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Replace This with the Actual Title Using All Caps MODELING NEW YORK STATE'S STOCKED STREAM TROUT FISHERY A Thesis Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Master of Science by Benjamin Marcy-Quay May 2015 © 2015 Benjamin Marcy-Quay ABSTRACT A population dynamics model has been used in New York State since the 1980's to explore trout stocking scenarios, but the input information has become obsolete due to changes in predator communities and angler practices. We surveyed nine streams for a three year period and using a combination of methods. Creel surveys allowed us to estimate effort, harvest, and catch rates, while electrofishing surveys provided estimates of total mortality. Geostatistical methods were used to explore patterns of angler origin. The effect of angler specialization was assessed using regression to compare calculated travel distance to angler income, gear, and stream choice. All three factors were found to be significant (P<0.05).Using nonlinear parameter estimation, we obtained estimates for apparent natural mortality and catchability nearly an order of magnitude higher than historical estimates. Predictions from the updated model exhibited much better fit than those from the model previously used to inform stocking decisions. BIOGRAPHICAL SKETCH Born in Ann Arbor, Michigan in 1988, Ben spent the majority of his childhood exploring the woods, streams, and lakes around his home and abroad. While on family vacations that ranged from treks in Canada's Northwest Territories to houseboat trips down the Mississippi River, he cultivated a keen interest in the natural world around him. Ben's high school years were spent at a small boarding school on the shore of Lake Michigan where he took every science course offered, including volunteering as a teaching assistant for a marine biology course in the British Virgin Islands. In 2010, Ben earned his Bachelor's of Science in Environmental Science from Allegheny College. During summer breaks and after graduation, he spent time in Utah backpacking, climbing, and working as a counselor for a therapeutic wilderness program where he helped teens overcome problems such as substance abuse and depression. Ben came to New York in 2011 when he took a job as a research technician with the Department of Environmental Conservation. In fall 2012, after two enjoyable seasons of field work, Ben began graduate work at Cornell University in the Department of Natural Resources. iii ACKNOWLEDGMENTS This work would not have been possible without the help of many people. I would first and foremost like to thank my committee, Patrick Sullivan and Clifford Kraft, for their advice and knowledge. In the course of this project they have greatly deepened my understanding of ecology and statistics. Funding support was provided by the New York State Department of Environmental Conservation and the USGS New York Cooperative Fish and Wildlife Research Unit. The members of the DEC Trout Team were instrumental to the completion of the project, particularly Fred Henson and Shaun Keeler, who provided leadership and guidance. I owe heartfelt gratitude to all of the state biologists and managers involved in the process for their help with study design, data collection, and for providing "real world" interpretation of the results. The entire Cornell DNR community has helped and supported me along the way and I am grateful for their help and friendship. In particular I would like to thank Suzanne Beyeler for both encouraging me to apply to graduate school and being an excellent mentor during the last several years. Finally, I would like to thank my parents, Sherry Marcy and Nancy Quay, for their unfailing love and support. iv TABLE OF CONTENTS Biographical Sketch .......................................................................................... iii Acknowledgements ..........................................................................................iv Table of Contents ............................................................................................. v List of Figures ...................................................................................................vi List of Tables ................................................................................................... vii Chapter 1 – A Population Dynamics Model for Stocked Brown Trout (Salmo trutta) Using Nonlinear Parameter Estimation .................................................. 1 Abstract ......................................................................................................... 1 Introduction ................................................................................................... 2 Methods ........................................................................................................ 4 Results ........................................................................................................ 10 Discussion ................................................................................................... 18 References .................................................................................................. 23 Chapter 2 – Angler Specialization and Travel Distance: Applying Two Complementary Statistical Methods for Interpreting Spatially Referenced Creel Survey Data .................................................................................................... 29 Abstract ....................................................................................................... 29 Introduction ................................................................................................. 30 Methods ...................................................................................................... 33 Results ........................................................................................................ 37 Discussion ................................................................................................... 43 References .................................................................................................. 48 v LIST OF FIGURES Figure 1.1. Comparison of current and historical estimates of total annual angler effort. Historical estimates are taken from single year creel surveys conducted between 1985 and 1995. ............................................................ 11 Figure 1.2. Mean creel rate by year for all study streams. ............................ 12 Figure 1.3. Fit of model predictions (lines) to observed densities from surveys (points) for all streams and years. .............................................................. 16 Figure 1.4. Fit of model predictions (lines) to observed average daily angler catch-rates (points) for all streams and years. .............................................. 17 Figure 1.5. Current model fit versus the historical model for an example stream and year. ...................................................................................................... 18 Figure 2.1. Estimates and Bonferroni-corrected confidence intervals for all levels of the variable Stream.. ...................................................................... 38 Figure 2.2. Variogram model fits for each study stream............................... 41 Figure 2.3. Interpolated angler origination for all study streams with heat map transparency increasing with variation. ........................................................ 42 vi LIST OF TABLES Table 1.1. Candidate models ranked by lowest Akaike Information Criterion (AIC) score. .................................................................................................. 13 Table 1.2. Estimated parameter values by stream for the top model............ 14 Table 1.3. Estimated parameter values by DEC stream type compared to historical values used in the previous model.. .............................................. 14 Table 2.1. Number of anglers surveyed per stream from 2011-2013.. ......... 34 Table 2.2. ANCOVA analysis of angler travel distance against angler specialization variables................................................................................. 39 Table 2.3. Variogram models and parameter estimates for the study streams ..................................................................................................................... 40 vii CHAPTER 1 A Population Dynamics Model for Stocked Brown Trout (Salmo trutta) Using Nonlinear Parameter Estimation Abstract Stocking programs used to improve the quality of recreational fisheries can have positive effects on angler catch-rate and satisfaction, but may also negatively affect the local habitat and native fish community. A population dynamics model has been used in New York State since the 1980's to explore alternative stocking scenarios, but the input information for developing these forecasts has likely become obsolete due to changes in predator communities and angler practices. In this study we surveyed nine streams for a three year period and used a combination of methods to assess natural and angler-related mortality. Creel surveys allowed us to estimate angler effort, harvest, and catch rates, while depletion surveys of marked cohorts provided estimates of natural mortality. Angler effort was lower than historically recorded for nearly all streams and release rates were much greater (75-80%) than the 0% previously assumed. Using nonlinear parameter estimation, we obtained estimates for daily apparent natural mortality and catchability that
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