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Langmore NE, Grealy A, Noh HJ, Medina I, Skeels A, Grant J, Murray KD, Kilner RM, Holleley CE. Coevolution with hosts underpins speciation in brood-parasitic cuckoos. Science 2024; 384:1030-1036. [PMID: 38815013 DOI: 10.1126/science.adj3210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Coevolution between interacting species is thought to increase biodiversity, but evidence linking microevolutionary processes to macroevolutionary patterns is scarce. We leveraged two decades of behavioral research coupled with historical DNA analysis to reveal that coevolution with hosts underpins speciation in brood-parasitic bronze-cuckoos. At a macroevolutionary scale, we show that highly virulent brood-parasitic taxa have higher speciation rates and are more likely to speciate in sympatry than less-virulent and nonparasitic relatives. We reveal the microevolutionary process underlying speciation: Hosts reject cuckoo nestlings, which selects for mimetic cuckoo nestling morphology. Where cuckoos exploit multiple hosts, selection for mimicry drives genetic and phenotypic divergence corresponding to host preference, even in sympatry. Our work elucidates perhaps the most common, but poorly characterized, evolutionary process driving biological diversification.
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Affiliation(s)
- N E Langmore
- Research School of Biology, Australian National University, Canberra, Australia
| | - A Grealy
- Research School of Biology, Australian National University, Canberra, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
| | - H-J Noh
- Research School of Biology, Australian National University, Canberra, Australia
| | - I Medina
- School of Biosciences, The University of Melbourne, Melbourne, Australia
| | - A Skeels
- Research School of Biology, Australian National University, Canberra, Australia
| | - J Grant
- Research School of Biology, Australian National University, Canberra, Australia
| | - K D Murray
- Research School of Biology, Australian National University, Canberra, Australia
| | - R M Kilner
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - C E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
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2
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Yaka R, Maja Krzewińska, Lagerholm VK, Linderholm A, Özer F, Somel M, Götherström A. Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. Biotechniques 2024; 76:216-223. [PMID: 38530148 DOI: 10.2144/btn-2023-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.
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Affiliation(s)
- Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
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3
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Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [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: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
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4
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Bennett EA, Parasayan O, Prat S, Péan S, Crépin L, Yanevich A, Grange T, Geigl EM. Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea. Nat Ecol Evol 2023; 7:2160-2172. [PMID: 37872416 DOI: 10.1038/s41559-023-02211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Populations genetically related to present-day Europeans first appeared in Europe at some point after 38,000-40,000 years ago, following a cold period of severe climatic disruption. These new migrants would eventually replace the pre-existing modern human ancestries in Europe, but initial interactions between these groups are unclear due to the lack of genomic evidence from the earliest periods of the migration. Here we describe the genomes of two 36,000-37,000-year-old individuals from Buran-Kaya III in Crimea as belonging to this newer migration. Both genomes share the highest similarity to Gravettian-associated individuals found several thousand years later in southwestern Europe. These genomes also revealed that the population turnover in Europe after 40,000 years ago was accompanied by admixture with pre-existing modern human populations. European ancestry before 40,000 years ago persisted not only at Buran-Kaya III but is also found in later Gravettian-associated populations of western Europe and Mesolithic Caucasus populations.
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Affiliation(s)
- E Andrew Bennett
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Oğuzhan Parasayan
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Sandrine Prat
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Alliance Sorbonne Université, Musée de l'Homme, Palais de Chaillot, Paris, France
| | - Stéphane Péan
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Laurent Crépin
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Alexandr Yanevich
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
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5
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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6
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Żarczyńska M, Żarczyński P, Tomsia M. Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics. Genes (Basel) 2023; 14:1643. [PMID: 37628694 PMCID: PMC10454188 DOI: 10.3390/genes14081643] [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: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.
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Affiliation(s)
- Małgorzata Żarczyńska
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Piotr Żarczyński
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland
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7
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Essel E, Zavala EI, Schulz-Kornas E, Kozlikin MB, Fewlass H, Vernot B, Shunkov MV, Derevianko AP, Douka K, Barnes I, Soulier MC, Schmidt A, Szymanski M, Tsanova T, Sirakov N, Endarova E, McPherron SP, Hublin JJ, Kelso J, Pääbo S, Hajdinjak M, Soressi M, Meyer M. Ancient human DNA recovered from a Palaeolithic pendant. Nature 2023:10.1038/s41586-023-06035-2. [PMID: 37138083 DOI: 10.1038/s41586-023-06035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, London, UK
| | - Marie-Cécile Soulier
- Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Merlin Szymanski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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8
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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9
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de Flamingh A, Ishida Y, Pečnerová P, Vilchis S, Siegismund HR, van Aarde RJ, Malhi RS, Roca AL. Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Front Genet 2023; 13:1021004. [PMID: 36712847 PMCID: PMC9876978 DOI: 10.3389/fgene.2022.1021004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/05/2022] [Indexed: 01/13/2023] Open
Abstract
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
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Affiliation(s)
- Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sahara Vilchis
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Hans R. Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rudi J. van Aarde
- Department of Zoology and Entomology, Conservation Ecology Research Unit, University of Pretoria, Pretoria, South Africa
| | - Ripan S. Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Alfred L. Roca
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
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10
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Analysis of Ancient Microbial DNA. Methods Mol Biol 2022; 2605:103-131. [PMID: 36520391 DOI: 10.1007/978-1-0716-2871-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.
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11
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Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel. Sci Rep 2022; 12:14528. [PMID: 36008437 PMCID: PMC9411205 DOI: 10.1038/s41598-022-17399-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
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12
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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13
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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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14
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA. Genes (Basel) 2022; 13:genes13040687. [PMID: 35456493 PMCID: PMC9032354 DOI: 10.3390/genes13040687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.
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15
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Silvestrini S, Romandini M, Marciani G, Arrighi S, Carrera L, Fiorini A, López‐García JM, Lugli F, Ranaldo F, Slon V, Tassoni L, Higgins OA, Bortolini E, Curci A, Meyer M, Meyer MC, Oxilia G, Zerboni A, Benazzi S, Spinapolice EE. Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy. JOURNAL OF QUATERNARY SCIENCE 2022; 37:235-256. [PMID: 35874301 PMCID: PMC9290050 DOI: 10.1002/jqs.3341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/15/2023]
Abstract
The Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.
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Affiliation(s)
- Sara Silvestrini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Matteo Romandini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Giulia Marciani
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
| | - Simona Arrighi
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
| | - Lisa Carrera
- Università degli Studi di Bologna, Dipartimento di Scienze BiologicheGeologiche e AmbientaliBolognaItaly
| | - Andrea Fiorini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Juan Manuel López‐García
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES‐CERCA)TarragonaSpain
- Universitat Rovira i VirgiliDepartament d'Història i Història de l'ArtTarragonaSpain
| | - Federico Lugli
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Filomena Ranaldo
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
- Museo della Preistoria Nardò
| | - Viviane Slon
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and BiochemistrySackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- The Dan David Center for Human Evolution and Biohistory ResearchTel Aviv UniversityTel AvivIsrael
| | - Laura Tassoni
- Università degli Studi di Ferrara, Dipartimento di Studi UmanisticiSezione di Scienze Preistoriche e AntropologicheFerraraItaly
| | | | | | - Antonio Curci
- Università di BolognaDipartimento di Storia Culture CiviltàBolognaItaly
| | - Matthias Meyer
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | | | - Gregorio Oxilia
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Andrea Zerboni
- Università degli Studi di MilanoDipartimento di Scienze delle Terra “A. Desio”MilanoItaly
| | - Stefano Benazzi
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Enza Elena Spinapolice
- Università degli Studi di Roma “La Sapienza”Dipartimento di Scienze dell'AntichitàRoma00185Italy
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16
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Bennett EA, Weber J, Bendhafer W, Champlot S, Peters J, Schwartz GM, Grange T, Geigl EM. The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia. SCIENCE ADVANCES 2022; 8:eabm0218. [PMID: 35030024 PMCID: PMC8759742 DOI: 10.1126/sciadv.abm0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Before the introduction of domestic horses in Mesopotamia in the late third millennium BCE, contemporary cuneiform tablets and seals document intentional breeding of highly valued equids called kungas for use in diplomacy, ceremony, and warfare. Their precise zoological classification, however, has never been conclusively determined. Morphometric analysis of equids uncovered in rich Early Bronze Age burials at Umm el-Marra, Syria, placed them beyond the ranges reported for other known equid species. We sequenced the genomes of one of these ~4500-year-old equids, together with an ~11,000-year-old Syrian wild ass (hemippe) from Göbekli Tepe and two of the last surviving hemippes. We conclude that kungas were F1 hybrids between female domestic donkeys and male hemippes, thus documenting the earliest evidence of hybrid animal breeding.
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Affiliation(s)
- E. Andrew Bennett
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Jill Weber
- Near East Section, The University Museum of Archaeology and Anthropology, Philadelphia, PA 19103, USA
| | - Wejden Bendhafer
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Sophie Champlot
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Joris Peters
- ArchaeoBioCenter, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- SNSB, Bavarian State Collection of Palaeoanatomy, 80333 Munich, Germany
| | - Glenn M. Schwartz
- Department of Near Eastern Studies, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thierry Grange
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
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17
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Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proc Natl Acad Sci U S A 2022; 119:2113666118. [PMID: 34969841 PMCID: PMC8740756 DOI: 10.1073/pnas.2113666118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/26/2023] Open
Abstract
DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments. Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.
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18
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Pedersen MW, Antunes C, De Cahsan B, Moreno-Mayar JV, Sikora M, Vinner L, Mann D, Klimov PB, Black S, Michieli CT, Braig HR, Perotti MA. Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits. Mol Biol Evol 2021; 39:6481551. [PMID: 34963129 PMCID: PMC8829908 DOI: 10.1093/molbev/msab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.
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Affiliation(s)
- Mikkel W Pedersen
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Catia Antunes
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Binia De Cahsan
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Martin Sikora
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Lasse Vinner
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Darren Mann
- Oxford University Museum of Natural History, Oxford, United Kingdom
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, USA
| | - Stuart Black
- Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom
| | - Catalina Teresa Michieli
- Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
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19
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Maixner F, Mitterer C, Jäger HY, Sarhan MS, Valverde G, Lücker S, Piombino‐Mascali D, Szikossy I, Molnár E, Pálfi G, Pap I, Cipollini G, Zink A. Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | | | - Heidi Y. Jäger
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | | | - Guido Valverde
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | - Sebastian Lücker
- Department of Microbiology IWWR Radboud University Nijmegen the Netherlands
| | - Dario Piombino‐Mascali
- Department of Anatomy, Histology and Anthropology Faculty of Medicine Vilnius University Vilnius Lithuania
| | - Ildikó Szikossy
- Department of Anthropology Hungarian Natural History Museum Budapest Hungary
| | - Erika Molnár
- Department of Biological Anthropology University of Szeged Szeged Hungary
| | - György Pálfi
- Department of Biological Anthropology University of Szeged Szeged Hungary
| | - Ildikó Pap
- Department of Anthropology Hungarian Natural History Museum Budapest Hungary
| | | | - Albert Zink
- Institute for Mummy Studies Eurac Research Bolzano Italy
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20
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Type VI secretion system mutations reduced competitive fitness of classical Vibrio cholerae biotype. Nat Commun 2021; 12:6457. [PMID: 34753930 PMCID: PMC8578542 DOI: 10.1038/s41467-021-26847-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
The gram-negative bacterium Vibrio cholerae is the causative agent of the diarrhoeal disease cholera and is responsible for seven recorded pandemics. Several factors are postulated to have led to the decline of 6th pandemic classical strains and the rise of El Tor biotype V. cholerae, establishing the current 7th pandemic. We investigated the ability of classical V. cholerae of the 2nd and 6th pandemics to engage their type six secretion system (T6SS) in microbial competition against non-pandemic and 7th pandemic strains. We report that classical V. cholerae underwent sequential mutations in T6SS genetic determinants that initially exposed 2nd pandemic strains to microbial attack by non-pandemic strains and subsequently caused 6th pandemic strains to become vulnerable to El Tor biotype V. cholerae intraspecific competition. The chronology of these T6SS-debilitating mutations agrees with the decline of 6th pandemic classical strains and the emergence of 7th pandemic El Tor V. cholerae.
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21
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Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021; 12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
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Affiliation(s)
- Yilan Wang
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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22
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Essel E, Korlević P, Meyer M. A method for the temperature-controlled extraction of DNA from ancient bones. Biotechniques 2021; 71:382-386. [PMID: 34164993 DOI: 10.2144/btn-2021-0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Contamination with microbial and other exogenous DNA poses a significant challenge in the generation of genome-wide sequence data from ancient skeletal remains. Here we describe a method for separating ancient DNA into multiple fractions during DNA extraction by sequential temperature-controlled release of DNA into sodium phosphate buffer. An evaluation of the effectiveness of the method using a set of three ancient bones resulted in between 1.6- and 32-fold enrichment of endogenous DNA compared with regular DNA extraction. For two bones, the method outperformed previous methods of decontaminating ancient bones, including hypochlorite treatment, which resulted in near-complete destruction of DNA in the worst-preserved sample. This extraction method expands the spectrum of methods available for depleting contaminant DNA from ancient skeletal remains.
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Affiliation(s)
- Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany
| | - Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany.,Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany
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23
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Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
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Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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24
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Hofreiter M, Sneberger J, Pospisek M, Vanek D. Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. Forensic Sci Int Genet 2021; 54:102538. [PMID: 34265517 DOI: 10.1016/j.fsigen.2021.102538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/07/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.
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Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Jiri Sneberger
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic.
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25
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Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
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Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
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26
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Martinón-Torres M, d'Errico F, Santos E, Álvaro Gallo A, Amano N, Archer W, Armitage SJ, Arsuaga JL, Bermúdez de Castro JM, Blinkhorn J, Crowther A, Douka K, Dubernet S, Faulkner P, Fernández-Colón P, Kourampas N, González García J, Larreina D, Le Bourdonnec FX, MacLeod G, Martín-Francés L, Massilani D, Mercader J, Miller JM, Ndiema E, Notario B, Pitarch Martí A, Prendergast ME, Queffelec A, Rigaud S, Roberts P, Shoaee MJ, Shipton C, Simpson I, Boivin N, Petraglia MD. Earliest known human burial in Africa. Nature 2021; 593:95-100. [PMID: 33953416 DOI: 10.1038/s41586-021-03457-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 03/16/2021] [Indexed: 02/03/2023]
Abstract
The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.
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Affiliation(s)
- María Martinón-Torres
- CENIEH (National Research Center on Human Evolution), Burgos, Spain. .,Anthropology Department, University College London, London, UK.
| | - Francesco d'Errico
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France.,SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway
| | - Elena Santos
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Instituto de Salud Carlos III, Madrid, Spain.,Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales - Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Ana Álvaro Gallo
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - Noel Amano
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - William Archer
- Department of Archaeology and Anthropology, National Museum, Bloemfontein, South Africa.,Department of Archaeology, University of Cape Town, Cape Town, South Africa.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Simon J Armitage
- SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway.,Department of Geography, Royal Holloway, University of London, Egham, UK
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José María Bermúdez de Castro
- CENIEH (National Research Center on Human Evolution), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | - James Blinkhorn
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Geography, Royal Holloway, University of London, Egham, UK.,Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Stéphan Dubernet
- UMR 5060 CNRS-Université Bordeaux Montaigne IRAMAT-CRP2A: Institut de recherche sur les Archéomatériaux - Centre de recherche en physique appliquée à l'archéologie, Maison de l'archéologie, Pessac, France
| | - Patrick Faulkner
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Faculty of Arts and Social Sciences, Department of Archaeology, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Nikos Kourampas
- Centre for Open Learning, University of Edinburgh, Edinburgh, UK.,Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jorge González García
- 3D Applications Engineer and Heritage Specialist Digital Heritage and Humanities Collections, University of South Florida, Tampa, FL, USA
| | - David Larreina
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - François-Xavier Le Bourdonnec
- UMR 5060 CNRS-Université Bordeaux Montaigne IRAMAT-CRP2A: Institut de recherche sur les Archéomatériaux - Centre de recherche en physique appliquée à l'archéologie, Maison de l'archéologie, Pessac, France
| | - George MacLeod
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Laura Martín-Francés
- CENIEH (National Research Center on Human Evolution), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julio Mercader
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer M Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Emmanuel Ndiema
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,National Museums of Kenya, Department of Earth Sciences, Nairobi, Kenya
| | - Belén Notario
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - Africa Pitarch Martí
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France.,Seminari d'Estudis i Recerques Prehistòriques (SERP), Facultat de Geografia i Història, Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | | | - Alain Queffelec
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France
| | - Solange Rigaud
- UMR 5199 CNRS De la Préhistoire à l'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Mohammad Javad Shoaee
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ceri Shipton
- Institute of Archaeology, University College London, London, UK.,Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ian Simpson
- Centre for Open Learning, University of Edinburgh, Edinburgh, UK
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. .,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia. .,Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada. .,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Michael D Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. .,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia. .,Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA. .,Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, Queensland, Australia.
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27
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Zhang M, Cao P, Dai Q, Wang Y, Feng X, Wang H, Wu H, Ko AMS, Mao X, Liu Y, Yu L, Roos C, Nadler T, Xiao W, Bennett EA, Fu Q. Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples. Zool Res 2021; 42:280-286. [PMID: 33855818 PMCID: PMC8175948 DOI: 10.24272/j.issn.2095-8137.2020.377] [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] [Indexed: 11/07/2022] Open
Abstract
DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Yongqiang Wang
- Institute of cultural relics and archaeology in Xinjiang, Urumqi, Xinjiang 830011, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Tilo Nadler
- Wildlife Consultant, Cuc Phuong Commune, Nho Quan, Ninh Binh 430000, Vietnam
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan 671003, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China. E-mail:
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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28
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Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proc Natl Acad Sci U S A 2021; 118:2022466118. [PMID: 33798098 DOI: 10.1073/pnas.2022466118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.
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29
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Harney É, Cheronet O, Fernandes DM, Sirak K, Mah M, Bernardos R, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Candilio F, Constantinescu M, Coppa A, Ciobanu I, Dani J, Gallina Z, Genchi F, Nagy EG, Hajdu T, Hellebrandt M, Horváth A, Király Á, Kiss K, Kolozsi B, Kovács P, Köhler K, Lucci M, Pap I, Popovici S, Raczky P, Simalcsik A, Szeniczey T, Vasilyev S, Virag C, Rohland N, Reich D, Pinhasi R. A minimally destructive protocol for DNA extraction from ancient teeth. Genome Res 2021; 31:472-483. [PMID: 33579752 PMCID: PMC7919446 DOI: 10.1101/gr.267534.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
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Affiliation(s)
- Éadaoin Harney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the City of Cagliari and the Provinces of Oristano and South Sardinia, 09121 Cagliari, Italy
| | | | - Alfredo Coppa
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
- Department of Environmental Biology, Sapienza University, 00185 Rome, Italy
| | - Ion Ciobanu
- Cultural-Natural Reserve "Orheiul Vechi", 3552 Orhei, Republic of Moldova
- Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova
| | | | - Zsolt Gallina
- Ásatárs Kulturális, Régészeti Szolgáltató és Kereskedelmi Limited, 6000 Kecskemét, Hungary
| | - Francesco Genchi
- Department of Environmental Biology, Sapienza University, 00185 Rome, Italy
| | | | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | | | | | - Ágnes Király
- Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary
| | - Krisztián Kiss
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | | | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary
| | - Michaela Lucci
- Department of History, Anthropology, Religion, Arts and Performing Arts, Sapienza University, 00185 Rome, Italy
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | - Sergiu Popovici
- National Agency for Archaeology, 2012 Chișinău, Republic of Moldova
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary
| | - Angela Simalcsik
- Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova
- Olga Necrasov Center for Anthropological Research, Romanian Academy, 700481 Iasi, Romania
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology of the Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Egyptological Studies of the Russian Academy of Sciences, 119071 Moscow, Russia
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
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30
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Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age. Genes (Basel) 2021; 12:genes12020146. [PMID: 33499220 PMCID: PMC7911526 DOI: 10.3390/genes12020146] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.
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31
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Petr M, Hajdinjak M, Fu Q, Essel E, Rougier H, Crevecoeur I, Semal P, Golovanova LV, Doronichev VB, Lalueza-Fox C, de la Rasilla M, Rosas A, Shunkov MV, Kozlikin MB, Derevianko AP, Vernot B, Meyer M, Kelso J. The evolutionary history of Neanderthal and Denisovan Y chromosomes. Science 2020; 369:1653-1656. [PMID: 32973032 DOI: 10.1126/science.abb6460] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 12/31/2022]
Abstract
Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.
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Affiliation(s)
- Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,The Francis Crick Institute, NW1 1AT London, UK
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hélène Rougier
- Department of Anthropology, California State University, Northridge, Northridge, CA 91330-8244, USA
| | | | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoli P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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32
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Zhang D, Xia H, Chen F, Li B, Slon V, Cheng T, Yang R, Jacobs Z, Dai Q, Massilani D, Shen X, Wang J, Feng X, Cao P, Yang MA, Yao J, Yang J, Madsen DB, Han Y, Ping W, Liu F, Perreault C, Chen X, Meyer M, Kelso J, Pääbo S, Fu Q. Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science 2020; 370:584-587. [DOI: 10.1126/science.abb6320] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Dongju Zhang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Frontier Center for Eco-environment and Climate Change in Pan-third Pole Regions, Lanzhou University, Lanzhou 730000, China
| | - Huan Xia
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fahu Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Ting Cheng
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Xuke Shen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian Wang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- School of Earth Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Juanting Yao
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jishuai Yang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - David B. Madsen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Department of Anthropology, University of Nevada–Reno, Reno, NV 89557, USA
| | - Yuanyuan Han
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wanjing Ping
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Feng Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Charles Perreault
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoshan Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
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33
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Romandini M, Oxilia G, Bortolini E, Peyrégne S, Delpiano D, Nava A, Panetta D, Di Domenico G, Martini P, Arrighi S, Badino F, Figus C, Lugli F, Marciani G, Silvestrini S, Menghi Sartorio JC, Terlato G, Hublin JJ, Meyer M, Bondioli L, Higham T, Slon V, Peresani M, Benazzi S. A late Neanderthal tooth from northeastern Italy. J Hum Evol 2020; 147:102867. [DOI: 10.1016/j.jhevol.2020.102867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
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34
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Vinueza-Espinosa DC, Santos C, Martínez-Labarga C, Malgosa A. Human DNA extraction from highly degraded skeletal remains: How to find a suitable method? Electrophoresis 2020; 41:2149-2158. [PMID: 33002215 DOI: 10.1002/elps.202000171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/27/2020] [Accepted: 09/24/2020] [Indexed: 11/07/2022]
Abstract
Retrieving DNA from highly degraded human skeletal remains is still a challenge due to low concentration and fragmentation, which makes it difficult to extract and purify. Recent works showed that silica-based methods allow better DNA recovery and this fact may be attributed to the type of bones and the quality of the preserved tissue. However, more systematic studies are needed to evaluate the efficiency of the different silica-based extraction methods considering the type of bones. The main goal of the present study is to establish the best extraction method and the type of bone that can maximize the recovery of PCR-amplifiable DNA and the subsequent retrieval of mitochondrial and nuclear genetic information. Five individuals were selected from an archaeological site located in Catalonia-Spain dating from 5th to 11th centuries AD. For each individual, five samples from different skeletal regions were collected: petrous bone, pulp cavity and cementum of tooth, and rib and limb bones. Four extraction methods were tested, three silica-based (silica in-suspension, HE column and XS plasma column) and the classical method based on phenol-chloroform. Silica in-suspension method from petrous bone and pulp cavity showed the best results. However, the remains preservation will ultimately be the key to the molecular result success.
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Affiliation(s)
- Diana C Vinueza-Espinosa
- Biology Anthropology Research Group, Department of Animal Biology, Vegetal Biology and Ecology, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Cristina Santos
- Biology Anthropology Research Group, Department of Animal Biology, Vegetal Biology and Ecology, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Cristina Martínez-Labarga
- Department of Biology, Centre of Molecular Anthropology for Ancient DNA Studies, University of Rome Tor Vergata, Rome, Italy
| | - Assumpció Malgosa
- Biology Anthropology Research Group, Department of Animal Biology, Vegetal Biology and Ecology, Universidad Autónoma de Barcelona, Barcelona, Spain
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35
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Bokelmann L, Glocke I, Meyer M. Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. Genome Res 2020; 30:1449-1457. [PMID: 32963029 PMCID: PMC7605269 DOI: 10.1101/gr.263863.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.
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Affiliation(s)
- Lukas Bokelmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - 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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36
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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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37
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Karpinski E, Hackenberger D, Zazula G, Widga C, Duggan AT, Golding GB, Kuch M, Klunk J, Jass CN, Groves P, Druckenmiller P, Schubert BW, Arroyo-Cabrales J, Simpson WF, Hoganson JW, Fisher DC, Ho SYW, MacPhee RDE, Poinar HN. American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations. Nat Commun 2020; 11:4048. [PMID: 32873779 PMCID: PMC7463256 DOI: 10.1038/s41467-020-17893-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 07/24/2020] [Indexed: 12/27/2022] Open
Abstract
Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures. Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles.
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Affiliation(s)
- Emil Karpinski
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada. .,Department of Biology, McMaster University, Hamilton, ON, L8S 4L8, Canada.
| | - Dirk Hackenberger
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Department of Biochemistry, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, Whitehorse, YT, Y1A 2C6, Canada.,Research and Collections, Canadian Museum of Nature, Ottawa, ON, K2P 2R1, Canada
| | - Chris Widga
- Center of Excellence in Paleontology and Department of Geosciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Department of Anthropology, McMaster University, Hamilton, ON, L8S 4L9, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - Christopher N Jass
- Quaternary Palaeontology Program, Royal Alberta Museum, Edmonton, T5J 0G2, Canada
| | - Pam Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, AK, 99775, USA
| | - Patrick Druckenmiller
- Department of Geosciences, University of Alaska Fairbanks, Alaska, AK, 99775, USA.,University of Alaska Museum, University of Alaska Fairbanks, Alaska, AK, 99775, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology and Department of Geosciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, SLAA, Instituto Nacional de Antropología e Historia, Ciudad de México, 06600, México
| | - William F Simpson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | | | - Daniel C Fisher
- Museum of Paleontology and Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Ross D E MacPhee
- Department of Mammalogy/Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada. .,Department of Biochemistry, McMaster University, Hamilton, ON, L8S 4L8, Canada. .,Department of Anthropology, McMaster University, Hamilton, ON, L8S 4L9, Canada.
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38
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Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat Protoc 2020; 15:2279-2300. [PMID: 32612278 DOI: 10.1038/s41596-020-0338-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023]
Abstract
It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.
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39
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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40
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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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41
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Dolle D, Fages A, Mata X, Schiavinato S, Tonasso-Calvière L, Chauvey L, Wagner S, Der Sarkissian C, Fromentier A, Seguin-Orlando A, Orlando L. CASCADE: A Custom-Made Archiving System for the Conservation of Ancient DNA Experimental Data. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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42
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Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 2020; 581:299-302. [DOI: 10.1038/s41586-020-2259-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
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43
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McGaughran A. Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? BMC Genomics 2020; 21:188. [PMID: 32111157 PMCID: PMC7048091 DOI: 10.1186/s12864-020-6594-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/19/2020] [Indexed: 01/04/2023] Open
Abstract
Background Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years. Results I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
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Affiliation(s)
- Angela McGaughran
- Australian National University, Research School of Biology, Division of Ecology and Evolution, Acton, Canberra, ACT, 2600, Australia. .,CSIRO Land and Water, Integrated Omics Team, Black Mountain Laboratories, Canberra, ACT, 2600, Australia.
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44
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Hofreiter M, Hartmann S. Reconstructing protein-coding sequences from ancient DNA. Methods Enzymol 2020; 642:21-33. [DOI: 10.1016/bs.mie.2020.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Young JM, Higgins D, Austin JJ. Hybridization Enrichment to Improve Forensic Mitochondrial DNA Analysis of Highly Degraded Human Remains. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Gokcumen O. Archaic hominin introgression into modern human genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171 Suppl 70:60-73. [PMID: 31702050 DOI: 10.1002/ajpa.23951] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023]
Abstract
Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?
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Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, North Campus, University at Buffalo, Buffalo, New York
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Shinde V, Narasimhan VM, Rohland N, Mallick S, Mah M, Lipson M, Nakatsuka N, Adamski N, Broomandkhoshbacht N, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Jadhav N, Kim YJ, Chatterjee M, Munshi A, Panyam A, Waghmare P, Yadav Y, Patel H, Kaushik A, Thangaraj K, Meyer M, Patterson N, Rai N, Reich D. An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers. Cell 2019; 179:729-735.e10. [PMID: 31495572 PMCID: PMC6800651 DOI: 10.1016/j.cell.2019.08.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
Abstract
We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.
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Affiliation(s)
- Vasant Shinde
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nilesh Jadhav
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Yong Jun Kim
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Malavika Chatterjee
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Avradeep Munshi
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Amrithavalli Panyam
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Pranjali Waghmare
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Yogesh Yadav
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Himani Patel
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Amit Kaushik
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | | | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Bokelmann L, Hajdinjak M, Peyrégne S, Brace S, Essel E, de Filippo C, Glocke I, Grote S, Mafessoni F, Nagel S, Kelso J, Prüfer K, Vernot B, Barnes I, Pääbo S, Meyer M, Stringer C. A genetic analysis of the Gibraltar Neanderthals. Proc Natl Acad Sci U S A 2019; 116:15610-15615. [PMID: 31308224 PMCID: PMC6681707 DOI: 10.1073/pnas.1903984116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.
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Affiliation(s)
- Lukas Bokelmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Selina Brace
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Ian Barnes
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Svante Pääbo
- 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
| | - Chris Stringer
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
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49
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Zavala EI, Rajagopal S, Perry GH, Kruzic I, Bašić Ž, Parsons TJ, Holland MM. Impact of DNA degradation on massively parallel sequencing-based autosomal STR, iiSNP, and mitochondrial DNA typing systems. Int J Legal Med 2019; 133:1369-1380. [PMID: 31267160 DOI: 10.1007/s00414-019-02110-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Biological samples, including skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt) DNA sequencing and short tandem repeat (STR) analysis, which target segments of DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples as they target templates down to 60 to 170 bps. We performed a modeling study that demonstrates that SNPs can increase the significance of an identification when analyzing DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear DNA. Observations from this study were then compared with human skeletal material results (n = 14, ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples. The robustness of the Promega PowerSeq™ Mito System was also tested with human skeletal remains (n = 70, ninth to eighteenth centuries), resulting in successful coverage of 99.29% of the mtDNA control region at 50× coverage or more. This was accompanied by modifications to a mainstream DNA extraction technique for skeletal remains that improved recovery of shorter templates.
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Affiliation(s)
- Elena I Zavala
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.
| | - Swetha Rajagopal
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.,Department of Forensic Science, John Jay College of Criminal Justice, New York, NY, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, State College, PA, USA
| | - Ivana Kruzic
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Željana Bašić
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Thomas J Parsons
- International Commission on Missing Persons, The Hague, Netherlands
| | - Mitchell M Holland
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA
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50
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Delsuc F, Kuch M, Gibb GC, Karpinski E, Hackenberger D, Szpak P, Martínez JG, Mead JI, McDonald HG, MacPhee RDE, Billet G, Hautier L, Poinar HN. Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths. Curr Biol 2019; 29:2031-2042.e6. [PMID: 31178321 DOI: 10.1016/j.cub.2019.05.043] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/18/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.
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Affiliation(s)
- Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Gillian C Gibb
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Centennial Drive, Hokowhitu, Palmerston North 4410, New Zealand
| | - Emil Karpinski
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Dirk Hackenberger
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, ON K9L 0G2, Canada
| | - Jorge G Martínez
- Instituto Superior de Estudios Sociales, CONICET-Instituto de Arqueología y Museo, Universidad Nacional de Tucumán, San Martín 1545, CP4000 San Miguel de Tucumán, Argentina
| | - Jim I Mead
- The Mammoth Site, Hot Springs, Hot Springs, SD 57747, USA; East Tennessee State University Natural History Museum, 1212 Suncrest Drive, Johnson City, TN 37615, USA
| | - H Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South #500, Salt Lake City, UT 84101, USA
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, Central Park West & 79th Street, New York, NY 10024, USA
| | - Guillaume Billet
- Centre de Recherche en Paléontologie - Paris (CR2P), UMR CNRS 7207, Sorbonne Université, Muséum National d'Histoire Naturelle, 57 Rue Cuvier, 75005 Paris, France
| | - Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
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