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Application of next-generation sequencing (NGS) to DNA metabarcoding can greatly increase the understanding of predator–prey dynamics and the conflict between wildlife and humans, but remains underutilized for carnivores such as the threatened snow leopard (Panthera uncia). To date, this technique was hindered by the difficulty in discerning closely related caprines (Caprinae). We identified a segment of mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) to differentiate these prey, and used this marker in tandem with a portion of mitochondrial 12S rRNA (MT-RNR1) to determine dietary items in 165 genetically confirmed snow leopard scats from four range countries. Identified prey species consisted of ten medium to large mammals, three small mammals, and two birds. The dominant prey consumed varied by country, with markhor (Capra falconeri) most prevalent in Pakistan, Siberian ibex (C. sibirica) in Mongolia and Kyrgyzstan, and blue sheep (Pseudois nayaur) in China. Livestock comprised 31% of diet occurrences from Pakistan and 15% from Mongolia. Domestic livestock included goat (C. aegagrus hircus), sheep (Ovis aries), bovids (Bos taurus, B. grunniens, and potentially hybrids), and horse (Equus caballus). Protection and management of regionally specific wild prey is crucial for sustaining snow leopard populations, although overall dietary breadth suggests that snow leopards may exploit other species if necessary, including livestock. Additional sampling efforts across seasons, years, regions, and areas with varying degrees of livestock depredation are needed. MT-CO1 in conjunction with MT-RNR1 can be applied to other carnivore diet studies, making it an important tool for conservation and research, particularly in ecosystems with pastoral communities.

The Sichuan snub-nosed monkey (Rhinopithecus roxellana) is an endangered species endemic to China, where the smallest population resides in Shennongjia National Park, Hubei Province. In this study, the genetic diversity of the Sichuan snub-nosed monkeys from two areas, Qianjiaping (QJP) and Dalongtan (DLT) in Shennongjia National Park was evaluated using single nucleotide polymorphisms (SNPs) data derived from restriction site-associated DNA sequencing (RAD-seq). A total of 41,260 SNP loci were found in 29 Sichuan snub-nosed monkey individuals. The genome-wide nucleotide diversity (π) of the Shennongjia population was 0.001842. The genetic differentiation (FST) between the QJP and DLT subpopulations was 0.034. The heterozygosity of individuals from QJP was 0.3475 ± 0.03696 and 0.3148 ± 0.03501 for individuals from DLT. Although the DLT and QJP subpopulations did not show significant genetic differences, genetic differentiation between the two subpopulations was confirmed using Bayesian cluster analysis, neighbor-joining trees and principal component analysis. These results suggest that the Shennongjia population of Sichuan snub-nosed monkey has relatively low genetic diversity at the genomic level. The little genetic differentiation noted between the DLT and QJP subpopulations likely due to natural and anthropogenic barriers which may exacerbate loss of genetic diversity of this endangered subpopulation.

The wild Bactrian camel is one of the world’s rarest and most endangered animals and is facing hybridization threat due to human encroachment. Although captive breeding programs of the wild camel have been undertaken to save it from extinction, to succeed, we need to take into account many factors, e.g., maintain genetic diversity of captive populations similar to that found in wild populations. We applied restriction-site associated DNA sequencing (RAD-Seq) on a captive population in the most important wild camel conservation center in China—Gansu endangered animal conservation center—to investigate the genetic diversity, potential hybridization and inbreeding threats, and thus further guide population management. We sequenced a total of 44 Bactrian camels including 13 wild camels and 31 domestic camels and generated a genome-wide polymorphism dataset with 679,195 high-quality SNPs. This enabled us to detect wild camel individuals with recent genetic introgression from domestic camels. In addition, it revealed that the studied captive population suffers from inbreeding. We therefore suggest practical measures to improve the management of the wild camel and to protect its natural gene pool.

The dhole (Cuon alpinus), a canid, is categorized as Endangered (EN) on the IUCN Red List and is listed as a category II protected species in China. Presence-absence data are extremely rare in western China, and possible existence of remnant populations of dholes is not clear. Here, we document new records of dhole in a protected area in an arid region of the Altun Mountains in Xinjiang Autonomous Region in western China. From a total of 4517 camera-trap days at ten water sites between 2011 and 2013, we obtained seven independent records of dhole at three sites. Additionally, another reserve in Gansu Province which is located near Altun Mountains also recorded the species through camera-trap surveys. Our results indicate that dhole populations exist in the vast arid region of the Altun Mountains, and the current distribution of the dhole might be widespread in western China. We suggest that conservation efforts in this region should focus on minimizing the persecution and poaching of both dholes and their prey.

Group-living animals may need to spend less time being vigilant, consequently, having more time for other important activities such as foraging (i.e., group size effect). Przewalski’s gazelle (Procapra przewalskii) is a group-living social animal, and a study was conducted in Qinghai Province of China during June–August 2006 by using a continuous focal sampling method to investigate the influences of group size, sex, within-group spatial position, and nearest-neighbor distance on individual vigilance level (defined as scanning frequency per minute). Male gazelles were more vigilant than females. The gazelle’s vigilance level decreased with group size (group size effect), but only for females. The individuals at the central positions within a group were less vigilant than those at the peripheral positions, but the nearest-neighbor distance did not have any significant influence on the individual vigilance level. Our results support the hypotheses of group size effect and edge effects, but the sexual difference in vigilance level and in the response to group size effect on vigilance suggests that there may be sexual difference in the function and targets of vigilance behavior of Przewalski’s gazelles, which warrants more investigation, with incorporation of within-group spatial position, to better understand the mechanism underlying the group size effect and edge effect.

Background Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Results Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P

The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P

This is the first time to describe the diversity of denitrifying bacteria in Sanjiangyuan natural reserve in Tibet Plateau by investigating the molecular diversity and phylogenetic analysis of nirK and nosZ genes using PCR-RFLP and sequencing. Four soil samples were collected from alpine meadow communities from over an altitude of 4600 m which had different physicochemical properties by principal component analysis (PCA). For the genes fragment of nirK and nosZ, the diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequenced. A total of 253 nirK clones and 283 nosZ clones were received in four samples, and 78 operational taxonomic units (OTUSs) of nirK and 120 OTUs of nosZ by the restriction enzymes Mspl and Rsal digested. The analysis of environmental factors showed that altitude and C/N ratio in soil may be the key factors to the denitrifying bacteria community. 36 nirK clones and 17 nosZ clones were sequenced, and their levels of nucleotide identity were from 69% to 98% and 57% to 97%, respectively. The phylogenetic tree was constructed using the Clustal W and Mega softwares, and all the sequenced clones could be subdivided into 4 groups. Some of clone sequences were related to the nirK and nosZ genes belonging to three phylogenetic subdivisions (α-, β-and γ subclasses of the Proteobacteria), while most of the clones were closely related to the genes of the uncultured bacteria. The sequence distributions were not clear relating to the sample sites in the tree.

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.

The Przewalski's gazelle, Procapra przewalskii, is now isolated in four local populations on the east and northwest shores of Qinghai Lake. We have been being conducting field surveys in the Qinghai Lake region since 1994. Based on the information we gathered from those surveys, we carried out a Population Viability Analysis (PVA) on the Przewalski's gazelle. We discovered that the Przewalski's gazelle would be extinct within 200 years if no management measures were taken. Since the local population size of the gazelle is small, the most effective measures are to control the wolf density and to reduce the impact of climatic catastrophes. In order to increase the population of the gazelle, we should also take measures to increase primary production of the grassland, to establish a habitat corridor, and to increase the rate of migration of individuals among different local populations.

Background GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. Results A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P Conclusions High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.