Shelter visits vs availability for Sonoran Desert Tortoises in 2 Arizona populations

At Sugarloaf we monitored female tortoises (range 184–289 mm midline carapace length [CL]) weekly using radio telemetry in 1991–1993 and 1997–2005 as part of a reproductive ecology study (Averill-Murray 2002; Averill-Murray et al. 2018). During the 11 years of radio-tracking, all burrows used by both telemetered and opportunistically encountered tortoises were marked with numbered aluminum tags (n = 522). We use the term “burrow” specifically to refer to a subsurface cavity &gt;1/2 the tortoise’s length either formed by erosion or excavated by a tortoise or another animal (Burge 1978). We categorized burrow types as “rock” (cover provided by rocks or boulders, including large boulder piles in which the tortoise could not be visualized), “soil” (cover provided by soil or vegetation with no substantial rock component), and “packrat” (freestanding white-throated woodrat Neotomoa albigula nest independent of other shelter types; packrat nests inside rock shelters were categorized as “rock”). We did not individually mark “pallets” (shallow, scraped out areas &lt;1/2 tortoise length) or other temporary shelters unmodified by the tortoise (e.g., under trees, shrubs, or rock overhangs).At FMR, as part of a habitat-use study we attached radio transmitters (ATS, AVM, Telonics, or Wildlife Materials) to the anterior carapace of adult tortoises as above (Riedle et al. 2008). During the winter months (November through February) when tortoises were inactive, we located tortoises once a week. During the activity season (March through October) we located tortoises 2–3 times weekly, obtaining both morning and evening locations. From 2000 to 2003, we searched areas in which tortoises might occur within FMR, concentrating on sites suitable for burrow excavation, especially including incised washes with caliche caves and the volcanic hill. We also searched all washes within the study area, whether incised or not, and spent considerable time on the alluvial fans. We marked burrows in which we observed tortoises with individually numbered aluminum tags (n = 124), and we mapped locations of all caliche caves large enough to shelter a tortoise ≥180 mm CL (n = 463). Burrow types included caliche, rock, soil, and packrat.We tested hypotheses that shelter use did not differ by different shelter types. We used linear mixed-effects models in R package <i>nlme</i> to assess whether the number of shelters used (including pallets) varied by shelter type or sex, with individual tortoise ID specified as a random effect. We used GLMMs with a binomial distribution in R package <i>lme4</i> to determine whether tortoises used different types of burrows in proportion to their availability within their home ranges, again with tortoise ID as a random effect. We used permutation-based sign tests with R package <i>phuassess</i> to assess whether tortoises visited different shelter types relative to their availability. We conducted these analyses separately for FMR and Sugarloaf due to the lack of caliche burrows at Sugarloaf.