THE ECOLOGY OF LAKES AND RIVERS IN THE SOUTHERN BOREAL SHIELD: WATER QUALITY, COMMUNITY STRUCTURE, AND CUMULATIVE EFFECTS by Fredric Christopher Jones A thesis submitted in partial fullfillment of the requirements for the degree of doctor of philosophy (PhD) in Boreal Ecology Faculty of Graduate Studies, Laurentian University, Sudbury, Ontario © Fredric Christopher Jones, 2018 THESIS DEFENCE COMMITTEE/COMITÉ DE SOUTENANCE DE THÈSE Laurentian Université/Université Laurentienne Faculty of Graduate Studies/Faculté des études supérieures Title of Thesis Titre de la thèse THE ECOLOGY OF LAKES AND RIVERS IN THE SOUTHERN BOREAL SHIELD: WATER QUALITY, COMMUNITY STRUCTURE, AND CUMULATIVE EFFECTS Name of Candidate Nom du candidat Jones, Fredric Christopher Degree Diplôme Doctor of Philosophy Department/Program Date of Defence Département/Programme Boreal Ecology Date de la soutenance June 07, 2018 APPROVED/APPROUVÉ Thesis Examiners/Examinateurs de thèse: Dr. John Gunn (Co-Supervisor/Co-directeur de thèse) Dr. Brie Edwards (Co-Supervisor/Co-directrice de thèse) Dr. John Bailey (Committee member/Membre du comité) Dr. Richard Johnson (Committee member/Membre du comité) Approved for the Faculty of Graduate Studies Approuvé pour la Faculté des études supérieures Dr. David Lesbarrères Monsieur David Lesbarrères Dr. Garry Scrimgeour Dean, Faculty of Graduate Studies (External Examiner/Examinateur externe) Doyen, Faculté des études supérieures Dr. Yves Alaire (Internal Examiner/Examinateur interne) ACCESSIBILITY CLAUSE AND PERMISSION TO USE I, Fredric Christopher Jones, hereby grant to Laurentian University and/or its agents the non-exclusive license to archive and make accessible my thesis, dissertation, or project report in whole or in part in all forms of media, now or for the duration of my copyright ownership. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also reserve the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that this copy is being made available in this form by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner. ii ABSTRACT Cumulative effects are the collective ecological effects of multiple human activities. Cumulative effects assessment (CEA) is concerned with quantifying effects of natural environmental factors and human activities. CEA has not lived up to its promise as a precautionary instrument for sustainability, in part because our knowledge of stressors and their effects is elementary; monitoring systems (needed to characterize ecological condition and how it changes over time) are insufficient; and numerical methods for associating stressors and effects, and for forecasting development outcomes, are lacking. This thesis reviews the environmental appraisal literature to synthesize CEA’s theoretical underpinnings, articulate its impediments, and establish that ecological monitoring and modelling activities are critical to success. Three research chapters overcome several scientific barriers to effective CEA. Data from spatial and temporal surveys of lake and stream water chemistry and benthic community structure are used to evaluate candidate monitoring indicators, identify minimally impacted reference waterbodies, characterize baseline water quality and biological condition, and quantify cumulative effects of land use and natural environmental variation (spatial survey: 107 lakes and 112 streams sampled in 2012 or 2013; temporal survey: 19 lakes sampled between 1993 and 2016). The research was conducted in Canada’s Muskoka River Watershed, a 5660 km2 area of Precambrian Shield that drains to Lake Huron. This area’s combination of extensive remaining natural areas and pervasive human influence makes it ideal for studying cumulative effects. It is also characterized by many lakes and their connecting stream and river channels, which integrate effects of stressors in their catchments and constitute logical focal points for CEA. Moreover, the local planning authority (District iii Municipality of Muskoka) is striving to implement CEA and establish a cumulative effects monitoring program centered on water as its foremost resource; therefore, practical applications of the research have, been identified. Universal numerical methods, which are transferrable to other study areas, are used. Random forest models (an extension of the algorithm used to produce classification or regression trees) are shown to model the singular and collective effects of land-use and natural factors on water chemistry and benthic community structure, and to quantify the sensitivities, and identify the important drivers of various chemical and biological indicators of aquatic ecosystem condition. Partial dependencies from the random forests (i.e., the mean predicted values of a given indicator that occurred across the observed range of a selected predictor) are paired with TITAN (Threshold Indicator Taxa Analysis) to investigate biological and chemical “onset-of-effect” thresholds along gradients of human development. Declining calcium concentrations and amphipod abundances are demonstrated in lakes, and generalized linear models forecast an average 57% decrease in the abundances of these animals to occur by the time lake- water calcium concentrations reach expected minima. As its key findings, the thesis highlights sensitive indicators that should be included in a cumulative effects monitoring program, and are to be preferred when forecasting outcomes of changed land-use or environmental attributes. Empirical break- points, where effects of stressor exposures become detectable, are also identified. These thresholds can be used to distinguish reference and impacted conditions, so that normal indicator ranges and associated assessment criteria (important CEA precursors) can be objectively derived. In addition, the potential severity of cumulative effects is exemplified by marked declines in the abundances of lake dwelling amphipods, which could propagate through food webs to substantially alter soft-water Boreal ecosystems. iv ACKNOWLEDGEMENTS I thank my academic supervisor, John Gunn, co-supervisors, John Bailey and Brie Edwards, and graduate committee members, Richard Johnson and Simon Linke, for their guidance. I’m grateful to Ontario’s Ministry of Environment and Climate Change and the Canadian Water Network for funding this project. Thanks to Keith Somers, Melissa Robillard, and Rachael Fletcher for seeing the value of this project and allowing me some flexibility in my work schedule to undertake the research. I acknowledge Keith Somers, Jim Rusak, Simon Courtenay, and Jan Ciborowski for sharing their ideas, and providing encouragement. Thanks also to Sarah Sinclair and several other technicians who assisted with stream and lake sampling, and sample processing activities. I acknowledge my long-suffering family and friends for tolerating me and this project. v TABLE OF CONTENTS ABSTRACT…………………………………………………………………………… iii ACKNOWLEDGEMENTS ………………………………………………………….. v TABLE OF CONTENTS ………………………………………………………….… 1 PART 1: INTRODUCTION …………………………………………………………. 2 PART 2: CUMULATIVE EFFECTS ASSESSMENT ― THEORETICAL UNDERPINNINGS AND BIG PROBLEMS ………………………………………. 24 PART 3: RANDOM FORESTS AS CUMULATIVE EFFECTS MODELS ― A CASE STUDY OF LAKES AND RIVERS IN MUSKOKA CANADA …………… 43 PART 4: ONSET-OF-EFFECT THRESHOLDS AND REFERENCE CONDITIONS ― A CASE STUDY OF THE MUSKOKA RIVER WATERSHED, CANADA………………………………………………………….... 62 PART 5: DECLINING AMPHIPOD ABUNDANCE IS LINKED TO LOW AND DECLINING CALCIUM CONCENTRATIONS IN LAKES OF THE SOUTH PRECAMBRIAN SHIELD …………………………………………………………... 104 PART 6: SUMMARY, CONCLUSIONS AND DISCUSSION ..………………….. 143 1 Part 1: INTRODUCTION 2 Background As the branch of biology that deals with interactions of organisms with one another, and with their physical environment, Ecology’s fundamental goal is to explain and predict the occurrences and abundances of taxa (Townsend 1989, Belovsky et al. 2004, Temperton and Hobbs 2004). Its sub-discipline, Community Ecology, is concerned with explaining the distributions, abundances, and interactions of taxa (Liebold et al. 2004) that co-occur as assemblages at different places or times. Community assembly refers to the processes by which communities arise. Current paradigms emphasize dispersal, niche limitation (taxa not capable of tolerating the physical conditions present at a given location being excluded from that location), biotic interactions (e.g., predation, competition), evolution, and neutral (random) processes of extirpation and colonization as most important (Belyea and Lancaster 1999, Hubbell 2001, Fussmann et al. 2007)1. Stressor exposures and natural disturbances are universal determinants of the taxonomic structure and functions of ecosystems (Hutchinson 1957). The term ecological effect describes a change to the structure or function of