I © Copyright 2017 Christine Stawitz
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i © Copyright 2017 Christine Stawitz ii Understanding the effects of growth and size-at-age variation on the dynamics of fish populations Christine Stawitz A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2017 Reading Committee: Timothy Essington, Chair Trevor Branch Melissa Haltuch Program Authorized to Offer Degree: Quantitative Ecology and Resource Management iii University of Washington Abstract Understanding the effects of growth and size-at-age variation on the dynamics of fish populations Christine Stawitz Chair of the Supervisory Committee: Professor Timothy E. Essington School of Aquatic and Fishery Sciences Understanding drivers of populations is of tantamount importance across a broad scale of researchers, from theoretical ecologists to tactical resource managers. Drivers may be internal feedbacks (density-dependent) or external (density-independent) processes, such as changes in prey, predator, or competitor populations, or environmental stochasticity. In a closed population, these drivers affect populations by altering demographic rates (i.e. mortality, reproduction, somatic growth). Although there is increasing evidence that no demographic rates are static, at least in patchy and stochastic aquatic environments, it is an ongoing question to identify the most important types and scale of variation for population dynamics models. In this dissertation, I seek to quantify the magnitude and effect of growth and size-at-age variation on fish population dynamics using a variety of different modeling techniques. In the first chapter, I use a state-space iv statistical model to quantify the magnitude and type of temporal size-at-age variation experienced by a number of Pacific groundfish populations. In the second chapter, I use these estimates of growth variation, along with parameters taken from fisheries stock assessment models, to illustrate how both growth and recruitment variation may introduce fluctuations into simulated populations with otherwise static demographic rates. In the third chapter, I use an integrated analysis model to simulate and estimate patterns of growth variation in Petrale sole (Eopsetta jordani) to examine the effect of growth misspecification on estimates of population status. In the final chapter, I adapt a size-structured ecosystem model to Tonlé Sap Lake, Cambodia, and explore ways to validate model accuracy in a species-rich, data-poor ecosystem. This work highlights the importance of accounting for multiple types of demographic stochasticity across life history type and how appropriate model complexity scales with data quality and quantity. i TABLE OF CONTENTS List of Figures ................................................................................................................................. v List of Tables ............................................................................................................................... viii Introduction ..................................................................................................................................... 1 Chapter 1. A state-space approach for detecting growth variation and application to North Pacific groundfish ....................................................................................................................................... 4 1.1 Introduction ..................................................................................................................... 5 1.2 Methods........................................................................................................................... 9 1.2.1 Growth model framework ........................................................................................... 9 1.2.2 Simulation study ....................................................................................................... 12 1.2.3 Bayesian methods ..................................................................................................... 13 1.2.4 Model application ..................................................................................................... 14 1.3 Results ........................................................................................................................... 17 1.3.1 Simulation study ....................................................................................................... 17 1.3.2 Estimated growth mode and pattern ......................................................................... 18 1.3.3 Effect of survey data ................................................................................................. 19 1.3.4 Growth anomaly magnitude ...................................................................................... 20 1.4 Discussion ..................................................................................................................... 20 Chapter 2. Somatic growth contributes to population variation in marine fishes ......................... 38 2.1 Introduction ................................................................................................................... 39 2.2 Methods......................................................................................................................... 41 i ii 2.2.1 Species selection and life history traits ..................................................................... 42 2.2.2 Population model ...................................................................................................... 43 2.2.3 Early life history ....................................................................................................... 43 2.2.4 Growth ...................................................................................................................... 45 2.2.5 Scaling of growth deviations .................................................................................... 46 2.2.6 Simulation ................................................................................................................. 47 2.3 Results ........................................................................................................................... 48 2.3.1 Empirical and simulated demographic variability .................................................... 48 2.3.2 Importance of growth or recruitment variability ...................................................... 49 2.3.3 Interaction effect with age truncation ....................................................................... 50 2.3.4 Comparison to alternative population models .......................................................... 51 2.3.5 Relation to life history characteristics....................................................................... 51 2.4 Discussion ..................................................................................................................... 52 Chapter 3. How does growth misspecification affect management advice derived from integrated fisheries stock assessment models? .............................................................................................. 65 3.1 Introduction ................................................................................................................... 66 3.2 Methods......................................................................................................................... 69 3.2.1 Model adaptation ...................................................................................................... 70 3.2.2 Specification of operation model growth parameters ............................................... 71 3.2.3 Simulation framework .............................................................................................. 73 3.2.4 Response metrics and convergence criteria .............................................................. 74 3.3 Results ........................................................................................................................... 75 3.3.1 Bias in management quantities in data-rich case ...................................................... 76 ii iii 3.3.2 Increase in uncertainty in data-rich case ................................................................... 78 3.3.3 Effect of data limitation ............................................................................................ 78 3.3.4 Convergence ............................................................................................................. 79 3.4 Discussion ..................................................................................................................... 79 Chapter 4. Testing the applicability of size-spectrum food models to a species-rich tropical lake ....................................................................................................................................................... 91 Abstract .................................................................................................................................... 91 4.1 Introduction ................................................................................................................... 93 4.2 Methods......................................................................................................................... 96 4.2.1 Ecosystem model ...................................................................................................... 96 4.2.2 Dynamics .................................................................................................................