A global perspective on the origins of agriculture: the importance of unconscious selection Thomas Kluyver Department of Animal and Plant Sciences A thesis submitted for the degree of Doctor of Philosophy July 2013 1 Acknowledgements My primary supervisor, Colin Osborne, has provided advice, encouragement and inspiration throughout my PhD. My supervisors in the Department of Archaeology, Glynis Jones and Mike Charles, have patiently helped me to get to grips with a field which I had never studied before this project. Mark Rees’ advice about statistics has also been invaluable. I am grateful to Irene Johnson, for her eminently practical help with growing all kinds of plants, and to Emily Mockford and Chris Bennett, for painstakingly dissecting beet seed capsules to weigh individual seeds. Katherine Haynes and Rebecca Crabtree weighed seed of modern garden vegetables for chapter 3, and that chapter also could not have been written without people and organisations around the world who shared their data with me, including Benoît Pujol (Laboratoire Évolution et Diversité Biologique, France), the Botanical Information Section at RBG Kew, the USDA National Genetic Resources Program, the International Potato Centre (CIP) in Peru, and EMBRAPA in Brazil. Over the last few years, I have enjoyed a warm, friendly and intellectually stimulating environment in Sheffield. It has been a pleasure to work with the people in Colin Osborne’s lab group, as well as the many others who I have got to know. My PhD research was funded by a university studentship from the University of Sheffield, for which I am very thankful. Last but not least, my thanks to my girlfriend and my family, for their support both during my PhD and in the years of education which prepared me to undertake it. i Abstract The protracted model of agricultural origins proposes that farming developed gradually in broad regions, rather than being invented and adopted rapidly in small ‘core areas’. This view points to an important role for unconscious selection in the evolution of crop plants, wherein humans unintentionally modified the environment of plants in cultivation, setting up selection pressures different from those acting in the wild. This thesis examines the role of unconscious selection on seed mass and photosynthesis, especially in grass and legume crops. Domestication is known to have increased seed mass in many seed crops, while studies that have compared photosynthetic rate have mostly, but not universally, found no difference between wild and domestic forms. An important aspect of this work has been making comparisons among a range of crop species and geographic regions. This is not to presume that the same processes were acting in these different cases: it is important to study each crop and each region individually. However, it is also natural to look for larger patterns. Agriculture in widely separated parts of the world appears to have started more-or-less simultaneously, and in many cases to have used plants from the same families, especially the grasses and the legumes. I have therefore chosen to examine how far these similarities extend, and how great the differences between the regions and crop species are. Analysing seed mass data shows that crop progenitors already have large seeds in comparison to other wild species, but only the centre of agricultural origins in Western Asia has ii an unusual abundance of large-seeded species. A variety of vegetable crops, including vegetatively propagated species, have larger seeds than their wild progenitors, providing evidence that unconscious selection has acted on seed mass; the difference, however, is smaller than that seen in seed crops. A comparative experiment tested the hypothesis that seed burial and the need to emerge from deeper in the soil drove the evolution of larger seeds, the results of which support this mechanism in some, but not all, of the grain legume species tested. Finally, photosynthetic rate has not changed in domestication in any of a range of grass and legume crops; possible explanations for this are discussed. In summary, I find broad taxonomic and geographic patterns in the seed mass of crop progenitors, increased seed mass in both seed and vegetable crops, and no change in photosynthesis during domestication, while the effect of seed mass on emergence depth differs among species, and the availability of wild large-seeded grass and legume species differs markedly among regions. iii Table of Contents Acknowledgements.............................................................i Abstract.............................................................................ii List of Figures...................................................................vi List of Tables.....................................................................ix 1 Introduction.....................................................................1 1.1 Context.......................................................................................1 1.2 Sources of Evidence....................................................................2 1.3 The domestication syndrome......................................................3 1.4 Unconscious Selection................................................................3 1.5 Where agriculture started...........................................................5 1.6 Causes of the Transition to Agriculture.......................................6 1.7 Groups of Cultivated Plants.........................................................7 1.7.1 Grasses................................................................................7 1.7.2 Legumes...............................................................................7 1.7.3 Pseudocereals......................................................................8 1.7.4 ‘Root’ crops..........................................................................8 1.7.5 Other crops..........................................................................9 1.8 Selection of Plants for Cultivation...............................................9 1.9 Aims and objectives..................................................................10 1.9.1 Chapter 2: The taxonomic and geographic distributions of seed mass in wild legumes and grasses.....................................11 1.9.2 Chapter 3: Unconscious selection on seed size in vegetable crops...........................................................................................11 1.9.3 Chapter 4: Did greater burial depth increase the seed size of domesticated legumes?..........................................................12 1.9.4 Chapter 5: Comparison of photosynthetic parameters among crop species and progenitors..........................................12 2 The taxonomic and geographic distributions of seed mass in wild legumes and grasses..................................................13 2.1 Introduction...............................................................................13 2.2 Methods....................................................................................14 2.2.1 Data Sources......................................................................14 2.2.2 Accessing DELTA Data........................................................14 2.2.3 Combining Data.................................................................14 iv 2.2.4 Data Preparation................................................................16 2.2.5 Domesticates and centres of origin....................................17 2.3 Results......................................................................................22 2.3.1 Structure............................................................................22 2.3.2 Progenitors and congeners................................................22 2.3.3 Species from the centres of origin of agriculture...............24 2.3.4 Geography and seed size distribution................................26 2.3.5 Geography and large-seeded species................................29 2.4 Discussion.................................................................................35 3 Unconscious selection on seed size in vegetable crops......39 3.1 Introduction...............................................................................39 3.2 Materials and Methods..............................................................40 3.3 Results......................................................................................42 3.3.1 Seed Crops.........................................................................42 3.3.2 Vegetable crops..................................................................43 3.4 Discussion.................................................................................45 3.5 Conclusion................................................................................48 4 Did greater burial depth increase the seed size of domesticated legumes?.....................................................49 4.1 Introduction...............................................................................49 4.2 Materials and methods.............................................................50 4.2.1 Plant material.....................................................................50 4.3 Emergence depth trial..............................................................51 4.3.1 Statistical analysis..............................................................52 4.4 Results......................................................................................52 4.4.1