreme variation, depicting a range of multiple magnitudes of mtDNA molecules per hair fragment. Furthermore, degradation can lead to fewer fragments being available for PCR. The results call for parallel determination of the quantity and quality of mtDNA prior to downstream genotyping assays.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Steffen Hörer
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; Forensic Science Program, The Pennsylvania State University, USA.
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
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8
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S D Corrêa H, Alessandri I, Verzeletti A. Assessing the usefulness of Raman spectroscopy and lipid analysis of decomposed human bones in forensic genetics and molecular taphonomy. Forensic Sci Int 2024; 354:111881. [PMID: 38000148 DOI: 10.1016/j.forsciint.2023.111881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/18/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023]
Abstract
Bones are among the structures most likely to be recovered after death. However, the low quantity of preserved DNA and complex processing from sample to DNA profile make forensic DNA analysis of bones a challenging task. Raman spectroscopy and gas chromatography-mass spectrometry (GC/MS), have the potential to be useful as screening tools for DNA analysis and in decomposition studies. The objective of this research was to assess the usefulness of such molecular investigations. Femur samples collected from 50 decomposing human bodies were subjected to Raman spectroscopy and GC/MS. Assessment of nuclear DNA quantity and short tandem repeat (STR) genotyping efficiency were also performed. Raman parameters (crystallinity, carbonate-to-phosphate ratio, mineral-to-matrix ratio) and detected lipids were recorded. Background fluorescence proved problematic for Raman analysis of forensic bones. Regardless, it was not associated with less preserved DNA or less detected STR alleles. Fatty acids, hydrocarbons, and five types of fatty acid methyl esters (FAMEs) were detected. The main phosphate peak position in Raman spectra was significantly correlated with preserved DNA (p = 0.03713), while significantly more STR alleles were detected in bones containing methyl hexadecenoate (p = 0.04236). Detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which are not associated with the level of preservation of endogenous DNA. The techniques assessed have shown to be useful in molecular taphonomy studies and forensic genetics.
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Affiliation(s)
- Heitor S D Corrêa
- Institute of Legal Medicine, Department of Medico-surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy; Forensic DNA Laboratory, Politec/MT, Cuiabá, Brazil.
| | - Ivano Alessandri
- INSTM and Sustainable Chemistry and Materials Laboratory, Department of Information Engineering, University of Brescia, Brescia, Italy
| | - Andrea Verzeletti
- Institute of Legal Medicine, Department of Medico-surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
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9
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Zupanič Pajnič I, Mlinšek T, Počivavšek T, Leskovar T. Genetic sexing of subadult skeletal remains. Sci Rep 2023; 13:20463. [PMID: 37993531 PMCID: PMC10665466 DOI: 10.1038/s41598-023-47836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Teo Mlinšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tadej Počivavšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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10
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Rahmat RA, Humphries MA, Saedon NA, Self PG, Linacre AMT. Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth. Int J Legal Med 2023; 137:1353-1360. [PMID: 37306739 DOI: 10.1007/s00414-023-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Melissa A Humphries
- School and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, 5006, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, the University of Adelaide, Adelaide, South Australia, Australia
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor, 46661, Malaysia
| | - Peter G Self
- CSIRO, Land and Water, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
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11
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Inkret J, Zupanc T, Zupanič Pajnič I. A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology. Genes (Basel) 2023; 14:1449. [PMID: 37510353 PMCID: PMC10379588 DOI: 10.3390/genes14071449] [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: 06/08/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
It is very important to generate phenotypic results that are reliable when processing chronological old skeletal remains for cases involving the identification of missing persons. To improve the success of pigmentation prediction in Second World War victims, three bones from each of the eight skeletons analyzed were included in the study, which makes it possible to generate a consensus profile. The PowerQuant System was used for quantification, the ESI 17 Fast System was used for STR typing, and a customized version of the HIrisPlex panel was used for PCR-MPS. The HID Ion Chef Instrument was used for library preparation and templating. Sequencing was performed with the Ion GeneStudio S5 System. Identical full profiles and identical hair and eye color predictions were achieved from three bones analyzed per skeleton. Blue eye color was predicted in five skeletons and brown in three skeletons. Blond hair color was predicted in one skeleton, blond to dark blond in three skeletons, brown to dark brown in two skeletons, and dark brown to black in two skeletons. The reproducibility and reliability of the results proved the multisample analysis method to be beneficial for phenotyping chronological old skeletons because differences in DNA yields in different bone types provide a greater possibility of obtaining a better-quality consensus profile.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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12
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [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: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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13
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Bonfigli A, Cesare P, Volpe AR, Colafarina S, Forgione A, Aloisi M, Zarivi O, Poma AMG. Estimation of DNA Degradation in Archaeological Human Remains. Genes (Basel) 2023; 14:1238. [PMID: 37372418 DOI: 10.3390/genes14061238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.
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Affiliation(s)
- Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Rita Volpe
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alfonso Forgione
- Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy
| | - Massimo Aloisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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14
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Zupanič Pajnič I, Leskovar T, Črešnar M. Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med 2023:10.1007/s00414-023-03003-3. [PMID: 37127762 DOI: 10.1007/s00414-023-03003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 107 (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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15
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Zupanič Pajnič I, Leskovar T, Zupanc T, Podovšovnik E. A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples. Forensic Sci Int Genet 2023; 65:102882. [PMID: 37141673 DOI: 10.1016/j.fsigen.2023.102882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/20/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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16
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Zupanič Pajnič I, Geršak ŽM, Leskovar T, Črešnar M. Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. Forensic Sci Int Genet 2023; 65:102886. [PMID: 37137206 DOI: 10.1016/j.fsigen.2023.102886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Živa Miriam Geršak
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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17
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Eaton K, Sidhu RK, Klunk J, Gamble JA, Boldsen JL, Carmichael AG, Varlık N, Duchene S, Featherstone L, Grimes V, Golding GB, DeWitte SN, Holmes EC, Poinar HN. Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. Curr Biol 2023; 33:1147-1152.e5. [PMID: 36841239 DOI: 10.1016/j.cub.2023.01.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.1,2 A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.3 Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.4,5 To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.
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Affiliation(s)
- Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Ravneet K Sidhu
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Daicel Arbor Biosciences, Ann Arbor, MI 48103, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, 5260 Odense, Denmark
| | - Ann G Carmichael
- Department of History, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Nükhet Varlık
- Department of History, Rutgers University - Newark, Newark, NJ 07102, USA
| | - Sebastian Duchene
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Leo Featherstone
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, SC A1C 5S7, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC 29208, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney 2006, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biochemistry, McMaster University, Hamilton, ON L82 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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18
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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Mullin VE, Stephen W, Arce AN, Nash W, Raine C, Notton DG, Whiffin A, Blagderov V, Gharbi K, Hogan J, Hunter T, Irish N, Jackson S, Judd S, Watkins C, Haerty W, Ollerton J, Brace S, Gill RJ, Barnes I. First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria E. Mullin
- Department of Earth Sciences The Natural History Museum London UK
- Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland
| | - William Stephen
- Department of Earth Sciences The Natural History Museum London UK
| | - Andres N. Arce
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
- School of Engineering, Arts, Science & Technology University of Suffolk Ipswich UK
| | - Will Nash
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Calum Raine
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | | | | | | | - Karim Gharbi
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - James Hogan
- Oxford University Museum of Natural History Oxford UK
| | | | - Naomi Irish
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Simon Jackson
- Tullie House Museum and Art Gallery Trust Carlisle UK
- Ipswich Museum (Colchester and Ipswich Museums) Ipswich UK
| | | | - Chris Watkins
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Wilfried Haerty
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology University of Northampton Northampton UK
| | - Selina Brace
- Department of Earth Sciences The Natural History Museum London UK
| | - Richard J. Gill
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
| | - Ian Barnes
- Department of Earth Sciences The Natural History Museum London UK
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20
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A 16 th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 2022; 5:599. [PMID: 35710940 PMCID: PMC9203756 DOI: 10.1038/s42003-022-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past. Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
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21
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Żyła A. DNA: prawie niezniszczalny i najbardziej pojemny nośnik danych. ARCHEION 2021. [DOI: 10.4467/26581264arc.21.014.14494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dzięki ewolucji technologicznej prawie całkowicie zrezygnowano współcześnie z analogowej archiwizacji informacji (papier, klisza, obraz) na rzecz zapisu cyfrowego. Obecnie potrzeba magazynowania wytwarzanych i przetwarzanych informacji wzrasta w eksponencjalnym tempie. Coraz większą popularnością cieszą się tzw. chmury (cloud) internetowe. Rozwój naukowy podsuwa inne rozwiązanie, zainspirowane najstarszym, ale także niesamowicie trwałym nośnikiem informacji, czyli ciągiem kwasów nukleinowych: DNA. Co więcej, DNA jest bardzo trwałe, a zakonserwowane w odpowiednich warunkach niemal niezniszczalne w odniesieniu do długości ludzkiego życia. Ponadto informacja zawarta w kwasach nukleinowych jest bardzo skondensowana. Oznacza to, że w kilku probówkach możemy zapisać informację o całych serwerach danych. Naukowcy od lat myślą o zastąpieniu cyfrowych nośników danych informacjami zapisanymi w kodzie genetycznym. Dzięki rozwojowi nauki ta perspektywa staje się atrakcyjna.
DNA: an almost indestructible data carrier with incomparable capacity
Thanks to the technological evolution, analog methods of archiving information (paper, film, image) have been almost entirely replaced by digital storage. Currently, the need for storage of generated and processed information is growing at an exponential rate. The so-called clouds are becoming increasingly popular. Scientific advances suggest yet another solution, inspired by the oldest but also incredibly durable information carrier, i.e. a sequence of nucleic acids: DNA. Moreover, DNA is very durable, and preserved in appropriate conditions, almost indestructible in relation to human lifespan. Further, the information contained in nucleic acids is very condensed. This means that in a scant few test tubes we could store servers’ worth of information. Scientists have been thinking for years about replacing digital data carriers with information stored in the genetic code. Thanks to new scientific developments, this prospect is becoming attractive.
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22
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Leskovar T, Zupanič Pajnič I, Jerman I. Dealing with minor differences in bone matrix: can spectra follow the DNA preservation? AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1948102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ivan Jerman
- Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
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23
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Rossi C, Ruß-Popa G, Mattiangeli V, McDaid F, Hare AJ, Davoudi H, Laleh H, Lorzadeh Z, Khazaeli R, Fathi H, Teasdale MD, A'ali A, Stöllner T, Mashkour M, Daly KG. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran. Biol Lett 2021; 17:20210222. [PMID: 34256582 PMCID: PMC8278039 DOI: 10.1098/rsbl.2021.0222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022] Open
Abstract
Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole-genome sequences (3.94 X) of an approximately 1600-year-old naturally mummified sheep recovered from Chehrābād, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed the remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination are substantially reduced, likely owing to the high salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high-salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the remarkable preservation of the sample. Applying population genomic analyses, we find clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the presence of an ancestral 'hairy' allele, consistent with hair fibre imaging. This, along with derived alleles associated with the fat-tail phenotype, provides genetic evidence that Sasanian-period Iranians maintained specialized sheep flocks for different uses, with the 'hairy', 'fat-tailed'-genotyped sheep likely kept by the rural community of Chehrābād's miners.
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Affiliation(s)
- Conor Rossi
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Gabriela Ruß-Popa
- Austrian Academy of Sciences, Austrian Archaeological Institute, Archaeological Sciences, Hollandstraße 11-13, 1020 Vienna, Austria
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Fionnuala McDaid
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Hossein Davoudi
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Haeedeh Laleh
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
- Faculty of Humanities, Department of Archaeology, University of Tehran, 1417935840 Tehran, Iran
| | - Zahra Lorzadeh
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Roya Khazaeli
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Homa Fathi
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Matthew D. Teasdale
- McDonald Institute for Archaeological Research, Dept. of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | - Abolfazl A'ali
- Zanjan Cultural Heritage Centre, Archaeological Museum of Zanjan, Emaarate Zolfaghari, Taleghani St., Zanjan, Iran
| | - Thomas Stöllner
- Research Department, Haus der Archäologien, Ruhr University Bochum, Institute for Archaeological Studies and Deutsches Bergbau-Museum Bochum, Am Bergbaumuseum 31, D-44791 Bochum, Germany
| | - Marjan Mashkour
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, Sorbonne Université, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
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24
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Zupanič Pajnič I, Leskovar T, Jerman I. Bone fragment or bone powder? ATR-FTIR spectroscopy-based comparison of chemical composition and DNA preservation of bones after 10 years in a freezer. Int J Legal Med 2021; 135:1695-1707. [PMID: 34031722 DOI: 10.1007/s00414-021-02620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Freezing bone samples to preserve their biomolecular properties for various analyses at a later time is a common practice. Storage temperature and freeze-thaw cycles are well-known factors affecting degradation of molecules in the bone, whereas less is known about the form in which the tissue is most stable. In general, as little intervention as possible is advised before storage. In the case of DNA analyses, homogenization of the bone shortly before DNA extraction is recommended. Because recent research on the DNA yield from frozen bone fragments and frozen bone powder indicates better DNA preservation in the latter, the aim of the study presented here was to investigate and compare the chemical composition of both types of samples (fragments versus powder) using ATR-FTIR spectroscopy. Pairs of bone fragments and bone powder originating from the same femur of 57 individuals from a Second World War mass grave, stored in a freezer at - 20 °C for 10 years, were analyzed. Prior to analysis, the stored fragments were ground into powder, whereas the stored powder was analyzed without any further preparation. Spectroscopic analysis was performed using ATR-FTIR spectroscopy. The spectra obtained were processed and analyzed to determine and compare the chemical composition of both types of samples. The results show that frozen powdered samples have significantly better-preserved organic matter and lower concentrations of B-type carbonates, but higher concentrations of A-type carbonates and stoichiometric apatite. In addition, there are more differences in the samples with a low DNA degradation index and less in the samples with a high DNA degradation index. Because the results are inconsistent with the current understanding of bone preservation, additional research into optimal preparation and long-term storage of bone samples is necessary.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000, Ljubljana, Slovenia.
| | - Ivan Jerman
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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25
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Keighley X, Bro‐Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals. Mol Ecol Resour 2021; 21:1149-1166. [PMID: 33463014 PMCID: PMC8248401 DOI: 10.1111/1755-0998.13331] [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: 10/14/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.
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Affiliation(s)
- Xénia Keighley
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Arctic Centre/Groningen Institute of ArchaeologyFaculty of ArtsUniversity of GroningenAS GroningenThe Netherlands
| | - Maiken Hemme Bro‐Jørgensen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Hans Ahlgren
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Paul Szpak
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
| | - Marta Maria Ciucani
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
| | | | - Lesley Howse
- Archaeology CentreUniversity of TorontoTorontoOntarioCanada
| | | | - Aikaterini Glykou
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Peter Jordan
- Department of Archaeology and Ancient HistoryLund UniversityLundSweden
| | - Kerstin Lidén
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
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Aznar-Cormano L, Bonnald J, Krief S, Guma N, Debruyne R. Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics. Sci Rep 2021; 11:7227. [PMID: 33790303 PMCID: PMC8012363 DOI: 10.1038/s41598-021-86010-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 11/24/2022] Open
Abstract
It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.
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Affiliation(s)
- Laetitia Aznar-Cormano
- CNRS, Centre de Recherche en Paléontologie Paris (CR2P), Muséum national d'Histoire naturelle, Sorbonne Université, 57 rue Cuvier, CP 38, 75005, Paris, France
| | - Julie Bonnald
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | - Sabrina Krief
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | | | - Régis Debruyne
- Direction Générale Déléguée à la Recherche, à l'Expertise, la Valorisation et l'Enseignement (DGD-REVE), Muséum national d'Histoire naturelle, 57 rue Cuvier, CP 17, 75005, Paris, France.
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27
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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28
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Peyrégne S, Peter BM. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol 2020; 21:246. [PMID: 32933569 PMCID: PMC7490890 DOI: 10.1186/s13059-020-02123-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022] Open
Abstract
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
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29
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Peyrégne S, Prüfer K. Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays 2020; 42:e2000081. [PMID: 32648350 DOI: 10.1002/bies.202000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
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30
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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31
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Mckinnon M, Henneberg M, Simpson E, Higgins D. A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling. Forensic Sci Int 2020; 313:110328. [PMID: 32502739 DOI: 10.1016/j.forsciint.2020.110328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
Standard protocols for extracting DNA from bone are variable and are largely dependent on the state of preservation. In archaic samples, endogenous DNA is believed to be tightly bound to crystal aggregates in the Hydroxyapatite (HAp) matrix requiring prolonged demineralisation to allow its release. By comparison, fresh bone contains abundant cellular material, discounting the need for demineralisation. Recommendations for incinerated bone, specifically how viable sampling sites should be selected and the ideal techniques for DNA recovery are unclear, and the protocol used is often selected based on macroscopic sample appearance. It has been postulated that like archaic bone, burned bone is 'highly degraded' and therefore aDNA techniques may present better results for DNA recovery than using fresh protocols. However, little research has been undertaken comparing the crystal structure of burnt, fresh and archaic bone. This study uses a combination of XRPD and SEM analysis to compare the crystalline profile and microscopic appearance of burned bone subjected to temperatures ranging from 100-1000°C, with archaic and fresh samples. Although macroscopically visually different, fresh samples and samples heated up to 500°C showed no microscopic differences or significant changes in crystallinity. By comparison, samples heated above 500°C became significantly more crystalline, with HAp crystal size increasing dramatically. Archaic samples were different again, more closely resembling the amorphous fresh samples than the highly crystalline incinerated samples. These results suggests that, potentially, samples burned at 500°C or lower can be treated as fresh samples, whilst samples exposed to higher temperatures may require adapted protocols. Whether or not these highly burned samples require demineralisation needs to be investigated.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Frome Road, Adelaide, SA 5000, Australia
| | | | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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32
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Gonzalez A, Cannet C, Zvénigorosky V, Geraut A, Koch G, Delabarde T, Ludes B, Raul JS, Keyser C. The petrous bone: Ideal substrate in legal medicine? Forensic Sci Int Genet 2020; 47:102305. [PMID: 32446165 DOI: 10.1016/j.fsigen.2020.102305] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.
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Affiliation(s)
- Angéla Gonzalez
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Catherine Cannet
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Vincent Zvénigorosky
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France; CNRS, FRE2029-BABEL, Université Paris Descartes, France.
| | - Annie Geraut
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Guillaume Koch
- Institut d'Anatomie Normale, Hôpitaux Universitaires de Strasbourg, Faculté de médecine de Strasbourg, France.
| | | | - Bertrand Ludes
- CNRS, FRE2029-BABEL, Université Paris Descartes, France; Institut Médico-Légal de Paris, France; Institut National de la Transfusion Sanguine, Paris, France.
| | - Jean-Sébastien Raul
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Christine Keyser
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France; CNRS, FRE2029-BABEL, Université Paris Descartes, France; Institut National de la Transfusion Sanguine, Paris, France.
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Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
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Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
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34
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ATR-FTIR spectroscopy combined with data manipulation as a pre-screening method to assess DNA preservation in skeletal remains. Forensic Sci Int Genet 2020; 44:102196. [DOI: 10.1016/j.fsigen.2019.102196] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/20/2022]
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35
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Caputo M, Corach D. Reply to comment “A DNA extraction method of small quantities of bone for high-quality genotyping”. Forensic Sci Int Genet 2019; 41:e18-e19. [DOI: 10.1016/j.fsigen.2019.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/26/2022]
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36
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Cafiero C, Re A, Stigliano E, Bassotti E, Moroni R, Grippaudo C. Optimization of DNA extraction from dental remains. Electrophoresis 2019; 40:1820-1823. [PMID: 31111969 PMCID: PMC6771583 DOI: 10.1002/elps.201900142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/18/2022]
Abstract
Efficient DNA extraction procedures is a critical step involved in the process of successful DNA analysis of such samples. Various protocols have been devised for the genomic DNA extraction from human tissues and forensic stains, such as dental tissue that is the skeletal part that better preserves DNA over time. However DNA recovery is low and protocols require labor‐intensive and time‐consuming step prior to isolating genetic material. Herein, we describe an extremely fast procedure of DNA extraction from teeth compared to classical method. Sixteen teeth of 100‐year‐old human remains were divided into two groups of 8 teeth and we compared DNA yield, in term of quantity and quality, starting from two different sample preparation steps. Specifically, teeth of group 1 were treated with a classic technique based on several steps of pulverization and decalcification, while teeth of group 2 were processed following a new procedure to withdraw dental pulp. In the next phase, the samples of both group underwent the same procedure of extraction, quantification and DNA profile analysis. Our findings provide an alternative protocol to obtain a higher amount of good quality DNA in a fast time procedure, helpful for forensic and anthropological studies.
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Affiliation(s)
- Concetta Cafiero
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Agnese Re
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Egidio Stigliano
- Università Cattolica del Sacro Cuore-Institute of Pathological Anatomy, Rome, Italy
| | - Ezio Bassotti
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Rossana Moroni
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Cristina Grippaudo
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
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37
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Sigwart JD, Garbett A. Biodiversity Assessment, DNA Barcoding, and the Minority Majority. Integr Comp Biol 2019; 58:1146-1156. [PMID: 30053016 DOI: 10.1093/icb/icy076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The majority of species on Earth are in "under-studied" groups, and indeed probably the majority of species remain undiscovered and undescribed. Species are natural units of evolution, and they are formed from branching phylogenetic processes that have a mathematical structure. So it follows that we should be able to develop a set of general principles that describe global patterns of species groups, like genera. Understanding such patterns would lend considerable power to the approach of "taxonomic surrogacy." In environmental assessments, ecology, and paleontology, it is common to substitute genus-level or family-level identification where definitive species identification is impractical. Clarity and confidence in fundamental patterns, based on a robust null model for species and genus level diversity, can accelerate species discovery: there are more species in the tropics, species-poor genera are very common, large genera are rare. Much hope has been placed in DNA barcoding as an effective tool to increase the pace of species discovery, but it is abundantly clear that certain mitochondrial DNA (mtDNA) markers are more or less variable in different clades and universal threshold values are impractical to delimit species. This study further examines the patterns of divergence in one common mtDNA barcode fragment, cytochrome c oxidase subunit 1at the genus level. We compared pairwise divergence in this fragment between two animal clades that have similar species richness but different evolutionary histories: birds and bivalves. We analyzed quality controlled alignments of over 39,000 published sequences in 1223 genera. Median pairwise differences at the genus level are positively correlated with the species richness of a genus, and this is not dependent of the number of sequences sampled. Unsurprisingly, sequence divergence in vertebrates was far more constrained than in evolutionarily more ancient non-vertebrate clades. Differences among the groups examined highlight the need for DNA barcode approaches to be considered in the context of specific biological groups. Vertebrates are better studied, but not necessarily representative of the majority of biodiversity. A technique that provides powerful insights for vertebrate species may be ineffective for the majority of organisms.
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Affiliation(s)
- Julia D Sigwart
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
| | - Amy Garbett
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
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Abstract
Youtube.com has become one of the most popular places to share videos on the Internet, storing a large amount of audiovisual materials. People all over the world can upload their videos and watch videos of others. The research potential of this information source has received increasing popularity across scientific disciplines. In this contribution, we explore the top viewed videos containing selected cryospheric keywords, both general (cryosphere, glacier, ice, permafrost, snow), and specific, focusing on different types of cryospheric hazards (avalanche, blizzard and glacial lake outburst flood/jokulhlaup). Searching 100 top-viewed videos for each keyword, our database consists of 859 videos. Each video is described by several qualitative characteristics (e.g., video type, geographical focus) as well as quantitative characteristics (e.g., views per day, likes). A total of 310 videos in our database (36.1% of all) are classified as videos with factual cryospheric content. We show that the broader audience represented by YouTube users is particularly interested in videos capturing dynamic processes such as calving of glaciers. While videos found for general cryosphere keywords have attracted a generally higher attention of YouTube users (total views), videos found for specific keywords are ranked among the most liked. Further, we analyze where the videos with cryospheric content are filmed, revealing several hotspots for different keywords located in all continents except for Africa. Finally, we discuss the potentials of cryosphere videos for educational and research purposes, pointing out that videos filmed by incidental witnesses of low-frequency processes such as glacial lake outburst floods might contribute to the elucidation of their dynamics, magnitude and behavior as well as the occurrence in space and time.
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39
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Rohland N, Glocke I, Aximu-Petri A, Meyer M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat Protoc 2019; 13:2447-2461. [PMID: 30323185 DOI: 10.1038/s41596-018-0050-5] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA preserved in ancient bones, teeth and sediments is typically highly fragmented and present only in minute amounts. Here, we provide a highly versatile silica-based DNA extraction protocol that enables the retrieval of short (≥35 bp) or even ultrashort (≥25 bp) DNA fragments from such material with minimal carryover of substances that inhibit library preparation for high-throughput sequencing. DNA extraction can be performed with either silica spin columns, which offer the most convenient choice for manual DNA extraction, or silica-coated magnetic particles. The latter allow a substantial cost reduction as well as automation on liquid-handling systems. This protocol update replaces a now-outdated version that was published 11 years ago, before high-throughput sequencing technologies became widely available. It has been thoroughly optimized to provide the highest DNA yields from highly degraded samples, as well as fast and easy handling, requiring not more than ~15 min of hands-on time per sample.
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Affiliation(s)
- Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Ayinuer Aximu-Petri
- 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
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40
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Klunk J, Duggan AT, Redfern R, Gamble J, Boldsen JL, Golding GB, Walter BS, Eaton K, Stangroom J, Rouillard JM, Devault A, DeWitte SN, Poinar HN. Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:240-252. [PMID: 30964548 DOI: 10.1002/ajpa.23820] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVES In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark. MATERIALS AND METHODS Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis. RESULTS We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing. DISCUSSION The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.
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Affiliation(s)
- Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Rebecca Redfern
- Center for Human Bioarchaeology, Museum of London, London, UK
| | - Julia Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense, Denmark
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Brittany S Walter
- Defense POW/MIA Accounting Agency Laboratory, Offutt AFB, Omaha, Nebraska
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Julianna Stangroom
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Marie Rouillard
- Arbor Biosciences, Ann Arbor, Michigan.,Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, Michigan
| | | | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, South Carolina
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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41
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Decorte R, Polet C, Boudin M, Tilquin F, Matroule JY, Dieu M, Charles C, Carlier A, Lebecque F, Deparis O. An interdisciplinary study around the reliquary of the late cardinal Jacques de Vitry. PLoS One 2019; 14:e0201424. [PMID: 30794540 PMCID: PMC6386372 DOI: 10.1371/journal.pone.0201424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022] Open
Abstract
The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th century, has experienced several transfers over the last centuries, which seriously question the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth poses an additional question regarding his age at death in 1240. The reliquary, located in the Saint Marie d'Oigines church, Belgium, was reopened in 2015 for an interdisciplinary study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage notably built from Jacques de Vitry's donation. Anthropological, isotopic and genetic analyses were performed independently on the remains found in the reliquary. Results of the analyses provided evidence that the likelihood that these remains are those of Jacques de Vitry is very high: the remains belong to the same human male individual and the historical tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry's mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen was analysed by a proteomic method in order to determine the animal species. The results showed that, surprisingly, not all parts of the mitre were made from the same species. All together, these findings are expected to fertilize knowledge carried by historical tradition around the relics of Jacques de Vitry and his related cultural heritage.
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Affiliation(s)
- Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven (KUL), Leuven, Belgium
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Forensic Medicine, UZ Leuven (UZL), Leuven, Belgium
| | - Caroline Polet
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mathieu Boudin
- Radiocarbon Dating Laboratory, Royal Institute for Cultural Heritage (KIK-IRPA), Brussels, Belgium
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Catherine Charles
- Moretus Plantin University Library, University of Namur, Namur, Belgium
| | | | | | - Olivier Deparis
- Heritages, Transmissions, Inheritances (PaTHs) Institute & Department of Physics, University of Namur, Namur, Belgium
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42
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Kavlick MF. Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers. Mitochondrion 2018; 46:41-50. [PMID: 30261278 DOI: 10.1016/j.mito.2018.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 09/18/2018] [Indexed: 01/11/2023]
Abstract
A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice.
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Affiliation(s)
- Mark F Kavlick
- Counterterrorism and Forensic Science Research Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, United States.
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43
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Furtwängler A, Reiter E, Neumann GU, Siebke I, Steuri N, Hafner A, Lösch S, Anthes N, Schuenemann VJ, Krause J. Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis. Sci Rep 2018; 8:14075. [PMID: 30232341 PMCID: PMC6145933 DOI: 10.1038/s41598-018-32083-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022] Open
Abstract
In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.
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Affiliation(s)
- Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
| | - Ella Reiter
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Gunnar U Neumann
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Inga Siebke
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Nils Anthes
- Institute of Ecology and Evolution, Animal Evolutionary Ecology group University of Tübingen, Tübingen, Germany
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Jena, Germany.
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44
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Alberti F, Gonzalez J, Paijmans JLA, Basler N, Preick M, Henneberger K, Trinks A, Rabeder G, Conard NJ, Münzel SC, Joger U, Fritsch G, Hildebrandt T, Hofreiter M, Barlow A. Optimized DNA sampling of ancient bones using Computed Tomography scans. Mol Ecol Resour 2018; 18:1196-1208. [DOI: 10.1111/1755-0998.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Federica Alberti
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Javier Gonzalez
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | | | - Nikolas Basler
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Michaela Preick
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Alexandra Trinks
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
- Evolutionary Biology; IRI for the Life Sciences; Humboldt University Berlin; Berlin Germany
| | - Gernot Rabeder
- Department of Palaeontology; Geozentrum; University of Vienna; Vienna Austria
| | - Nicholas J. Conard
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Susanne C. Münzel
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum Braunschweig; Braunschweig Germany
| | - Guido Fritsch
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
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45
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Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T, Guichoux E, Chancerel E, Bech-Hebelstrup I, Bernard V, Billard C, Billaud Y, Bolliger M, Croutsch C, Čufar K, Eynaud F, Heussner KU, Köninger J, Langenegger F, Leroy F, Lima C, Martinelli N, Momber G, Billamboz A, Nelle O, Palomo A, Piqué R, Ramstein M, Schweichel R, Stäuble H, Tegel W, Terradas X, Verdin F, Plomion C, Kremer A, Orlando L. High-Throughput DNA sequencing of ancient wood. Mol Ecol 2018; 27:1138-1154. [PMID: 29412519 DOI: 10.1111/mec.14514] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023]
Abstract
Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.
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Affiliation(s)
- Stefanie Wagner
- BIOGECO, INRA, University of Bordeaux, Cestas, France.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Vincent Bernard
- Dendro-Archaeology, CNRS, UMR 6566 CReAAH, University of Rennes, Rennes cedex, France
| | | | - Yves Billaud
- MCC/DRASSM, Marseille, France.,Edytem, University of Savoie, Le Bourget-du-Lac, France
| | | | - Christophe Croutsch
- Archéologie Alsace 11, Sélestat, France.,UMR 7044, ARCHIMEDE, Strasbourg Cedex, France
| | - Katarina Čufar
- Biotechnical Faculty, Department of Wood Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Karl Uwe Heussner
- Deutsches Archäologisches Institut, Zentrale, Referat Naturwissenschaften/Dendrochronologie, Berlin, Germany
| | - Joachim Köninger
- Janus Verlag Freiburg im Breisgau, Freiburg im Breisgau, Germany
| | | | - Frédéric Leroy
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | - Christine Lima
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | | | - Garry Momber
- National Oceanography Centre, Maritime Archaeology Trust, Southampton, UK
| | - André Billamboz
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Oliver Nelle
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Antoni Palomo
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Piqué
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | - Willy Tegel
- Institute for Forest Growth, University of Freiburg, Freiburg, Germany
| | - Xavier Terradas
- Spanish National Research Council, IMF - Archaeology of Social Dynamics, Barcelona, Spain
| | - Florence Verdin
- CNRS, UMR 5607 Ausonius, Maison de l'Archéologie, Pessac cedex, France
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
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46
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Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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47
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Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 2018; 14:e1006750. [PMID: 29300782 PMCID: PMC5754119 DOI: 10.1371/journal.ppat.1006750] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.
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Affiliation(s)
- Zoe Patterson Ross
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sebastian Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Mark W. Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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48
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Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.
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Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
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50
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Glocke I, Meyer M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res 2017; 27:1230-1237. [PMID: 28408382 PMCID: PMC5495074 DOI: 10.1101/gr.219675.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
Abstract
The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with single-strand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material.
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Affiliation(s)
- Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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