Wednesday, June 24, 2020

[Mammalogy • 2020] Faecal DNA to the Rescue: Shotgun Sequencing of Non-invasive Samples reveals Two Subspecies of Southeast Asian Primates (Presbytis femoralis group) to be Critically Endangered Species

 Robinson’s banded langur  Presbytis robinsoni  

in Ang, Roesma, Nijman, et al., 2020. 
 Photo: Andie Ang.

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.

Three subspecies of Presbytis femoralis;
clockwise from East Sumatran banded langur P. f. percura (1), Raffles’ banded langur P. f. femoralis (2), to Robinson’s banded langur P. f. robinsoni (3).
Photos: Andie Ang.

Resurrection of Presbytis femoralis, P. percura and P. robinsoni 

Based on multiple species delimitation methods, high genetic divergence, placement in the mitochondrial phylogenies, as well as distinct morphological differences, we here resurrect the three species of P. femoralis from their current subspecific status (Table 2). The newly circumscribed Raffles’ banded langur P. femoralis is now only known from southern Peninsular Malaysia (states of Johor and Pahang) and Singapore. The East Sumatran banded langur P. percura only occurs in Riau Province of east-central Sumatra. Lastly, Robinson’s banded langur P. robinsoni has the widest distribution and ranges from northern Peninsular Malaysia (states of Kedah and Perak) through southern Thailand (provinces of Surat Thani, Phetchaburi, and Prachuap Khiri Khan) to southern Myanmar (Tanintharyi Region). These changes to species status mean that Presbytis now comprises 19 species.


Presbytis siamensis siamensis and Presbytis s. cana 

(images: Lee Zan Hui & Andie Ang).

white-thighed langur Presbytis siamensis
 photo: Lee Zan Hui  

We here demonstrate the value of non-invasive faecal samples for addressing taxonomic questions that are of significant conservation importance. Based on mitochondrial DNA (mitogenomes, cyt-b and d-loop), we resurrect three species within the Presbytis femoralis group. The new species limits also led to a change in the conservation status of P. femoralis and P. percura which now have to be considered Critically Endangered. We further urge researchers to include the collection of non-invasive faecal samples into their field protocols.

Andie Ang, Dewi Imelda Roesma, Vincent Nijman, Rudolf Meier, Amrita Srivathsan and Rizaldi. 2020. Faecal DNA to the Rescue: Shotgun Sequencing of Non-invasive Samples reveals Two Subspecies of Southeast Asian Primates to be Critically Endangered Species. Scientific Reports. 10, 9396. DOI: 10.1038/s41598-020-66007-8