Abstract
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.
Highlights
Human impacts on the environment have rapidly accelerated species extinction via habitat degradation and climate change and the recent report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) predicts that climate change has already affected the distribution of nearly half (47%) of land-mammals[1]
In order to investigate to what extent faecal samples have been used in addressing taxonomic problems, we surveyed the literature as captured in Zoological Record
Illumina sequencing of faecal metagenomes yielded 60.3–69.7 million sequences for each sample from Sumatra (Presbytis femoralis percura: ESBL1–8, P. siamensis cf. cana: Pres[2]; Table 3)
Summary
Human impacts on the environment have rapidly accelerated species extinction via habitat degradation and climate change and the recent report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) predicts that climate change has already affected the distribution of nearly half (47%) of land-mammals[1]. Recent review by Srivathsan et al.[8] estimates that it is possible to obtain data on host genetics and natural history for nearly 1,000 species of mammals in the decade if faecal samples were to be collected routinely during field surveys and evaluated using metagenomics. Asian colobines (langurs and odd-nosed monkeys) are a diverse group of mammals, with 55 recognized species (87 spp.) belonging to seven genera (Nasalis, Presbytis, Pygathrix, Rhinopithecus, Semnopithecus, Simias, Trachypithecus)[11]; i.e., nearly half of all primate species in Asia are colobines. Many of these species are dependent on habitats that are quickly disappearing. Presbytis f. robinsoni is widespread and ranges from northern Peninsular Malaysia to southern Thailand and Myanmar
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