THE UNIVERSITY OF CHICAGO CHARACTERIZING AND QUANTIFYING HABITAT HETEROGENEITY, EXTINCTION, AND PERSISTENCE OF HABITAT PREFERENCE IN PHANEROZOIC REEFS A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE PHYSICAL SCIENCES IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF THE GEOPHYSICAL SCIENCES BY PETER WARD TIERNEY CHICAGO, ILLINOIS DECEMBER 2018 TABLE OF CONTENTS LIST OF FIGURES v LIST OF TABLES vii ABSTRACT viii ACKNOWLEDGMENTS ix INTRODUCTION ....................................................................................................................................................................... 1 CHAPTER 1 Characterizing and quantifying habitat heterogeneity in fossil reefs: case studies from the Ordovician of Newfoundland, and the Pleistocene of Florida ....................................................................... 4 1.1 Abstract ........................................................................................................................................................................... 4 1.2 Introduction ................................................................................................................................................................... 4 1.3 Background .................................................................................................................................................................... 6 1.3.1 Heterogeneity and biodiversity in the reef system ............................................................................. 6 1.3.2 Measurement of habitat heterogeneity in modern reefs .................................................................. 7 1.3.3 At what scales is heterogeneity important? ........................................................................................... 8 1.4 The challenges of identifying habitat heterogeneity in deep time.......................................................... 9 1.4.1 The taphonomic limitations on identifying heterogeneity in fossil reefs ............................... 10 1.4.2 The limits of spatial scale in identifying heterogeneity in fossil reefs ...................................... 11 1.5 A new protocol for measuring habitat heterogeneity in fossil reefs.................................................... 12 1.5.1 Trait 1: Reef-builder morphotype as a measure of local heterogeneity .................................. 13 1.5.2 Trait 2: Diversity of reef building morphotypes ................................................................................ 15 1.5.3 Trait 3: Facies-variation as a measure of reef heterogeneity ....................................................... 16 1.5.4 Trait 4: Original topography above surrounding sediment .......................................................... 17 1.5.5 Trait 5: Potential rugosity measured using stretched-line transects-- adapting a Structural Complexity Index (SCI) ...................................................................................................................... 18 1.6 Results: Application of the protocol to Ordovician and Pleistocene case studies .......................... 22 1.6.1 Heterogeneity in Ordovician patch reefs .............................................................................................. 22 1.6.2 Heterogeneity in a Pleistocene barrier reef......................................................................................... 26 1.7 Discussion ..................................................................................................................................................................... 29 1.7.1 Limitations: When can and can’t these measurements be made? .............................................. 29 1.7.2 Challenges in comparing Paleozoic reefs .............................................................................................. 30 1.7.3 Challenges in comparing reefs between time periods .................................................................... 32 1.7.4 Potential utility across non-analogous reefs and adaptation to nonreef framework carbonates .................................................................................................................................................................... 33 1.8 Conclusions .................................................................................................................................................................. 33 ii CHAPTER 2 Facies development and increasing habitat heterogeneity in Middle Ordovician to Late Devonian reefs: A recapitulation of individual reef-building dynamics ......................................................... 35 2.1 Abstract ......................................................................................................................................................................... 35 2.2 Introduction ................................................................................................................................................................. 35 2.3 Background .................................................................................................................................................................. 38 2.3.1 Autogenic sedimentary dynamics and spatial contingency .......................................................... 38 2.4 Methods ......................................................................................................................................................................... 40 2.4.1 Reef builder morphotypes .......................................................................................................................... 41 2.4.2 Facies description and facies diversity .................................................................................................. 42 2.4.3 Relief .................................................................................................................................................................... 43 2.4.4 Final Notes on Literature-Based Data .................................................................................................... 44 2.5 Results ............................................................................................................................................................................ 44 2.5.1 Occupancy and taxonomic associations of reef-builder morphotypes .................................... 44 2.5.2 Dominance by single reef-builder morphotype ................................................................................. 49 2.5.3 Reefs that are not dominated by a single morphotype ................................................................... 50 2.5.4 Multivariate associations of reef builders ............................................................................................ 52 2.5.5 Original topographic relief and preserved thickness ...................................................................... 52 2.5.6 Lateral and vertical facies variation within reefs .............................................................................. 56 2.5.7 Relationship between facies diversity and the original relief and preserved size of reefs ................................................................................................................................................................................. 56 2.5.8 Relationship between facies diversity and reef-builder morphologies ................................... 58 2.6 Discussion ..................................................................................................................................................................... 60 2.6.1 Impact of literature bias .............................................................................................................................. 60 2.6.2 Taxonomic membership of morphotypes: change over time, and relevance to patch- scale habitat heterogeneity ................................................................................................................................... 61 2.6.3 Reef builder morphotypes in combination, and relevance to patch-scale habitat heterogeneity .............................................................................................................................................................. 62 2.6.4 Development of habitat heterogeneity at the facies (landscape) scale .................................... 64 2.6.5 Reef development underlies facies-scale heterogeneity within reefs ...................................... 65 2.6.6 Role of sea level change in reef trends ................................................................................................... 66 2.6.7 Examining biological controls on relief ................................................................................................. 68 2.7 Conclusions .................................................................................................................................................................. 69 CHAPTER 3 On extinction within the reef fauna during Phanerozoic reef crises, and the variable persistence of habitat preference among reef-builders and reef-dwellers ................................................... 71 3.1 Abstract: ........................................................................................................................................................................ 71 3.2 Introduction 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