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Yaka R, Maja Krzewińska, Lagerholm VK, Linderholm A, Özer F, Somel M, Götherström A. Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. Biotechniques 2024; 76:216-223. [PMID: 38530148 DOI: 10.2144/btn-2023-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.
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Affiliation(s)
- Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
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2
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Mulder KP, Savage AE, Gratwicke B, Longcore JE, Bronikowski E, Evans M, Longo AV, Kurata NP, Walsh T, Pasmans F, McInerney N, Murray S, Martel A, Fleischer RC. Sequence capture identifies fastidious chytrid fungi directly from host tissue. Fungal Genet Biol 2024; 170:103858. [PMID: 38101696 DOI: 10.1016/j.fgb.2023.103858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.
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Affiliation(s)
- Kevin P Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Ed Bronikowski
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Matthew Evans
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Naoko P Kurata
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA; Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, USA; Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Tim Walsh
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Frank Pasmans
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Suzan Murray
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - An Martel
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
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3
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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4
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White LC. Shallow sequencing can mislead when evaluating hybridization capture methods. CONSERV GENET RESOUR 2023. [DOI: 10.1007/s12686-023-01298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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5
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Loreille O, Tillmar A, Brandhagen MD, Otterstatter L, Irwin JA. Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family. Genes (Basel) 2022; 13:genes13020202. [PMID: 35205247 PMCID: PMC8872530 DOI: 10.3390/genes13020202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina’s lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the lock were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas’ maternal lineage, including the well-known point heteroplasmy at position 16169.
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Affiliation(s)
- Odile Loreille
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
- Correspondence:
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, SE-587 58 Linkoping, Sweden;
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-582 25 Linkoping, Sweden
| | - Michael D. Brandhagen
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
| | - Linda Otterstatter
- Federal Bureau of Investigation Laboratory, Trace Evidence Unit, Quantico, VA 22135, USA;
| | - Jodi A. Irwin
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
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6
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Hofreiter M, Sneberger J, Pospisek M, Vanek D. Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. Forensic Sci Int Genet 2021; 54:102538. [PMID: 34265517 DOI: 10.1016/j.fsigen.2021.102538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/07/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.
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Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Jiri Sneberger
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic.
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7
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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8
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Bravo-Lopez M, Villa-Islas V, Rocha Arriaga C, Villaseñor-Altamirano AB, Guzmán-Solís A, Sandoval-Velasco M, Wesp JK, Alcantara K, López-Corral A, Gómez-Valdés J, Mejía E, Herrera A, Meraz-Moreno A, Moreno-Cabrera MDLL, Moreno-Estrada A, Nieves-Colón MA, Olvera J, Pérez-Pérez J, Iversen KH, Rasmussen S, Sandoval K, Zepeda G, Ávila-Arcos MC. Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190580. [PMID: 33012233 PMCID: PMC7702795 DOI: 10.1098/rstb.2019.0580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Carolina Rocha Arriaga
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Ana B. Villaseñor-Altamirano
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Axel Guzmán-Solís
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Julie K. Wesp
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC 27695, USA
| | - Keitlyn Alcantara
- Department of Anthropology, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Aurelio López-Corral
- Department of Archeology, National Institute of Anthropology and History, Tlaxcala, 90000, Mexico
| | | | - Elizabeth Mejía
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | - Alberto Herrera
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Maria A. Nieves-Colón
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Joel Olvera
- Graduate Program of Physical Anthropology, National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Julia Pérez-Pérez
- National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Katrine Højholt Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Gabriela Zepeda
- National Institute of Anthropology and History, Guanajuato, 36250, Mexico
| | - María C. Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
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9
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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.
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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.
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10
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Hiltbrunner M, Heckel G. Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples. Viruses 2020; 12:v12070749. [PMID: 32664593 PMCID: PMC7412162 DOI: 10.3390/v12070749] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.
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Affiliation(s)
- Melanie Hiltbrunner
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
- Swiss Institute of Bioinformatics, Quartier Sorge, 1011 Lausanne, Switzerland
- Correspondence:
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11
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Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
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Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
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12
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Lang PLM, Weiß CL, Kersten S, Latorre SM, Nagel S, Nickel B, Meyer M, Burbano HA. Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Mol Ecol Resour 2020; 20:1228-1247. [PMID: 32306514 DOI: 10.1111/1755-0998.13168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.
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Affiliation(s)
- Patricia L M Lang
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, London, UK
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13
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White LC, Fontsere C, Lizano E, Hughes DA, Angedakin S, Arandjelovic M, Granjon AC, Hans JB, Lester JD, Rabanus-Wallace MT, Rowney C, Städele V, Marques-Bonet T, Langergraber KE, Vigilant L. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Mol Ecol Resour 2019; 19:609-622. [PMID: 30637963 DOI: 10.1111/1755-0998.12993] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 11/30/2022]
Abstract
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%-3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.
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Affiliation(s)
- Lauren C White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne-Céline Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jörg B Hans
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Carolyn Rowney
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Veronika Städele
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute of Human Origins, Arizona State University, Tempe, Arizona
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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14
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Ziesemer KA, Ramos‐Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar‐García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM, Hofman CL, Warinner C, Schroeder H. The efficacy of whole human genome capture on ancient dental calculus and dentin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:496-509. [PMID: 30586168 PMCID: PMC6519167 DOI: 10.1002/ajpa.23763] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 11/10/2018] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
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Affiliation(s)
| | | | - Allison E. Mann
- Laboratories of Molecular Anthropology and Microbiome Research and Department of AnthropologyUniversity of OklahomaNormanOklahoma
| | - Bernd W. Brandt
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam, University of Amsterdam and VU University AmsterdamAmsterdamThe Netherlands
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research and Department of AnthropologyUniversity of OklahomaNormanOklahoma
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahoma
| | - Andrew T. Ozga
- School of Human Evolution and Social ChangeArizona State UniversityTempeArizona
- Institute for Human OriginsArizona State UniversityTempeArizona
- Center for Evolution and MedicineArizona State UniversityTempeArizona
| | - Menno Hoogland
- Faculty of ArchaeologyLeiden UniversityLeidenThe Netherlands
| | - Courtney A. Hofman
- Laboratories of Molecular Anthropology and Microbiome Research and Department of AnthropologyUniversity of OklahomaNormanOklahoma
| | - Domingo C. Salazar‐García
- Department of ArchaeogeneticsMax Planck Institute for the Science of Human HistoryJenaGermany
- Grupo de Investigación en Prehistoria IT‐622‐13 (UPV‐EHU)/IKERBASQUE‐Basque Foundation for ScienceVitoriaSpain
| | | | - George R. Milner
- Department of AnthropologyPennsylvania State UniversityUniversity ParkPennsylvania
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeArizona
- Institute for Human OriginsArizona State UniversityTempeArizona
- Center for Evolution and MedicineArizona State UniversityTempeArizona
| | - Mark Aldenderfer
- Department of Anthropology and Heritage StudiesUniversity of CaliforniaMercedCalifornia
| | - Cecil M. Lewis
- Laboratories of Molecular Anthropology and Microbiome Research and Department of AnthropologyUniversity of OklahomaNormanOklahoma
| | | | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research and Department of AnthropologyUniversity of OklahomaNormanOklahoma
- Department of ArchaeogeneticsMax Planck Institute for the Science of Human HistoryJenaGermany
| | - Hannes Schroeder
- Faculty of ArchaeologyLeiden UniversityLeidenThe Netherlands
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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15
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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16
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Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE. An environmental DNA sampling method for aye-ayes from their feeding traces. Ecol Evol 2018; 8:9229-9240. [PMID: 30377496 PMCID: PMC6194247 DOI: 10.1002/ece3.4341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye's mitochondrial genome and used these to isolate aye-aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye's geographic range that had not been sampled previously. Our method demonstrates the application of next-generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-ayes.
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Affiliation(s)
- Megan L. Aylward
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Alexis P. Sullivan
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
| | - George H. Perry
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
- Department of AnthropologyPennsylvania State UniversityState CollegePennsylvania
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Edward E. Louis
- Grewcock Center for Conservation and ResearchOmaha's Henry Doorly Zoo and AquariumOmahaNebraska
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17
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Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. BMC Genomics 2018; 19:608. [PMID: 30107783 PMCID: PMC6092841 DOI: 10.1186/s12864-018-4945-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries’ initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round. Electronic supplementary material The online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana I Cruz-Dávalos
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - María A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | | | | | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA.,Institute of Human Origins, Arizona State University, Tempe, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, USA.,Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Anna-Sapfo Malaspinas
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.
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18
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Gates DJ, Pilson D, Smith SD. Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae). Mol Phylogenet Evol 2018; 123:26-34. [DOI: 10.1016/j.ympev.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 10/18/2022]
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19
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Bose N, Carlberg K, Sensabaugh G, Erlich H, Calloway C. Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples. Forensic Sci Int Genet 2018. [DOI: 10.1016/j.fsigen.2018.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, Stone AC. Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:824-836. [PMID: 29603124 DOI: 10.1002/ajpa.23472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/15/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). MATERIALS AND METHODS All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step. RESULTS No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments. DISCUSSION Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.
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Affiliation(s)
- Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287
| | - William J Pestle
- Department of Anthropology, University of Miami, Coral Gables, Florida 33124
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Vera Tiesler
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Travis W Stanton
- Department of Anthropology, University of California Riverside, Riverside, California 92521
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287.,Center for Bioarchaeological Research, Arizona State University, Tempe, Arizona 85287
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21
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Marshall C, Sturk-Andreaggi K, Daniels-Higginbotham J, Oliver RS, Barritt-Ross S, McMahon TP. Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure. Forensic Sci Int Genet 2017; 31:198-206. [DOI: 10.1016/j.fsigen.2017.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
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22
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Der Sarkissian C, Pichereau V, Dupont C, Ilsøe PC, Perrigault M, Butler P, Chauvaud L, Eiríksson J, Scourse J, Paillard C, Orlando L. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour 2017; 17:835-853. [PMID: 28394451 DOI: 10.1111/1755-0998.12679] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023]
Abstract
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Vianney Pichereau
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | | | - Peter C Ilsøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mickael Perrigault
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Paul Butler
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Laurent Chauvaud
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Jón Eiríksson
- Institute of Earth Sciences, University of Iceland, Askja, Reykjavík, Iceland
| | - James Scourse
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Christine Paillard
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
- Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France
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23
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Sánchez Barreiro F, Vieira FG, Martin MD, Haile J, Gilbert MTP, Wales N. Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes. Mol Ecol Resour 2016; 17:209-220. [DOI: 10.1111/1755-0998.12610] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/17/2016] [Accepted: 08/29/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Fátima Sánchez Barreiro
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Filipe G. Vieira
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Michael D. Martin
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- NTNU University Museum; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - James Haile
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- PalaeoBARN; Research Lab for Archaeology and the History of Art; University of Oxford; Oxford OX1 3QY UK
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- NTNU University Museum; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
- Trace and Environmental DNA Laboratory; Department of Environment and Agriculture; Curtin University; GPO Box U1987, Perth WA 6845 Australia
| | - Nathan Wales
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
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24
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Cruz-Dávalos DI, Llamas B, Gaunitz C, Fages A, Gamba C, Soubrier J, Librado P, Seguin-Orlando A, Pruvost M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Scheu A, Beneke N, Ludwig A, Cooper A, Willerslev E, Orlando L. Experimental conditions improving in-solution target enrichment for ancient DNA. Mol Ecol Resour 2016; 17:508-522. [PMID: 27566552 DOI: 10.1111/1755-0998.12595] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/29/2016] [Accepted: 08/05/2016] [Indexed: 11/30/2022]
Abstract
High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.
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Affiliation(s)
- Diana I Cruz-Dávalos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.,Undergraduate Program on Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, 62210, Cuernavaca, Mexico
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, 31000, Toulouse, France
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.,National High-Throughput DNA Sequencing Center, University of Copenhagen, Øster Farimagsgade 2D, 1353K, Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, 75205, Paris cédex 13, France
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland
| | - Norbert Beneke
- Naturwissenschaftliches Referat an der Zentrale, Deutsches Archäologisches Institut, Im Dol 2-6, 14195, Berlin, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, 31000, Toulouse, France
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25
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Mohandesan E, Speller CF, Peters J, Uerpmann HP, Uerpmann M, De Cupere B, Hofreiter M, Burger PA. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel. Mol Ecol Resour 2016; 17:300-313. [PMID: 27289015 PMCID: PMC5324683 DOI: 10.1111/1755-0998.12551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 12/29/2022]
Abstract
The performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
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Affiliation(s)
- Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.,Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joris Peters
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität München (LMU Munich), 80539, Munich, Germany.,Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Hans-Peter Uerpmann
- Abteilung Archäozoologie, Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 7207, Tübingen, Germany
| | - Margarethe Uerpmann
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
| | - Michael Hofreiter
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.,Evolutionary and Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, Potsdam, 14476, Germany
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
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26
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Guimaraes S, Pruvost M, Daligault J, Stoetzel E, Bennett EA, Côté NML, Nicolas V, Lalis A, Denys C, Geigl EM, Grange T. A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa. Mol Ecol Resour 2016; 17:405-417. [PMID: 27374145 DOI: 10.1111/1755-0998.12565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/12/2016] [Accepted: 06/24/2016] [Indexed: 11/29/2022]
Abstract
We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high-throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.
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Affiliation(s)
- S Guimaraes
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - M Pruvost
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - J Daligault
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - E Stoetzel
- Département Systématique & Evolution, UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, CP51-Mammifères & Oiseaux, Muséum National d'Histoire Naturelle, 55, rue Buffon, 75005, Paris, France
| | - E A Bennett
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - N M-L Côté
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - V Nicolas
- Département Systématique & Evolution, UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, CP51-Mammifères & Oiseaux, Muséum National d'Histoire Naturelle, 55, rue Buffon, 75005, Paris, France
| | - A Lalis
- Département Systématique & Evolution, UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, CP51-Mammifères & Oiseaux, Muséum National d'Histoire Naturelle, 55, rue Buffon, 75005, Paris, France
| | - C Denys
- Département Systématique & Evolution, UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, CP51-Mammifères & Oiseaux, Muséum National d'Histoire Naturelle, 55, rue Buffon, 75005, Paris, France
| | - E-M Geigl
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
| | - T Grange
- Epigenome and Paleogenome Group, Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France
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27
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The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol 2016; 99:16-33. [DOI: 10.1016/j.ympev.2016.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
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28
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Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. Genetics 2016; 203:699-714. [PMID: 27098910 PMCID: PMC4896188 DOI: 10.1534/genetics.116.187492] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.
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29
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Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MTP, Lalueza-Fox C. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Mol Biol Evol 2015; 32:3132-42. [PMID: 26337550 PMCID: PMC4652622 DOI: 10.1093/molbev/msv181] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Marcela Sandoval-Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lobón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pablo García Borja
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain
| | - Domingo C Salazar-García
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain Department of Archaeology, University of Cape Town, Cape Town, South Africa LAMPEA UMR 7269, Maison Méditerranéenne des Sciences de l'Homme (MMSH), Aix-en-Provence, France Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Josep María Fullola
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Xavier Oms
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Pedro
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Pablo Martínez
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Col·Lectiu per a la Investigació de la Prehistòria i l'Arqueologia del Garraf-Ordal, CIPAG, Begues, Spain
| | - Montserrat Sanz
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal
| | - Joan Daura
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal GRQ, Grup de Recerca del Quaternari, Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - João Zilhão
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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30
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Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet 2015; 16:395-408. [PMID: 26055157 DOI: 10.1038/nrg3935] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Affiliation(s)
- Ludovic Orlando
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark
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