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Russulas of Southern Vancouver Island Coastal Forests

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Russulas of Southern Vancouver Island Coastal Forests Russulas of Southern Vancouver Island Coastal Forests Volume 1 by Christine Roberts B.Sc. University of Lancaster, 1991 M.S. Oregon State University, 1994 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY in the Department of Biology © Christine Roberts 2007 University of Victoria All rights reserved. This dissertation may not be reproduced in whole or in part, by photocopying or other means, without the permission of the author. Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-47323-8 Our file Notre reference ISBN: 978-0-494-47323-8 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. In compliance with the Canadian Conformement a la loi canadienne Privacy Act some supporting sur la protection de la vie privee, forms may have been removed quelques formulaires secondaires from this thesis. ont ete enleves de cette these. While these forms may be included Bien que ces formulaires in the document page count, aient inclus dans la pagination, their removal does not represent il n'y aura aucun contenu manquant. any loss of content from the thesis. Canada ii Russulas of Southern Vancouver Island Coastal Forests by Christine Roberts B.Sc. University of Lancaster, 1991 M.S. Oregon State University, 1994 Supervisory Committee Dr. William E. Hintz, Supervisor (Department of Biology) Dr. Bryce W. Kendrick, Additional Member (School of Environmental Studies) Dr. Barbara Hawkins, Departmental Member (Department of Biology) Dr. Geraldine A. Allen, Departmental Member (Department of Biology) Dr. Stanton E. Tuller, Outside Member (Geography Department) Dr. John A. Trofymow, Additional Member (Department of Biology) 111 Supervisory Committee Dr. William E. Hintz, Supervisor (Department of Biology) Dr. Bryce W. Kendrick, Additional Member (School of Environmental Studies) Dr. Barbara Hawkins, Departmental Member (Department of Biology) Dr. Geraldine A. Allen, Departmental Member (Department of Biology) Dr. Stanton E. Tuller, Outside Member (Geography Department) Dr. John A. Trofymow, Additional Member (Department of Biology) Abstract The Russula flora of Vancouver Island is diverse, colourful, abundant, ecologically important, but poorly documented, with the literature spread in many diverse journals and books from across North America and Europe in various languages. Keys and field guides to local species emphasise macroscopic and spore characters but distinctive structures in the epicutis are not described. As Russulas are prone to environmentally affected colour variation and a number of species have a similar appearance, correct identification may require microscopic examination and a suite of chemicals, a barrier to many people. The existence of synonyms and conflicting concepts for several species adds to the frustration in identification. Presented here are detailed illustrated descriptions of locally collected species, with discussions on nomenclatural and taxonomic issues where these cause confusion, some of iv these confirm past records, and some are new records or new species. Three aids to identification are examined: 1. A simplified chromatography method is described that identifies Russulas to subgenus and in some cases section and subsection level, enabling differentiation between some lookalike species without recourse to microscopy. 2. A method often used to match ectomycorrhizae with nearby basidiomata by comparing their restriction fragment length polymorphisms (RFLPs) of amplified ITS rDNA, can also be compared with virtual RFLP's from sequence data downloaded from NCBI and EMBI to aid identification. The restriction enzymes Hinfl, Alul and Sau3 A, resolved identities to subgeneric and section level, rarely to species. 3. Using published sequence data and Bayesian analysis, a phylogeny was sought with better resolution in the upper clades than had been found with other analysis methods. Various characters from published descriptions and from Vancouver Island collections were then examined for correlation with branching order or clade in this phylogeny, with basidia width, spore colour, pileocystidia shape and spore shape having highest correlation. V Table of Contents Supervisory Committee ii Abstract iii Table of Contents v List of Figures xiii List of Tables xxii Acknowledgments xxiv Chapter 1 1 Introduction 1 The environment of the Southern Vancouver Island coastal forests 4 Taxonomy of the genus Russula 7 North American knowledge of Russulas 12 The current level of knowledge of Russulas in western Canada 14 Questions addressed by this dissertation 15 Chapter 2 19 Chromatographic analyses of cuticle pigments 19 Introduction 19 Comparison of naturally occurring pigments with watercolour pigments 19 Materials and Methods 23 Extraction of Pigments 23 Chromatography 24 Results 25 Conclusions and Discussion 38 Chapter 3 42 DNA analyses Part 1: Evaluation of the RFLP of the ITS region of Russulas as a means of differentiating among them, and confirming their identity by comparison with published sequence data 42 Introduction 42 The use of rDNA genes and spacer regions for RFLP comparisons 43 Primers 44 I vi Restriction enzymes used in ITS-RFLP studies 45 Extraction protocols 46 Materials and Methods 50 Selection of restriction enzymes 50 DNA extraction procedure 51 Amplification protocol 53 Digestions 58 Determining the size of DNA fragments 59 Creation of RFLP data from published sequences 61 Results and Discussion 62 The PCR product 63 Hinfl 63 Alul 65 Sau3AI and overall patterns 66 Conclusions 73 DNA Analyses Part 2: Generating a phylogenetic tree from previously published sequence data as a basis for establishing the relative taxonomic importance of morphological characters 81 DNA Analyses Part 2: Generating a phylogenetic tree from previously published sequence data as a basis for establishing the relative taxonomic importance of morphological characters 82 Introduction 82 Methods 86 Sequence selection and treatment 86 Bayesian analysis 87 Re-alignment and analysis of upper clades 89 Mapping characters 89 Results 90 Trees 90 Clade and character relationships 91 Macroscopic characters 93 vii Conclusions and Discussion 94 Most useful characters 94 Anomalous clade members 95 General taxonomic observations and recommendations based on these analyses.... 96 Character variability - hypotheses on developmental processes 99 Chapter 4 116 Examination of character trends in Vancouver Island collections 116 Introduction 116 Methods 116 Estimating clade positions of Vancouver Island species 116 Evaluation and examination of characters of Vancouver Island collections 117 Trends 119 Correlations between characters 121 Conclusions 131 Chapter 5 133 Summary 133 Russula species found in Vancouver Island coastal forests 133 Habitat specificity 134 Evaluation of the various tools of identification 138 Evaluation of morphological characters in relation to phylogenetic relationships and clade structure 139 Morphological characters and clade structure 139 Taxonomic observations and recommendations 142 Bibliography 144 Appendix 1 160 Appendix 2 166 Output files of the Bambe program running from the Pasteur Institute server 179 Summary of sequence data of all 111 sequences in the alignment and the initial parameters selected 179 Summary of sequence data and the initial parameters selected of the top clade of 55 sequences which have been stripped of all identical positions in the alignment 186 viii Output generated by BAMBE version 2.03 Beta 186 Appendix 3 191 Keys and Descriptions of Russulas found in southern Vancouver Island coastal forests.. 191 Diagnostic characters 191 Keys to Russulas of Vancouver Island and the Pacific Northwest 197 Polychotomous keys to major groups." 197 Key 1: Compactae -Clade lb 199 Key 2: Lactaroides -Clade 2b 200 Key 3 Ingratae -Clade 3 201 Key 4 Heterophyllidia 203 Key 5 Other Russula subgenera 206 Synoptic keys 221 Descriptions of Vancouver Island Russulas 235 Clade lb 235 Subgenus Compactae (Fries) Bon 235 Section Compactae Fries (= Nigricantinae in Romagnesi 1967) 23 5 Russula adnsta (Pers.) Fr 235 Russula anthracina var. insipida Romagnesi nom. inval., art. 37.1 ICBN 242 Russula albonigra (Krombh.) Fries 249 Russula dissimulans Shaffer 255 Clade 2b 262 Subgenus
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