Reliability, clinical performance and trending ability of a pulse oximeter and pulse co-oximeter, in monitoring blood oxygenation, at two measurement sites, in immobilised white rhinoceros (Ceratotherium simum).

BACKGROUND: Monitoring blood oxygenation is essential in immobilised rhinoceros, which are susceptible to opioid-induced hypoxaemia. This study assessed the reliability, clinical performance and trending ability of the Nonin PalmSAT 2500 A pulse oximeter's and the Masimo Radical-7 pulse co-oximeter's dual-wavelength technology, with their probes placed at two measurement sites, the inner surface of the third-eyelid and the scarified ear pinna of immobilised white rhinoceroses. Eight white rhinoceros were immobilised with etorphine-based drug combinations and given butorphanol after 12 min, and oxygen after 40 min, of recumbency. The Nonin and Masimo devices, with dual-wavelength probes attached to the third-eyelid and ear recorded arterial peripheral oxygen-haemoglobin saturation (SpO2) at pre-determined time points, concurrently with measurements of arterial oxygen-haemoglobin saturation (SaO2), from drawn blood samples, by a benchtop AVOXimeter 4000 co-oximeter (reference method). Reliability of the Nonin and Masimo devices was evaluated using the Bland-Altman and the area root mean squares (ARMS) methods. Clinical performance of the devices was evaluated for their ability to accurately detect clinical hypoxemia using receiver operating characteristic (ROC) curves and measures of sensitivity, specificity, and positive and negative predictive values. Trending ability of the devices was assessed by calculating concordance rates from four-quadrant plots. RESULTS: Only the Nonin device with transflectance probe attached to the third-eyelid provided reliable SpO2 measurements across the 70 to 100% saturation range (bias - 1%, precision 4%, ARMS 4%). Nonin and Masimo devices with transflectance probes attached to the third-eyelid both had high clinical performance at detecting clinical hypoxaemia [area under the ROC curves (AUC): 0.93 and 0.90, respectively]. However, the Nonin and Masimo devices with transmission probes attached to the ear were unreliable and provided only moderate clinical performance. Both Nonin and Masimo devices, at both measurement sites, had concordance rates lower than the recommended threshold of ≥ 90%, indicating poor trending ability. CONCLUSIONS: The overall assessment of reliability, clinical performance and trending ability indicate that the Nonin device with transflectance probe attached to the third-eyelid is best suited for monitoring of blood oxygenation in immobilised rhinoceros. The immobilisation procedure may have affected cardiovascular function to an extent that it limited the devices' performance.

GUT MICROBIOME DIVERSITY OF THREE RHINOCEROS SPECIES IN EUROPEAN ZOOS.

The wild rhinoceros populations have declined drastically in the past decades because the rhinoceros are heavily hunted for their horns. Zoological institutions aim to conserve rhinoceros populations in captivity, but one of the challenges of ex situ conservation is to provide food sources that resemble those available in the wild. Considering that the mammalian gut microbiota is a pivotal player in their host's health, the gut microbiota of rhinoceros may also play a role in the bioavailability of nutrients. Therefore, this study aims to characterize the fecal microbiome composition of grazing white rhinoceros (WR; Ceratotherium simum) and greater one-horned rhinoceros (GOHR; Rhinoceros unicornis) as well as the browsing black rhinoceros (BR; Diceros bicornis) kept in European zoos. Over the course of 1 yr, 166 fecal samples in total were collected from 9 BR (n = 39), 10 GOHR (n = 56), and 14 WR (n = 71) from 23 zoological institutions. The bacterial composition in the samples was determined using 16S rRNA gene Illumina sequencing. The fecal microbiomes of rhinoceros clustered by species, with BR clustering more distantly from GOHR and WR. Furthermore, the data report clustering of rhinoceros microbiota according to individual rhinoceros and institutional origin, showing that zoological institutions play a significant role in shaping the gut microbiome of rhinoceros species. In addition, BR exhibit a relatively higher microbial diversity than GOHR and WR. BR seem more susceptible to microbial gut changes and appear to have a more diverse microbiome composition among individuals than GOHR and WR. These data expand on the role of gut microbes and can provide baseline data for continued efforts in rhinoceros conservation and health status.

Rhinoceros horn mineral and metal concentrations vary by sample location, depth, and color.

Poaching is again driving rhinos to the brink of extinction due to the demand for rhino horn products consumed for cultural, medicinal, and social purposes. Paradoxically, the same horn for which rhinos are killed may contain valuable clues about the species' health. Analyses of horn composition could reveal such useful bioindicators while elucidating what people actually ingest when they consume horn derivatives. Our goals were to quantify minerals (including metals) in rhino horn and investigate sampling factors potentially impacting results. Horns (n = 22) obtained during necropsies of white (n = 3) and black (n = 13) zoo rhinos were sampled in several locations yielding 182 specimens for analysis. Initial data exposed environmental (soil) contamination in the horn's exterior layer, but also confirmed that deep (≥ 1 cm), contaminant-free samples contained measurable concentrations of numerous minerals (n = 18). Of the factors examined in deep samples, color-associated mineral differences were the most profound with dark samples higher in zinc, copper, lead, and barium (p < 0.05). Our data demonstrate that rhino horns contain both essential and potentially toxic minerals that could be relevant to rhino health status, but low concentrations make their human health benefits or risks unlikely following consumption.

Poaching pressure on African rhinos is still at an all-time high.

The decrease in African rhino poaching incidents since 2015 has prompted many to praise the effectiveness of anti-poaching efforts. To test the validity of this statement, we calculated how far poachers moved on average from 2007 to 2022 to find a rhino in the context of the dwindling rhino densities. These calculations demonstrate that the total poaching pressure has remained persistently high since 2013. Given the concurrently declining arrest rates, our results show that the rhino protection practices of the past decade have been insufficient. Instead, we propose that rhinos can best be protected in small and well-monitored "safe havens" while focusing on long-term rhino horn demand reduction.

52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.

The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.

Inter-annual variation in the microplastics abundance in feces of the Baird's tapir (Tapirus bairdii) from the Selva Maya, México.

Microplastics (MPs) are found in a wide range of ecosystems, from the Arctic to the deep ocean. However, there is no data on their presence in terrestrial mammals that inhabit the Selva Maya. The aim of this study is to detect the presence of MPs in the feces of the Baird's tapir (Tapirus bairdii) from the region of Calakmul, located in the Yucatan Peninsula, Mexico. We analyzed 129 fecal samples collected during 2017 and 2018, obtaining 57 and 72 samples during the rainy and dry seasons respectively. Sixty-eight percent of the samples contained 743 MPs with a mean of 19.3 ± 28.1 MPs/kg of dry weight (DW) feces in both years. An inter-annual variation in the average abundance of microplastic was observed during the two-year period (2017-2018), with a 72 % increase in these plastic particles in feces. Fourteen polymers were identified, with ethylene vinyl acetate (EVA), polypropylene (PP) and polyester (PES) being the most abundant during both years. Although the effects of MPs on the health of tapirs are not known, their presence is cause for concern. There is an urgent need for the implementation of appropriate plastic waste management programs in communities of the Selva Maya to diminish the consumption of MPs in species including humans where they pose a significant risk to health. ENVIRONMENTAL IMPLICATIONS: The use of plastics worldwide is increasing every day, so the presence of microplastics is and will continue to be a major environmental problem. It is known that contaminants can adhere to plastics, making them hazardous materials. Microplastics can contaminate remote areas such as Biosphere Reserves. Terrestrial species such as the tapir can ingest microplastics, putting their health at risk. Knowing the dispersion of microplastics is very important in order to manage them properly, taking into account their emission sources and type of polymer.

Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov.

Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.

ONT read assembly of the black rhino genome.

OBJECTIVES: The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo's often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced and assembled the genome of a captive male black rhino using ONT sequencing data only. DATA DESCRIPTION: This work produced over 100 Gb whole genome sequencing reads from whole blood. These were assembled into a 2.47 Gb draft genome consisting of 834 contigs with an N50 of 29.53 Mb. The genome annotation was lifted over from an available genome annotation for black rhino, which resulted in the retrieval of over 99% of gene features. This new genome assembly will be a valuable resource in for conservation genetic research in this species.

CT based 3D reconstruction of the forefoot's blood supply in a white rhinoceros.

BACKGROUND: The white rhinoceros (Ceratotherium simum) is close to extinction, listed as "Near Threatened", with a decreasing population on the Red List of Threatened Species of the International Union for Conservation of Nature. In at least 50% of the specimens in captivity, podiatric diseases, such as osteitis, osteomyelitis, chip fractures, enthesophytes, fractures and osteoarthritis were found during necropsy. These osteal deformations cause further pathogenic alterations in the soft tissues, particularly in the digital cushion. The literature provides good description of the skeleton of the rhino's limbs, but similar for the vascular system is non-existent. In order to recognize the symptoms in an early state and for a successful surgical treatment, precise knowledge of the vascular anatomy is essential. The purpose of our study was to provide detailed anatomical description of the blood supply of the digits and that of the digital cushion. RESULTS: The blood supply of the distal foot, digits and digital cushions were perfectly visible on the reconstructed and coloured 3D models. The deep palmar arch provided not only the blood supply to the digits but had a palmaro-distal running branch which developed a trifurcation proximal to the proximal sesamoid bones of the third digit. Two of its branches participated in the blood supply of the digits' proximal palmar surface, while the major branch supplied the digital cushion from proximal direction. CONCLUSIONS: Our findings show a unique blood supply: the main vessels of the digital cushion stem both directly from the deep palmar arch and from the digits' own arteries. The detailed description of vessels may be useful in planning surgery of the region and also in cases where the veins of the ear are not accessible.

How can research on modern and fossil bones help us build more resistant columns?

Bone is an economical material. Indeed, as moving a heavy skeleton is energetically costly, the vertebrate skeleton is adapted to maximise resistance to the stresses imposed with a minimum amount of material, so that bone tissue is deposited where it is needed. Using bone as a source of inspiration should therefore reduce the manufacturing cost (both financial and ecological) and increase the strength (and lifespan) of bioinspired (BI) structures. This study proposes to investigate which adaptive features of the outer shape and inner structure of bone, related to compressive strength, could be used to build BI support structures. To do so, we explain the choice of the bones to be analysed and present the results of the biomechanical analyses (finite element analysis) carried out on virtual models built from the structures of the different bone models and of the mechanical tests carried out on 3D-printed versions of these models. The compressive strength of these direct bone BI columns was compared with each other, and with those of a conventional filled cylindrical column, and of a cylindrical column whose internal structure is BI from the radius of the white rhinoceros. The results of our comparative analyses highlight that the shape of long bones is less effective than a cylinder in resisting compression but underline the relevance in designing BI cylindrical columns with heterogeneous structures inspired by the radius of the white rhinoceros and the tibia of the Asian elephant, and raise the interest in studying the fossil record using the radius of the giant rhinocerotoidParaceratherium.

Rhinoceros beetle (Trypoxylus dichotomus) cuticular hydrocarbons contain information about body size and sex.

Japanese rhinoceros beetle (Trypoxylus dichotomus) males have exaggerated horns that are used to compete for territories. Larger males with larger horns tend to win these competitions, giving them access to females. Agonistic interactions include what appears to be assessment and often end without escalating to physical combat. However, it is unknown what information competitors use to assess each other. In many insect species chemical signals can carry a range of information, including social position, nutritional state, morphology, and sex. Specifically, cuticular hydrocarbons (CHCs), which are waxes excreted on the surface of insect exoskeletons, can communicate a variety of information. Here, we asked whether CHCs in rhinoceros beetles carry information about sex, body size, and condition that could be used by males during assessment behavior. Multivariate analysis of hydrocarbon composition revealed patterns associated with both sex and body size. We suggest that Rhinoceros beetles could be communicating information through CHCs that would explain behavioral decisions.

Dehorning Does Not Alter the Stress Response in Southern White Rhinoceroses (Ceratotherium simum simum) during Transport: A Preliminary Investigation.

Translocation and dehorning are common and important practices for rhinoceros management and conservation. It is not known if dehorning causes a stress response or negatively affects rhinoceroses during transport. Twenty-three subadult wild Southern white rhinoceros (Ceratotherium simum simum) bulls were immobilized and translocated >280 km for population management reasons. Ten animals were dehorned at capture, and 13 animals were transported without dehorning. For transport, five dehorned and six nondehorned rhinoceroses were sedated with azaperone (62.38±9.54 µg/kg) and five dehorned and seven nondehorned rhinoceroses with midazolam (64.61±9.28 µg/kg). Blood samples were collected at capture, start of transport, and after 6 h of transport. Measurements included 10 physiologic variables: hematocrit, total serum protein, creatine kinase (CK), aspartate aminotransferase, gamma-glutamyl transferase (GGT), creatinine, urea, cholesterol, ß-hydroxybutyrate, and glucose; and four stress response variables: cortisol, epinephrine, neutrophil-to-lymphocyte ratio, and leukocyte coping capacity. Using a linear mixed model, CK and GGT were higher in dehorned compared with nondehorned rhinoceroses. There were no significant differences in the other variables between the two groups. The likely cause of these differences is that dehorned animals spent more time in the crate before the start of transport than nondehorned rhinoceroses (3:11±0:54 h vs. 1:12±0:56 h, P<0.001). These results indicate that dehorning does not negatively alter the white rhinoceros' physiologic and stress responses during translocation, supporting its use for antipoaching measures.

Vesicular stomatitis virus in two species of rhinoceros at a California zoological park.

OBJECTIVE: To describe an outbreak of vesicular stomatitis virus (VSV) in southern white rhinoceros (SWR; Ceratotherium simum simum) and greater one-horned rhinoceros (GOHR; Rhinoceros unicornis) at a safari park in San Diego, CA, from May to September 2023. ANIMALS: 21 SWR and 5 GOHR in professionally managed care. METHODS: Rhinoceros of both species presented with a range of clinical signs and severities. Lesion locations were categorized as cutaneous (coronary bands, heels and soles, limbs, ventrum, neck folds, and ears) and mucocutaneous (lips, nostrils, mucous membranes of the oral cavity, and vulva). Clinical signs included lethargy, lameness, difficulty with prehension, hyporexia to anorexia, and hypersalivation. Severely affected rhinoceros had clinical pathology findings consistent with systemic inflammation. RESULTS: Vesicular stomatitis New Jersey virus was confirmed via PCR from swabs of lesions in 10/26 (38%) rhinoceros. Of these 10 confirmed cases, 9 (90%) were SWR and 1 (10%) was a GOHR. A further 6/26 (24%) were considered probable cases, and 10/26 (38%) were considered suspect cases based on clinical signs, but the inability to appropriately sample due to the housing environment precluded confirmation. Histopathology samples from 3 rhinoceros were consistent with VSV, and viral RNA was localized in histologic lesions via RNA in situ hybridization for 1 case. All rhinoceros survived infection despite severe systemic illness in 2 animals. CLINICAL RELEVANCE: This case series describes the clinical appearance and progression of VSV in 2 rhinoceros species. To the authors' knowledge, this is the first report of VSV in a rhinoceros.

New materials of plesiacerathere (Perissodactyla, Rhinocerotidae) from the late Early Miocene of Northern China.

As a member of Aceratheriinae, the genus Plesiaceratherium in Europe is widely distributed and highly diverse. However, only one species of Plesiaceratherium (i.e., P. gracile) exists in China with a discontinuous distribution range. Recently, we have discovered new materials of Plesiaceratherium in the lower layers of the Zhang'enbao Formation exposed in Miaoerling in Tongxin County, China. The new materials are well-preserved and can be separated from other Plesiaceratherium species by the following combination of features: the long and generally flat skull, with closed frontoparietal crests; the deep nasal notch at the level of P4; the high supraorbital margin, with its anterior margin at the level of the M1/M2 boundary; the medium-sized upper I1, with an oval abraded surface; the semi-molarized upper premolars with the protocone and hypocone joined by a lingual bridge; the strong constrictions of protocone on the upper molars; the absent buccal cingulum on upper cheek teeth; the cheek teeth are covered by cement on the buccal walls; the convex base of mandibular corpus; the inclined backward ramus; and the mandibular foramen above the teeth neck. Based on the combination of characteristics and phylogenetic analysis, we herein establish the new species as Plesiaceratherium tongxinense sp. nov. living in the late Early Miocene. Phylogenetic analysis reveals that P. tongxinense is in the basal position of the genus Plesiaceratherium, providing more detailed morphological characteristics of the plesiaceratheres.

Effects of Butorphanol on Respiration in White Rhinoceros (Ceratotherium simum) Immobilized with Etorphine-Azaperone.

This article reports on respiratory function in white rhinoceros (Ceratotherium simum) immobilized with etorphine-azaperone and the changes induced by butorphanol administration as part of a multifaceted crossover study that also investigated the effects of etorphine or etorphine-butorphanol treatments. Six male white rhinoceros underwent two immobilizations by using 1) etorphine-azaperone and 2) etorphine-azaperone-butorphanol. Starting 10 min after recumbency, arterial blood gases, limb muscle tremors, expired minute ventilation, and respiratory rate were evaluated at 5-min intervals for 25 min. Alveolar to arterial oxygen gradient, expected respiratory minute volume, oxygen consumption, and carbon dioxide production were calculated. Etorphine-azaperone administration resulted in hypoxemia and hypercapnia, with increases in alveolar to arterial oxygen gradient, oxygen consumption, and carbon dioxide production, and a decrease in expired minute ventilation. Muscle tremors were also observed. Intravenous butorphanol administration in etorphine-azaperone-immobilized white rhinoceros resulted in less hypoxemia and hypercapnia; a decrease in oxygen consumption, carbon dioxide production, and expired minute ventilation; and no change in the alveolar to arterial oxygen gradient and rate of breathing. We show that the immobilization of white rhinoceros with etorphine-azaperone results in hypoxemia and hypercapnia and that the subsequent intravenous administration of butorphanol improves both arterial blood oxygen and carbon dioxide partial pressures.

The impact of induced pluripotent stem cells in animal conservation.

It is widely acknowledged that we are currently facing a critical tipping point with regards to global extinction, with human activities driving us perilously close to the brink of a devastating sixth mass extinction. As a promising option for safeguarding endangered species, induced pluripotent stem cells (iPSCs) hold great potential to aid in the preservation of threatened animal populations. For endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni), supply of embryos is often limited. After the death of the last male in 2019, only two females remained in the world. IPSC technology offers novel approaches and techniques for obtaining pluripotent stem cells (PSCs) from rare and endangered animal species. Successful generation of iPSCs circumvents several bottlenecks that impede the development of PSCs, including the challenges associated with establishing embryonic stem cells, limited embryo sources and immune rejection following embryo transfer. To provide more opportunities and room for growth in our work on animal welfare, in this paper we will focus on the progress made with iPSC lines derived from endangered and extinct species, exploring their potential applications and limitations in animal welfare research.

Phylogenetic congruence of Plasmodium spp. and wild ungulate hosts in the Peruvian Amazon.

Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%, 1/2). We performed PCR-based analysis of blood samples from 47 ungulates of five different species collected during subsistence hunting by an indigenous community in the Peruvian Amazon. We detected Plasmodium malariae/brasilianum lineage in a sample from red-brocket deer. However, no parasite DNA was detected in collared peccary (Pecari tajacu; 0.0%, 0/10), white-lipped peccary (Tayassu pecari; 0.0%, 0/15), and tapir (Tapirus terrestris; 0.0%, 0/11). Concordant phylogenetic analyses suggested a possible co-evolutionary relationship between the Plasmodium lineages found in American deer and their hosts.

Antemortem detection of Mycobacterium bovis in nasal swabs from African rhinoceros.

Mycobacterium bovis (M. bovis) infection has been identified in black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros populations in Kruger National Park, South Africa. However, it is unknown whether M. bovis infected rhinoceros, like humans and cattle, can shed mycobacteria in respiratory secretions. Limited studies have suggested that rhinoceros with subclinical M. bovis infection may present minimal risk for transmission. However, recent advances that have improved detection of Mycobacterium tuberculosis complex (MTBC) members in paucibacillary samples warranted further investigation of rhinoceros secretions. In this pilot study, nasal swab samples from 75 rhinoceros with defined infection status based on M. bovis antigen-specific interferon gamma release assay (IGRA) results were analysed by GeneXpert MTB/RIF Ultra, BACTEC MGIT and TiKa-MGIT culture. Following culture, speciation was done using targeted PCRs followed by Sanger sequencing for mycobacterial species identification, and a region of difference (RD) 4 PCR. Using these techniques, MTBC was detected in secretions from 14/64 IGRA positive rhinoceros, with viable M. bovis having been isolated in 11 cases, but not in any IGRA negative rhinoceros (n = 11). This finding suggests the possibility that MTBC/M. bovis-infected rhinoceros may be a source of infection for other susceptible animals sharing the environment.

Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution.

Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome.

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.