The systematics and genetics of tomatoes on the Galápagos Islands (Solanum, Solanaceae) By Sarah Catherine Darwin A thesis submitted for the degree of Doctor of Philosophy at University College London August 2009 Department of Genetics, Evolution and Environment University College London 1 Declaration I, Sarah Darwin confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Chapter 2 is a reprint from a paper on the taxonomy of the tomatoes of the Galápagos Islands published in Systematics and Biodiversity in 2003. This was a collaborative project, and the authors were Sarah Darwin, Sandra Knapp and Iris Peralta. I was the lead author as this was part of my thesis work, and I carried out most of the work towards the paper. Below I list the contributions of each author for Chapter 2. Morphological analysis I undertook the analysis of the herbarium specimens, with particular guidance from Sandy Knapp and Iris Peralta for the S. lycopersicum and S. pimpinellifolium collected from the mainland of South America. Morphometrics Morphological characters were selected by all of us based on my experience from fieldwork, Dr Peralta’s experience from greenhouse grown accessions and Dr Knapp’s experience from herbarium specimens. I undertook the measurement of the living plants and herbarium specimens with the assistance/guidance of Drs Peralta and Knapp Statistics I and Dr Peralta undertook the PCA, with advice from Drs Claudio Galmarini and Clive Moncrieff. Taxonomic treatment Dr Knapp and Dr Norman Robson wrote the Latin for the taxonomic treatment. 2 Artwork The illustration of S. galapagense for the taxonomic treatment was undertaken by C. Scoones the rest of the illustrations and figures were undertaken by me and formatted for the paper by Derek Adams and myself. Writing I wrote the first draft of the paper, and it went through repeated editorial cycles among all three authors. Sarah Darwin Prof. James Mallet Candidate UCL Supervisor 3 Abstract Galápagos tomatoes (Solanum section Lycopersicon) have long interested scientists and plant breeders. Several morphological and physiological characters found in the endemic Galápagos tomatoes have been bred into the cultivated Solanum lycopersicum, making the native plants an invaluable resource for the development of this important global crop. Extensive fieldwork was carried out on twelve islands, old records were confirmed, new records added, but several previously recorded populations of endemic tomatoes could not be confirmed. I collected tomatoes from 12 islets and Islands. Detailed morphometric analysis on c.400 plants and extensive genetic studies on c.1,200 plants were carried out in addition to fieldwork and natural history studies. Observations and experiments were carried out on herbarium specimens, field collected and green house grown accessions. I confirmed the presence of four taxa in the Galápagos Islands – two endemic species S. cheesmaniae and S. galapagense, the latter here described as new, and two introduced species S. pimpinellifolium and S. lycopersicum. Hybrids were found involving all taxa growing in the Galápagos Islands. Of particular interest is an extensive hybrid zone between S. cheesmaniae and S. pimpinellifolium spanning 20km along the Baltra Road on Isla Santa Cruz. Hybridization raises the threat of extinction by introgression and the possibility of the evolution of a serious invasive species. Conservation recommendations are proposed. In addition, a genetic analysis was undertaken of 60 seed bank accessions of all four tomato species from the Galápagos. Again, indications of hybridization were found, raising the potential of introgression within the seed bank collections, occurring potentially during rejuvenation cycles. Furthermore, I propose a new outline for a generic invasive species threat/impact scoring system. Applying this new system I class Solanum pimpinellifolium as an alien invasive species and assess its impact on Isla Santa Cruz in the Galápagos Islands. 4 Acknowledgments I would like to thank my supervisors Dr Sandy Knapp and Professors Jim Mallet and Ziheng Yang for their support and advice during this thesis. I would like to thank all the many people in the Galápagos Islands for their enthusiasm, invaluable support, advice and help with fieldwork, they are too numerous to mention by name. The Galápagos National Parks, in Islas Santa Cruz and Isabela, for advice, field assistance and field permits. The staff at the Charles Darwin Research Station in the Galápagos Islands, in particular Alan Tye and Mark Gardener for their collaboration and on the ground support. Tina and Daniel Fitter and Virginia Appleton for joining me and guiding me on field excursions. Godfrey Merlin, Jenny and David Day, Felipe Cruz for their general advice and assistance in the Galápagos Islands. I would like to thank the Tomato Genetic Resource Center and Cornell seed bank for their kind donation of seed accessions. Clive Moncrieff, Clem Maidment, Iris Peralta, Claudio Galmarini, Steve Ansell, Harald Schneider and Kanchon Dasmahapatra for their advice on analytical packages and statistics and the Department of Botany at the Natural History Museum for giving me desk space on which to undertake this research and in particular my friends Juliet Brodie, Gabrielle To and Rhina and Holger Thüs for their general support. Teamwork in the allozyme laboratory was supported by Johannes Vogel, Steve Russell, Michael Grundmann, Steve Ansell and Harriet Hunt. Pat Hart and David McCann who helped with the maps and layout of figure 3.11. Lorraine Porch who assisted with the thesis layout. Financial support was received from the BBSRC (PhD grant) and the Hubbard Foundation. The latter funded the first part of the research and the field trips. Special thanks goes to my family, wonderful husband Johannes, my lovely sons Leo and Josiah, my parents Ras and Shuna for their continued belief and patience and to my mother-in-law Edith Vogel. I would like to dedicate this thesis to my mother who made our lives such fun. 5 Table of contents Title page 1 Declaration 2 Abstract 4 Acknowledgments 5 Table of contents 6 List of figures 7 List of tables 9 Preface 11 Chapter 1 Plant invasions on oceanic islands 28 Chapter 2 Taxonomy of tomatoes in the Galápagos Islands: 69 native and introduced species of Solanum section Lycopersicon (Solanaceae) Chapter 3 Galápagos tomato genetics and hybridization 96 Chapter 3a The genetic diversity in tomatoes from the 105 Galápagos Islands Chapter 3b Galápagos tomato soup: hybridization between 142 tomato species Chapter 3c Genetics of tomatoes in seed banks 202 Chapter 4 General discussion and conclusions 221 Appendix 1 Box plots 244 6 List of figures a Greenhouse grown plants. Perceived wisdom in 2000 13 b Map of the Galápagos Islands. SCD field collection sites 15 from 2000 c Map of the Galápagos Islands. SCD field collection sites 18 from 2002 d Solanum pimpinellifolium at the Basura, Baltra Road, Isla 19 Santa Cruz e Solanum cheesmaniae at the Basura, Baltra Road, Isla 19 Santa Cruz f Solanum cheesmaniae x S. pimpinellifolium hybrids at the 20 Basura, Baltra Road, Isla Santa Cruz g Map of the Galápagos Islands. SCD field collection sites 23 from 2000 and 2002 1.1 Transitions of an alien species into an invasive and 39 dominant species 2.1 Distribution map of tomatoes in the Galápagos Islands 72 2.2 History of classification of tomatoes in the Galápagos 74 2.3 Results of the morphological analysis 80 2.4 Leaf morphology variation in the Galápagos tomatoes 83 2.5 Solanum galapagense 86 2.6 Solanum section Lycopersicon in the Galápagos 87 3.1 Ne arranged from East to West for S. cheesmaniae and S. 123 galapagense 3.2 Plot of likelihood value of different values of k 124 3.3 STRUCTURE bar charts 125 3.4 Flower measurements 154 3.5 Sepal score, description, and illustration 158 3.6 PCO of morphological characters using field circumscription 175 as symbol 3.7 Likelihood scores for STRUCTURE for k=1 to k=8 176 3.8 STRUCTURE bar charts 177 7 3.9 PCO of morphological characters using STRUCTURE as 178 symbol 3.10 Likelihood scores for STRUCTURE hybrid work 179 3.11 Distribution of S. cheesmaniae, S. pimpinellifolium and 180 hybrids along the Baltra road, Santa Cruz 3.12 Stigma exsertion for S. cheesmaniae, S. pimpinellifolium 183 and S. cheesmaniae x S. pimpinellifolium 3.13 Percentage mixed offspring from field collected accessions 185 8 List of tables 1.1 Tens rule (sensu Williamson 1996) 31 1.2 Terms to describe alien plants suggested by Richardson et 37 al. (2000) 1.3 Proposed outline for invasive plant species threat/impact 42 scoring system 1.4 The alien plant definition, stage and ‘threat/impact score’ for 43 Solanum pimpinellifolium in the Galápagos Islands 2.1 Galápagos Island names and synonyms 73 2.2 Characters measured for morphometric analysis 77 2.3 Locality groups as OTUs for accessions 79 2.4 Means of leaf character ratios 79 3.1 Population localities, names, numbers, coordinates and 103 altitudes 3.2 Populations used for each species in this analysis 112 3.3 Allele frequencies for variable loci in Galápagos tomatoes 115 3.4 Allele presence in SCD bulk data set 119 3.5 Summary of within population genetic diversity measures 122 3.6 Summary of F-statistics 123 3.7 Results for some of the life history traits (Hamrick and Godt, 139 1996) 3.8 He and Fst of S. cheesmaniae and S. galapagense 139 compared Hamrick and Godt (1996) results 3.9 Populations