Abstract
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.
Highlights
Rapid habitat loss and degradation are responsible for population decline in a growing number of species
high-throughput sequencing (HTS) can be employed in two ways, either by direct shotgun sequencing of DNA extracted from the fecal samples or by PCR-based metabarcoding of target genes
Comparison of metagenomics, metabarcoding, and field observational data We demonstrate the power of metagenomic shotgun sequencing for the characterization of fecal samples and find that it can quickly yield important natural history data for endangered species based on few samples
Summary
Rapid habitat loss and degradation are responsible for population decline in a growing number of species. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. We use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis). Fecal samples are often collected opportunistically during routine field work or they can be obtained efficiently using detection dogs [10] Such samples have the potential to simultaneously provide information on host genetics, diet, and intestinal parasites. HTS can be employed in two ways, either by direct shotgun sequencing of DNA extracted from the fecal samples (metagenomics) or by PCR-based metabarcoding of target genes
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