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.

To improve our understanding of health and immune function in tortoises, we evaluated both standard blood diagnostic (body condition, hematologic, plasma biochemistry values, trace elements, plasma proteins, vitamin A levels) and gene transcription profiles in 21 adult tortoises (11 clinically abnormal; 10 clinically normal) from Clark County, NV, USA. Necropsy and histology evaluations from clinically abnormal tortoises revealed multiple physiological complications, with moderate to severe rhinitis or pneumonia being the primary cause of morbidity in all but one of the examined animals. Improved methods for health assessments are an important element of monitoring tortoise population recovery and can support the development of more robust diagnostic measures for ill animals, or individuals directly impacted by disturbance.

To improve our understanding of health and immune function in tortoises, we evaluated both standard blood diagnostic (body condition, hematologic, plasma biochemistry values, trace elements, plasma proteins, vitamin A levels) and gene transcription profiles in 21 adult tortoises (11 clinically abnormal; 10 clinically normal) from Clark County, NV, USA. Necropsy and histology evaluations from clinically abnormal tortoises revealed multiple physiological complications, with moderate to severe rhinitis or pneumonia being the primary cause of morbidity in all but one of the examined animals. Improved methods for health assessments are an important element of monitoring tortoise population recovery and can support the development of more robust diagnostic measures for ill animals, or individuals directly impacted by disturbance.

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

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

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.

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.

This work is part of a study of the immunological effects of exposure to alternative flame retardants in avian species. For the pathology portion of the study, spleens and bursas from American kestrels (Falco sparverius) exposed by egg injection to varying doses of short-chain chlorinated paraffins (SCCPs) and the flame retardant TBBPA-BDBPE were examined microscopically for architectural and cellular abnormalities. At euthanasia, spleen and bursa of Fabricius were collected and fixed in 10% neutral buffered formalin for histopathological assessment. Slides were processed and stained with hematoxalin and eosin as per standard procedure (Luna 1968). Quantitative and qualitative B and T cell parameters were assessed by light microscopy. Specifically, variables assessed included the following: spleen: total area; number, thickness and area of peri-arteriolar lymphoid sheaths; number and diameter of lymphoid follicles; bursa: follicular and medullary area; cellular density; apoptosis; heterophil infiltration; presence of follicular cysts. Evaluation of the architecture and cellular population of immune organs will shed light on potential functional immunological effects of exposure that may lead to increased susceptibility to infectious disease or affect normal growth and development of the chick. (Luna LG. 1968. Manual of histologic staining methods of the armed forces institute of pathology, 3rd edn. McGraw-Hill, New York, NY.)