Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

Polyomaviruses infect a wide variety of mammalian and avian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. Viral metagenomics and general PCR methods were used to detected viral nucleic acid in the samples from a diseased and healthy giant pandas. A novel polyomavirus, the giant panda polyomavirus 1 (GPPyV1) from the nasal cavity of a dead giant panda (Ailuropoda melanoleuca) was characterized. The GPPyV1 genome is 5144 bp in size and reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. Phylogenetic analyses of the large T antigen of the GPPyV1 indicated GPPyV1 belonged to a putative new species within genus Deltapolyomavirus, clustering with four human polyomavirus species. The GPPyV1 VP1 and VP2 clustered with genus Alphapolyomavirus. Our epidemiologic study indicated that this novel polyomavirus was also detected in nasal swabs and fecal samples collected from captive healthy giant pandas. A novel polyomavirus was detected in giant pandas and its complete genome was characterized, which may cause latency infection in giant pandas.

Physiological indexes like blood parameters have been widely used to monitor the health of free-roaming animals. Attempts to reintroduce one of China’s most endangered species, the giant panda (Ailuropoda melanoleuca), have been hampered by a lack of data on its ecology and physiology. We examined three giant pandas’ hematological and blood chemistry parameters in a soft release program and 30 captive giant pandas as controls and determined the reference intervals (RIs) for those blood parameters in the captive animals. Elevation, captivity status and the interaction of those factors were statistically significant for hematologic measures. Release pandas had significantly higher hemoglobin and hematocrit values after they moved to high elevation locations. We also found significant difference in the enzyme parameters between high and low elevation pandas such as higher aspartate aminotransferase, alanine aminotransferase, creatinine kinase, amylase and lower lactate dehydrogenase and alkaline phosphatase. Release pandas also had higher nutrition parameter values such as higher albumin, globulin and creatinine. The RI for blood parameters in our study provides a baseline to monitor the health of captive animals and forms the basis for assessing the health of free-roaming giant pandas in future reintroduction efforts.

As apex predators, felids (Felidae) face unresolved phylogenetic controversies due to their recent rapid speciation and remarkable morphological conservatism. Previous studies, often relying on a limited number of genetic markers, were constrained by insufficient data and conflicting phylogenetic signals, leaving these disputes unresolved. Therefore, establishing a robust phylogenetic framework based on larger-scale genomic data is crucial. This study integrated complete mitogenomes from 37 species representing all major felid genera to characterize genomic diversity, selection pressures, and phylogenetic relationships. Results revealed conserved gene content and arrangement patterns but significant intergenic variation in nucleotide composition, with the light-strand encoded ND6 exhibiting pronounced strand-specific bias. Nucleotide diversity was highest in ND4L (Pi = 0.132) and ATP6 (Pi = 0.131), suggesting their utility as novel markers for species delimitation and population studies. Selection pressure analysis indicated strong purifying selection on cytochrome oxidase subunits (e.g., COX1 Ka/Ks = 0.00327) but relaxed constraints on ATP8 (Ka/Ks = 0.12304). Phylogenies reconstructed from the complete 13PCGs + 2rRNAs dataset (showing high congruence between maximum likelihood and Bayesian methods) clearly delineated Felidae into two primary clades (Pantherinae and Felinae), confirming monophyly of all genera and positioning Neofelis nebulosa as the basal lineage within Pantherinae. Crucially, exclusion of ND6 (12PCGs + 2rRNAs) yielded topologies congruent with the complete 13PCGs + 2rRNAs dataset, whereas single-gene or limited multi-gene datasets produced inconsistent trees (particularly at genus-level nodes). This demonstrates that near-complete mitogenomic data (≥12PCGs + 2rRNAs) are essential for reconstructing robust felid phylogenetic frameworks. Our study provides insights into carnivoran mitogenome evolution.

The poor reproductive capacity of giant pandas significantly hinders the development of captive populations, with 80.88% of adult individuals being unable to successfully become pregnant and deliver offspring. The disturbance of vaginal microbiota has been proven to potentially lead to miscarriage, abortion, and stillbirth in mammals. To elucidate the potential relationship between the vaginal microbiota and the reproductive capacity of giant pandas, we performed high-throughput sequencing of vaginal microbiota at the time of fertilization and conducted comparative analyses based on different pregnancy outcomes. We found that the microbial diversity in the delivery (D) group exceeded that in the non-delivery (ND) group and the vaginal microbial community structure was statistically different between the two groups. The vaginal microbiota in the delivery pandas consisted of unclassified Pseudomonadaceae which was gradually replaced by the Escherichia-Shigella type of vaginal microbiota in the ND group. A function predictions analysis showed that infectious disease, glycan biosynthesis, and metabolism were significantly enriched in the ND group. Additionally, an analysis of the microbial community phenotypic categories indicated that the ND group exhibited a significantly higher abundance of Gram-negative bacteria, facultative anaerobes, potential pathogens, and stress-tolerant species compared to the D group, predominantly driven by the elevated abundance of Escherichia-Shigella. Escherichia-Shigella can be used within LDA and ROC analyses to diagnostically distinguish the vaginal microflora associated with bad pregnancy outcomes during estrus. Our results will help to identify potential pathogens causing reproductive tract diseases, reduce the number of reproductive tract disease infections in pandas, and increase the birth rate of giant pandas in conservation breeding programs.

Managing endangered wildlife in pre-release or semi-wild training programs requires an understanding of how animals balance strict energetic constraints against environmental health risks. We investigated the behavioral and spatial coping mechanisms of giant pandas (Ailuropoda melanoleuca) during semi-wild adaptation training exposed to intense seasonal tick (Ixodes ovatus) parasitism. Integrating high-resolution 3D-GPS telemetry, fine-scale microhabitat architecture mapping, and longitudinal daily tick counts, we evaluated the relative efficacy of behavioral hypoactivity versus microhabitat selection using Generalized Estimating Equations (GEE). During the high-risk summer season, individuals exhibited pronounced baseline behavioral suppression. However, GEE models revealed that fine-scale microhabitat selection—rather than localized movement reduction—was the primary determinant of parasite avoidance. Actively shifting to higher-elevation microhabitats with minimal leaf litter and dense bamboo coverage significantly minimized daily tick burdens. Conversely, remaining sedentary within low-elevation, thick-litter zones yielded the highest predicted parasite loads. These findings demonstrate that physical stillness alone is insufficient to mitigate ectoparasite exposure without access to structural habitat refugia. For conservation and reintroduction programs, providing structurally complex, topographically heterogeneous enclosures is essential. Ensuring access to natural altitudinal gradients empowers managed herbivores to autonomously regulate parasitological risks, thereby enhancing pre-release animal welfare and health.