I Phylogenetic, Taxonomic, and Functional Diversity of Wetland
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Phylogenetic, taxonomic, and functional diversity of wetland Diptera communities Amélie Grégoire Taillefer Department of Natural Resource Sciences McGill University Montreal, Quebec, Canada December 2016 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctorate of Philosophy © Amélie Grégoire Taillefer, 2016. All rights reserved i TABLE OF CONTENTS LIST OF TABLES ............................................................................................. v LIST OF FIGURES ........................................................................................... v LIST OF APPENDICES .................................................................................. vii ABSTRACT ...................................................................................................... ix RÉSUMÉ .......................................................................................................... xi PREFACE ....................................................................................................... xiii ACKNOWLEDGMENTS ............................................................................... xv CHAPTER 1: Introduction and literature review 1.1. INTRODUCTION ...................................................................................... 1 1.2. LITERATURE REVIEW ............................................................................ 3 1.2.1. CONCEPTS ...................................................................................... 3 1.2.1.1. Community analysis.................................................................. 3 1.2.1.2. Phylogenetic structure ............................................................... 3 1.2.1.3. Functional traits ........................................................................ 4 1.2.1.4. Landscape structure .................................................................. 4 1.2.1.5. Scales ........................................................................................ 5 1.2.2. STUDY HABITATS AND ORGANISMS .............................................. 6 1.2.2.1. Wetlands in Canada ................................................................... 6 1.2.2.2. Arthropods in wetlands ............................................................. 8 1.2.2.3. Ecological diversity of wetland Diptera ................................... 9 1.2.2.4. Diptera phylogenetic relationships ........................................... 9 1.3. OBJECTIVES ........................................................................................... 11 1.4. HYPOTHESES AND PREDICTIONS..................................................... 12 1.5. REFERENCES ......................................................................................... 13 1.6. CONNECTING STATEMENT ................................................................ 23 CHAPTER 2: Effect of habitat type on taxonomic, phylogenetic and functional diversity of wetland Diptera ii 2.1. ABSTRACT .............................................................................................. 24 2.2. INTRODUCTION .................................................................................... 25 2.3. MATERIALS AND METHODS .............................................................. 28 2.4. STATISTICAL ANALYSES ..................................................................... 29 2.4.1. Diptera diversity and community structure .................................... 29 2.4.2. Phylogeny reconstruction ............................................................... 31 2.4.3. Phylogenetic and functional community structure ......................... 32 2.4.4. Phylobetadiversity .......................................................................... 33 2.5. RESULTS .................................................................................................. 34 2.5.1. Alpha taxonomic structure .............................................................. 34 2.5.2 Beta taxonomic structure ................................................................. 35 2.5.3. Alpha phylogenetic structure .......................................................... 35 2.5.4. Beta phylogenetic structure ............................................................ 36 2.6. DISCUSSION ........................................................................................... 37 2.6.1. Taxonomic structure ....................................................................... 37 2.6.2. Phylogenetic structure .................................................................... 38 2.6.3. Taxonomic vs phylogenetic structure ............................................. 40 2.6.4. Rarity effect .................................................................................... 41 2.7. CONCLUSIONS AND CONSERVATION IMPLICATIONS ................. 42 2.8. ACKNOWLEDGMENTS......................................................................... 43 2.9. REFERENCES ......................................................................................... 43 2.10. CONNECTING STATEMENT .............................................................. 64 CHAPTER 3: Latitudinal patterns in phylogenetic and functional diversity of Diptera in temperate bogs 3.1. ABSTRACT .............................................................................................. 65 3.2. INTRODUCTION .................................................................................... 65 3.3. MATERIALS AND METHODS .............................................................. 69 3.3.1. Study sites, sampling and processing ............................................. 69 3.3.2. Habitat and vegetation variables ..................................................... 70 3.4. STATISTICAL ANALYSES ..................................................................... 71 iii 3.4.1. Taxonomic and functional composition .......................................... 71 3.4.2. Phylogeny reconstruction ............................................................... 72 3.4.3. Phylogenetic community structure ................................................. 74 3.4.4. Phylogenetic signals in trait diversity ............................................. 74 3.5. RESULTS .................................................................................................. 76 3.5.1. Species and functional alpha and beta diversity ............................. 76 3.5.2. Phylogenetic alpha and beta composition ....................................... 77 3.6. DISCUSSION ........................................................................................... 79 3.7. CONCLUSIONS....................................................................................... 82 3.8. ACKNOWLEDGMENTS......................................................................... 83 3.9. REFERENCES ......................................................................................... 84 CHAPTER 4: General discussion, conclusion and future directions 4.1. INTRODUCTION .................................................................................. 108 4.2. SUMMARY OF RESEARCH ................................................................ 108 4.2.1. Phylogenetic and taxonomic responses of Diptera communities to wetland habitats ...................................................................................... 108 4.2.2. Spatial patterns of taxonomic, functional and phylogenetic structure in peatlands .............................................................................. 109 4.3. SYNTHESIS AND RECOMMENDATIONS FOR FUTURE WORK .. 109 4.4. REFERENCES ........................................................................................111 5. APPENDICES: Supplementary materials for Chapter 2 and 3 .......... 113 iv LIST OF TABLES Table 2.1. Ground cover variables reduced with principal component analysis. Variables with loadings larger than 0.32 in principal components (PC) 1 to 4 are in bold ..... 55 Table 2.2. Abundance (N), species richness (Sobs) and rarefied species richness ± standard error (Sest) for each of the 12 wetland sites. Rarefied species richness was standardized at 196 individuals (PIN_BG) ...................................................................................... 57 Table 3.1. Life-history and ecological traits considered in this study including categories, abbreviations and trait determination notes. Traits were assigned at the species level and adult stage except for feeding habits and specialization (larval stage) ...................98 Table 3.2. Abundance (Abun), observed species richness (S), Chao1 indices (Chao1), rarefied species richness (Srare), functional richness (FRic), functional evenness (FEve) and functional divergence (FDiv) for all sites and mean diversity for each ecoregion .........100 Table 3.3. Dominant functional composition of each site, represented by community-level weighted means (CWM). For continuous traits the mean trait value is weighted by abundance, while for categorical traits the dominant class is returned. For description of traits and associated codes refer to table 3.1 ...................................................................................101 Table 3.4. Phylogenetic diversity (PD), net relatedness index (NRI) and nearest taxon index (NTI) for Diptera communities in 15 sites across three ecoregions at three spatial scales (trap, site, ecoregion). Fisher’s combined probability tests were performed to assess if overall P-values were significant at the trap and site scales.