BackgroundRapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history of these species is important for designing conservation strategies, such as habitat enhancements or ex-situ conservation. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. Here we use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis).ResultsWe conducted metagenomics via shotgun sequencing on six fecal samples obtained from a remnant population of P. femoralis in a species-rich rainforest patch in Singapore. Shotgun sequencing and identification against a plant barcode reference database reveals a broad dietary profile consisting of at least 53 plant species from 33 families. The diet includes exotic plant species and is broadly consistent with > 2 years of observational data. Metagenomics identified 15 of the 24 plant genera for which there is observational data, but also revealed at least 36 additional species. DNA traces for the diet species were recovered and identifiable in the feces despite long digestion times and a large number of potential food plants within the rainforest habitat (>700 species). We also demonstrate that metagenomics provides greater taxonomic resolution of food plant species by utilizing multiple genetic markers as compared to single-marker metabarcoding. In addition, full mitochondrial genomes of P. femoralis individuals were reconstructed from fecal metagenomic shotgun reads, showing very low levels of genetic diversity in the focal population, and the presence of gut parasites could also be confirmed. Metagenomics thus allows for the simultaneous assessment of diet, population genetics and gut parasites based on fecal samples.ConclusionsOur study demonstrates that metagenomic shotgun sequencing of fecal samples can be successfully used to rapidly obtain natural history data for understudied species with a complex diet. We predict that metagenomics will become a routinely used tool in conservation biology once the cost per sample reduces to ~100 USD within the next few years.Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-016-0150-4) contains supplementary material, which is available to authorized users.

A significant number of Southeast Asian mammal species described in the 19th and 20th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss which creates an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking and difficult to obtain for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in IUCN status to Critically Endangered due to small population sizes and fragmented habitats. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.

Understanding local community attitudes toward wildlife is critical for making context-sensitive conservation planning and management decisions that may facilitate better human-wildlife coexistence. We conducted questionnaire-based interviews with local households in the Qinglong village of Mayanghe National Nature Reserve (MNNR) in China from March to August 2015. We used a mixed analysis technique based on a theoretical framework of categorical variables to explain attitudes to investigate the key factors that influenced local attitudes toward Endangered François' langurs (Trachypithecus francoisi). We found that 53% (40, N = 75) of interviewees liked François' langurs presence around the village; 27% did not; and 20% were neutral. Respondents with favorable attitudes to langurs associated them mainly with tangible benefits from local tourism and their positive aesthetic and emotional values. Respondents with negative attitudes to langurs associated them with tangible costs such as crop feeding and the destruction of their houses. Over half (N = 9) of respondents with neutral attitudes associated langurs with various cost and benefit trade-offs. Overall, local people tended to have slightly negative perceptions of the langurs' impacts at the household level, while they had very positive perceptions of their impacts at the community level. Ordinal logistic regression models revealed that age, gender, and impact perceptions were significantly associated with local residents' attitudes towards the langurs at the household and community levels. We suggest that such socioeconomic monitoring efforts should be periodically conducted in protected areas like MNNR, especially in the context of rapid economic and infrastructure development.

16A significant number of Southeast Asian mammal species described in the 19 th and 20 th 17 century were subsequently synonymized and are now considered subspecies. Many are 18 affected by rapid habitat loss and there is thus an urgent need to re-assess the conservation 19 status based on species boundaries established with molecular data. However, such data are 20 lacking for many populations and subspecies. We document via a literature survey and 21 empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful 22 tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three 23 subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. 24 femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the 25 resurrection of all three subspecies to species based on multiple species delimitation 26 algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 27 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. 28 percura), the results lead to an immediate change in the IUCN status to Critically Endangered 29 due to small population estimates and fragmented habitat. We conclude that faecal DNA 30 should be more widely used for clarifying species boundaries in endangered mammals. 32 Human impacts on the environment have rapidly accelerated species extinction via habitat 33 degradation and climate change. Recent report by Intergovernmental Science-Policy Platform 34 on Biodiversity and Ecosystem Services (IPBES) predicts that climate change has already 35 affected the distribution of nearly half (47%) of land-mammals 1 . Conservation efforts are 36 urgently needed but are hampered by the lack of data for a large number of mammal species, 37 subspecies, and populations which face imminent extinction 2,3,4 . A typical example is Asian 38 primates for which 70% of the species are threatened with extinction 5 . Effective conservation 39 programs are needed but they require a robust understanding of species numbers and 40 boundaries based on up-to-date taxonomic information 6,7 . Unfortunately, this information is 41 lacking for many rare, globally threatened, and elusive mammalian species. Many lack 42 molecular data and collecting these data is difficult because invasive sampling that would 43 yield fresh tissues is often not feasible. 44This leaves only three alternative sources of DNA. The first is museum specimens, but the 45 number of samples in museums tends to be small and many were collected in the 19 th or early 46 20 th century thus reflecting (historic) genetic diversity prior to extensive habitat loss. The 47 second is tissue samples obtained from specimens that died of "natural causes" such as road 48 accidents. The third source of genetic material is non-invasive samples such as hair and 49 faeces. Arguably, faecal samples are still an underappreciated source of information although 50 they could be collected in good numbers during ro...

Roads that dissect natural habitats present risks to wildlife, creating gaps or barriers which animals have to traverse in order to move within and between their habitats. Restoring habitat connectivity can be achieved naturally by planting trees and vines to reconnect forest gaps, or artificially by creating culverts for small ground vertebrates, building overpasses for large terrestrial animals, or installing canopy bridges for arboreal fauna. The 3-km Old Upper Thomson Road borders the eastern side of the Central Catchment Nature Reserve, the largest nature reserve in Singapore, and isolates it from neighbouring forest patches. To facilitate safe crossing for tree-dwelling animals such as the critically endangered Raffles’ banded langurs (Presbytis femoralis) along Old Upper Thomson Road, two rope bridges were installed. We monitored the use of these rope bridges by vertebrates from April 2020 to August 2021 through surveillance cameras attached on one end of each bridge. A total of 64 118 videos were processed, with 6218 (9.70%) containing vertebrates. Seven species, including three primates, two squirrels and two reptiles, utilised the bridges to travel between the forests. In particular, Raffles’ banded langurs made a total of 293 successful crossings. We have shown that these rope bridges are useful for arboreal species and can complement national efforts to restore connectivity in fragmented habitats.