UNIVERSITY OF CALIFORNIA SANTA CRUZ CONSERVATION BIOGEOGRAPHY, MECHANISMS OF DECLINE, AND CLIMATE RELATIONSHIPS OF CALIFORNIA WILDLIFE A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in ECOLOGY AND EVOLUTIONARY BIOLOGY by Joseph A. E. Stewart September 2018 The Dissertation of Joseph A. E. Stewart is approved: Professor A. Marm Kilpatrick Professor Barry Sinervo Professor Kristy Kroeker Professor M. Tim Tinker Dr. David Wright Dr. James Thorne Lori Kletzer Vice Provost and Dean of Graduate Studies Table of Contents Table of Contents iii List of Figures iv List of Tables ix Abstract xii Acknowledgements xiii Introduction 1 Chapter 1 — Revisiting the past to foretell the future: summer temperature 7 and habitat area predict pika extirpations in California Chapter 2 — Apparent climate-mediated loss and fragmentation of core 50 habitat of the American pika in the Northern Sierra Nevada, California Chapter 3 — A climate change vulnerability assessment for twenty 88 California mammal taxa Chapter 4 — Habitat restoration opportunities, climatic niche contraction, 216 and conservation biogeography in California's San Joaquin Desert iii List of Figures 1.1 Location and occupancy status of 67 historical pika sites in California. 16 1.2 Pika occupancy as a function of the best predictor variables. 24 1.3 Map of predicted pika occupancy status under 6 climate scenarios for 2070. 26 1.S1 Illustration of the method used set historical site centroid locations. 40 1.S2 Historical photo retake from ‘4 miles southwest of McDonald Peak’, Lassen Co., CA. 42 1.S2 Historical photo retake from Emerald Lake, Lassen Co., CA. 43 1.S3 Pictures of fresh and old pika fecal pellets. 34 1.S4 Projected decline in pika occupancy at historical sites under various degrees of 47 summer warming. 1.S5 Locations of sites incorrectly classified by the best-performing model. 49 2.1 Sites surveyed for pikas in the north Lake Tahoe area, California, USA. 55 2.2 Calibrated radiocarbon age ranges for each of the remnant pika scat samples. 63 2.3 Mean annual temperature data from weather station at Tahoe City, California, USA. 64 2.4 Inundation of sky islands surrounding Lake Tahoe by rising tides of warm air. 66 2.S1 Snow depth measurements for weather station at Tahoe City, CA, USA. 82 2.S2 Graphical comparison of pika occupancy models. 83 2.S3 Current and historical mean summer temperature and pika occupancy status. 84 3.1 Range of component climate vulnerability scores for taxa assessed in this chapter. 97 3.2 Range of overall climate vulnerability scores under four climate scenarios. 99 3.3 Comparison of 12 CMIP5 GCM projections under the RCP 4.5 emission scenario. 112 3.4 Comparison of 12 CMIP5 GCM projections under the RCP 8.5 emission scenario. 113 3.5 Flow chart of hydroclimatic variables calculated by the Basin Characterization 114 Model. 3.6 Estimated dispersal ability and phylogenetic relationships for terrestrial mammal 117 species. 3.7 Occurrence locations, climatic suitability, and modelled distribution of Tamias 118 alpinus. iv 3.8 Projected change in climatically suitable habitat for Tamias alpinus under four 120 climate scenarios. 3.9 A shrew (Genus: Sorex). 131 3.10 Occurrence locations, climatic suitability, and modelled distribution of Sorex lyelli. 134 3.11 Projected change in climatically suitable habitat for Sorex lyelli under four climate 134 scenarios. 3.12 An ornate shrew (Sorex ornatus). 135 3.13 Occurrence locations, climatic suitability, and modelled distribution of Sorex ornatus 138 salicornicus. 3.14 Projected change in climatically suitable habitat for Sorex ornatus salicornicus under 138 four scenarios. 3.15 Projected loss of habitat from one meter of sea level rise for Sorex ornatus 139 salicornicus. 3.16 A wandering shrew (Sorex vagrans). 140 3.17 Occurrence locations, climatic suitability, and modelled distribution of Sorex vagrans 143 halicoetes. 3.18 Projected change in climatically suitable habitat for Sorex vagrans halicoetes under 143 four scenarios. 3.19 Projected loss of habitat from one meter of sea level rise for Sorex vagrans 144 halicoetes. 3.20 An American pika (Ochotona princeps). 145 3.21 Occurrence locations, climatic suitability, and modelled distribution of Ochotona 148 princeps. 3.22 Projected change in climatically suitable habitat for Ochotona princeps under four 148 scenarios. 3.23 A Mountain Beaver (Aplodontia rufa). 149 3.24 Occurrence locations, climatic suitability, and modelled distribution of Aplodontia 152 rufa phaea. 3.25 Projected change in climatically suitable habitat for Aplodontia rufa phaea under 152 four scenarios. 3.26 Projected loss of habitat from one meter of sea level rise for Aplodontia rufa phaea. 153 3.27 A Belding's ground squirrel (Urocitellus beldingi). 154 v 3.28 Occurrence locations, climatic suitability, and modelled distribution of Urocitellus 157 beldingi. 3.29 Projected change in climatically suitable habitat for Urocitellus beldingi under four 157 scenarios. 3.30 A golden-mantled ground squirrel (Callospermophilus lateralis). 158 3.31 Occurrence locations, climatic suitability, and modelled distribution of 161 Callospermophilus lateralis bernardinus. 3.32 Projected change in climatically suitable habitat for Callospermophilus lateralis 161 bernardinus under four scenarios. 3.33 An alpine chipmunk (Tamias alpinus). 162 3.34 Occurrence locations, climatic suitability, and modelled distribution of Tamias 165 alpinus. 3.35 Projected change in climatically suitable habitat for Tamias alpinus under four 165 scenarios. 3.36 A Mount Pinos lodgepole chipmunk (Tamias speciosus callipeplus). 166 3.37 Occurrence locations, climatic suitability, and modelled distribution of Tamias 169 speciosus callipeplus. 3.38 Projected change in climatically suitable habitat for Tamias speciosus callipeplus 169 under four scenarios. 3.39 A Western Jumping Mouse (Zapus princeps). 170 3.40 Occurrence locations, climatic suitability, and modelled distribution of Zapus 173 princeps. 3.41 Projected change in climatically suitable habitat for Zapus princeps under four 173 scenarios. 3.42 A red tree vole (Arborimus pomo). 174 3.43 Occurrence locations, climatic suitability, and modelled distribution of Arborimus 177 pomo. 3.44 Projected change in climatically suitable habitat for Arborimus pomo under four 177 scenarios. 3.45 Projected loss of habitat from one meter of sea level rise for Arborimus pomo. 178 3.46 A California vole (Microtus californicus). 179 3.47 Occurrence locations, climatic suitability, and modelled distribution of Microtus 182 californicus halophilus. vi 3.48 Projected change in climatically suitable habitat for Microtus californicus halophilus 182 under four scenarios. 3.49 Projected loss of habitat from one meter of sea level rise for Microtus californicus 183 halophilus. 3.50 A California vole (Microtus californicus). 184 3.51 A California vole (Microtus californicus). 186 3.52 Occurrence locations, climatic suitability, and modelled distribution of Microtus 189 californicus sanpabloensis. 3.53 Projected change in climatically suitable habitat for Microtus californicus 189 sanpabloensis under four scenarios. 3.54 Projected loss of habitat from one meter of sea level rise for Microtus californicus 190 sanpabloensis. 3.55 A Montane vole (Microtus montanus). 191 3.56 Occurrence locations, climatic suitability, and modelled distribution of Microtus 194 montanus. 3.57 Projected change in climatically suitable habitat for Microtus montanus under four 194 scenarios. 3.58 A San Joaquin kit fox (Vulpes macrotis mutica). 195 3.59 Occurrence locations, climatic suitability, and modelled distribution of Vulpes 198 macrotis mutica. 3.60 Projected change in climatically suitable habitat for Vulpes macrotis mutica under 198 four scenarios. 3.61 A Sierra Nevada red fox (Vulpes vulpes necator). 199 3.62 Occurrence locations, climatic suitability, and modelled distribution of Vulpes vulpes 202 necator. 3.63 Projected change in climatically suitable habitat for Vulpes vulpes necator under four 202 scenarios. 3.64 A Humboldt marten (Martes caurina humboldtensis). 203 3.65 Occurrence locations, climatic suitability, and modelled distribution of Martes 206 caurina humboldtensis. 3.66 Projected change in climatically suitable habitat for Martes caurina humboldtensis 206 under four scenarios. 3.67 An American marten (Martes caurina). 207 vii 3.68 Occurrence locations, climatic suitability, and modelled distribution of Martes 210 caurina sierrae. 3.69 Projected change in climatically suitable habitat for Martes caurina sierrae under 210 four scenarios. 3.70 A Desert bighorn sheep (Ovis canadensis nelsoni). 211 3.71 Occurrence locations, climatic suitability, and modelled distribution of Ovis 214 canadensis nelsoni. 3.72 Projected change in climatically suitable habitat for Ovis canadensis nelsoni under 214 four scenarios. 4.1 The historical distribution of habitat for Gambelia sila, extant sites, extirpated sites, 229 lost habitat, and sites where persistence of G. sila has not been confirmed since before 1995. 4.2 Geographic information on habitat suitability models for Gambelia sila. 231 4.3 Area of Gambelia sila habitat lost over time from 1850 to present. 233 4.4 Apparent climatic-niche contraction away from the mesic margin in Gambelia sila. 234 4.S1 Hours of restriction and hours of activity for Gambelia sila. 255 4.S2 Density plots for 11 candidate predictor variables. 256 4.S3 Habitat suitability in the Westlands Water District. 257 4.S4 Modeled