A long-term research project was conducted on Agassiz’s desert tortoises (Gopherus agassizii) at a 7.77 square kilometer plot at the Desert Tortoise Research Natural Area, Western Mojave Desert, California, USA. The plot included tortoise populations and habitat both inside and outside the protective fence at the Research Natural Area. Databases used in the research and publications from the research project are assembled here and include: census (survey) database used for the demographic analysis and Bayesian modeling of the desert tortoise population; shell-skeletal remains of desert tortoises; clinical signs of health, disease, and trauma in desert tortoises; perennial (shrubs, perennial grasses) and annual plant data from transects within the study area; potential avian predators of desert tortoises at the study area; evidence of mammalian carnivores at the study area; and evidence of anthropogenic impacts to desert tortoise and their habitats inside and outside the fenced Natural Area. These data support the following publications: 1) Berry, K.H., and Yee, J.L., 2021, Development of demographic models to analyze populations with multi-year data-Using Agassiz’s Desert Tortoise (Gopherus agassizii) as a case study: U.S. Geological Survey Open-File Report 2018-1094, 55 p., https://doi.org/10.3133/ofr20181094. 2) Berry, K.H., Yee, J.L., Shields, T.A., and Stockton, L. 2020. The catastrophic decline of tortoises at a fenced Natural Area. Wildlife Monographs 205:1-53. DOI:10.1002/wmon.1052

This dataset provides spatial predictions of habitat suitability for Gopherus agassizii (Agassiz’s desert tortoise), Gopherus morafkai (Morafka’s desert tortoise) and a pooled-species model under current conditions (1950 – 2000 yr). The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to evaluate subtle ecological niche differences between Gopherus agassizii and Gopherus morafkai, and identify local species-environment relationships. Spatial predictions of habitat suitability were created using MaxEnt version 3.4.0 (Phillips et al., 2006), a widely-used software for SDM in presence-background frameworks. Detailed methods are provided in Inman et al. 2019. Inman et al. 2019. Local niche differences predict genotype associations in sister taxa of desert tortoise. Diversity and Distributions. https://doi.org/10.1111/ddi.12927

We developed a model for analyzing multi-year demographic data for long-lived animals and used data from a population of Agassiz’s desert tortoise (Gopherus agassizii) at the Desert Tortoise Research Natural Area in the western Mojave Desert of California, USA, as a case study. The study area was 7.77 square kilometers and included two locations: inside and outside the fenced boundary. The wildlife-permeable, protective fence was designed to prevent entry from vehicle users and sheep grazing. We collected mark-recapture data from 1,123 tortoises during 7 annual surveys consisting of two censuses each over a 34-year period. We used a Bayesian modeling framework to develop a multistate Jolly-Seber model because of its ability to handle unobserved (latent) states and modified this model to incorporate the additional data from non-survey years. For this model we incorporated 3 size-age states (juvenile, immature, adult), sex (female, male), two location states (inside and outside the fenced boundary) and 3 survival states (not-yet-entered, entered/alive, and dead/removed). We calculated population densities and estimated probabilities of growth of the tortoises from one size-age state to a larger size-age state, survival after 1 year and 5 years, and detection. Our results show a declining population with low estimates for survival after 1 year and 5 years. The probability for tortoises to move from outside to inside the boundary fence was greater than for tortoises to move from inside the fence to outside. The probability for detecting tortoises differed by size-age state and was lowest for the smallest tortoises and highest for the adult tortoises. The framework for the model can be used to analyze other animal populations where vital rates are expected to vary depending on multiple individual states. The model was incorporated into the manuscript that included several other databases for publication in Wildlife Monographs in 2020 by Berry et al.

We developed a model for analyzing multi-year demographic data for long-lived animals and used data from a population of Agassiz’s desert tortoise (Gopherus agassizii) at the Desert Tortoise Research Natural Area in the western Mojave Desert of California, USA, as a case study. The study area was 7.77 square kilometers and included two locations: inside and outside the fenced boundary. The wildlife-permeable, protective fence was designed to prevent entry from vehicle users and sheep grazing. We collected mark-recapture data from 1,123 tortoises during 7 annual surveys consisting of two censuses each over a 34-year period. We used a Bayesian modeling framework to develop a multistate Jolly-Seber model because of its ability to handle unobserved (latent) states and modified this model to incorporate the additional data from non-survey years. For this model we incorporated 3 size-age states (juvenile, immature, adult), sex (female, male), two location states (inside and outside the fenced boundary) and 3 survival states (not-yet-entered, entered/alive, and dead/removed). We calculated population densities and estimated probabilities of growth of the tortoises from one size-age state to a larger size-age state, survival after 1 year and 5 years, and detection. Our results show a declining population with low estimates for survival after 1 year and 5 years. The probability for tortoises to move from outside to inside the boundary fence was greater than for tortoises to move from inside the fence to outside. The probability for detecting tortoises differed by size-age state and was lowest for the smallest tortoises and highest for the adult tortoises. The framework for the model can be used to analyze other animal populations where vital rates are expected to vary depending on multiple individual states. The model was incorporated into the manuscript that included several other databases for publication in Wildlife Monographs in 2020 by Berry et al.

During a multi-year demographic study of Agassiz’s desert tortoise (Gopherus agassizii) at the Desert Tortoise Research Natural Area (Natural Area), in the western Mojave Desert, USA, we recorded evidence of evidence of mesocarnivores that commonly prey on desert tortoises on a 7.77 square-kilometer study area. The study area included land inside and outside the fenced boundary of the Natural Area. We recorded locations, condition and recency of sign, and type of sign present at burrows, dens, and den complexes used by desert kit foxes (Vulpes macrotis), coyotes (Canis latrans), American badgers (Taxidea taxus), and bobcats (Lynx rufus). We also recorded scat piles by species using them, amount, and relative ages of the scats. Scats were checked for evidence of desert tortoise remains. Observations of live mesocarnivores were noted also. We compared differences in predator pressure inside and outside the boundary fence of the Natural Area and whether mesocarnivores were a driver for changes in tortoise demography.

These data were acquired from 7 study sites distributed across the range of Gopherus agassizii. Data were collected from 1997 to 2002 as part of three separate studies, although data were not collected at all sites in each year. Radio-transmitters were attached to the carapace of 151 females and VHF radio-telemetry was used to relocate animals to assess reproductive status. Egg production was determined from X-radiographs taken weekly/biweekly intervals (depending on the study) using a portable X-ray machine between April and July or August of each year. In addition, the mean carapace length (MCL) of each tortoise was measured at each time of capture or recapture using calipers (mm). A nesting event was recorded if a female previously observed with eggs was observed without eggs during a subsequent X-ray session.

This dataset provides spatial predictions of clustering and the genotype association index for the Mojave genotype in local species-environment relationships of Desert Tortoises (Gopherus agassizi and Gopherus morafkaii) for individuals in the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space. Inman et al. 2019. Local niche differences predict genotype associations in sister taxa of desert tortoise. Diversity and Distributions. https://doi.org/10.1111/ddi.12927

Data on annual and perennial plants were collected during four survey years (1989, 1993, 1997, and 2012) at a 7.77 sq. km the Desert Tortoise Research Natural Area in the western Mojave Desert as part of a long-term research project on populations and habitat of the threatened desert tortoise (Gopherus agassizii) spanning 34 years. The data collection and analysis involved comparisons of vegetation inside and outside the fenced Desert Tortoise Research Natural Area.

Data on annual and perennial plants were collected during four survey years (1989, 1993, 1997, and 2012) at a 7.77 sq. km the Desert Tortoise Research Natural Area in the western Mojave Desert as part of a long-term research project on populations and habitat of the threatened desert tortoise (Gopherus agassizii) spanning 34 years. The data collection and analysis involved comparisons of vegetation inside and outside the fenced Desert Tortoise Research Natural Area.

These estimated precipitation data were compiled using the WestMap web site (http://www.cefa.dri.edu/Westmap/). We selected pixels on the map shown on their web site that were in the core of our study areas: one near Palm Springs, California and the other at Sugarloaf Mountain in the Tonto National Forest of Arizona. WestMap uses PRISM data to make point measurements of climate data and a digital elevation model of terrain to create estimates of monthly climate elements. Estimates are derived for a 4km grid, for ease in mapping and GIS applications. PRISM is an integrated set of rules, decision making, and calculations designed to imitate the process an expert climatologist would go through when mapping climate data. We were interested in precipitation data for two hydroperiods: winter precipitation (October-March) and summer precipitation (June-September). These two periods are important for desert tortoise ecology since they trigger germination of food plants in the spring and in the summer.