Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.

Forest musk deer (Moschus berezovskii), one of the world's most endangered ruminants, faces extinction risks, with captive populations additionally threatened by prevalent diseases including digestive and immune disorders. This study employed comparative metagenomic sequencing to analyze intestinal microbiota structure and function between wild populations in Chongqing and Hunan and captive individuals. Wild musk deer exhibited a Pseudomonadota-dominated gut microbiota (significantly higher than captive), enriched in lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, captive groups showed increased abundances of Firmicutes/Bacteroidota, with abnormal proliferation of Escherichia and Clostridium. Alpha and beta diversity analyses revealed significant differences in gut microbial community composition among the three groups, with wild cohorts exhibiting higher diversity than captive groups. Although substantial disparities in microbial abundance existed between the two wild populations due to differential vegetation in their habitats, convergence was observed in core microbial diversity and carbohydrate metabolic functions. Functional analyses have revealed significant divergences in metabolic pathways，Captive deer microbiota was enriched in translation and glycan metabolism pathways, while wild populations exhibited superior enrichment in immune regulation and environmental sensing pathways. This research provides a theoretical foundation for optimizing wild conservation strategies and developing scientifically informed feeding regimens for captive Moschus berezovskii.

The tufted deer (Elaphodus cephalophus), a Near-Threatened (NT) species endemic to China and Myanmar, requires robust genetic data for effective conservation. However, the genetic landscape of key populations, such as those in Chongqing, remains poorly understood. This study aimed to comprehensively evaluate the genetic diversity, population structure, gene flow, and demographic history of tufted deer across this critical region. We analyzed mitochondrial DNA (mtDNA) from 46 non-invasively collected fecal samples from three distinct populations: Jinfo Mountain (JF, n = 13), Simian Mountain (SM, n = 21), and the Northeastern Mountainous region (NEM, n = 12). Genetic variation was assessed using the cytochrome b (Cyt b) and D-loop regions, with analyses including F_st, gene flow (N_m), neutrality tests, and Bayesian Skyline Plots (BSP). Our results revealed the highest genetic diversity in the SM population, establishing it as a genetic hub. In contrast, the JF population exhibited the lowest diversity and significant genetic differentiation (>0.23) from the SM and NEM populations, indicating profound isolation. Gene flow was substantial between SM and NEM but severely restricted for the JF population. Demographic analyses, including BSP, indicated a long history of demographic stability followed by a significant expansion beginning in the Middle to Late Pleistocene. We conclude that the SM/NEM metapopulation serves as the genetic core for the species in this region, while the highly isolated JF population constitutes a distinct and vulnerable Management Unit (MU). This historical demographic expansion is likely linked to climatic and environmental changes during the Pleistocene, rather than recent anthropogenic factors. These findings underscore the urgent need for a dual conservation strategy: targeted management for the isolated JF population and the establishment of ecological corridors to connect the Jinfo Mountain and Simian Mountain populations, ensuring the long-term persistence of this unique species.

DNA methylation is a common epigenetic modification of DNA levels in the genome of eukaryotic cells, and an aberrant elevation of DNA methylation in gene promoter regions can inhibit gene expression. DNA methyltransferases (DNMTs) are involved in genomic DNA methylation, divided into maintenance DNA methyltransferases and de novo methylases, which are expressed to different degrees in the testis and ovaries. 5-aza-2′-deoxycytidine (5-aza-dC) is a cytidine analog with a strong methylation inhibition. In this experiment, medaka fish fries were treated with 5-aza-dC at 0 μg/L, 50 μg/L, and 100 μg/L. It was found that 100 g/L concentration of 5-aza-dC inhibited both body length and body weight of the adult fish, while 50 g/L concentration had no significant difference. In addition, paraffin section observation and gonad index statistics showed that after 100 g/L concentration of 5-aza-dC treatment, the gonad index of female fish increased significantly, but the gonad index of male fish had no significant difference. And the development of sperms and ovaries was normal without significant difference. Finally, we found that 5-aza-dC not only significantly decreased the transcription levels of dnmt1 and dnmt3bb.1, but also significantly increased the expression levels of female-related genes such as foxl2, cyp19a1 and wnt4, and significantly decreased the expression levels of male-related genes such as dmrt1, sox9a and amh. The DNA methylation patterns of foxl2 and dmrt1 genes were altered. This work provides more references for understanding the mechanism of DNA methylation affecting sex determination in fish.

Effective conservation and management of the endangered tufted deer (Elaphodus cephalophus) necessitate genetic diversity research. This study systematically assessed the genetic diversity, population structure, gene flow, and demographic history of three representative tufted deer populations in Chongqing, China (Jinfo Mountain, Simian Mountain, Northeastern Mountainous area) using combined mitochondrial Cytochrome b (Cyt b) gene and D-loop region analysis. Our findings reveal the D-loop region demonstrates significantly higher genetic variability and a faster mutation rate than Cyt b. The Simian Mountain population consistently displayed the highest haplotype diversity, suggesting its role as a genetic diversity hotspot and crucial hub for regional gene flow. Haplotype network analysis showed frequent gene exchange between Simian Mountain and Northeastern Mountainous populations, while the Jinfo Mountain population exhibits significant genetic isolation, likely due to unique topographical features. Historical demographic analyses suggest a likely slow expansion, with evidence for recent population expansion despite concurrent regional genetic isolation. This study underscores the critical importance of multi-scale genetic markers for deciphering species’ evolutionary histories and provides essential groundwork for tufted deer conservation. We recommend prioritizing Simian Mountain conservation, enhancing Jinfo Mountain genetic management, and maintaining regional population connectivity through ecological corridors and continuous monitoring.

Reeves’ muntjac (Muntiacus reevesi Ogilby, 1839) is a small deer species native to China, primarily residing in the mountainous regions of the southeastern part of the country. In this study, the mitochondrial genome of a Reeves’ muntjac specimen from Chongqing, southeastern China, was sequenced. The genome consists of 16,356 base pairs (GenBank: PP506676), including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, OL, and control region. Phylogenetic analysis disclosed significant genetic differences between the Reeves’ muntjac from Chongqing and those previously reported, indicating that its population may possess rich genetic diversity or there might be undiscovered, geographically isolated groups.