Faecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red-shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~ 10,000 (0.014%) and ~ 44,000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.

Red-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural lifestyle, including dietary habits such as consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure and lifestyle. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, biodiversity, and microbial function. We also identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella, which may be related to health. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.

Humans and long-tailed macaques (Macaca fascicularis) interface in several locations in Singapore. We investigated six of these interface zones to assess the level of conflict between the two species. We observed macaque-to-human interactions and distributed questionnaires to residents and visitors of nature reserves. We observed an average of two macaque-to-human interactions per hour at the sites, which included affiliative or submissive behaviors (46.9%), aggression (19.1%), taking food and other items (18.5%) searching bins, cars, and houses (13.4%), and nonaggressive contact (2.1%). Two-thirds of interactions occurred when a human was carrying food or food cues, and one-quarter occurred when a human provoked macaques. Only 8% of interactions occurred without a clear human-triggered context. Our interview showed one-third of respondents experienced nuisance problems from macaques. They had items taken from them (50.5%) and received threats (31.9%). Residents reported more nuisance problems than visitors, and their perceptions toward macaques differed. Residents were more aware of the consequences of food provisioning and that there were regulations against feeding. Residents fed macaques less and held more negative sentiments toward macaques. Nearly half of the interviewed people held neutral attitudes toward macaques and only 26.2% of respondents thought conflict with macaques warranted urgent action. Nearly two-thirds of the respondents supported education programs to ameliorate human–macaque conflict, and less than 15% supported removing or eradicating macaques. 87.6% felt that it is importance to conserve and protect macaques. Our results show that human–macaque conflict exists in Singapore, but that it may not be severe. Human behavior is largely responsible for macaque-to-human interactions, and thus could be lessened with management of human behavior in interface zones (i.e. restrict food carrying and provocation). Moreover, our interviews shows people living in Singapore value macaques, do not wish them entirely removed, prefer education-based solutions, and consider conservation and protection of them important.

The long-tailed macaque (Macaca fascicularis) population of the island-state of Singapore consists of ca. 1,218-1,454 individuals. About seventy percent of the population (ca. 1,027 individuals) is concentrated in both Bukit Timah and Central Catchment Nature Reserves, a system of reservoirs and forest reserves located in the center of Singapore. This core population resides mainly along perimeter forest areas of the reserve system, which is bordered by residential and recreational areas (e.g., parks and golf courses) and encircled by expressways. Periphery sub-populations (ca. 427 individuals) persist in forest fragments throughout Singapore mainland and on 5 offshore islands. Much of the Singaporean macaque population overlaps with human settlement and these commensal groups are mainly distributed close to roads, parks and residential areas. At least 70% of these groups are habituated to human presence and at least 50% to food provisioning. Moreover, commensal groups have more individuals and have higher infant:adult female ratios than non-commensal groups. The close association of habituated macaque groups living in human environments has led to increasing human-macaque conflict in Singapore. The overlap is also associated with human-induced population loss resulting from road accidents (2.4%); and trapping efforts (14%) aimed at ameliorating conflict issues. Consequently, it is important to better understand how humans are affecting macaque populations. In order to mitigate human-macaque conflict and at the same maintain a sustainable macaque population in Singapore, there is an urgent need for wildlife management strategies aimed at minimizing the extent of human-macaque conflict. Such strategies should include designing appropriate buffers around reserve areas, revised urban development plans, and managing the behavior of people interfacing with macaques.

We conducted observations of two neighboring groups of food-enhanced long-tailed macaques (Macaca fascicularis) over a period of one year. We examined their diet, behavior, habitat use, and ranging and how within-population variability reflected differential utilization of anthropogenic food resources. The group that consumed more anthropogenic food spent less time feeding on wild fruits and flowers, less time resting, and more time locomoting. They used forest habitats less often, and had a larger total home range and mean monthly home range. Some of these results contrasted with previous studies of food-enhanced primates which reported that food-enhancement resulted in smaller home ranges, shorter daily ranges, less time traveling and feeding, and more time resting. These contrasting patterns may relate to the nature of anthropogenic foods. In most studies of food-enhanced primates, anthropogenic food resources were abundant and concentrated but the macaques in this study used anthropogenic foods mainly from a few refuse sites where they had limited access, and from dispersed and irregular human provisioning. The group consuming more anthropogenic food therefore showed more spatially dispersed feeding activity and home range use, an effect that was likely further enhanced by lower natural food resource availability within their home range. The Singapore macaque population shows small-scale variability in feeding and ranging behavior, contributing to the complexity of their adaptive variability in a human-altered habitat. Our findings could have important implications for mitigating human-macaque conflict as measures applied at a higher spatial or population level may achieve highly inconsistent results, intensifying the challenges for wildlife managers.