51
|
'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species. Sci Rep 2020; 10:19109. [PMID: 33154397 PMCID: PMC7644772 DOI: 10.1038/s41598-020-75431-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/28/2020] [Indexed: 11/08/2022] Open
Abstract
Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.
Collapse
|
52
|
Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020; 10:18225. [PMID: 33106554 PMCID: PMC7588426 DOI: 10.1038/s41598-020-75163-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
Collapse
Affiliation(s)
- Cody Parker
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam B Rohrlach
- Max Planck Institute for the Science of Human History, Jena, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.
| |
Collapse
|
53
|
Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2020; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
Collapse
Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
| |
Collapse
|
54
|
Maguire S, Lohman GJS, Guan S. A low-bias and sensitive small RNA library preparation method using randomized splint ligation. Nucleic Acids Res 2020; 48:e80. [PMID: 32496547 PMCID: PMC7641310 DOI: 10.1093/nar/gkaa480] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
Small RNAs are important regulators of gene expression and are involved in human development and disease. Next generation sequencing (NGS) allows for scalable, genome-wide studies of small RNA; however, current methods are challenged by low sensitivity and high bias, limiting their ability to capture an accurate representation of the cellular small RNA population. Several studies have shown that this bias primarily arises during the ligation of single-strand adapters during library preparation, and that this ligation bias is magnified by 2′-O-methyl modifications (2′OMe) on the 3′ terminal nucleotide. In this study, we developed a novel library preparation process using randomized splint ligation with a cleavable adapter, a design which resolves previous challenges associated with this ligation strategy. We show that a randomized splint ligation based workflow can reduce bias and increase the sensitivity of small RNA sequencing for a wide variety of small RNAs, including microRNA (miRNA) and tRNA fragments as well as 2′OMe modified RNA, including Piwi-interacting RNA and plant miRNA. Finally, we demonstrate that this workflow detects more differentially expressed miRNA between tumorous and matched normal tissues. Overall, this library preparation process allows for highly accurate small RNA sequencing and will enable studies of 2′OMe modified RNA with new levels of detail.
Collapse
Affiliation(s)
- Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| |
Collapse
|
55
|
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.
Collapse
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
| |
Collapse
|
56
|
New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland). Sci Rep 2020; 10:14778. [PMID: 32901061 PMCID: PMC7479612 DOI: 10.1038/s41598-020-71504-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/17/2020] [Indexed: 02/03/2023] Open
Abstract
The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.
Collapse
|
57
|
Sabin S, Herbig A, Vågene ÅJ, Ahlström T, Bozovic G, Arcini C, Kühnert D, Bos KI. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol 2020; 21:201. [PMID: 32778135 PMCID: PMC7418204 DOI: 10.1186/s13059-020-02112-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
Collapse
Affiliation(s)
- Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Torbjörn Ahlström
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Gracijela Bozovic
- Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00 Lund, Sweden
| | - Caroline Arcini
- Arkeologerna, National Historical Museum, 226 60 Lund, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| |
Collapse
|
58
|
Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
Collapse
Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
59
|
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
|
60
|
Weiß CL, Gansauge MT, Aximu-Petri A, Meyer M, Burbano HA. Mining ancient microbiomes using selective enrichment of damaged DNA molecules. BMC Genomics 2020; 21:432. [PMID: 32586278 PMCID: PMC7318760 DOI: 10.1186/s12864-020-06820-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains. Results We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach. Conclusions Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.
Collapse
Affiliation(s)
- Clemens L Weiß
- Department of Molecular Biology, Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Ayinuer Aximu-Petri
- 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
| | - Hernán A Burbano
- Department of Molecular Biology, Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany. .,Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
61
|
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
|
62
|
Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq. Mol Cell 2020; 78:975-985.e7. [PMID: 32320643 PMCID: PMC7276987 DOI: 10.1016/j.molcel.2020.03.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/13/2020] [Accepted: 03/20/2020] [Indexed: 12/03/2022]
Abstract
DNA single-strand breaks (SSBs) are among the most common lesions in the genome, arising spontaneously and as intermediates of many DNA transactions. Nevertheless, in contrast to double-strand breaks (DSBs), their distribution in the genome has hardly been addressed in a meaningful way. We now present a technique based on genome-wide ligation of 3′-OH ends followed by sequencing (GLOE-Seq) and an associated computational pipeline designed for capturing SSBs but versatile enough to be applied to any lesion convertible into a free 3′-OH terminus. We demonstrate its applicability to mapping of Okazaki fragments without prior size selection and provide insight into the relative contributions of DNA ligase 1 and ligase 3 to Okazaki fragment maturation in human cells. In addition, our analysis reveals biases and asymmetries in the distribution of spontaneous SSBs in yeast and human chromatin, distinct from the patterns of DSBs. GLOE-Seq detects 3′-OH ends with nucleotide resolution in purified genomic DNA GLOE-Seq maps single-strand breaks, lesions, and replication and repair intermediates GLOE-Seq reveals insight into the use of ligases 1 and 3 in human cells GLOE-Seq detects asymmetries in spontaneous nicks in yeast and human chromatin
Collapse
|
63
|
Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
Collapse
|
64
|
Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020; 4:94-108. [PMID: 32313686 PMCID: PMC7156104 DOI: 10.1002/evl3.165] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 01/01/2023] Open
Abstract
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
Collapse
Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - María C. Ávila‐Arcos
- International Laboratory for Human Genome Research (LIIGH)UNAM JuriquillaQueretaro76230Mexico
| | - David Díez‐del‐Molino
- Centre for Palaeogenetics10691StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park CampusImperial College LondonAscotSL5 7PYUnited Kingdom
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Science for Life LaboratoryUppsala University75236UppsalaSweden
| | | | - Anna‐Sapfo Malaspinas
- Department of Computational BiologyUniversity of Lausanne1015LausanneSwitzerland
- SIB Swiss Institute of Bioinformatics1015LausanneSwitzerland
| | - Tomas Marques‐Bonet
- Institut de Biologia Evolutiva(CSIC‐Universitat Pompeu Fabra), Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
- National Centre for Genomic Analysis—Centre for Genomic RegulationBarcelona Institute of Science and Technology08028BarcelonaSpain
- Institucio Catalana de Recerca i Estudis Avançats08010BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Michael D. Martin
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Gemma G. R. Murray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB2 1TNUnited Kingdom
| | - Alexander S. T. Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
| | | | - Daniel Wegmann
- Department of BiologyUniversité de Fribourg1700FribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Love Dalén
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
| |
Collapse
|
65
|
Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Pușcaș M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM, Coissac E. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. PLANTS (BASEL, SWITZERLAND) 2020; 9:E432. [PMID: 32244605 PMCID: PMC7238428 DOI: 10.3390/plants9040432] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
Collapse
Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Sebastien Lavergne
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | - Marti Boleda
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - Youri Lammers
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Charles Pouchon
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Iva Pitelkova
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Mihai Pușcaș
- A. Borza Botanical Garden and Faculty of Biology and Geology, Babeș-Bolyai University, 400015 Cluj-Napoca, Romania;
| | - Cristina Roquet
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Wilfried Thuiller
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | | | - Eric Coissac
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| |
Collapse
|
66
|
Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020. [PMID: 32098773 DOI: 10.1101/654749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
Collapse
Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- 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
| | - 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
| | - Swapan Mallick
- 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
| | - Nadin Rohland
- Department of Genetics, 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
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - 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, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
- National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- 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
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| |
Collapse
|
67
|
Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020; 30:427-436. [PMID: 32098773 PMCID: PMC7111520 DOI: 10.1101/gr.260141.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/11/2020] [Indexed: 12/29/2022]
Abstract
DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
Collapse
Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,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
| | - 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
| | - Swapan Mallick
- 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
| | - Nadin Rohland
- Department of Genetics, 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
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - 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, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia.,National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- 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
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| |
Collapse
|
68
|
Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, Khokhlov A, Chizhevsky A, Hansen S, Belinsky AB, Kalmykov A, Kantorovich AR, Maslov VE, Stockhammer PW, Vai S, Zavattaro M, Riga A, Caramelli D, Skeates R, Beckett J, Gradoli MG, Steuri N, Hafner A, Ramstein M, Siebke I, Lösch S, Erdal YS, Alikhan NF, Zhou Z, Achtman M, Bos K, Reinhold S, Haak W, Kühnert D, Herbig A, Krause J. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat Ecol Evol 2020; 4:324-333. [PMID: 32094538 PMCID: PMC7186082 DOI: 10.1038/s41559-020-1106-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022]
Abstract
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight Salmonella enterica subsp.
enterica genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of S.
enterica all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific S. enterica Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica is linked to human cultural
transformations.
Collapse
Affiliation(s)
- Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Luis R Esquivel-Gomez
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tuebingen, Tuebingen, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russian Federation
| | - Andrey Chizhevsky
- Institute of Archaeology named after A.Kh. Khalikov of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russian Federation
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Alexey Kalmykov
- 'Nasledie' Cultural Heritage Unit, Stavropol, Russian Federation
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence, Italy
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | | | | | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Inga Siebke
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | | | | | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| |
Collapse
|
69
|
The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol 2020; 4:334-345. [PMID: 32094539 PMCID: PMC7080320 DOI: 10.1038/s41559-020-1102-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
Abstract
Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
Collapse
|
70
|
Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics 2019; 20:1023. [PMID: 31881841 PMCID: PMC6935139 DOI: 10.1186/s12864-019-6355-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming. Results Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding. Conclusions SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
Collapse
Affiliation(s)
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Varsha Rao
- Claret Bioscience LLC, Santa Cruz, CA, 95060, USA
| | | | - Charles Cole
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| |
Collapse
|
71
|
Narasimhan VM, Patterson N, Moorjani P, Rohland N, Bernardos R, Mallick S, Lazaridis I, Nakatsuka N, Olalde I, Lipson M, Kim AM, Olivieri LM, Coppa A, Vidale M, Mallory J, Moiseyev V, Kitov E, Monge J, Adamski N, Alex N, Broomandkhoshbacht N, Candilio F, Callan K, Cheronet O, Culleton BJ, Ferry M, Fernandes D, Freilich S, Gamarra B, Gaudio D, Hajdinjak M, Harney É, Harper TK, Keating D, Lawson AM, Mah M, Mandl K, Michel M, Novak M, Oppenheimer J, Rai N, Sirak K, Slon V, Stewardson K, Zalzala F, Zhang Z, Akhatov G, Bagashev AN, Bagnera A, Baitanayev B, Bendezu-Sarmiento J, Bissembaev AA, Bonora GL, Chargynov TT, Chikisheva T, Dashkovskiy PK, Derevianko A, Dobeš M, Douka K, Dubova N, Duisengali MN, Enshin D, Epimakhov A, Fribus AV, Fuller D, Goryachev A, Gromov A, Grushin SP, Hanks B, Judd M, Kazizov E, Khokhlov A, Krygin AP, Kupriyanova E, Kuznetsov P, Luiselli D, Maksudov F, Mamedov AM, Mamirov TB, Meiklejohn C, Merrett DC, Micheli R, Mochalov O, Mustafokulov S, Nayak A, Pettener D, Potts R, Razhev D, Rykun M, Sarno S, Savenkova TM, Sikhymbaeva K, Slepchenko SM, Soltobaev OA, Stepanova N, Svyatko S, Tabaldiev K, Teschler-Nicola M, Tishkin AA, Tkachev VV, Vasilyev S, Velemínský P, Voyakin D, Yermolayeva A, Zahir M, Zubkov VS, Zubova A, Shinde VS, Lalueza-Fox C, Meyer M, Anthony D, Boivin N, Thangaraj K, Kennett DJ, Frachetti M, Pinhasi R, Reich D. The formation of human populations in South and Central Asia. Science 2019; 365:365/6457/eaat7487. [PMID: 31488661 DOI: 10.1126/science.aat7487] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 02/19/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
Collapse
Affiliation(s)
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. .,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Luca M Olivieri
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University, Rome 00185, Italy
| | - Massimo Vidale
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.,Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, Italy
| | - James Mallory
- School of Natural and Built Environment, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Egor Kitov
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.,A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Janet Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Neel Alex
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca Candilio
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Beatriz Gamarra
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona 43007, Spain
| | - Daniel Gaudio
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Denise Keating
- Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mario Novak
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Institute for Anthropological Research, Zagreb 10000, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.,Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Earth Institute, University College Dublin, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gaziz Akhatov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | - Anatoly N Bagashev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Alessandra Bagnera
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan
| | | | - Julio Bendezu-Sarmiento
- CNRS-EXT500, Directeur de la Delegation Archaologique Francaise en Afghanistan (DAFA), Embassy of France in Kabul, Afghanistan
| | - Arman A Bissembaev
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Aktobe Regional Historical Museum, Aktobe 030006, Kazakhstan
| | - Gian Luca Bonora
- Archaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental Studies, Rome RM00186, Italy
| | | | - Tatiana Chikisheva
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr K Dashkovskiy
- Department of Political History, National and State-Confessional Relations, Altai State University, Barnaul 656049, Russia
| | - Anatoly Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.,Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Nadezhda Dubova
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Dmitry Enshin
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Andrey Epimakhov
- Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, Russia.,South Ural State University, Chelyabinsk 454080, Russia
| | - Alexey V Fribus
- Department of Archaeology, Kemerovo State University, Kemerovo 650043, Russia
| | - Dorian Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, UK.,School of Cultural Heritage, Northwest University, Shanxi, 710069, China
| | - Alexander Goryachev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Sergey P Grushin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul 656049, Russia
| | - Bryan Hanks
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margaret Judd
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Erlan Kazizov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | - Aleksander Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Aleksander P Krygin
- West Kazakhstan Regional Center for History and Archaeology, Uralsk 090000, Kazakhstan
| | - Elena Kupriyanova
- Scientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk State University, Chelyabinsk 454021, Russia
| | - Pavel Kuznetsov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy
| | - Farhod Maksudov
- Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan
| | - Aslan M Mamedov
- Center for Research, Restoration and Protection of Historical and Cultural Heritage of Aktobe Region, Aktobe 030007, Kazakhstan
| | - Talgat B Mamirov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | | | - Deborah C Merrett
- Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Roberto Micheli
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.,MiBAC - Ministero per i Beni e le Attività Culturali - Soprintendenza Archeologia, belle arti e paesaggio del Friuli Venezia Giulia, 34135 Trieste, Italy
| | - Oleg Mochalov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Samariddin Mustafokulov
- Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan.,Afrosiab Museum, Samarkand 140151, Uzbekistan
| | - Ayushi Nayak
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Dmitry Razhev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Marina Rykun
- National Research Tomsk State University, Tomsk 634050, Russia
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy
| | - Tatyana M Savenkova
- F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Kulyan Sikhymbaeva
- Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan
| | - Sergey M Slepchenko
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | | | - Nadezhda Stepanova
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana Svyatko
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia.,CHRONO Centre for Climate, the Environment, and Chronology, Queen's University of Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | | | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.,Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul 656049, Russia
| | | | - Sergey Vasilyev
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Egyptological Studies RAS, Moscow 119991, Russia
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Dmitriy Voyakin
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Archaeological Expertise LLP, Almaty 050060, Kazakhstan
| | | | - Muhammad Zahir
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.,Department of Archaeology, Hazara University, Mansehra 21300, Pakistan
| | - Valery S Zubkov
- N.F. Katanov Khakassia State University, Abakan 655017, Russia
| | - Alisa Zubova
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Vasant S Shinde
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - David Anthony
- Anthropology Department, Hartwick College, Oneonta, NY 13820, USA
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Douglas J Kennett
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA. .,Spatial Analysis, Interpretation, and Exploration Laboratory, Washington University in St. Louis, St. Louis, MO 63112, USA
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland. .,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA
| |
Collapse
|
72
|
Interactions between earliest Linearbandkeramik farmers and central European hunter gatherers at the dawn of European Neolithization. Sci Rep 2019; 9:19544. [PMID: 31863024 PMCID: PMC6925266 DOI: 10.1038/s41598-019-56029-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/01/2019] [Indexed: 01/19/2023] Open
Abstract
Archaeogenetic research over the last decade has demonstrated that European Neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early Neolithic central European Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had a mixture of WHG-related and ANF-related ancestry, one of them with approximately 50% of each, while the third individual had approximately all ANF-related ancestry. Stable carbon and nitrogen isotope ratios for all three individuals were within the range of variation reflecting diets of other Neolithic agrarian populations. Strontium isotope analysis revealed that the ~50% WHG-ANF individual was non-local to the Brunn 2 area. Overall, our data indicate interbreeding between incoming farmers, whose ancestors ultimately came from western Anatolia, and local HGs, starting within the first few generations of the arrival of the former in central Europe, as well as highlighting the integrative nature and composition of the early LBK communities.
Collapse
|
73
|
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
|
74
|
Miura F, Fujino T, Kogashi K, Shibata Y, Miura M, Isobe H, Ito T. Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA. Nucleic Acids Res 2019; 46:e95. [PMID: 29846671 PMCID: PMC6144795 DOI: 10.1093/nar/gky452] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/11/2018] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing of single-stranded DNA (ssDNA) is attracting increased attention from a wide variety of research fields. Accordingly, various methods are actively being tested for the efficient adaptor-tagging of ssDNA. We conceived a novel chemo-enzymatic method termed terminal deoxynucleotidyl transferase (TdT)-assisted, copper-catalyzed azide-alkyne cycloaddition (CuAAC)-mediated ssDNA ligation (TCS ligation). In this method, TdT is used to incorporate a single 3′-azide-modified dideoxyribonucleotide onto the 3′-end of target ssDNA, followed by CuAAC-mediated click ligation of the azide-incorporated 3′-end to a 5′-ethynylated synthetic adaptor. This report presents the first proof-of-principle application of TCS ligation with its use in the preparation of a next-generation sequencing library.
Collapse
Affiliation(s)
- Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tomoko Fujino
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kanako Kogashi
- Department of Chemistry, Tohoku University, 6-3 Aramaki-aza-aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Yukiko Shibata
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Miki Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroyuki Isobe
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
75
|
Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, Soares P, Ferrando-Bernal M, Adamski N, Broomandkhoshbacht N, Cheronet O, Culleton BJ, Fernandes D, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zhang Z, Jiménez Arenas JM, Toro Moyano IJ, Salazar-García DC, Castanyer P, Santos M, Tremoleda J, Lozano M, García Borja P, Fernández-Eraso J, Mujika-Alustiza JA, Barroso C, Bermúdez FJ, Viguera Mínguez E, Burch J, Coromina N, Vivó D, Cebrià A, Fullola JM, García-Puchol O, Morales JI, Oms FX, Majó T, Vergès JM, Díaz-Carvajal A, Ollich-Castanyer I, López-Cachero FJ, Silva AM, Alonso-Fernández C, Delibes de Castro G, Jiménez Echevarría J, Moreno-Márquez A, Pascual Berlanga G, Ramos-García P, Ramos-Muñoz J, Vijande Vila E, Aguilella Arzo G, Esparza Arroyo Á, Lillios KT, Mack J, Velasco-Vázquez J, Waterman A, Benítez de Lugo Enrich L, Benito Sánchez M, Agustí B, Codina F, de Prado G, Estalrrich A, Fernández Flores Á, Finlayson C, Finlayson G, Finlayson S, Giles-Guzmán F, Rosas A, Barciela González V, García Atiénzar G, Hernández Pérez MS, Llanos A, Carrión Marco Y, Collado Beneyto I, López-Serrano D, Sanz Tormo M, Valera AC, Blasco C, Liesau C, Ríos P, Daura J, de Pedro Michó MJ, Diez-Castillo AA, Flores Fernández R, Francès Farré J, Garrido-Pena R, Gonçalves VS, Guerra-Doce E, Herrero-Corral AM, Juan-Cabanilles J, López-Reyes D, McClure SB, Merino Pérez M, Oliver Foix A, Sanz Borràs M, Sousa AC, Vidal Encinas JM, Kennett DJ, Richards MB, Werner Alt K, Haak W, Pinhasi R, Lalueza-Fox C, Reich D. The genomic history of the Iberian Peninsula over the past 8000 years. Science 2019; 363:1230-1234. [PMID: 30872528 DOI: 10.1126/science.aav4040] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
Collapse
Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for the Science of Human History, Jena, Germany.,Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Zaragoza, Spain
| | - Marina Silva
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Francesca Gandini
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Pedro Soares
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | | | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Brendan J Culleton
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra, Portugal
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Juan Manuel Jiménez Arenas
- Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain.,Instituto Universitario de la Paz y los Conflictos, Universidad de Granada, Granada, Spain.,Department of Anthropology - Anthropologisches Institut and Museum, Universität Zürich, Zürich, Switzerland
| | | | - Domingo C Salazar-García
- Departamento de Geografía, Prehistoria y Arqueología, Grupo de Investigación en Prehistoria, (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Pere Castanyer
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | - Marta Santos
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | | | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Pablo García Borja
- Departamento de Prehistoria e Historia Antigua, Universidad Nacional de Educación a Distancia, Valencia, Spain
| | - Javier Fernández-Eraso
- Departamento de Geografía, Prehistoria y Arqueología, Universidad del País Vasco, Vitoria, Spain
| | | | - Cecilio Barroso
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | - Francisco J Bermúdez
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | | | - Josep Burch
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Neus Coromina
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - David Vivó
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Artur Cebrià
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Josep Maria Fullola
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Oreto García-Puchol
- PREMEDOC Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | - Juan Ignacio Morales
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - F Xavier Oms
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Tona Majó
- Archaeom. Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | | | | | - F Javier López-Cachero
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,UNIARQ, Faculdade de Letras, Universidade de Lisboa, Lisboa, Portugal.,CEF, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Germán Delibes de Castro
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | - Adolfo Moreno-Márquez
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain.,Departamento de Geografía, Historia y Humanidades, Universidad de Almería, Almería, Spain
| | | | | | - José Ramos-Muñoz
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Eduardo Vijande Vila
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Gustau Aguilella Arzo
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Ángel Esparza Arroyo
- GIR PrehUSAL, Departamento de Prehistoria, Historia Antigua y Arqueología, Universidad de Salamanca, Salamanca, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Jennifer Mack
- Office of the State Archaeologist, University of Iowa, Iowa City, IA, USA
| | - Javier Velasco-Vázquez
- Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | - Luis Benítez de Lugo Enrich
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Prehistoria y Arqueología, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - María Benito Sánchez
- Departamento de Medicina Legal, Psiquiatría y Anatomía Patológica, Universidad Complutense de Madrid, Madrid, Spain
| | - Bibiana Agustí
- INSITU S.C.P., Centelles, Spain.,Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | - Ferran Codina
- Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | | | - Almudena Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria-Gobierno de Cantabria-Santander), Santander, Spain
| | | | - Clive Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Anthropology, University of Toronto, Toronto, ON, Canada.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Geraldine Finlayson
- The Gibraltar National Museum, Gibraltar.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Stewart Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | | | - Antonio Rosas
- Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales (MNCN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Virginia Barciela González
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Gabriel García Atiénzar
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Mauro S Hernández Pérez
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | | | - Yolanda Carrión Marco
- Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | | | | | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Joan Daura
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | - Agustín A Diez-Castillo
- GRAM Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | - Rafael Garrido-Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | | | | | - Sarah B McClure
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Marta Merino Pérez
- Unitat d'Antropologia Física, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Arturo Oliver Foix
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Montserrat Sanz Borràs
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Douglas J Kennett
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Kurt Werner Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
76
|
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.
Collapse
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
| |
Collapse
|
77
|
Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
Collapse
|
78
|
Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019; 10:E509. [PMID: 31284503 PMCID: PMC6679096 DOI: 10.3390/genes10070509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
Collapse
Affiliation(s)
- Tian Ming Lan
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Ren Gui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Hai Meng Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunil Kumar-Sahu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Juan Yang
- Heilongjiang Provincial Museum, Harbin 150001, China
| | - Hua Bing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China
| | - Wen Hao Xu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yan Chun Xu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China.
| |
Collapse
|
79
|
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.
Collapse
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
| |
Collapse
|
80
|
Peyrégne S, Slon V, Mafessoni F, de Filippo C, Hajdinjak M, Nagel S, Nickel B, Essel E, Le Cabec A, Wehrberger K, Conard NJ, Kind CJ, Posth C, Krause J, Abrams G, Bonjean D, Di Modica K, Toussaint M, Kelso J, Meyer M, Pääbo S, Prüfer K. Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. SCIENCE ADVANCES 2019; 5:eaaw5873. [PMID: 31249872 PMCID: PMC6594762 DOI: 10.1126/sciadv.aaw5873] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.
Collapse
Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Adeline Le Cabec
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | | | - Nicholas J. Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, Tübingen72070, Germany
| | - Claus Joachim Kind
- State Office for Cultural Heritage Baden-Württemberg Berliner Strasse 12, Esslingen 73728 Germany
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
| | | | | | | | | | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena07745, Germany
| |
Collapse
|
81
|
Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZP, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 2019; 365:science.aaw6275. [PMID: 31147405 DOI: 10.1126/science.aaw6275] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Abstract
How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
Collapse
Affiliation(s)
- Mary E Prendergast
- Division of Humanities, Saint Louis University, 28003 Madrid, Spain. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Elizabeth A Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11790, USA.
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine A Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendra A Sirak
- 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
| | - Rebecca Bernardos
- Department of Genetics, 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J Culleton
- Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, 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
| | - 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
| | - 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
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley H Ambrose
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - George Ayodo
- Department of Public and Community Health, School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Emmanuel K Ndiema
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Charles Nelson
- Academy for Lifelong Learning, Western Washington University, Bellingham, WA 98225, USA
| | - Peter Robertshaw
- Department of Anthropology, California State University, San Bernardino, CA 92407, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - 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
| |
Collapse
|
82
|
Liu X, Liu L, Ji Y, Li C, Wei T, Yang X, Zhang Y, Cai X, Gao Y, Xu W, Rao S, Jin D, Lou W, Qiu Z, Wang X. Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer. EBioMedicine 2019; 41:345-356. [PMID: 30857943 PMCID: PMC6442234 DOI: 10.1016/j.ebiom.2019.02.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 02/08/2023] Open
Abstract
Background Analysis of cell-free DNA (cfDNA) is promising for broad applications in clinical settings, but with significant bias towards late-stage cancers. Although recent studies have discussed the diverse and degraded nature of cfDNA molecules, little is known about its impact on the practice of cfDNA analysis. Methods We developed single-strand library preparation and hybrid-capture-based cfDNA sequencing (SLHC-seq) to analysis degraded cfDNA fragments. Next we used SLHC-seq to perform cfDNA profiling in 112 pancreatic cancer patients, and the results were compared with 13 previous reports. Extensive analysis was performed in terms of cfDNA fragments to explore the reasons for higher detection rate of KRAS mutations in the circulation of pancreatic cancers. Findings By applying the new approach, we achieved higher efficiency in analysis of mutations than previously reported using other detection assays. 791 cancer-specific mutations were detected in plasma of 88% patients with KRAS hotspots detected in 70% of all patients. Only 8 mutations were detected in 28 healthy controls without any known oncogenic or truncating alleles. cfDNA profiling by SLHC-seq was largely consistent with results of tissue-based sequencing. SLHC-seq rescued short or damaged cfDNA fragments along to increase the sensitivity and accuracy of circulating-tumour DNA detection. Interpretation We found that the small mutant fragments are prevalent in early-stage patients, which provides strong evidence for fragment size-based detection of pancreatic cancer. The new pipeline enhanced our understanding of cfDNA biology and provide new insights for liquid biopsy.
Collapse
Affiliation(s)
- Xiaoyu Liu
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China; Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Lingxiao Liu
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Changyu Li
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Xuerong Yang
- Department of Radiology, Shuguang Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuefang Zhang
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xuyu Cai
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Weihong Xu
- Stanford Genome Technology Center, Palo Alto, CA, USA
| | - Shengxiang Rao
- Department of Radiology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Dayong Jin
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai, China; Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai, China; Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai, China.
| | - Zilong Qiu
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiaolin Wang
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China.
| |
Collapse
|
83
|
Devièse T, Massilani D, Yi S, Comeskey D, Nagel S, Nickel B, Ribechini E, Lee J, Tseveendorj D, Gunchinsuren B, Meyer M, Pääbo S, Higham T. Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia. Nat Commun 2019; 10:274. [PMID: 30700710 PMCID: PMC6353915 DOI: 10.1038/s41467-018-08018-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 12/04/2022] Open
Abstract
A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950-33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia.
Collapse
Affiliation(s)
- Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK.
| | - Diyendo Massilani
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Seonbok Yi
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| | - Sarah Nagel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Birgit Nickel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Erika Ribechini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Jungeun Lee
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Damdinsuren Tseveendorj
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Byambaa Gunchinsuren
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Matthias Meyer
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Svante Pääbo
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| |
Collapse
|
84
|
Pollpeter D, Sobala A, Malim MH. Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells. J Vis Exp 2019:10.3791/58715. [PMID: 30774124 PMCID: PMC6682491 DOI: 10.3791/58715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, and high-resolution assay that is capable of defining retroviral reverse transcription intermediates within the physiological context of virus infection. The described method captures the 3'-termini of nascent complementary DNA (cDNA) molecules within HIV-1 infected cells at single nucleotide resolution. The protocol involves harvesting of whole cell DNA, targeted enrichment of viral DNA via hybrid capture, adaptor ligation, size fractionation by gel purification, PCR amplification, deep sequencing, and data analysis. A key step is the efficient and unbiased ligation of adaptor molecules to open 3'-DNA termini. Application of the described method determines the abundance of reverse transcripts of each particular length in a given sample. It also provides information about the (internal) sequence variation in reverse transcripts and thereby any potential mutations. In general, the assay is suitable for any questions relating to DNA 3'-extension, provided that the template sequence is known.
Collapse
Affiliation(s)
- Darja Pollpeter
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London;
| | - Andrew Sobala
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
| |
Collapse
|
85
|
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nat Methods 2018; 16:59-62. [PMID: 30559431 PMCID: PMC6378878 DOI: 10.1038/s41592-018-0259-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
We describe Droplet Assisted RNA Targeting by single cell sequencing (DART-seq), a versatile technology that enables multiplexed amplicon sequencing and transcriptome profiling in single cells. We applied DART-seq to simultaneously characterize the non-A-tailed transcripts of a segmented dsRNA virus and the transcriptome of the infected cell. In addition, we used DART-seq to simultaneously determine the natively paired, variable region heavy and light chain amplicons and the transcriptome of B lymphocytes.
Collapse
|
86
|
|
87
|
Abstract
Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.
Collapse
|
88
|
Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Sci Rep 2018; 8:9822. [PMID: 29959351 PMCID: PMC6026117 DOI: 10.1038/s41598-018-28091-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022] Open
Abstract
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
Collapse
|
89
|
Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
Collapse
Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| |
Collapse
|
90
|
Abstract
Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material.
Collapse
|
91
|
Wu J, Dai W, Wu L, Wang J. SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states. BMC Genomics 2018; 19:143. [PMID: 29439663 PMCID: PMC5811972 DOI: 10.1186/s12864-018-4530-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. RESULTS This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 105 to 500 cells. CONCLUSIONS This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.
Collapse
Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China.
| |
Collapse
|
92
|
Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Collapse
Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| |
Collapse
|
93
|
Carøe C, Gopalakrishnan S, Vinner L, Mak SST, Sinding MHS, Samaniego JA, Wales N, Sicheritz‐Pontén T, Gilbert MTP. Single‐tube library preparation for degraded
DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12871] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Carøe
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | | | - Lasse Vinner
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Sarah S. T. Mak
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Mikkel Holger S. Sinding
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Natural History MuseumUniversity of Oslo Blindern Oslo Norway
| | - José A. Samaniego
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Nathan Wales
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Thomas Sicheritz‐Pontén
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | - M. Thomas P. Gilbert
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Trace and Environmental DNA LaboratoryDepartment of Environment and AgricultureCurtin University Perth WA Australia
- NTNU University Museum Trondheim Norway
| |
Collapse
|
94
|
Devièse T, Karavanić I, Comeskey D, Kubiak C, Korlević P, Hajdinjak M, Radović S, Procopio N, Buckley M, Pääbo S, Higham T. Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition. Proc Natl Acad Sci U S A 2017; 114:10606-10611. [PMID: 28874524 PMCID: PMC5635904 DOI: 10.1073/pnas.1709235114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000-29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1-G3 These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.
Collapse
Affiliation(s)
- Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, HR-10000 Zagreb, Croatia
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
| | - Cara Kubiak
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
| | - Petra Korlević
- 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
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology, Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia
| | - Noemi Procopio
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
| |
Collapse
|
95
|
Wu DC, Lambowitz AM. Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching. Sci Rep 2017; 7:8421. [PMID: 28827600 PMCID: PMC5566474 DOI: 10.1038/s41598-017-09064-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/20/2017] [Indexed: 01/30/2023] Open
Abstract
High-throughput single-stranded DNA sequencing (ssDNA-seq) of cell-free DNA from plasma and other bodily fluids is a powerful method for non-invasive prenatal testing, and diagnosis of cancers and other diseases. Here, we developed a facile ssDNA-seq method, which exploits a novel template-switching activity of thermostable group II intron reverse transcriptases (TGIRTs) for DNA-seq library construction. This activity enables TGIRT enzymes to initiate DNA synthesis directly at the 3′ end of a DNA strand while simultaneously attaching a DNA-seq adapter without end repair, tailing, or ligation. Initial experiments using this method to sequence E. coli genomic DNA showed that the TGIRT enzyme has surprisingly robust DNA polymerase activity. Further experiments showed that TGIRT-seq of plasma DNA from a healthy individual enables analysis of nucleosome positioning, transcription factor-binding sites, DNA methylation sites, and tissues-of-origin comparably to established methods, but with a simpler workflow that captures precise DNA ends.
Collapse
Affiliation(s)
- Douglas C Wu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA. .,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA.
| |
Collapse
|
96
|
Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
Collapse
Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| |
Collapse
|
97
|
Slon V, Hopfe C, Weiß CL, Mafessoni F, de la Rasilla M, Lalueza-Fox C, Rosas A, Soressi M, Knul MV, Miller R, Stewart JR, Derevianko AP, Jacobs Z, Li B, Roberts RG, Shunkov MV, de Lumley H, Perrenoud C, Gušić I, Kućan Ž, Rudan P, Aximu-Petri A, Essel E, Nagel S, Nickel B, Schmidt A, Prüfer K, Kelso J, Burbano HA, Pääbo S, Meyer M. Neandertal and Denisovan DNA from Pleistocene sediments. Science 2017; 356:605-608. [DOI: 10.1126/science.aam9695] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/07/2017] [Indexed: 12/11/2022]
|
98
|
Glocke I, Meyer M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res 2017; 27:1230-1237. [PMID: 28408382 PMCID: PMC5495074 DOI: 10.1101/gr.219675.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
Abstract
The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with single-strand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material.
Collapse
Affiliation(s)
- Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| |
Collapse
|