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GEOGRAPHIC ANALYSIS for SUPPORTING CONSERVATION STRATEGIES of CROP WILD RELATIVES By

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GEOGRAPHIC ANALYSIS for SUPPORTING CONSERVATION STRATEGIES of CROP WILD RELATIVES By GEOGRAPHIC ANALYSIS FOR SUPPORTING CONSERVATION STRATEGIES OF CROP WILD RELATIVES by NORA PATRICIA CASTAÑEDA ÁLVAREZ A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Biosciences College of Life and Environmental Sciences The University of Birmingham March 2016 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Crop wild relatives are important for agriculture due to the genetic richness they possess. They have been used in plant breeding to develop high yielding varieties; varieties with im- proved resistance to biotic and abiotic stresses, and enhanced nutritional content. Securing their conservation in the long-term is critical to enable the continuous development of crops’ vari- eties able to respond to future challenges. The work presented in this thesis is a contribution to the effort of understanding the ex situ conservation gaps of crop wild relatives, their expected response to climate change and their needs for conservation. Methods used in this thesis include species distribution modelling, gap analyses, a case study assessing the preliminary IUCN Red List categories, species distribution projections onto future climate change scenarios, and an estimation of the global value of crop wild relatives based on their likelihood of being used in plant breeding, and the contributions of their associated crops to human diets and agricultural production systems. The methods used here can be applied to more crop gene pools for global conservation planning, and can also be adapted for analysis at the regional and national level. The results presented here are being used to improve the conservation of the wild relatives of 29 crops. To Nora, Elías and Fernando ACKNOWLEDGEMENTS First, I would like to thanks Dr. Andy Jarvis, who gave me the opportunity of being part of his team, and who has constantly challenged me to prove I can do better. Special thanks to my supervisor, Dr. Nigel Maxted for his support, guidance and patience during this PhD. My gratitude goes to Luigi Guarino, Hannes Dempewolf and Jane Toll from the Global Crop Diversity Trust, for the financial support, but also for being an inspiration to continue working towards the conservation of plant genetic resources. I also extend my thanks to Ruth Eastwood and Jonas Müller from the Millennium Seed Bank, Kew, for their support during the completion of this study. Special thanks to the International Center for Tropical Agriculture (CIAT) and the team that has been always willing and available to help and collaborate: Chrystian Camilo Sosa, Harold A. Achicanoy, Steven Sotelo, Edward Guevara, Shirley Calderón, Ingrid Vanegas, Vi- vian Bernau, Ovidio Rivera, David Arango, Hugo Dorado and Carlos Navarro-Racines. Special thanks to Colin who has been my “partner in crime” during the last four years. My gratitude also goes to all the fantastic and inspiring people I met during the preparation of this thesis: David Spooner (University of Wisconsin), Alberto Salas, Stef de Haan, Henry Juárez, Bettina Heider and Reinhard Simon (International Potato Center); Sandy Knapp, Tiina Särkinen and Mindy Syfert from the National History Museum, London; and all the genebank and database managers and herbaria curators that facilitated access to the data they maintain, specially those from the herbaria I visited personally: CUVC (Universidad del Valle, Cali, Colombia); JABOT and GUA (Rio de Janeiro, Brazil); MA (Madrid, Spain); LISC, LISI and LISU (Lisboa, Portugal); COI (Coimbra, Portugal), and E (Edinburgh, UK). Special thanks to Dr. Daniel Debouck and Dr. Mauricio Parra-Quijano. Both of them have guided me one a way or another before starting and during this PhD. Thanks to my friends, who have been supportive during the process of completing this PhD: Carolina González, Julie Hernández, Sergio Angulo and Carolina Navarrete. Special thanks to Meike Andersson and Julian Ramirez-Villegas for their constant support, and for putting aside some of their free time to proof-read parts of this thesis. Profound thanks to Sandy Knapp for letting me be part of her team during the time spent at the National History Museum: these periods were an inspiration to continue working towards the understanding of plants and their conservation needs. Thanks to the Parker family for having me during my visits to London, to Richard Barrie for the cuppas and for the Sundays when we kneaded bread, and to Isabella Römer, Paulo Ávila, Carlos Flores, Javier Juárez, and Aremi Contreras for their companion and friendship. I am specially thankful to Marcela Quintero for all the support, counselling and coaching provided during the final stages of this PhD. Special thanks to Paul Struik who has been always available to provide insightful comments of my writing and the way I present information. I also extend my gratitude to Sara Oldfield OBE and Dr. Eugenio Sanchez-Moran for ac- cepting being my reviewers. I did enjoy our discussions during my viva. This work was undertaken as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives" which is supported by the Govern- ment of Norway. The project is managed by the Global Crop Diversity Trust with the Millen- nium Seed Bank of the Royal Botanic Gardens, Kew UK and implemented in partnership with national and international genebanks and plant breeding institutes around the world. For further information, go to the project website: http://www.cwrdiversity.org/ CONTENTS 1 Introduction 1 1.1 Context . 1 1.2 Relevance of agriculture in the world . 2 1.3 Constraints and challenges for agriculture . 3 1.4 Plant genetic resources and agriculture . 4 1.5 Crop wild relatives . 6 1.5.1 Definition of CWR . 6 1.5.2 Utilization of CWR . 7 1.5.3 Threats affecting CWR . 8 1.5.4 Policies supporting the conservation of CWR . 9 1.5.5 Conservation assessments for CWR . 11 1.6 Aims of the study . 15 2 A global occurrence dataset for crop wild relatives 22 2.1 Abstract . 23 2.2 Background and summary . 23 2.3 Methods . 26 2.3.1 Data collection . 26 2.3.2 Data preparation . 33 2.3.3 Code availability . 36 2.4 Data Records . 36 2.5 Technical Validation . 36 2.5.1 Nomenclature validation . 38 2.5.2 Geographic validation . 39 2.6 Usage Notes . 42 2.7 Discussion . 43 3 Ex situ conservation priorities for the wild relatives of potato (Solanum L. section Petota) 44 3.1 Abstract . 45 3.2 Introduction . 45 3.3 Materials and Methods . 49 3.3.1 Wild relative species and geographic area of study . 49 3.3.2 Environmental niche modelling . 50 3.3.3 Gap analysis . 51 3.3.4 Identification of geographic areas of priority for further collecting . 52 3.4 Results . 52 3.4.1 Wild relative species and geographic area of study . 52 3.4.2 Environmental niche modelling . 58 3.4.3 Gap analysis . 58 3.5 Discussion . 62 4 Crop wild relatives of the brinjal eggplant (Solanum melongena: Solanaceae): poorly represented in genebanks and many species at risk of extinction 65 4.1 Abstract . 66 4.2 Introduction . 67 4.3 Materials and methods . 72 4.3.1 Gene pool concept and selection of species . 72 4.3.2 Occurrence data . 72 4.3.3 Species distribution modelling . 74 4.3.4 Ex situ conservation analysis . 75 4.3.5 In situ conservation assessment . 77 4.4 Results . 78 4.4.1 Gene pool concept definition . 78 4.4.2 Occurrence data . 83 4.4.3 Species distribution models . 83 4.4.4 Ex situ conservation analysis . 84 4.4.5 In situ conservation assessment . 85 4.5 Discussion . 90 5 Global conservation priorities for crop wild relatives 96 5.1 Abstract . 97 5.2 Introduction . 97 5.3 Methods . 99 5.4 Results . 99 5.5 Discussion . 103 6 Climate change impacts on the distributions of crop wild relatives 108 6.1 Summary . 108 6.2 Introduction . 108 6.3 Methodology . 111 6.3.1 Crops and species selection . 111 6.3.2 Occurrence data . 112 6.3.3 Current and future climate data . 113 6.3.4 Environmental niche modelling . 114 6.3.5 Impacts . 117 6.3.6 Taxa richness . 117 6.4 Results . 118 6.4.1 Crops and species selection . 118 6.4.2 Occurrence data . 118 6.4.3 Environmental niche modelling . 118 6.4.4 Impacts . 119 6.5 Discussion . 125 7 Complementary dimensions for refining global conservation priorities for crop wild relatives 128 7.1 Summary . 128 7.2 Introduction . 129 7.3 Methodology . 132 7.3.1 Selection of associated crops and their wild relative taxa . 132 7.3.2 Gathering and preparation of occurrence data . 133 7.3.3 Modelling the distributions of wild relative taxa . 134 7.3.4 Estimating the value of associated crops . 135 7.3.5 Richness maps per importance categories . ..
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