Small and fragmented populations are at high risk of local extinction, in part because of elevated inbreeding and subsequent inbreeding depression. A major conservation priority is to identify the mechanisms and extent of inbreeding depression in small populations. The eastern massasauga (Sistrurus catenatus) rattlesnake is listed as Federally Threatened in the United States, having experienced significant habitat fragmentation and concomitant population declines over the past 200 years. Here, we use long-term monitoring of two wild populations of eastern massasaugas in Michigan to estimate the extent of inbreeding in each population, identify mechanisms that generate inbreeding, and test for the impact of inbreeding on fitness. Using targeted genomic data and spatial coordinates of capture locations from over 1000 individuals, we find evidence of inbreeding and link inbreeding to spatial kinship structure within populations, possibly driven by limited dispersal. We reconstruct multigenerational pedigrees for each population to measure reproductive output and use long-term capture-recapture data to estimate individual survival (i.e., the two major components of fitness). We find evidence of inbreeding depression in both fitness metrics. The 5% most inbred individuals are 13.5% less likely to have any surviving offspring and have 11.6% lower annual survival compared to all less inbred individuals. By combining genomics and long-term monitoring data, we are able to link the life history of eastern massasaugas to inbreeding and detect relationships between fitness and inbreeding. These insights provide important conservation context for future management and for understanding how spatial structure can generate inbreeding depression even at fine spatial scales.

Evidence from captive populations indicates that lemurs are particularly vulnerable to toxoplasmosis, a parasitic disease caused by Toxoplasma gondii. In wild populations, however, seroprevalence in lemurs remains low. This may be partly due to their predominantly arboreal behavior, which limits exposure to environmentally transmitted oocysts. Alternatively, or additionally, low seroprevalence could reflect high mortality following infection due to limited evolutionary exposure to the parasite and, consequently, a lack of evolved resistance. In this study, we assess whether the evolutionary history of primates with felids influences susceptibility to T. gondii infection, independent of ecological exposure. Specifically, we predicted that (1) species with greater terrestriality would exhibit higher exposure risk, (2) species longevity would be positively associated with their seroprevalence to T. gondii and (3) primate superfamilies with longer histories of co-occurrence with felids would show higher seroprevalence than Lemuroidea at similar levels of terrestriality and longevity. Serum samples from 435 free-ranging lemurs were tested for T. gondii antibodies and a literature review of T. gondii seroprevalence in free-ranging primates was conducted. The overall seroprevalence in Lemuroidea was 5.4 %, significantly lower than that observed in Ceboidea (11.8 %) and Cercopithecoidea (27.6 %). Notably, seroprevalence in lemurs was lower than expected based on their terrestriality, suggesting that evolutionary isolation from felids may underlie heightened vulnerability. Longevity modifies the risk profile in a lineage-specific way where seroprevalence increases with lifespan in Cercopithecoidea but not for lemurs. Collectively, our findings support the hypothesis that lemurs are immunologically naïve to T. gondii, and in the face of expanding domestic cat populations and increasing habitat fragmentation, the parasite may pose an underrecognized conservation threat.

Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a specific association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.

Osteoarthritis is a common cause of morbidity and mortality in geriatric gazelles. Propionibacterium australiense has been reported as a cause of systemic granulomas in cattle, but there are no descriptions of this bacteria infecting other species nor causing osteoarthritis, to our knowledge. An 8-y-old, castrated male, sand gazelle ( Gazella leptoceros leptoceros) was managed for chronic, intermittent, progressive osteoarthritis of the right tarsus. Serial biopsies revealed pyogranulomatous dermatitis with intralesional bacteria. Serial diagnostic imaging identified osseous and soft tissue proliferation with draining tracts. Treatments over 1 y included broad-spectrum antibiotics, anti-inflammatories, joint debridement, and infusion with platelet-rich plasma and stem cells. Despite therapy, lameness persisted, azotemia developed, and subsequently, the animal was euthanized. On postmortem examination, the periarticular tissue of the right tarsus was markedly expanded by pyogranulomas and fibrosis. Histologically, the synovium, joint capsule, and overlying soft tissues were markedly expanded by pyogranulomas and numerous gram-positive and acid-fast–negative filamentous bacteria surrounded by Splendore–Hoeppli material. Within the joint, there was regionally extensive cartilage ulceration, osteonecrosis, osteolysis, and pannus formation. PCR assay of affected formalin-fixed, paraffin-embedded tissue amplified segments of 16S rRNA and β subunit of bacterial RNA polymerase ( rpoB) genes with 99.7% and 95.6% identity to P. australiense. This bacterium should be considered a differential for chronic pyogranulomatous osteoarthritis in gazelles.

Feline infectious peritonitis (FIP) is a systemic disease in felid species caused by infection with mutated forms of feline coronavirus (FCoV), and outbreaks can devastate exotic felid populations in human care. Feline infectious peritonitis was diagnosed in three of four related juvenile sand cats (Felis margarita) from a single institution over a 6-wk period. Case 1 was a 7-mon-old male found deceased with no premonitory signs. Case 2, an 8-mon-old male (littermate to Case 1), and Case 3, a 6-mon-old male (from a different litter with identical parentage), were evaluated for lethargy and anorexia 1 mon after Case 1. Both exhibited transient anisocoria and progressive lethargy, anorexia, and dehydration despite antibiotic and supportive treatment. Approximately 1 wk after initial presentation, Case 2 was humanely euthanized, and Case 3 was found deceased. Necropsy findings included intrathoracic and/or intra-abdominal lymphadenopathy (3/3 cases), bicavitary effusion (2/3), multifocal tan hepatic and intestinal nodules (1/3), and multifocal yellow renal nodules (1/3). Histologically, all cats had severe pyogranulomatous vasculitis in multiple organs, and the presence of FCoV antigen was confirmed using immunohistochemical staining. Next-generation sequencing of the virus from Case 3's affected kidney demonstrated ∼93% homology to the UG-FH8 virus, a serotype 1 feline alphacoronavirus isolated from Denmark. Future research will focus on comparative viral genomic sequencing with the goals of identifying potential sources of FCoV infection and identifying features that may have contributed to the development of FIP in this species.

Dental disease is a common finding in pygmy slow lorises (Nycticebus pygmaeus) under human care, but the etiology is not fully understood. The small oral cavity in this species can make diagnosis of dental disease difficult. This retrospective study evaluated medical records and diet and husbandry protocols from 18 participating institutions with the objective of describing the signalment, clinical signs, physical exam findings, tooth type, tooth location, diagnostics used, and treatments performed to help guide care for dental disease. In addition, the study aimed to identify potential contributing factors to dental disease in this species. Of 59 animals with medical records evaluated, 42 (71.2%) had dental disease: 19 (44.2%) males, 20 (46.5%) females, and 3 (9.3%) without gender documented. Average age at onset of dental disease was 7.6 yr in males and 9 yr in females. Multiple lorises with dental disease (n = 12; 28.6%) had no premonitory clinical signs, and dental disease was found incidentally on examination. On dental examination, 30 lorises (71.4%) had evidence of gingivitis. In 13 cases skull radiographs were taken, but the majority of images (n = 8; 61.5%) were nondiagnostic for pathologic dental changes. A small proportion of cases with dental abnormalities (n = 4; 9.5%) were diagnosed using computed tomography. In total, 175 teeth were extracted from 31 patients; molars were the most frequently extracted tooth (n = 55; 31.4%). No substantial differences in diets were noted among many of the participating institutions, and not all slow lorises evaluated developed dental disease (n = 17; 28.8%). This retrospective study provides clinical findings on slow loris dental disease and guidance for the veterinary care and management of slow lorises under human care.

Background Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium—CZA; Denver Zoo—DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility. Results We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified  Clostridium perfringens type A (CZA and DZ) and C. colinum  (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis ) associated with susceptibility to clostridial enteritis. Conclusions We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

Among the primate malaria parasites, those found in lemurs have been neglected. Here, six Plasmodium lineages were detected in 169 lemurs. Nearly complete mitochondrial genomes (mtDNA, & AP;6Kb) and apicoplast loci (& AP;6Kb) were obtained from these parasites and other Haemosporida species. Plasmodium spp. in lemurs are a diverse clade that shares a common ancestor with other primate parasites from continental Africa. Time-trees for the mtDNA were estimated under different scenarios, and the origin of the lemur clade coincides with the proposed time of their host species' most recent common ancestor (Lemuridae-Indriidae). A time tree with fewer taxa was estimated with mtDNA + Apicoplast loci. Those time estimates overlapped but were younger and had narrower credibility intervals than those from mtDNA alone. Importantly, the mtDNA + Apicoplast estimates that the clade including the most lethal malaria parasite in humans, Plasmodium falciparum, may have originated with Homininae (African apes). Finally, the phylogenetic congruence of the lemurs and their parasites was explored. A statistically significant scenario identified four cospeciation, two duplications, four transfer (host switches), and zero loss events. Thus, the parasite species sampled in lemurs seem to be radiating with their hosts.

Soft tissue sarcomas (STSs) are common well-described cutaneous neoplasms in many domestic species. Few cutaneous neoplasms have been reported in cervids, other than papilloma virus–induced benign cutaneous fibromas (BCFs). Two wild-caught Alaskan moose ( Alces alces), housed at different North American zoos, were both presented with lameness and a mass. The gross appearance of each mass varied greatly; case 1 had a distinct, exophytic, ulcerated mass near the right carpal joint similar in appearance to a BCF, and case 2 had a pronounced swelling over the left hip. Based on histologic evaluation, both masses were diagnosed as STS. The clinical presentation of these masses included rapid growth and associated lameness; however, gross appearance was markedly different. Histopathology revealed characteristics typical of STS in other species, including spindle-shaped cells arranged in streaming sheets with ovoid nuclei. STS should be included as a differential diagnosis for moose with a cutaneous or subcutaneous soft tissue mass or swelling.

The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex.

Complete medical examinations were performed on 25 wild golden-crowned sifaka (Propithecus tattersalli) from northeastern Madagascar. Each animal received a complete physical examination and weight, body temperature, heart rate, and respiratory rate were documented. Blood samples were collected for packed cell volume, estimated total white blood cell count, serum biochemical profile, fat-soluble vitamin analysis, trace mineral analysis, and Toxoplasma gondii serology. All animals examined were adults and determined to be in good health and body condition. No ectoparasites were observed. Fecal samples were collected for endoparasite examination and bacterial culture; while no endoparasites were observed, fecal samples from two females cultured positive for Bacillus cereus. One male lemur had a positive antibody titer to Toxoplasma gondii immunoglobulin G. These baseline health data provide an important foundation for continued monitoring of this critically endangered species.

The Anthropocene is a major threat to biodiversity worldwide. Human pressures including climate change and emerging infectious diseases are presenting new challenges to wildlife, requiring vigilance and monitoring of wild populations to ensure their persistence. In order to monitor fluctuations in health, baseline data from long-term studies are required. Clinical laboratory data on 80 black-and-white ruffed lemurs (Varecia variegata), derived from the capture of 98 individuals spanning six field seasons are presented. Serum biochemical profiles showed variation between years that remained within published reference intervals for the species, with the exception of total bilirubin in 2008, and creatine kinase and chloride in 2019. Serum trace minerals and fat-soluble vitamin values also fluctuated between years and are within ranges seen in other lemur species. These results, combined with previously published data on ectoparasite load and population genetic diversity, suggest that the Mangevo ruffed lemur population is healthy and can provide important and valuable baseline data for comparisons moving forward.

The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1 , a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus ; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a d N /d S value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.

If gut microbes influence host behavioral ecology in the short term, over evolutionary time, they could drive host niche differentiation. We explored this possibility by comparing the gut microbiota of Madagascar’s folivorous lemurs from Indriidae and Lepilemuridae. Occurring sympatrically in the eastern rainforest, our four, target species have different dietary specializations, including frugo-folivory (sifakas), young-leaf folivory (indri and woolly lemurs), and mature-leaf folivory (sportive lemurs). We collected fecal samples, from 2013 to 2017, and used amplicon sequencing, metagenomic sequencing, and nuclear magnetic resonance spectroscopy, respectively, to integrate analyses of gut microbiome structure and function with analysis of the colonic metabolome. The lemurs harbored species-specific microbiomes, metagenomes, and metabolomes that were tuned to their dietary specializations: Frugo-folivores had greater microbial and metagenomic diversity, and harbored generalist taxa. Mature-leaf folivores had greater individual microbiome variation, and taxa and metabolites putatively involved in cellulolysis. The consortia even differed between related, young-leaf specialists, with indri prioritizing metabolism of fiber and plant secondary compounds, and woolly lemurs prioritizing amino-acid cycling. Specialized gut microbiota and associated gastrointestinal morphologies enable folivores to variably tolerate resource fluctuation and support nutrient extraction from challenging resources (e.g., by metabolizing plant secondary compounds or recalcitrant fibers), perhaps ultimately facilitating host species’ diversity and specialized feeding ecologies.

Freshwater turtle species are suffering from anthropocentric-caused population declines, making preservation of professionally managed populations increasingly important. Turtles under professional care have an increased risk to develop hepatic lipidosis, potentially resulting in early death. Computed tomography can provide an antemortem screening for increased fatty liver composition. A goal of this prospective analytical cross-sectional study was to assess the hepatic attenuation measured as Hounsfield units (HU) in a wild population of a freshwater turtle species, and then compare hepatic HU to freshwater turtles under professional care. Ninety-five wild Blanding's turtles (BT; Emydoidea blandingii) as well as 10 Vietnamese Pond turtles (VPT; Mauremys annamensis) and six Northern Snake-Necked turtles (NSNT; Chelodina oblonga) under professional care underwent CT with quantification of hepatic HU. Hepatic HU were correlated to serum chemistry findings and the presence of follicles was recorded in BT. The mean (+/- SD) hepatic attenuation for 95 wild BT was 97.5 HU +/- 9.6. There were significant differences in hepatic attenuation among VPT, NSNT, and BT, with median HU values (range) of 5.39 HU (-6.45 to 61.50), 71.74 HU (59.44-94.49), and 95.43 HU (74.41-124.56), respectively. Aspartate aminotransferase (AST) values had a weak negative correlation to HU with a coefficient of -0.85 (P < .001). The hepatic attenuation was significantly higher for individuals undergoing folliculogenesis (P = .007). The decreased HU values were significantly negatively correlated with AST values. Findings supported the use of CT as an aid for guiding future management practices in freshwater turtles.

Pronghorn (Antilocapra americana) are native to western North America and are found in 24 Association of Zoos and Aquariums (AZA)-accredited institutions. Acute-phase proteins (APP) are a broad class of proteins that are stimulated in response to inflammation and have been shown to be a sensitive measure of inflammation in equids and ruminants. In this study, blood samples from clinically normal free-ranging and captive populations of pronghorn were analyzed using assays for protein electrophoresis (EPH) and APP, including serum amyloid A (SAA) and haptoglobin (HP), to develop preliminary ranges to gauge potential differences between these populations. Additional samples were taken from clinically abnormal captive pronghorn with facial abscesses. By EPH measurements, albumin: globulin ratio mean and SE were significantly different (P <0.05) with 1.02 (0.08) for captive populations and 1.91 (0.05) for free-ranging populations. Total protein mean and SE were significantly different (P <0.05) for captive and free-ranging populations, respectively 5.6 (0.3) g/dl and 6.9 (0.1) g/dl. Mean and SD of SAA for captive pronghorn were 1.4 (3.2) mg/L, and were significantly different from the free-ranging population, which was below the limits of detection for (P <0.05). There was no difference in HP levels between these groups. In a case study of a pronghorn with facial abscesses, elevated levels of HP, but not SAA, suggested that HP maybe useful in certain disease states. Future studies should explore the use of these biomarkers as tools to monitor general health, prognosis, and subclinical disease.

Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5’ and 3’ untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.