Monitoring population connectivity to inform management is especially important in regions at the very edges of wilderness where native fauna and flora face habitat reduction, degradation, and fragmentation. One such region is the Ivanpah valley along the California/Nevada border, where development (i.e., solar facilities, recreational utility vehicle use) continues to encroach on the habitat of its inhabitants, including the iconic Mojave Desert tortoise, Gopherus agassizi. A long-lived, elusive animal, this species poses an array of challenges to monitoring direct movement, including the challenging terrain in which it resides and the fact that individuals can spend as much as 95 percent of their time in burrows. Thus, genetic monitoring of gene flow and population structure can be an ideal complement to direct monitoring of tortoise movement. Our group has previously evaluated the spatial population genetic structure of the tortoise in the Ivanpah region using a dataset of 299 individuals sampled between 2011 and 2019 and genotyped at 20 microsatellite loci (Dutcher et al., 2020). We found support for historical gene flow with isolation-by-resistance and suggested that connectivity may have been reduced by a railway and highway bisecting the region. We continued to follow up on these findings, collecting additional samples and developing a set of 125 high-throughput microsatellite loci designed specifically for G. agassizi. This data release contains multilocus genotypes collected by high-throughput genotyping for 722 tortoises collected in the region and will be used to explore fine-scale population genetic dynamics, reconstruct pedigrees, and infer movement patterns.

These data show the multilocus genotypes, as well as extraction and sample genotype quality assessments for desert tortoise (Gopherus agassizii) scat samples.

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

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

These data include environmental covariates used to develop species distribution models for Gopherus agassizii and Gopherus morafkai, along with PCA-reduced environmental covariates used to explore local species-environment relationships within a subregion of the ectone between the two species. We also provide the genotype association used to test the mapped clusters of multiscale geographically weighted regression coefficients against models of (i) a geographically-based taxonomic designation these two sister species, and (ii) an environmental ecoregion designation. These data support the following publication: 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

These data include environmental covariates used to develop species distribution models for Gopherus agassizii and Gopherus morafkai, along with PCA-reduced environmental covariates used to explore local species-environment relationships within a subregion of the ectone between the two species. We also provide the genotype association used to test the mapped clusters of multiscale geographically weighted regression coefficients against models of (i) a geographically-based taxonomic designation these two sister species, and (ii) an environmental ecoregion designation. These data support the following publication: 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

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

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.

These data show multilocus genotypes, banding age, and territory for coastal cactus wrens (Campylorhynchus brunneicapillus) sampled in coastal Southern California between 2009 and 2019.