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Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. A Multifaceted Overview of Apple Tree Domestication. TRENDS IN PLANT SCIENCE 2019; 24:770-782. [PMID: 31296442 DOI: 10.1016/j.tplants.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.
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Affiliation(s)
- Amandine Cornille
- Génétique Quantitative et Evolution- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Ferran Antolín
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Elena Garcia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, USA
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Alice Fietta
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Otto Brinkkemper
- Cultural Heritage Agency, PO Box 1600, 3800 BP Amersfoort, The Netherlands
| | - Wiebke Kirleis
- Institute for Prehistoric and Protohistoric Archeology/Graduate School Human Development in Landscapes, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angela Schlumbaum
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
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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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Wales N, Andersen K, Cappellini E, Ávila-Arcos MC, Gilbert MTP. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS One 2014; 9:e86827. [PMID: 24475182 PMCID: PMC3903575 DOI: 10.1371/journal.pone.0086827] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/14/2013] [Indexed: 11/24/2022] Open
Abstract
Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.
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Affiliation(s)
- Nathan Wales
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, United States of America
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Kenneth Andersen
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | - M. Thomas P. Gilbert
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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