Modeling Neotropical Ecosystems during the Last Glacial Maximum by Hiromitsu Sato A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Earth Sciences University of Toronto c Copyright 2019 by Hiromitsu Sato Abstract Modeling Neotropical Ecosystems during the Last Glacial Maximum Hiromitsu Sato Doctor of Philosophy Graduate Department of Earth Sciences University of Toronto 2019 Rich biodiversity and biogeochemical significance has long motivated research on Neotropical ecosys- tems, though regionally-focused modeling studies remain relatively sparse and limited in scope. Three individual projects were performed to address potential issues in the modeling of Neotropical ecosystems in past and present contexts with particular emphasis on the Last Glacial Maximum. The first project was focused on discerning the effects of low CO2 and temperature on the carbon exchange of a well- watered tropical forest using a canopy-scale ecophysiological model. The radiative transfer regime and canopy energy balance were used to interpret the effect of environmental variables on carbon fluxes, as well as the reproduction of an observed phenomena where leaf temperature drops below air temperature. The second project was an analysis of a four-year data set of ecosystem fluxes designed to assess the seasonal patterns of carbon uptake and the impacts of drought from a tropical dry forest site in Santa Rosa National Park, Costa Rica. A hyperbolic light response function was used to partition net ecosys- tem exchange into gross primary productivty and ecosystem respiration, while extracting estimates of ecosystem-level photosynthetic radiation and saturated rates of uptake. Bursts of carbon dioxide were observed at the onset of the rainy season suggesting the occurrence of the `Birch Effect' within tropical dry forest ecosystems. The third project was a regional-scale modeling study of vegetation cover in the Neotropics during the Last Glacial Maximum, focusing on the individual and interactive effects of fire and low CO2 on biome distribution and tree cover. Inclusion of fire and the effects of low CO2 improved agreement with pollen records and suggest the past prevalence of grassier, more open ecosystems. Mod- eling evidence was found to support the existence of hypothesized routes and barriers to dispersal during the Last Glacial Maximum, bolstering theories of range expansion and diversification over Pleistocene climatic oscillations. ii Acknowledgements First off, I would like to thank my supervisor Sharon Cowling for the freedom and support that helped me finally perform and enjoy original research. My time in the Cowling lab taught me how much boldness and personal interest could fertilize and sustain good research. Thanks to my labmates who shared this funky journey through deep time. I would like to thank my friends for making life fun and lovely even when I was very much preoccupied with compilation errors and how lizards speciate. Thank you to my frequent study buddies, Nem and Mario, who shared the coffees, quick meals and mundane grind. Also, I'd like to thank my committee, Charly, Sean, and J¨org,for the nudges and suggestions that sometimes made a world of difference. Oh yes, also thank you to the many profs and post-docs and experts who responded to my impromptu emails kindly and constructively. I'd also like to thank my examination committee for taking the time to read and edit my thesis, and helping me understand my results in a larger context. I'd like to thank Douglas Kelley and Stephen Mayor for their guidance and technical support, which was a godsend that made me realize how important collaboration can be. I'd like to thank my fianc´eJackie for the love and confidence to follow my heart. Thank you to my family, for the love and encouragement and belief in me, even when the chips were down. Its been a long road baby, but we've only just begun. iii Contents 0.1 List of Tables . vi 0.2 List of Figures . vi 0.3 List of Symbols and Abbreviations . vii 1 Introduction 1 1.1 Overview . 1 1.2 Earth Systems Models and Palaeoecology . 2 1.3 Motivation and Research Goals . 3 2 Glacial Amazonia at the Canopy-Scale 5 2.1 Abstract . 5 2.2 Introduction . 5 2.3 Methods . 6 2.3.1 Canopy Model . 6 2.3.2 Climate Data and Ecosystem Parameters . 8 2.4 Results and Discussion . 9 2.4.1 Validation and LGM Carbon Processes . 9 2.4.2 Mechanisms behind Carbon Uptake Enhancement . 14 2.4.3 Effects on Glacial Amazonia . 16 2.4.4 Adaptation and Dry Forest . 17 2.4.5 Implications for Future Forests . 18 2.5 Conclusion . 18 2.6 Acknowledgments . 19 3 Interpreting Carbon Fluxes from a Costa Rican Tropical Dry Forest 20 3.1 Abstract . 20 3.2 Introduction . 20 3.3 Methods . 22 3.3.1 Study Site . 22 3.3.2 Eddy Covariance Measurements . 23 3.3.3 Flux Partitioning and Empirical Parameter Estimation . 24 3.4 Results and Discussion . 26 3.4.1 Phenology and the Impact of Drought from Ecosystem Carbon Fluxes . 26 3.4.2 Comparison with Tropical Rainforest . 26 3.4.3 The Birch Effect in Tropical Dry Forest . 29 iv 3.4.4 Connections with Model Representations of Tropical Dry Forest . 30 3.5 Conclusion . 31 4 Amazonian Dry Corridors opened by Fire and Low CO2 33 4.1 Abstract . 33 4.2 Introduction . 33 4.3 Results . 35 4.3.1 Comparison of Model Reconstructions with Palynological Data . 35 4.3.2 Fire and Low CO2 Activation Drives Expansions of Grasslands and Reductions of Forest . 37 4.3.3 Fire and Low CO2 Open Dry Corridors . 38 4.3.4 Interactive Effects of Fire and low CO2 on Tree Cover . 41 4.3.5 Low CO2 Intensifies the Fire-Forced Bimodality of Tree Cover . 43 4.4 Discussion . 44 4.5 Methods . 46 4.5.1 Model Description and Protocol . 46 4.5.2 Model-Pollen Biome Correspondence . 47 4.5.3 Discrete Manhattan Metric . 49 4.5.4 Stein-Alpert Decomposition . 50 4.6 Acknowledgments . 53 5 Conclusion 54 v 0.1 List of Tables • 4.1 Affinity matrix for LPX biomes to compute `distance' between biomes in trait space (p. 48) • 4.2 Correspondance legend between pollen reconstructed and model assigned biomes (p. 49) 0.2 List of Figures • 2.1 Flow of submodules used by CANOAK to compute carbon, energy, and microclimatic profiles (p. 6) • 2.2 a) Daily averages of Net Ecosystem Exchange at hourly intervals computed by CANOAK b) Theoretical computations of carbon fluxes (p. 9) • 2.3 Regression test between model output driven by modern values and measured values of Net Ecosystem Exchange with the equation for the line of best fit and regression coefficient (p. 10) • 2.4 The dependence and sensitivity (slope) of average hourly rates of canopy photosynthesis (carbon uptake) and respiration (carbon release) to air temperature (p. 11) • 2.5 a) The dependence and sensitivity of sensible and latent energy uxes to air temperature. b) The dependence and sensitivity of sunlit and mean leaf temperature to air temperature (p. 12) • 3.1 Eddy covariance system mounted on a tower in Santa Rosa National Park, Guanacaste, Costa Rica (p. 21) • 3.2 Tropical dry forest in study site during the dry season (February, 2016) (p. 22) • 3.3 Sample of fits of hyperbolic light response function to NEE and PAR data (p. 23) • 3.4 Time series for NEE, GPP, and Reco for the four year study period (p. 25) • 3.5 Time series for photosynthetic efficiency and saturated uptake for the four year study pe- riod,with blue shaded regions representing the wet season and red shaded regions representing the dry season (p. 26) • 3.6 a) Net ecosystem exchange and soil moisture measurements at half-hourly intervals spanning from April 26th, 2016 (0:00) to April 28th, 2016 (02:00) b) Precipitation measurements for the same time period (p. 28) • 4.1 Summary of model-data comparison scenarios from the fire and low CO2 factorial experiment for each LGM climate reconstruction (p. 35) • 4.2 LPX model reconstruction of biome distributions in the Neotropics during the LGM for four scenarios (p. 38) • 4.3 Whittaker plots showing occurrence of biomes in climate space for four scenarios designed by the fire/CO2 factorial experiment (p. 39) • 4.4 Identification of reconstructed biogeographical formations in the ensemble fire and low CO2 scenario (p. 40) vi • 4.5 Results from the Stein-Alpert Decomposition showing individual and interactive effects of fire and low CO2 in terms of fractional changes in tree cover (p. 41) • 4.6 Fractional tree cover against mean annual precipitation aggregated by runs driven by four AOGCM LGM reconstructions (p. 42) • 4.7 Flow of model protocol from spin-up to biome assignment for each factorial experiment run (p. 45) • 4.8 Diagram representing the biome assignment scheme (p. 47) 0.3 List of Symbols and Abbreviations • LGM: Last Glacial Maximum • GPP: Gross Primary Productivity • Reco: Ecosystem Respiration • NEE: Net Ecosystem Exchange • α: Photosynthetic Efficiency • A2000: Light-Saturated Rate of Uptake • gs: Stomatal Conductance • A: Rate of photosynthetic uptake • Vc: Rate of carboxylation • Vo: Rate of oxygenation • Rd: Rate of dark respiration • Wc: Rate of carboxylation when RuBP is saturated • Wj: Rate of carboxylation when limited by electron transport • PAR: Photosynthetically Active Radiation • SRNP: Santa Rosa National Park • AOGCM: Atmosphere-Ocean General Circulation Model • DGVM: Dynamic Global Vegetation Model • LPX: Land Processes and eXchanges model vii Chapter 1 Introduction 1.1 Overview The objective of my thesis was to perform the most advanced model reconstruction analysis of vegetation of the Neotropics during the Last Glacial Maximum (LGM), which I duly accomplished.