Hughes, Mark (2002) Population structure and speciation in Begonia L. PhD thesis http://theses.gla.ac.uk/6194/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] Population structure and speciation in Begonia L. A thesis submitted to the University of Glasgow for the degree of Doctor of Philosophy Mark Hughes Division of Environmental and Evolutionary Biology June 2002 Declaration I hereby declare that this thesis is composed of work carried out by myself unless otherwise acknowledged and cited and that this thesis is of my own composition. This research was carried out in the period of October 1998 to June 2002. This dissertation has not in whole or in part been previously presented for any other degree. ABSTRACT Biodiversityis unequally distributed between higher taxa; for example a small n~mber of angiosperm genera contain the majority of angiosperm species. Begonia is one of the largest angiosperm genera with ca. 1400 species. Studies of such genera can give insights into the processess that cause diversification. A number of features of the spatial distribution of biodiversity in Begonia suggest gene flow between populations is poor and has affected larger-scale patterns of diversity in the genus. These are (i) sporadic distribution of populations, which are usually restricted to a specific micro-habitat, (ii) a high degree of narrow endemism at the species level, (iii) widespread species being rare and also highly morphologically variable unless they show atypical adaptations that promote gene flow, and (iv) geographical restriction of monophyletic groups. Restricted gene flow betwee~ populations allows them to diverge in response to weaker selection pressures than they would be able to respond to in the face of gene flow from other populations. In order to examine population structure (micro-evolution) in Begonia and its congruence to higher patterns of diversity (macro-evolution), nuclear microsatellite markers have been isolated and applied to two Begonia species, B. socotrana and B. sutherlandii. Begonia socotrana is endemic to the Haggeher Mountains of the island of Socotra in the Indian Ocean, where it has a total range of less than lOx 15 km. PopUlation surveys have highlighted the need for its conservation status to be re­ assessed, and it is proposed to reduce its status from 'endangered' to 'least concern'. Population genetic analyses using microsatellite data show a significant degree of population structure (R sr 0.081, P<O.Ol; 9=0.096, P<O.Ol) and significant isolation by distance, even over small spatial scales. The pattern of isolation by distance could be due to restricted gene flow, or the result of small . scale vicariance events in the fragmented peaks of the Haggeher Mountains during climate change and resulting altitudinal migration. Begonia sutherlandii is native to eastern and southern Africa, where it is restricted to shaded, moist banks in indigenous forest. A high degree of Population structure was found (9=0.482, P<O.OOl; RsrO.634, P<O.OOl), which along with a high number of private alleles reflects the severe isolation of populations in a patchily distributed forest habitat. Population relationships appear to be strongly governed by the history and continuity of forest cover in the region. The population genetic studies of B. socotrana and B. sutherlandii show a stnmg correlation of genetic variation with geography which reflect patterns seen at larger scales. The correlation of micro and macro evolutionary patterns is congruent with a hypothesis of restricted gene flow promoting speciation in Begonia. ACKNOWLEDGEMENTS Without the philanthropy of the late Mr and Mrs Macintyre in setting up the M.L. MacIntye Begonia Trusts, I would not have been able to spend three years studying Begonia evolution. I am extremely grateful to them and to the trustees, in particular Prof. Malcolm Wilkins and Dr. Chris Wheeler, for giving me this opportunity. My supervisor, Pete Hollingsworth, deserves thanks (and no doubt a drink) for writing the initial project proposal and for guiding it through its subsequent changes, and for reading through this entire thesis, giving helpful comments and pointing out mildy amusing double entendres where relevant. This research involved some interesting fieldwork, and I am grateful to Tony Miller and Miranda Morris for organising the expedition to the Socotra archipelago, which was no mean feat; Roger Hyam and Diccon Alexander for being amiable travelling companions; and the people of Socotra for their hospitality and for killing dozens of goats for us. My collecting trip in South Africa was assisted by many people, particularly Tracy McLellan who provided air-conditioned transport and company; Trevor Edwards and Christina Potgeiter who looked after me in Pietermaritsburg when I arrived sans luggage and slightly the worse for wear from in-flight tranquilisers; Chris Randle for driving to Tygerskloof; Tony Abbott for a splendid stay in Umtamvuna, and Dirk Bellstedt for being a mine of information and for getting me to some very interesting forest patches. I also received a great deal of help on localities, transport and accomodation from the KZN parks board, particularly Sharon Luow, Barry, Dennis Eckhart (contacts kindly given to me by Michael Moeller), and Neil Crouch. Olive Hilliard and Bill Burtt also provided helpful advice and maps during the planning of the trip. The large amount of living material resulting from the fieldwork was carefully tended to in quarantine by Fiona Inches and Andrea Fowler, apd maintained in excellent condition upon its release by Steve Scott, Neil Watherston and Fred Mobeck among others. Becky Govier patiently went through the mess that was my collectors book and got most of it on BG BASE. The staff at Glasgow Botanic Garden also deserve a mention for maintaining the national Begonia collection, which made any trip through to Glasgow worthwhile. This project also involved a great deal of labwork, which was made less of a chore due to the excellent lab facilities at RBGE, provided by Michelle Hollingsworth and Alex Ponge, who risked boredom and dermatitis in making up the dozens of polyacrylamide gels I got through. Joanne Russell (SCRI) and Jane Squirrell were both of great assistance in the tricky development of the microsatellite markers. Ruth Hollands patiently dealt with the dozens of orders for oligos and consumables. Thanks also to Jill Harrison for looking after me whilst I invaded her bench space at Edinburgh University, and for being elsewhere when I started a not inconsiderable fire in the PhD office. I would also like to thank everyone in the lab and herbarium at RBGE for making it such a pleasant place to work. Assistance during the writing up phase came from many sources, including Rod Page and Richard Ennos for providing data analysis advice, and Neil Brummitt for heated debates on species-area relationships. All the RBGE library staff (in particular Graham Hardy) have been very helpful in finding material and sorting out copies and loans with spectacular efficiency. The latter stages of writing were carried out whilst also working on a post doctoral project on Streptocarpus at RBGE; Michael Moeller deserves a special mention for (i) employing me and (ii) for being a very understanding boss during a busy time. This project would not have been half as enjoyable were it not for the two other Begonia students Laura Forrest and Vanessa Plana. Thanks especially to Vanessa for knowledge of African Begonia, and to Laura for continuous and welcome distraction by email, (including the odd academic one) and both for drinks and good humour. I hope the two current Begonia students, Will Goodall­ Copestake and Sophie Neale, enjoy their projects as much as I have. Thanks also, of course, to my family and RG for their continuing support. PREFACE This thesis is an investigation of population structure in Begonia, and its relevance to evolution and speciation in the genus. There are four introductory chapters. The first is a general discussion of large scale patterns of biodiversity, and possible causes for the unequal distribution of biodiversity between higher taxa. The second is an account of the ecology and systematics of the Begoniaceae, and aspects of Begonia biodiversity that may be of relevance to popUlation structure and speciation processes. The third chapter is a discussion of the effects of gene flow on population differentation and speciation, and the fourth is a review of methods of analysing and interpreting population genetic data obtained from micro satellite markers. The next chunk of the thesis consists of five parts that are written as papers intended for pUblication. As each is a complete paper in its own right, this inevitably involves a small amount of repetition. The formatting for the submitted papers in terms of tables, figures and references is according to the format of the journal to which they were submitted. The first paper is a monograph of two species of Begonia from the Socotra archipelago, and an assessment of their conservation status. This has been accepted for publication by the Edinburgh Journal of Botany. Papers two and three are technical papers which describe the isolation and development of nuclear micro satellite markers from two Begonia species, B. socotrana and B. sutherlandii. These have been accepted for publication by Molecular Ecology Notes.