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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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2
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Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.
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Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
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3
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Alves‐Pereira A, Clement CR, Picanço‐Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, de Souza AP, Zucchi MI. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. Evol Appl 2020; 13:342-361. [PMID: 31993081 PMCID: PMC6976959 DOI: 10.1111/eva.12873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.
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Affiliation(s)
- Alessandro Alves‐Pereira
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
| | | | | | - Elizabeth Ann Veasey
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Gabriel Dequigiovanni
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Santiago Linorio Ferreyra Ramos
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - José Baldin Pinheiro
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Anete Pereira de Souza
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
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4
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Wagner S, Plomion C, Orlando L. Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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5
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Gutaker RM, Weiß CL, Ellis D, Anglin NL, Knapp S, Luis Fernández-Alonso J, Prat S, Burbano HA. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol 2019; 3:1093-1101. [PMID: 31235927 DOI: 10.1038/s41559-019-0921-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/10/2019] [Indexed: 12/30/2022]
Abstract
Potato, one of the most important staple crops, originates from the highlands of the equatorial Andes. There, potatoes propagate vegetatively via tubers under short days, constant throughout the year. After their introduction to Europe in the sixteenth century, potatoes adapted to a shorter growing season and to tuber formation under long days. Here, we traced the demographic and adaptive history of potato introduction to Europe. To this end, we sequenced 88 individuals that comprise landraces, modern cultivars and historical herbarium samples, including specimens collected by Darwin during the voyage of the Beagle. Our findings show that European potatoes collected during the period 1650-1750 were closely related to Andean landraces. After their introduction to Europe, potatoes admixed with Chilean genotypes. We identified candidate genes putatively involved in long-day pre-adaptation, and showed that the 1650-1750 European individuals were not long-day adapted through previously described allelic variants of the CYCLING DOF FACTOR1 gene. Such allelic variants were detected in Europe during the nineteenth century. Our study highlights the power of combining contemporary and historical genomes to understand the complex evolutionary history of crop adaptation to new environments.
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Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | | | | | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany.
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6
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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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7
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Zhou Y, Chen Z, Cheng M, Chen J, Zhu T, Wang R, Liu Y, Qi P, Chen G, Jiang Q, Wei Y, Luo M, Nevo E, Allaby RG, Liu D, Wang J, Dvorák J, Zheng Y. Uncovering the dispersion history, adaptive evolution and selection of wheat in China. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:280-291. [PMID: 28635103 PMCID: PMC5785339 DOI: 10.1111/pbi.12770] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 05/18/2023]
Abstract
Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.
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Affiliation(s)
- Yong Zhou
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Zhongxu Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Jian Chen
- Chengdu City Institute of ArchaeologyChengduSichuanChina
| | - Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Rui Wang
- State Key Lab of CAD&CGZhejiang UniversityHangzhouZhejiangChina
| | - Yaxi Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | | | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jan Dvorák
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
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8
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Roucou A, Violle C, Fort F, Roumet P, Ecarnot M, Vile D. Shifts in plant functional strategies over the course of wheat domestication. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13029] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Agathe Roucou
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
| | - Cyrille Violle
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Florian Fort
- CEFE; Montpellier SupAgro; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Pierre Roumet
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Martin Ecarnot
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Denis Vile
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
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9
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Smith O, Palmer SA, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG. Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment. Mol Biol Evol 2017; 34:2555-2562. [PMID: 28655202 PMCID: PMC5850308 DOI: 10.1093/molbev/msx175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought. Its microRNA profile is broadly similar to 19 globally distributed modern barley samples with the exception of three microRNAs (miRNA159, miRNA319, and miR396), all of which are known to have variable expression under stress conditions. We also found retrotransposon activity to be significantly reduced in the archeological barley compared with the controls, where one would expect the opposite under stress conditions. We suggest that the archeological barley's conflicting stress signals could be the result of long-term adaptation to its local environment.
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Affiliation(s)
- Oliver Smith
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Sarah A. Palmer
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Alan J. Clapham
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Pamela Rose
- The Austrian Archaeological Institute, Cairo Branch, Zamalek, Cairo, Egypt
| | - Yuan Liu
- BGI-Europe-UK, London, United Kingdom
| | | | - Robin G. Allaby
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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10
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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11
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Gutaker RM, Burbano HA. Reinforcing plant evolutionary genomics using ancient DNA. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:38-45. [PMID: 28160617 DOI: 10.1016/j.pbi.2017.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/07/2016] [Accepted: 01/13/2017] [Indexed: 05/11/2023]
Abstract
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place. Comparison of historical samples of barley (Hordeum vulgare) and maize (Zea mays ssp. mays) with their present-day counterparts enabled assessment of selection during different stages of domestication. These examples show how aDNA already improved our evolutionary inferences. Increasing quality and amount of sequencing data retrieved from historical plants will further advance our understanding of plant evolution.
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Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany.
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12
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The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol 2016; 99:16-33. [DOI: 10.1016/j.ympev.2016.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
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13
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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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14
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Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet 2015; 16:395-408. [PMID: 26055157 DOI: 10.1038/nrg3935] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Affiliation(s)
- Ludovic Orlando
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark
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15
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep 2014; 4:5559. [PMID: 24993353 PMCID: PMC4081896 DOI: 10.1038/srep05559] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/16/2014] [Indexed: 11/08/2022] Open
Abstract
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
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