The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.
Gut mycobiota are part of the gut microbiome, typically derived from the host diet and living environment. In this study, we examined the gut mycobiota of three snub-nosed monkeys: Rhinopithecus roxellana, R. bieti, and R. strykeri using next-generation amplicon sequencing targeting the fungal internal transcribed spacer. The alpha diversity indexes of gut mycobiota in R. bieti were significantly higher than R. roxellana and R. strykeri, the beta diversity indicated that R. roxellana and R. bieti had more similar feeding habits. Core mycobiota demonstrated commonalities among the three species and potentially associated with feeding habits. Mycobiota displaying significant differences exhibited the respective characteristics of the host, likely associated with the hosts’ living environment. Among them, animal and plant pathogenic fungi and lichen parasites are potential threats to the survival of snub-nosed monkeys for their pathogenicity to both monkeys and their food plants. Functionally, fungal trophic modes and functional guilds revealed a strong association between gut mycobiota and host diet. We found a higher abundance and more significant correlations with lichen parasitic fungi in R. strykeri than the other two species, indicating potential threats to their foods. Accordingly, this study revealed the basic structures of gut mycobiota of three wild Rhinopithecus species and highlighted the associations between gut mycobiota and their feeding habits and living environments. Furthermore, due to the close connection between fungi and the environment, animals could ingest fungi from their diet; thus, we speculate that gut mycobiota may serve a role in environmental monitoring for wildlife.
The Gansu zokor (Eospalax cansus), a subterranean rodent endemic to the Loess Plateau of China, exhibits remarkable adaptability to hypoxic environments. While gut microbiota are known to regulate lipid metabolism through bile acid (BA) pathways, this phenomenon has not been investigated in subterranean rodents exposed to hypoxia. This study employed 16SrRNA sequencing, targeted analysis of BA metabolites in colonic contents, and assessments of BA and lipid metabolites alongside molecular analyses in the liver and ileum under conditions of acute and chronic hypoxia in Gansu zokors. The results revealed that hypoxia altered the composition of gut microbiota and BA pools in Gansu zokors. Hypoxia-induced changes increased the abundance of gut microbiota associated with BA metabolism, thereby modulating lipid metabolism via farnesoid X receptor (FXR) signaling in the distal ileum and liver cells. Under acute hypoxia, FXR upregulated lipid synthesis and suppressed fatty acid β-oxidation by downregulating the carnitine palmitoyl-transferase1A (CPT1A) expression. Conversely, during chronic hypoxia, particularly under long-term exposure, FXR reduced lipid synthesis and enhanced fatty acid β-oxidation by upregulating acyl-CoA oxidase (ACOX1) expression. In both hypoxic conditions, FXR facilitated lipoprotein metabolism. In summary, this study elucidates that gut microbiota–mediated BA metabolic pathways contribute to the Gansu zokor's ability to maintain lipid metabolic homeostasis and adaptation to hypoxia.
Understanding the density-dependent immune response is an important theme in ecological and evolutionary studies. Animals may elevate their immune response with an increase in population density. There is substantial evidence supporting the density-dependent immune response in some insects, reptiles, and birds, but evidence is still lacking in wild rodents. Here, we tested the density-dependent immune response on Brandt's voles by manipulating their population change under both laboratory (with none or little parasite infection) and field conditions (with strong parasite infection). In the field experiment, we found that the parasite prevalence and infection intensity as well as the IgG levels increased with population density, suggesting evidence of density-dependent immune response. In the lab experiment, Brandt's voles in the high-density group experienced high crowding stress exhibited by a high frequency of locomotion and aggression, and they had a higher IgG level than those in the low-density group, but with no significant difference in parasite infection. Brandt's voles in the field had significantly higher parasite intensity and higher IgG levels than Brandt's voles in the lab. Sheep grazing and rainfall supplmentation increased IgG level but food supplementation had no significant effect on IgG level. Our study confirms density-dependent immune response in Brandt's voles, likely driven by increasing agressive behavior of voles and parasite transmission, and provides novel insight into density-dependent population regulation in small rodents oscillations.
The family Erinaceidae encompasses 27 extant species in two subfamilies: Erinaceinae, which includes spiny hedgehogs, and Galericinae, which comprises silky-furred gymnures and moonrats. Although they are commonly recognized by the general public, their phylogenetic history remains incompletely understood, and several species have never been included in any molecular analyses. Additionally, previous research suggested that the species diversity of Erinaceidae might be underestimated. In this study, we sequenced the mitochondrial genomes of 29 individuals representing 18 erinaceid species using 18 freshly collected tissue and 11 historical museum specimens. We also integrated previously published data for a concatenated analysis. We aimed to elucidate the evolutionary relationships within Erinaceidae, estimate divergence times, and uncover potential underestimated species diversity. Our data finely resolved intergeneric and interspecific relationships and presented the first molecular evidence for the phylogenetic position of Mesechinus wangi, Paraechinus micropus, and P. nudiventris. Our results revealed a sister relationship between Neotetracus and Neohylomys gymnures, as well as a sister relationship between Hemiechinus and Mesechinus, supporting previous hypotheses. Additionally, our findings provided a novel phylogenetic position for Paraechinus aethiopicus, placing it in a basal position within the genus. Furthermore, our study uncovered cryptic species diversity within Hylomys suillus as well as in Neotetracus sinensis, Atelerix albiventris, P. aethiopicus, and Hemiechinus auratus, most of which have been previously overlooked.
This study thoroughly examines biodiversity and aquatic ecosystems across 14 sampled sites within the Shitou River basin by utilizing environmental DNA technology. Through integrated analysis and high-throughput sequencing, the study elucidates a diverse array of biodiversity, encompassing 27 fish species and 341 freshwater benthic macroinvertebrates (FBM) species. Using various biodiversity indices, we found significant differences in diversity and stability across different environments. Regions with more complex habitats had higher species richness and evenness. Further analyses showed complex relationships between diversity metrics for FBM and fish, indicating potential interactions between these groups. The standardized mean score (SMS) was developed to aid in the assessment of water quality. Specifically, SMS scoring revealed that sites STH3, STH4, and STH14 excelled across multiple dimensions, earning an “Excellent” rating, while site STH12 was rated as “Poor” due to subpar performance across several metrics. This project not only enhances current understanding regarding aquatic ecological dynamics but also establishes a strong foundation for detailed environmental evaluation and monitoring, aligned with the priorities of contemporary ecological management and caution.
A species' vulnerability to extinction is influenced by both extrinsic threats (e.g., habitat loss and invasive species) and intrinsic biological traits (such as life-history traits, reproductive mode, and reproductive output). In this study, we investigated the roles of intrinsic biological traits in determining the risk of extinction across 960 oviparous species of non-avian reptiles. Our findings revealed that vulnerability to extinction is negatively correlated with clutch size, but positively correlated with egg size when controlling for body size. Surprisingly, we found that body size alone is not a predictor of extinction risk. Additionally, we observed a nonsignificant relationship between the activity phase and vulnerability to extinction across oviparous species. These results suggest that the increased risk of endangerment in oviparous reptiles may stem from declining population density due to decreasing clutch size and increasing egg mass.
Spatiotemporal interactions between predators and prey are central to maintaining sustainable functioning ecosystems and community stability. For wild ungulates and their predators, livestock grazing is an important anthropogenic disturbance causing population declines and modifying their interactions over time and space. However, it is poorly understood how fine-scale grazing affects the spatiotemporal responses of predators, prey, and their interactions. Two opposing hypotheses describe a dichotomy of possible effects. The human shield hypothesis states that people can protect prey because predators avoid areas with high human-induced mortality risk, whereas in the human competitor hypothesis, humans compete for prey and negatively impact predators through reduced prey availability. We used camera-trapping data from the Gansu Qilianshan National Nature Reserve in Northwest China to measure occupancy, daily activity patterns, and spatiotemporal interactions between snow leopards (Panthera uncia), the dominant predator, and their ungulate prey in areas with contrasting grazing intensities. The results of grazing were consistent with both the human-shield and human-competitor hypotheses, affecting spatiotemporal patterns and interactions of predators and prey. For the primary prey species, blue sheep (Pseudois nayaur), their spatial and temporal patterns were affected by grazing, which led to a reduction in interaction frequencies with snow leopards. For secondary prey, grazing led to reduced interaction frequencies with snow leopards for white-lipped deer (Przewalskium albirostris) and red deer (Cervus yarkandensis), but increased frequencies for alpine musk deer (Moschus chrysogaster). Our results indicate how both competition among livestock and prey and predator or prey avoidance of grazed areas can impact populations and predator–prey interactions. Our findings are relevant to grazing management and snow leopard conservation.
In mammals, temporal and spatial variation in appendage sizes within and among species may be driven by variations in ambient temperature and allometric scaling. Here, we use two decades of morphological data on three rodent species distributed across vast latitudinal gradients in China to estimate temporal and spatial trends of tail, hind-foot, and ear lengths. Further, we test 14 climate variables to identify the critical drivers of these trends and use structural equation modeling (SEM) to analyze whether the effects of climate variables on the appendage lengths are direct or indirect, via effects on body length. Relative to body length, and in contradiction to Allen's rule, all appendage lengths remained unchanged over time and across space. By contrast, absolute appendage lengths increased in one species (Apodemus agrarius) over time and in two species (A. agrarius and Rattus norvegicus) across space; and most of the appendage lengths in the two species were associated with annual mean minimum temperature in the year preceding capture (PreAnnMinTemp). The SEM results suggest that PreAnnMinTemp affected absolute appendage lengths indirectly through body length. In addition, except for tail length in two species and both hind-foot and ear length in one species, absolute appendage lengths scaled allometrically with body length. These results suggest that the distinct temperature–appendage-length patterns among and within species arise from species-specific temperature sensitivities and appendage-specific ontogenetic rates and functions.
The population regulation of animals depends on fertility and survivorship. Hunting can affect population growth through changes in reproduction and survivorship. Understanding these changes in vital rates is crucial for the control of invasive mammals. With the objective to assess the influence of different population removal pressures on the finite population growth rate (λ) of an invasive mammal, this research used demographic data estimated from 922 invasive beavers (Castor canadensis) eradicated from seven areas from Isla Grande de Tierra del Fuego, Argentina. Areas were classified into four removal pressures: higher, high-intermediate, low-intermediate, and lower removal pressure. The hypothesis states that the higher removal pressure produces higher population growth and resilience. Leslie matrix models were used to estimate λ, generation time, damping ratio, stable age distribution, reproductive value, and the sensitivity–elasticity of survivorship and fertility of the females for each removal pressure. The λ and damping ratio increased with the removal pressure, as expected; the inverse occurred with the generation time. The survivorship of the younger age classes was the most sensitive and elastic vital rate regardless of removal pressure, followed by the breeding onset. The fertility was less relevant on λ. The beaver population would depend more on the survival of kits, 1-year-olds, and subadults, than the number of offspring produced. A management strategy is proposed focusing on affecting the survivorship of younger age classes, eliminating first the adult animals and then the younger beavers.
Desmans belong to the subfamily Desmaninae, which are members of the family Talpidae. Desmans and moles show limited sexual dimorphism, making unclear sex discrimination by phenotypic assessment. The Iberian desman (Galemys pyrenaicus) is an endangered species with a severe population decline. Knowledge of sex and sex ratio is essential for conservation and management. Based on these arguments and although previous conventional PCR studies amplifying DBX/DBY genes were relatively successful in sexing the desman, high-resolution sex-specific PCR has been requested. All these reasons encouraged us to develop new species-specific RT-qPCR assays by TaqMan probes to determine the sex in desman, especially with genetic material from non-invasive samples. Accordingly, efficiency, limit of detection (LOD), specificity, and DNA analysis from faeces were verified. The target genes DBX and DBY were amplified with gDNA from both sexes, with Y-chromosome consistently absent in the female. Despite the modest efficiency, regression analysis (R2 > 0.999) indicated a linear range of the DBX and DBY assays extending from 20 to 0.2 ng/µL DNA. LOD analyses estimated that twice as much gDNA was needed in males as in females for DBX detection. Paradoxically, the Y-chromosome required three times as much gDNA as the X-chromosome using a male sample. Therefore, an unexpected dosage imbalance in the genome in favour of the X chromosome was discussed in light of an apparent multicopy nature of the DBX gene and with a sexing success rate of 49.9% of the non-invasive samples, supporting Fisher's principle for the mammalian XX/XY sex system, as expected.
The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24 325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy–Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.
The small-island effect (SIE) has been used to quantify the increase of established non-native species richness with island area but has not yet been applied to explore the dynamics of non-native species abundance, which is important to develop timely mitigation strategies on established populations. Based on field surveys of established populations of the American bullfrog (Lithobates catesbeianus = Rana catesbeiana) across 92 permanent water bodies on 31 islands in the Zhoushan Archipelago, China, we explored the abundance–area relationship (AAR) of the invasive bullfrogs at the island and habitat (i.e., permanent still waters) scales, respectively. We did not detect the non-linear increase of bullfrog abundance with island area in the Zhoushan Archipelago, but found a piecewise trend of the bullfrog abundance with the area of invaded waters. Overall, bullfrogs were more abundant on larger islands, less isolated islands, and in waters with lower densities of native anurans. Our findings indicate that the invasive bullfrogs may have not reached the threshold of rapid increase of population abundance in the Zhoushan Archipelago and highlight the importance of continued close monitoring to prevent future population outbreaks.