These datasets (S2-S3) document the transmission of a bacterial pathogen (Mycoplasma agassizii) between desert tortoises (Gopherus agassizii) experimentally introduced in captivity and were used to create and compare models predicting transmission probability given data on the hosts and their interactions. Dataset S2 includes variables describing the individual tortoises interacting, e.g. id, sex; variables describing the length of their interaction, e.g., number of days cohabitating, hours of direct contact; and variables estimating the infection level (based on data in S3) of infected tortoises involved in the interaction with the focal host. Interaction time and the amount of bacteria present in an infected host were used to calculate “dose” variables that represent the intensity of exposure to the pathogen. These data were used to estimate model parameters for multiple generalized linear models (glm) with predictor variables related to exposure time to an infected host and host characteristics. The response variable or event of interest was the infection status of the exposed tortoise after a period of interaction. Infection status was defined in two ways (described in section 15) and determined using qPCR of tissue samples collected at intervals – the results of which are presented in the S3 dataset. The analyses allowed us to identify interactions that have high transmission likelihood, and so we explored the contact patterns of a wild tortoise population (25 individuals with overlapping or contiguous homeranges) to estimate how frequently high-risk contacts occur (Dataset S4). This dataset includes all interactions (tortoise ids of interacting pair, date & time interaction began, and interaction duration) documented between tortoises fitted with proximity logging devices. Each device detects other devices when tortoises are approximately 10 cm apart and ends an interaction when tortoises have remained further than 10 cm for 1 minute. These data are associated with the following publication: Aiello, C. M., Nussear, K. E., Esque, T. C., Emblidge, P. G., Sah, P., Bansal, S. and Hudson, P. J. (2016), Host contact and shedding patterns clarify variation in pathogen exposure and transmission in threatened tortoise Gopherus agassizii: implications for disease modelling and management. J Anim Ecol, 85: 829–842. doi:10.1111/1365-2656.12511

This product consists of multiple tabular datasets and associated metadata for clinical status, gene transcripts, and lab results related to presence of Mycoplasma spp. in desert reptiles. To better understand immune responses to pathogenic infections, we conducted an experiment to quantify innate and induced immune responses using gene transcript profiles and measured induced antibody levels for Mycoplasma spp. in Mojave Desert tortoises (Gopherus agassizii). Data consists of: - Clinical Status Data - Clinical status of presence or absence of nasal discharge, eroded nares, or labored respiration in 15 captive tortoises classified as naive, exposed, or infected. - Gene Transcript Data - Gene transcription values for 11 genes of interest for 14 adult captive male tortoises and 13 adult wild tortoises in Clark County, Nevada, USA. - Laboratory Data - Disease laboratory results for qPCR and ELISA test for five control, five exposed, and five infected captive adult tortoises and 14 reference wild adult tortoises in Clark County, Nevada, USA.

This product consists of multiple tabular datasets and associated metadata for clinical status, gene transcripts, and lab results related to presence of Mycoplasma spp. in desert reptiles. To better understand immune responses to pathogenic infections, we conducted an experiment to quantify innate and induced immune responses using gene transcript profiles and measured induced antibody levels for Mycoplasma spp. in Mojave Desert tortoises (Gopherus agassizii). Data consists of: - Clinical Status Data - Clinical status of presence or absence of nasal discharge, eroded nares, or labored respiration in 15 captive tortoises classified as naive, exposed, or infected. - Gene Transcript Data - Gene transcription values for 11 genes of interest for 14 adult captive male tortoises and 13 adult wild tortoises in Clark County, Nevada, USA. - Laboratory Data - Disease laboratory results for qPCR and ELISA test for five control, five exposed, and five infected captive adult tortoises and 14 reference wild adult tortoises in Clark County, Nevada, USA.

Clinical signs of health, disease, and trauma were collected as part of a long-term research program on Agassiz’s desert tortoises (Gopherus agassizii) at a 7.77 square km plot at the fenced Desert Tortoise Research Natural Area in the western Mojave Desert, USA. Surveys for health, infectious and non-infectious diseases were initiated in 1993, because of an outbreak of infectious upper respiratory tract disease caused by Mycoplasma agassizii, M. testudineum, and possibly herpesvirus (TeHV2). The disease outbreak was discovered in 1988-1989. Moderate to severe clinical signs of upper respiratory tract disease increased over time on four surveys, from 1993 through 2012. Moderate to severe signs of shell lesions (cutaneous dyskeratosis, fungal involvement) varied significantly by year. Moderate to severe clinical signs of healed, healing or moderate trauma varied from 29.8 to 42.3 percent in all sizes of tortoises. Evidence of trauma was best predicted by size-age class of the tortoises with rates increasing as size-class increased.

Clinical signs of health, disease, and trauma were collected as part of a long-term research program on Agassiz’s desert tortoises (Gopherus agassizii) at a 7.77 square km plot at the fenced Desert Tortoise Research Natural Area in the western Mojave Desert, USA. Surveys for health, infectious and non-infectious diseases were initiated in 1993, because of an outbreak of infectious upper respiratory tract disease caused by Mycoplasma agassizii, M. testudineum, and possibly herpesvirus (TeHV2). The disease outbreak was discovered in 1988-1989. Moderate to severe clinical signs of upper respiratory tract disease increased over time on four surveys, from 1993 through 2012. Moderate to severe signs of shell lesions (cutaneous dyskeratosis, fungal involvement) varied significantly by year. Moderate to severe clinical signs of healed, healing or moderate trauma varied from 29.8 to 42.3 percent in all sizes of tortoises. Evidence of trauma was best predicted by size-age class of the tortoises with rates increasing as size-class increased.

This database contains demographic and movement variables for 158 adult Agassiz's desert tortoises (Gopherus agassizii) translocated from the National Training Center (NTC), Fort Irwin, in the central Mojave Desert, California, in spring of 2008 and monitored through fall of 2018. The tortoises, fitted with radio transmitters, were translocated to plots south of Fort Irwin and followed monthly until fall of 2018, when transmittered were removed, and the project was ended. The database consists of unique identification numbers of the tortoises, sex and size, dates, details of locations, and status of the tortoises.

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 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 data set contains individual adult bighorn sheep entry and exit/censor times for 3 disease states and 2 mortality states: susceptible, infected and recovered and disease-caused death and non-disease related death. These times are used in a time-to-event analysis that employs a mixture model approach to characterize transition rates between states.

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