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The Evolutionary Ecology of Adaptation to Polluted Environments

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The Evolutionary Ecology of Adaptation to Polluted Environments THE EVOLUTIONARY ECOLOGY OF ADAPTATION TO POLLUTED ENVIRONMENTS Alessandra Loria Department of Biology McGill University, Montreal July 2020 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy © Alessandra Loria 2020 To my family. To my dad who fostered my love of animals and plants, to my mom who supported me in all possible ways, to my brothers and sister for always believing in me, and to my beloved Mother Nature for giving me life and showing me every day the beauty of all things. ii TABLE OF CONTENTS Abstract ............................................................................................................................ viii Résumé .................................................................................................................................x Acknowledgements ........................................................................................................... xii Preface.............................................................................................................................. xiii Thesis format ................................................................................................................... xiii Ethic statement ................................................................................................................. xiv Author contributions ........................................................................................................ xiv Statement of originality......................................................................................................xv List of tables .................................................................................................................... xvii List of figures ................................................................................................................. xviii General Introduction .........................................................................................................1 Biodiversity and its role in eco-evolutionary dynamics .......................................................2 Threats to biodiversity and their potential consequences....................................................3 Pollution as a driver of biodiversity and micro-evolutionary change .................................6 Experimental approaches for studying the effects of aquatic pollution ..............................7 Daphnia as a model organism in eco-evolutionary studies .................................................8 DNA metabarcoding and its potential use in eco-evolutionary studies ...............................9 Research gaps and thesis objectives ..................................................................................12 Literature cited ...................................................................................................................15 Chapter 1. Mixed evidence for adaptation to environmental pollution ......................38 1.1 Abstract ........................................................................................................................39 iii 1.2 Introduction ..................................................................................................................40 1.3 Methods........................................................................................................................42 1.4 Overview of the studies ...............................................................................................46 1.4.1 Type of pollution and geographic distribution of species .........................................47 1.4.2 Evidence from phenotypic, genetic, selection, and demographic assays .................49 1.4.3 Invertebrates and metals: a meta-analysis ...............................................................52 1.5 Summary ......................................................................................................................54 1.6 Conclusions ..................................................................................................................55 1.7 Acknowledgements ......................................................................................................56 1.8 Literature cited .............................................................................................................57 Connecting statement for Chapters 1 and 2 ..................................................................73 Literature cited ...................................................................................................................74 Chapter 2. Genotype diversity promotes persistence in Daphnia populations during copper stress .....................................................................................................................75 2.1 Abstract ........................................................................................................................76 2.2 Introduction ..................................................................................................................77 2.3 Methods........................................................................................................................79 2.3.1 Experimental populations .........................................................................................79 2.3.2 Experimental design..................................................................................................79 2.3.3 Microsatellite analysis ..............................................................................................81 2.3.4 Statistical analyses ....................................................................................................82 2.4 Results ..........................................................................................................................84 2.4.1 Population growth trend ...........................................................................................84 iv 2.4.2 Survival analysis .......................................................................................................85 2.4.3 Microsatellite analysis ..............................................................................................85 2.4.4 pH and Cu concentrations ........................................................................................86 2.5 Discussion ....................................................................................................................86 2.5.1 The limits of evolutionary rescue ..............................................................................87 2.5.2 Genetic diversity promoted longer persistence .........................................................89 2.5.3 Clonal responses to long-term exposure to Cu .........................................................89 2.5.4 Future directions .......................................................................................................90 2.6 Conclusions ..................................................................................................................91 2.7 Acknowledgements ......................................................................................................92 2.8 Literature cited .............................................................................................................93 Connecting statement for Chapters 2 and 3 ................................................................111 Literature cited .................................................................................................................112 Chapter 3. The performance of eDNA-based metabarcoding in estimating rapid zooplankton diversity changes during herbicide contamination ...............................113 3.1 Abstract ......................................................................................................................114 3.2 Introduction ................................................................................................................115 3.3 Methods......................................................................................................................119 3.3.1 Experimental design................................................................................................119 3.3.2 Library preparation ................................................................................................121 3.3.3 Bioinformatic analysis ............................................................................................122 3.3.4 Taxonomic assignment ............................................................................................123 3.3.5 Diversity estimates ..................................................................................................124 v 3.3.6 Comparison between metabarcoding and morphological assessment data ...........125 3.3.7 Statistical analyses ..................................................................................................126 3.4 Results ........................................................................................................................127 3.4.1 Metabarcoding output description ..........................................................................127 3.4.2 Comparison of detection rates between metabarcoding and morphological assessments ......................................................................................................................128 3.4.3 Analysis of Last Common Ancestor (LCA) output
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