Distribution and conservation status of Rhinopithecus strykeri in China

Genetic Diversity, Genetic Structure, and Demographic History of Black Snub-Nosed Monkey (Rhinopithecus strykeri) in the Gaoligong Mountains, Southwestern China

The Gaoligong Mountains, located in the southeastern Tibetan Plateau, is one of the world's biodiversity hotspots and provides a refugium for many endangered endemic animals. In this study, we reported a population genetic study on black snub-nosed monkey (Rhinopithecus strykeri), a critically endangered primate endemic to the Gaoligong Mountains, yet their large-scale population genetic study remains underexplored. Here, we performed population genetic analyses from two geographical populations (Pianma and Luoma) based on targeted genomic single-nucleotide polymorphism (SNP) data (37.7 K) and mitochondrial DNA (mtDNA) control region (842 bp). Both nuclear SNP data and mtDNA revealed relatively low levels of genetic variation in both populations compared to other reported primates, which is most likely to be explained by loss of historical genetic diversity due to inbreeding and long-term small effective population size, thus potentially aggravating the effects of inbreeding and genetic depression. Phylogenetic and population structure analyses for mtDNA revealed two deep lineages (approximately 0.69 million years ago), but limited genetic differentiation in nuclear data, which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau and glacial refuge, and subsequent secondary contact as a result of historically high and bidirectional gene flow between populations. Ecological niche modeling and landscape connectivity analyses also showed historical and recent connectivity between two geographical populations. The demographic history inferred from both mtDNA and nuclear data revealed at least two continuous declines in the effective population size occurring around 43 Kya and 8-10 Kya, respectively, probably due to Pleistocene glaciations and subsequent human activities. Our results provide the first detailed and comprehensive genetic insights into the genetic diversity, population structure, and demographic history of a critically endangered species, and provide essential baseline information to guide conservation efforts.

Gut Mycobiota of Three Rhinopithecus Species Provide New Insights Into the Association Between Diet and Environment

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.

Adaptations to a cold climate promoted social evolution in Asian colobine primates

The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder environments tend to live in larger, more complex groups. Specifically, glacial periods during the past 6 million years promoted the selection of genes involved in cold-related energy metabolism and neurohormonal regulation. More-efficient dopamine and oxytocin pathways developed in odd-nosed monkeys, which may have favored the prolongation of maternal care and lactation, increasing infant survival in cold environments. These adaptive changes appear to have strengthened interindividual affiliation, increased male-male tolerance, and facilitated the stepwise aggregation from independent one-male groups to large multilevel societies.

Identifying optimized on-the-ground priority areas for species conservation in a global biodiversity hotspot

Threatened species are inadequately represented within protected areas (PAs) across the globe. Species conservation planning may be improved by using public species-occurrence databases, but empirical evidence is limited of how that may be accomplished at local scales. We used the Three Parallel Rivers Region of China as a case to investigate the utility of public species data in improvement in conservation planning. We mapped the distribution of each species as suitable habitat ranges using species distribution models (for 261 plants and 29 animals with ≥5 occurrences) or as point locations (for 591 plants and 328 animals with <5 occurrences). Systematic conservation planning was then applied to identify three optimized portfolios of priority conservation areas (PCAs) for achieving increasing targets of 17, 31, and 50% of the total study area. We then compared the distributions of PCAs in this study with those in two existing PCA datasets. PCAs in this study covered greater areas in the southeastern highly-disturbed regions and along valleys of great rivers than two existing datasets that had a focus on intact ecosystems in remote mountain areas. The three portfolios of PCAs had some overlap with two existing PCA datasets, with the overlapping area accounting for 26.4-39.0% of the total areas of our PCAs. Our PCAs could complement existing PCAs by identifying more priority areas in developed landscapes; this is critical for protecting biodiversity in such areas as they face greater pressures. PCAs in this study received a much lower PA coverage (32.9-43.1%) than existing PCAs (60.2-60.8%) because of biased PA distribution toward mountain areas. Our results suggest that conservation planning based on limited public species data could improve local-scale priority-setting practices. The analysis supports effective integration of species targets in China's new national park system by identifying optimized networks of PCAs.

Uses of nonhuman primates by humans in northeastern Brazil

Humans have used non-human primates (hereafter referred to as primates) as food source, medicine, parts of rituals, pets, and models for various studies worldwide. Here we investigated the extent of the use of primates by humans in three areas in northeastern Brazil, the country's most impoverished region. We carried out our study in three biomes (Caatinga, Cerrado, and Atlantic Forest). The results showed that humans exploited all five primate species occurring in the study sites: Callithrix jacchus, Sapajus flavius, Sapajus libidinosus, Alouatta belzebul, and Alouatta ululata. They used the primates as a food source, as pets and medicines, and for leisure. Despite socioeconomic differences in the study areas, we found similarities in the use of primates. Larger primates were targeted for meat, whereas the small common marmosets were targeted as pets. We found conflicting interactions between humans and bearded capuchins due to crop raiding, but no such conflict was found between humans and blonde capuchins, reflecting the differences in crop type, pattern, and tradition in the sites. A. ululata was used as medicine. We suggest that environmental education actions in the study areas should focus on (i) raising awareness among local people of the ecological importance of primates, (ii) providing alternative activities to hunting whenever possible, and (iii) minimising conflicts.

Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis)

The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.

Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species.

The effective use of camera traps to document the northernmost distribution of the western black crested gibbon in China

Gibbons represent a highly successful radiation of four genera and 20 species of Asian apes that, in response to recent habitat fragmentation and deforestation, are threatened with extinction. China has six species of gibbons, each of which is critically endangered. We present new biogeographical information on the distribution of the black crested gibbon (Nomascus concolor). Four subspecies of N. concolor have been described: three of them are present east of the Mekong River (Nomascus concolor jingdongensis, N. c. concolor and N. c. lu); and another is found west of the Mekong River (N. c. furvogaster). In addition, there has been speculation that gibbons exist in the Biluo Snow Mountains, between the Mekong and Salween basins. To clarify the biogeography of this species, from April 2011 to January 2012 and from January 2016 to September 2018, we conducted interviews with local villagers, completed line transect surveys, monitored gibbon calls, and placed 30 camera traps in the forest canopy. On October 30, 2016, we recorded gibbon's calls. On July 5, 2016, our camera traps obtained one image of a male gibbon, and on February 1 and 8, 2017, we captured two independent images of an adult female gibbon on Zhiben Mountains. Based on the black crest on the head, clearly visible in the photographs, the gibbons are N. c. furvogaster. Evidence from interviews and survey records indicate that N. c. furvogaster once was present in the Zhiben Mountains, at an altitude of between 2000 and 2700 m. Between 1990 and 2000, some 6-7 groups still existed in Caojian, Laowo and adjacent areas. Unfortunately, in the absence of an effective conservation strategy, the population was extirpated by hunters. The remaining forest in the Zhiben Mountains is highly fragmented, and most of the suitable habitat for gibbons has been lost. Therefore, we expect that this newly found gibbon population is under extreme anthropogenic pressure. It is imperative that further investigations of this gibbon population be conducted immediately, and that the local and national governments implement effective conservation plans, including educating the local communities to protect this critically endangered primate population.

Modeling habitat suitability for Yunnan Snub-nosed monkeys in Laojun Mountain National Park

We provide new information on Yunnan snub-nosed monkey (Rhinopithecus bieti) behavioral ecology, contributing to future conservation efforts within the Laojun Mountain National Park. Habitat evaluation procedures are used to quantify the value of land as a habitat for a species. We analyzed environmental variables hypothesized to influence habitat suitability for Yunnan snub-nosed monkeys, and mapped the distribution of suitable habitats across the study area and adjacent areas. Spatial analysis with GPS data was conducted to investigate home-range change of these monkeys. Predictor variables were generated using ArcMap and R programming language. We prepared 34 environmental variables at 30-m spatial resolution. Maxent was used to analyze environmental variables that contributed to suitability. Using satellite remote sensing and GIS, we modeled the distribution of suitable habitat for Yunnan snub-nosed monkeys in the Jinsichang area of the Laojun Mountains in China. This study did not describe the frequency or intensity of habitat use. Habitat suitability was affected by several variables, the most influential, as determined by permutation importance, being mean diurnal temperature range (31.6%), precipitation during the wettest quarter of the year (30.4%), average annual precipitation (17%), normalized difference vegetation index (5%), wetness (4.6%), and aspect (4.5%). This habitat suitability model provides information about the current distribution of Yunnan snub-nosed monkeys, which is important for appropriate implementation of conservation actions.

First insights into the feeding habits of the Critically Endangered black snub-nosed monkey, Rhinopithecus strykeri (Colobinae, Primates)

Since its initial discovery in 2010 in the Gaoligong Mountains on the Sino-Myanmar border, there remains no direct information on the feeding habits of the black snub-nosed monkey (Rhinopithecus strykeri). This species is on the verge of extinction, with an estimated remaining population of < 400 individuals. Due to difficulties in following these monkeys across steep mountainous terrain, during 203 observation days (September 2015-January 2017) we recorded 80 h of behavioral records of a wild population (Luoma group). Our preliminary results identified 14 plant species and four lichen species consumed by the monkeys. In addition, we provided the only two captive individuals of this species with a cafeteria diet composed of > 600 wild-collected plant species that were gathered from known R. strykeri habitats to determine which plant species and food items were considered palatable. Our results indicate that the captive monkeys freely consumed young and mature leaves, fruits/seeds, buds, flowers, twigs, and bark from 170 different species of trees, bushes, and herbs representing 76 genera and 41 plant families, as well as 15 species of lichen. All foods consumed by the wild monkeys were also consumed by the captive individuals. Food plants consumed by R. strykeri were found principally in intact subtropical evergreen broadleaf forests and hemlock-broadleaf mixed forests at an altitude of 2200-3000 m. Strict enforcement of habitat protection and access to resources across this elevation zone appear to be essential for the conservation and survivorship of this critically endangered primate.

Ethical and Scientific Pitfalls Concerning Laboratory Research with Non-Human Primates, and Possible Solutions

Basic and applied laboratory research, whenever intrusive or invasive, presents substantial ethical challenges for ethical committees, be it with human beings or with non-human animals. In this paper we discuss the use of non-human primates (NHPs), mostly as animal models, in laboratory based research. We examine the two ethical frameworks that support current legislation and guidelines: deontology and utilitarianism. While human based research is regulated under deontological principles, guidelines for laboratory animal research rely on utilitarianism. We argue that the utilitarian framework is inadequate for this purpose: on the one hand, it is almost impossible to accurately predict the benefits of a study for all potential stakeholders; and on the other hand, harm inflicted on NHPs (and other animals) used in laboratory research is extensive despite the increasing efforts of ethics committees and the research community to address this. Although deontology and utilitarianism are both valid ethical frameworks, we advocate that a deontological approach is more suitable, since we arguably have moral duties to NHPs. We provide suggestions on how to ensure that research currently conducted in laboratory settings shifts towards approaches that abide by deontological principles. We assert that this would not impede reasonable scientific research.

Snub-nosed monkeys (Rhinopithecus): potential distribution and its implication for conservation

Many threatened species have undergone range retraction, and are confined to small fragmented populations. To increase their survival prospects, it is necessary to find suitable habitat outside their current range, to increase and interconnect populations. Species distribution models may be used to this purpose and can be an important part of the conservation strategies. One pitfall is that such mapping will typically assume that the current distribution represents the optimal habitat, which may not be the case for threatened species. Here, we use maximum entropy modelling (Maxent) and rectilinear bioclimatic envelope modelling with current and historical distribution data, together with the location of protected areas, and environmental and anthropogenic variables, to answer three key questions for the conservation of Rhinopithecus, a highly endangered genus of primates consisting of five species of which three are endemic to China, one is endemic to China and Myanmar and one is endemic to Vietnam; Which environmental variables best predict the distribution? To what extent is Rhinopithecus living in an anthropogenically truncated niche space? What is the genus’ potential distribution in the region? Mean temperature of coldest and warmest quarter together with annual precipitation and precipitation during the driest quarter were the variables that best explained Rhinopithecus’ distribution. The historical records were generally in warmer and wetter areas and in lower elevation than the current distribution, strongly suggesting that Rhinopithecus today survives in an anthropogenic truncated niche space. There is 305,800–319,325 km² of climatic suitable area within protected areas in China, of which 96,525–100,275 km² and 17,175–17,550 km² have tree cover above 50 and 75%, respectively. The models also show that the area predicted as climatic suitable using Maxent was 72–89% larger when historical records were included. Our results emphasise the importance of considering historical records when assessing restoration potential and show that there is high potential for restoring Rhinopithecus to parts of its former range.

The Critically Endangered Myanmar snub-nosed monkey Rhinopithecus strykeri found in the Salween River Basin, China

The Myanmar snub-nosed monkey Rhinopithecus strykeri was discovered in 2010 on the western slopes of the Gaoligong Mountains in the Irrawaddy River basin in Myanmar and subsequently in the same river basin in China, in 2011. Based on 2 years of surveying the remote and little disturbed forest of the Gaoligong Mountains National Nature Reserve in China, with outline transect sampling and infrared camera monitoring, a breeding group comprising > 70 individuals was found on the eastern slopes of the Gaoligong Mountains in the Salween River Basin. Given the Critically Endangered status of this primate (a total of < 950 individuals are estimated to remain in the wild), efforts to protect the relatively undisturbed habitat of this newly discovered population and to prevent hunting are essential for the long-term survival of this species.

No evidence for mitochondrial genetic variability in the largest population of critically endangered Tonkin snub-nosed monkeys in Vietnam

The Tonkin snub-nosed monkey (Rhinopithecus avunculus) with a global population of <250 is listed as critically endangered. It is endemic to northeastern Vietnam and was feared extinct until its rediscovery in 1989. The largest single population of R. avunculus consists of 125-130 individuals in an area of forest called Khau Ca in Ha Giang Province. We used non-invasively collected fecal samples to establish the amount of genetic diversity in this population based on mitochondrial information. We amplified and sequenced a 467- to 650-bp section of the hypervariable region I (HVI) of the mitochondrial D-loop for 201 samples and reconstructed the full mitochondrial genomes for five samples based on metagenomic data. All 201 HVI sequences were identical and no variability was found in the five mitochondrial genomes. Our results highlight the immediate need for a comprehensive assessment of the genetic diversity of all populations of R. avunculus based on mitochondrial and nuclear markers. The latter need to be developed for this species.

Distribution and conservation status of Shortridge's capped langurs Trachypithecus shortridgei in China

We conducted community interviews and field surveys to determine the distribution and population of the Endangered Shortridge's capped langur Trachypithecus shortridgei, and the threats to the species, in the Dulong and Nu River valleys of north-western Yunnan Province, China. We found that c. 19 groups of T. shortridgei reside in the Dulong valley, mostly located in the southern portion of the valley. According to interview and observational records in the Gaoligong Mountains to the west of the Nu River, 12 individuals and no groups were observed. Family groups consist of one adult male, 2–3 adult females and up to five young. We estimate the population of T. shortridgei in China to be c. 250–370 individuals. Threats to the species include habitat loss and poaching. We suggest several measures to conserve T. shortridgei, such as a review of the Gaoligong National Nature Reserve management strategy, and increasing engagement, education, inclusion of local people in forest management, and the consistency of enforcement.