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Morphotype broadening of the grapevine (Vitis vinifera L.) from Oxus civilization 4000 BP, Central Asia. Sci Rep 2022; 12:16331. [PMID: 36175486 PMCID: PMC9522827 DOI: 10.1038/s41598-022-19644-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
The region of Transoxiana underwent an early agricultural-demographic transition leading to the earliest proto-urban centers in Central Asia. The agronomic details of this cultural shift are still poorly studied, especially regarding the role that long-generation perennials, such as grapes, played in the cultivation system. In this paper, we present directly dated remains of grape pips from the early urban centers of Sapalli and Djarkutan, in south Uzbekistan. We also present linear morphometric data, which illustrate a considerable range of variation under cultivation that we divide into four distinct morphotypes according to pip shape. While some of the pips in these two assemblages morphologically fall within the range of wild forms, others more closely resemble modern domesticated populations. Most of the specimens measure along a gradient between the two poles, showing a mixed combination of domesticated and wild features. We also point out that the seeds recovered from the Djarkutan temple were, on average, larger and contained more affinity towards domesticated forms than those from domestic contexts. The potential preference of morphotypes seems to suggest that there were recognized different varieties that local cultivators might aware and possibly propagating asexually.
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2
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Pérez-Escobar OA, Tusso S, Przelomska NAS, Wu S, Ryan P, Nesbitt M, Silber MV, Preick M, Fei Z, Hofreiter M, Chomicki G, Renner SS. Genome sequencing of up to 6,000-yr-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Mol Biol Evol 2022; 39:6652436. [PMID: 35907246 PMCID: PMC9387916 DOI: 10.1093/molbev/msac168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use “egusi-type” watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.
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Affiliation(s)
| | - Sergio Tusso
- Faculty of Biology, Division of Genetics, University of Munich (LMU), 82152 Planegg- Martinsried, Germany
| | | | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | | | - Mark Nesbitt
- Royal Botanic Gardens, Kew, TW9 3AE, United Kingdom
| | - Martina V Silber
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Guillaume Chomicki
- Ecology and Evolutionary Biology, School of Bioscience, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany.,Department of Biology, Washington University, Saint Louis, MO 63130, USA
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3
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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4
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Marinček P, Wagner ND, Tomasello S. Ancient DNA extraction methods for herbarium specimens: When is it worth the effort? APPLICATIONS IN PLANT SCIENCES 2022; 10:e11477. [PMID: 35774991 PMCID: PMC9215277 DOI: 10.1002/aps3.11477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 06/15/2023]
Abstract
Premise Herbaria harbor a tremendous number of plant specimens that are rarely used for molecular systematic studies, largely due to the difficulty in extracting sufficient amounts of high-quality DNA from the preserved plant material. Methods We compared the standard Qiagen DNeasy Plant Mini Kit and a specific protocol for extracting ancient DNA (aDNA) (the N-phenacylthiazolium bromide and dithiothreitol [PTB-DTT] extraction method) from two different plant genera (Xanthium and Salix). The included herbarium materials covered about two centuries of plant collections. To analyze the success of DNA extraction using each method, a subset of samples was subjected to a standard library preparation as well as target-enrichment approaches. Results The PTB-DTT method produced a higher DNA yield of better quality than the Qiagen kit; however, extracts from the Qiagen kit over a certain DNA yield and quality threshold produced comparable sequencing results. The sequencing resulted in high proportions of endogenous reads. We were able to successfully sequence 200-year-old samples. Discussion This method comparison revealed that, for younger specimens, DNA extraction using a standard kit might be sufficient. For old and precious herbarium specimens, aDNA extraction methods are better suited to meet the requirements for next-generation sequencing.
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Affiliation(s)
- Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
| | - Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
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5
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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6
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Estrada O, Richards SM, Breen J. Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens. Methods Mol Biol 2022; 2512:261-267. [PMID: 35818010 DOI: 10.1007/978-1-0716-2429-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.
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Affiliation(s)
- Oscar Estrada
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse, France.
- Australian Centre for Ancient DNA (ACAD), School of Biological Science, The University of Adelaide, Adelaide, SA, Australia.
- Grupo de Agrobiotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
| | - Stephen M Richards
- Australian Centre for Ancient DNA (ACAD), School of Biological Science, The University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
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7
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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8
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Danneels B, Viruel J, Mcgrath K, Janssens SB, Wales N, Wilkin P, Carlier A. Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing. Curr Biol 2021; 31:2666-2673.e4. [PMID: 33852872 DOI: 10.1016/j.cub.2021.03.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae.1 This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).4-6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.3.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Juan Viruel
- Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Krista Mcgrath
- Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Autonomous University of Barcelona, 08193 Bellaterra, Spain; Department of Archaeology, University of York, Heslington, York YO10 5DD, UK
| | - Steven B Janssens
- Meise Botanic Garden, 1860 Meise, Belgium; Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Nathan Wales
- Department of Archaeology, University of York, Heslington, York YO10 5DD, UK
| | - Paul Wilkin
- Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Aurélien Carlier
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium; LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France.
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9
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Back to the Origins: Background and Perspectives of Grapevine Domestication. Int J Mol Sci 2021; 22:ijms22094518. [PMID: 33926017 PMCID: PMC8123694 DOI: 10.3390/ijms22094518] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.
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10
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Blanchette RA, Haynes DT, Held BW, Niemann J, Wales N. Fungal mycelial mats used as textile by indigenous people of North America. Mycologia 2021; 113:261-267. [PMID: 33605842 DOI: 10.1080/00275514.2020.1858686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The indigenous people of the United States and Canada long have used forest fungi for food, tinder, medicine, paint, and many other cultural uses. New information about historical uses of fungi continues to be discovered from museums as accessions of fungi and objects made from fungi collected over the last 150+ years are examined and identified. Two textiles thought to be made from fungal mats are located in the Hood Museum of Art, Dartmouth College, and the Oakland Museum of California. Scanning electron microscopy and DNA sequencing were used to attempt to identify the fungus that produced the mats. Although DNA sequencing failed to yield a taxonomic identification, microscopy and characteristics of the mycelial mats suggest that the mats were produced by Laricifomes officinalis. This first report of fungal mats used for textile by indigenous people of North America will help to alert museum curators and conservators as well as mycological researchers to their existence and hopefully lead to more items being discovered that have been made from fungal fabric.
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Affiliation(s)
- Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | | | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jonas Niemann
- Department of Archaeology, University of York, Heslington, York, UK Y010 5DD.,Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, University of York, Heslington, York, UK Y010 5DD
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11
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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12
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Latorre SM, Lang PLM, Burbano HA, Gutaker RM. Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA. ACTA ACUST UNITED AC 2020; 5:e20121. [PMID: 33211414 DOI: 10.1002/cppb.20121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA.
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Affiliation(s)
- Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, 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, United Kingdom
| | - Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, New York.,Royal Botanic Gardens, Kew, Richmond, London, United Kingdom
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13
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Rønsted N, Grace OM, Carine MA. Editorial: Integrative and Translational Uses of Herbarium Collections Across Time, Space, and Species. FRONTIERS IN PLANT SCIENCE 2020; 11:1319. [PMID: 32973855 PMCID: PMC7472523 DOI: 10.3389/fpls.2020.01319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 06/01/2023]
Affiliation(s)
- Nina Rønsted
- Science and Conservation, National Tropical Botanical Garden, Kalaheo, HI, United States
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Olwen M. Grace
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Mark A. Carine
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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14
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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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15
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Ramos-Madrigal J, Runge AKW, Bouby L, Lacombe T, Samaniego Castruita JA, Adam-Blondon AF, Figueiral I, Hallavant C, Martínez-Zapater JM, Schaal C, Töpfer R, Petersen B, Sicheritz-Pontén T, This P, Bacilieri R, Gilbert MTP, Wales N. Palaeogenomic insights into the origins of French grapevine diversity. NATURE PLANTS 2019; 5:595-603. [PMID: 31182840 DOI: 10.1038/s41477-019-0437-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/30/2019] [Indexed: 05/20/2023]
Abstract
The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent-offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to 'Savagnin Blanc', providing evidence for 900 years of uninterrupted vegetative propagation.
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Affiliation(s)
| | - Anne Kathrine Wiborg Runge
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Laurent Bouby
- ISEM-UMR 5554, CNRS-IRD-EPHE-Université Montpellier, Montpellier, France
| | - Thierry Lacombe
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | - Isabel Figueiral
- Inrap, Méditerranée and ISEM-UMR 5554, CNRS-IRD-EPHE-Université Montpellier, Montpellier, France
| | - Charlotte Hallavant
- Bureau d'études Hadès, laboratoire TRACES-UMR 5608 (pôle Terrae)-UT2J, Toulouse, France
| | | | - Caroline Schaal
- GéoArchEon Sarl, Laboratoire Chrono-Environnement-UMR 6249, Université de Franche Comté, Besançon, France
| | - Reinhard Töpfer
- Julius Kühn-Institut Bundesforschungsinstitut für Kulturpflanzen, Institut für Rebenzüchtung Geilweilerhof, Siebeldingen, Germany
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Patrice This
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- NTNU University Museum, Trondheim, Norway.
| | - Nathan Wales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- BioArCh, Department of Archaeology, University of York, York, UK.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse, France.
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16
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Zervas A, Petersen G, Seberg O. Mitochondrial genome evolution in parasitic plants. BMC Evol Biol 2019; 19:87. [PMID: 30961535 PMCID: PMC6454704 DOI: 10.1186/s12862-019-1401-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/22/2019] [Indexed: 11/10/2022] Open
Abstract
Background Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss. Results Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive. Conclusions We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales. Electronic supplementary material The online version of this article (10.1186/s12862-019-1401-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Athanasios Zervas
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark.
| | - Gitte Petersen
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark
| | - Ole Seberg
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark
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17
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Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 2019; 20:29. [PMID: 30744646 PMCID: PMC6369560 DOI: 10.1186/s13059-019-1627-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.
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Affiliation(s)
- Caroline Pont
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France
| | - Stefanie Wagner
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Antoine Kremer
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade, 1350K, Copenhagen, Denmark
| | - Christophe Plomion
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Jerome Salse
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.
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18
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Abstract
Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of aDNA. Plant tissues are anatomically and chemically diverse and therefore require optimized DNA extraction approaches. Here, we describe a plant DNA isolation protocol that performs well in most contexts. We include recommendations for optimization to retain the very short DNA fragments that are expected to be preserved in degraded tissues.
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Affiliation(s)
- Nathan Wales
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Laboratory of Molecular Anthropology and Image Synthesis, University Paul Sabatier, Toulouse, France
- Department of Archaeology, University of York, York, UK
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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19
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Wales N, Akman M, Watson RHB, Sánchez Barreiro F, Smith BD, Gremillion KJ, Gilbert MTP, Blackman BK. Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evol Appl 2019; 12:38-53. [PMID: 30622634 PMCID: PMC6304678 DOI: 10.1111/eva.12594] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/26/2017] [Indexed: 01/02/2023] Open
Abstract
Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.
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Affiliation(s)
- Nathan Wales
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Melis Akman
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Ray H. B. Watson
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Fátima Sánchez Barreiro
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | | | | | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Norwegian University of Science and TechnologyUniversity MuseumTrondheimNorway
| | - Benjamin K. Blackman
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
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20
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Kistler L, Maezumi SY, Gregorio de Souza J, Przelomska NAS, Malaquias Costa F, Smith O, Loiselle H, Ramos-Madrigal J, Wales N, Ribeiro ER, Morrison RR, Grimaldo C, Prous AP, Arriaza B, Gilbert MTP, de Oliveira Freitas F, Allaby RG. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 2018; 362:1309-1313. [DOI: 10.1126/science.aav0207] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9000 years before the present (yr B.P.), traversed Central America by ~7500 yr B.P., and spread into South America by ~6500 yr B.P. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then evolved within South America out of this partially domesticated progenitor population. Genomic, linguistic, archaeological, and paleoecological data suggest that the southwestern Amazon was a secondary improvement center for partially domesticated maize. Multiple waves of human-mediated dispersal are responsible for the diversity and biogeography of modern South American maize.
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21
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Estrada O, Breen J, Richards SM, Cooper A. Ancient plant DNA in the genomic era. NATURE PLANTS 2018; 4:394-396. [PMID: 29915330 DOI: 10.1038/s41477-018-0187-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Oscar Estrada
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, South Australia, Australia.
- University of Adelaide Bioinformatics Hub, School of Biological Sciences, University of Adelaide, South Australia, Australia.
| | - Stephen M Richards
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
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22
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Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 2018; 6:1-13. [PMID: 28854615 PMCID: PMC5570000 DOI: 10.1093/gigascience/gix049] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
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Affiliation(s)
- Sarah Siu Tze Mak
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.,The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | | | - Shujin Fu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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23
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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24
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Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T, Guichoux E, Chancerel E, Bech-Hebelstrup I, Bernard V, Billard C, Billaud Y, Bolliger M, Croutsch C, Čufar K, Eynaud F, Heussner KU, Köninger J, Langenegger F, Leroy F, Lima C, Martinelli N, Momber G, Billamboz A, Nelle O, Palomo A, Piqué R, Ramstein M, Schweichel R, Stäuble H, Tegel W, Terradas X, Verdin F, Plomion C, Kremer A, Orlando L. High-Throughput DNA sequencing of ancient wood. Mol Ecol 2018; 27:1138-1154. [PMID: 29412519 DOI: 10.1111/mec.14514] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023]
Abstract
Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.
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Affiliation(s)
- Stefanie Wagner
- BIOGECO, INRA, University of Bordeaux, Cestas, France.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Vincent Bernard
- Dendro-Archaeology, CNRS, UMR 6566 CReAAH, University of Rennes, Rennes cedex, France
| | | | - Yves Billaud
- MCC/DRASSM, Marseille, France.,Edytem, University of Savoie, Le Bourget-du-Lac, France
| | | | - Christophe Croutsch
- Archéologie Alsace 11, Sélestat, France.,UMR 7044, ARCHIMEDE, Strasbourg Cedex, France
| | - Katarina Čufar
- Biotechnical Faculty, Department of Wood Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Karl Uwe Heussner
- Deutsches Archäologisches Institut, Zentrale, Referat Naturwissenschaften/Dendrochronologie, Berlin, Germany
| | - Joachim Köninger
- Janus Verlag Freiburg im Breisgau, Freiburg im Breisgau, Germany
| | | | - Frédéric Leroy
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | - Christine Lima
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | | | - Garry Momber
- National Oceanography Centre, Maritime Archaeology Trust, Southampton, UK
| | - André Billamboz
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Oliver Nelle
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Antoni Palomo
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Piqué
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | - Willy Tegel
- Institute for Forest Growth, University of Freiburg, Freiburg, Germany
| | - Xavier Terradas
- Spanish National Research Council, IMF - Archaeology of Social Dynamics, Barcelona, Spain
| | - Florence Verdin
- CNRS, UMR 5607 Ausonius, Maison de l'Archéologie, Pessac cedex, France
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
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Lendvay B, Hartmann M, Brodbeck S, Nievergelt D, Reinig F, Zoller S, Parducci L, Gugerli F, Büntgen U, Sperisen C. Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest. THE NEW PHYTOLOGIST 2018; 217:1737-1748. [PMID: 29243821 DOI: 10.1111/nph.14935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.
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Affiliation(s)
- Bertalan Lendvay
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Martin Hartmann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Sabine Brodbeck
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Daniel Nievergelt
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Frederick Reinig
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Felix Gugerli
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Ulf Büntgen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
- Department of Geography, University of Cambridge, Downing Place, Cambridge, CB2 3EN, UK
- Global Change Research Centre, Masaryk University, 613 00, Brno, Czech Republic
| | - Christoph Sperisen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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Marciano MA, Panicker SX, Liddil GD, Lindgren D, Sweder KS. Development of a Method to Extract Opium Poppy (Papaver somniferum L.) DNA from Heroin. Sci Rep 2018; 8:2590. [PMID: 29416103 PMCID: PMC5803222 DOI: 10.1038/s41598-018-20996-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/29/2018] [Indexed: 01/03/2023] Open
Abstract
This study is the first to report the successful development of a method to extract opium poppy (Papaver somniferum L.) DNA from heroin samples. Determining of the source of an unknown heroin sample (forensic geosourcing) is vital to informing domestic and foreign policy related to counter-narcoterrorism. Current profiling methods focus on identifying process-related chemical impurities found in heroin samples. Changes to the geographically distinct processing methods may lead to difficulties in classifying and attributing heroin samples to a region/country. This study focuses on methods to optimize the DNA extraction and amplification of samples with low levels of degraded DNA and inhibiting compounds such as heroin. We compared modified commercial-off-the-shelf extraction methods such as the Qiagen Plant, Stool and the Promega Maxwell-16 RNA-LEV tissue kits for the ability to extract opium poppy DNA from latex, raw and cooked opium, white and brown powder heroin and black tar heroin. Opium poppy DNA was successfully detected in all poppy-derived samples, including heroin. The modified Qiagen stool method with post-extraction purification and a two-stage, dual DNA polymerase amplification procedure resulted in the highest DNA yield and minimized inhibition. This paper describes the initial phase in establishing a DNA-based signature method to characterize heroin.
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Affiliation(s)
- Michael A Marciano
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA.
| | - Sini X Panicker
- U.S. Drug Enforcement Administration, Special Testing and Research Laboratory, Dulles, VA, 20166, USA
| | - Garrett D Liddil
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
| | - Danielle Lindgren
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
| | - Kevin S Sweder
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
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27
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Di Donato A, Filippone E, Ercolano MR, Frusciante L. Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:441. [PMID: 29719544 PMCID: PMC5914272 DOI: 10.3389/fpls.2018.00441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/21/2018] [Indexed: 05/08/2023]
Abstract
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
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Aversano R, Basile B, Buonincontri MP, Carucci F, Carputo D, Frusciante L, Di Pasquale G. Dating the beginning of the Roman viticultural model in the Western Mediterranean: The case study of Chianti (Central Italy). PLoS One 2017; 12:e0186298. [PMID: 29140987 PMCID: PMC5687709 DOI: 10.1371/journal.pone.0186298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/28/2017] [Indexed: 11/19/2022] Open
Abstract
Although domestication of the grapevine (Vitis vinifera L.) has been extensively documented, the history of genotype selection and evolution of vineyard management remain relatively neglected fields of study. The find of 454 waterlogged grapevine pips from a well-dated Etrusco-Roman site in the Chianti district (Tuscany, Central Italy) is an extraordinary chance to gain insights into the progress of viticulture occurring in a key historical period in one of the world's most famous wine regions. The molecular and geometrical analyses of grape seeds showed (a) the presence in the site of different grapevine individuals and (b) a sudden increase in pip size, occurring at around 200 BC, whic explainable by the selection and introduction of new varieties. In this period, the Etruscans settlers in Chianti were stimulated by northward-expanding Roman culture to use novel vineyard management practices. We hypothesize that one of the most important innovations may have been the introduction of pruning, inducing vine physiological conditions more favorable to pip growth. Such changes were the consequence of specific entrepreneurial choices made by the Romans in a period of economic investment in grape cultivation and wine making to satisfy the increased trade demand after the conquest of the Central-Western Mediterranean basin.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | - Francesca Carucci
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Gaetano Di Pasquale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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29
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Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques 2017; 62:76-79. [PMID: 28193151 DOI: 10.2144/000114517] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 11/23/2022] Open
Abstract
DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.
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30
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Nistelberger HM, Smith O, Wales N, Star B, Boessenkool S. The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains. Sci Rep 2016; 6:37347. [PMID: 27881876 PMCID: PMC5121605 DOI: 10.1038/srep37347] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/25/2016] [Indexed: 11/08/2022] Open
Abstract
The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data - excluding false-positives due to background contamination or incorrect index assignments - indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains.
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Affiliation(s)
- H. M. Nistelberger
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, Oslo, NO-0316, Norway
| | - O. Smith
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - N. Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - B. Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, Oslo, NO-0316, Norway
| | - S. Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, Oslo, NO-0316, Norway
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31
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Postglacial viability and colonization in North America's ice-free corridor. Nature 2016; 537:45-49. [PMID: 27509852 DOI: 10.1038/nature19085] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/07/2016] [Indexed: 02/07/2023]
Abstract
During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by approximately 12.6 cal. kyr bp, followed by open forest, with evidence of moose and elk at about 11.5 cal. kyr bp, and boreal forest approximately 10 cal. kyr bp. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr bp, are unlikely to have travelled by this route into the Americas. However, later groups may have used this north-south passageway.
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32
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Ozga AT, Nieves‐Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:220-8. [PMID: 26989998 PMCID: PMC4866892 DOI: 10.1002/ajpa.22960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew T. Ozga
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | | | - Tanvi P. Honap
- School of Life SciencesArizona State UniversityTempeAZ85287
| | | | | | - George R. Milner
- Department of AnthropologyPennsylvania State University, University ParkPA16802
| | - Cecil M. Lewis
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeAZ85287
- Center for Bioarchaeological Research, Arizona State UniversityTempeAZ85287
- Institute of Human Origins, Arizona State UniversityTempeAZ85287
| | - Christina Warinner
- Department of AnthropologyUniversity of OklahomaNormanOK73019
- Institute of Evolutionary Medicine, University of Zurich8057 ZurichSwitzerland
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33
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da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MTP. The origin and evolution of maize in the Southwestern United States. NATURE PLANTS 2015; 1:14003. [PMID: 27246050 DOI: 10.1038/nplants.2014.3] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/08/2014] [Indexed: 05/18/2023]
Abstract
The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.
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Affiliation(s)
- Rute R da Fonseca
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
- The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bruce D Smith
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Nathan Wales
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matteo Fumagalli
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | | | - Christian Carøe
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, &Organismal Biology, Iowa State University, 50011, USA
| | | | - Filipe Garrett Vieira
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, 15101 Arica, Chile
| | - Eske Willerslev
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Rasmus Nielsen
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Integrative Biology and Statistics, University of California, Berkeley, California 94720-3140, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, &Organismal Biology, Iowa State University, 50011, USA
| | - Anders Albrechtsen
- The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, California 95616, USA
| | - M Thomas P Gilbert
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia
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