AN ABSTRACT OF THE THESIS OF Jessica Sáenz for the degree of Master of Science in Fisheries Science presented on March 21, 2014. Title: Patch Dynamics of Desert Fishes in the Arid Wetlands of Western Utah Abstract approved: ______________________________________________________ James T. Peterson The conservation of declining desert fish species requires the identification of relations between fish population dynamics and their environments. Dynamic occupancy modeling, an approach that requires less information than traditional mark-recapture studies, may help identify important factors affecting population processes and aid desert fish conservation and restoration efforts. I used dynamic multi-season occupancy models for two analyses (multi-state and multi-species) to evaluate the influence of patch-level characteristics (patch percent open water, average patch depth, patch area), grazing damage, species interactions, population differences, patch connectivity and environmental variation (seasonal precipitation and temperature) on the patch dynamics (colonization, persistence, reproduction) of two desert chub species found in Snake Valley, UT. My results indicate that there was the strongest evidence according to model weights that patch dynamics in this system were influenced by patch-level characteristics (patch percent open water and average patch depth), grazing damage, population differences, biotic interactions, and winter precipitation rather than landscape level features such as connectivity. I observed positive effects of patch percent open water and average patch depth on least chub and Utah chub persistence. I also found that grazing damage increased their persistence at the medium damage level but decreased least chub and Utah chub colonization at the high grazing damage level. Least chub and Utah chub colonization varied between the two populations (study areas) with a higher probability of colonization at Bishop Springs than at Gandy Salt Marsh. In addition, I found some evidence that biotic interactions between least chub and Utah chub may be occurring in this system. Least chub were less likely to colonize patches previously occupied by Utah chub but surprisingly there was little evidence that these species interactions affected least chub persistence. Least chub reproduction increased with winter precipitation and was higher at Gandy Salt Marsh than Bishop Springs. The use of dynamic occupancy modeling in desert spring wetland complexes may provide a valuable tool for managers tasked with conserving at- risk desert fish species. ©Copyright by Jessica Sáenz March 21, 2014 All Rights Reserved Patch Dynamics of Desert Fishes in the Arid Wetlands of Western Utah by Jessica Sáenz A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Master of Science Presented March 21, 2014 Commencement June 2014 Master of Science thesis of Jessica Sáenz presented on March 21, 2014 APPROVED: Major Professor, representing Fisheries Science Head of the Department of Fisheries and Wildlife Dean of the Graduate School I understand that my thesis will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my thesis to any reader upon request. Jessica Sáenz, Author ACKNOWLEDGEMENTS This research was a collaborative effort including many agencies but primarily with the Bureau of Land Management, US Fish and Wildlife Service, and Utah Department of Natural Resources. I would like to thank the Bureau of Land Management for funding this research as well as Utah Department of Natural Resources (Chris Crockett, Mark Grover, Paul Thompson, and Kevin Wheeler) for providing a long term data set and allowing me to join them on several sampling occasions. I would like to thank my major advisor, Jim Peterson, for all of his assistance in data analysis, painful thesis editing and of course learning R. I would also like to thank my committee Selina Heppell and Matthew Betts for their feedback, and comments on my proposal and thesis and Susan Carozza for serving as my graduate school representative. In addition, I would like to thank the Peterson Lab (a.k.a. Kevin McDonnell) for providing assistance with R code (you were a life saver) and general moral support throughout this process. Last but not least, I am very thankful to my friends and family for their unwavering support and love throughout this process. I would especially like to thank my mom for instilling in me the importance of an education and always pushing me to continue my studies. I would like to thank my friends, new and old, for their companionship and help in maintaining my sanity. I would like to thank my fiancé Cody McKee for being supportive of my decision to come to Oregon and sticking with me these last few years. I am very lucky to have such an amazing group of people in my life and I am forever thankful. TABLE OF CONTENTS Page INTRODUCTION .................................................................................................. 1 Research Objectives .................................................................................................. 3 LITERATURE REVIEW ....................................................................................... 5 Physical and Chemical Environment ............................................................................ 6 Environmental Variability .......................................................................................... 9 Life History and Biotic Interactions ............................................................................ 11 Anthropogenic Effects ............................................................................................. 12 Desert Chubs ......................................................................................................... 18 Fish Population Dynamics ........................................................................................ 23 METHODS ........................................................................................................... 28 Study Location ....................................................................................................... 28 Data Collection and Compilation ............................................................................... 29 Data Analysis ........................................................................................................ 32 Evaluation of spatial replicate sample design ............................................................ 34 Dynamic Multi-state Occupancy Analysis ................................................................ 37 Dynamic Multi-Species Occupancy Analysis ............................................................ 41 RESULTS ............................................................................................................. 62 Dynamic Multi-state Occupancy Analysis ................................................................... 65 Detection Probability ........................................................................................... 66 Initial Occupancy ................................................................................................ 66 Persistence ......................................................................................................... 66 Colonization ....................................................................................................... 67 Reproduction ...................................................................................................... 68 TABLE OF CONTENTS (Continued) Page Dynamic Multi-Species Occupancy Analysis .................................................................. 68 Probability of Detection ........................................................................................ 69 Initial Occupancy ................................................................................................ 69 Colonization ....................................................................................................... 70 Extinction .......................................................................................................... 71 DISCUSSION ....................................................................................................... 94 Patch Dynamics ..................................................................................................... 94 Reproduction ....................................................................................................... 100 Detection ............................................................................................................ 101 Management Implications ...................................................................................... 102 CONCLUSION ................................................................................................... 104 LITERATURE CITED ....................................................................................... 107 LIST OF FIGURES Figure Page 3.1. Boundary of the Bonneville Basin with Snake Valley, Utah and two least chub study populations…………………………………...……………… 59 3.2. Boundary of Snake Valley, UT with Gandy Salt Marsh and Bishop Springs wetland complexes. Inset shows individual patches within each wetland complex……………………………………………………………….. 60 3.3. Aerial photographs of Gandy Salt Marsh and Bishop Springs with waterbody locations.......................................................……………………...... 61 4.1.