Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

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.

First record of interspecies grooming between Raffles’ Banded Langur and Long-tailed Macaque

“…However, it also raises concerns about interspecies disease transmission as a spillover effect of the human-macaque interface (Gillespie et al 2008;Rushmore et al 2017;Balasubramaniam et al 2020a,b). When macaques engage in interactions and close proximity with threatened primates, such as RBLs who are Critically Endangered, the risk of transmitting J TT zoonotic diseases adds to the factors that already threaten this rare species (Ang et al 2012(Ang et al , 2020.…”

“…Anecdotal records of interspecies allogrooming have been reported from the field, usually for species of the same genus and/ or within mixed species groups with hybrids (e.g., M. nemestrina x M. fascicularis at Sepilok, Sabah; Gilhooly & Colquhoun 2018) but, to the authors' knowledge, published observations of intergeneric grooming in wild sympatric primates are not available. Interspecies grooming between primates of different genera is rarely reported from the wild, and has, to our knowledge, not been documented for the Critically Endangered (Ang et al 2020; status currently being revised, A. Ang, pers.…”

“…J TT and Malaysian White-handed Gibbon Hybolates l. lar. Specifically, the Raffles' Banded Langur is Critically Endangered (Ang et al 2020) due to its small population size and restricted distribution in fragmented habitats. This species is only found in southern Peninsular Malaysia (states of Johor and Pahang) and the Republic of Singapore with an estimated global population size of fewer than 400 individuals (Ang et al 2020).…”

The importance of addressing different Red Lists in conservation studies: an analysis comparing the conservation status of Brazilian mammals

“…Fernandes et al, 2007;Attias et al, 2009;Hirsch and Chiarello, 2012), and taxonomic revisions (especially in cases where a single species is divided into two or more, e.g. Agapow et al, 2004;Nascimento and Feijó, 2017;Ang et al, 2020). The Brazilian Red Book (ICMBio/MMA, 2018) also mentions that more recent and accurate information (especially regarding declines or recoveries of populations) and adjustments in the method itself may be responsible for changes in the conservation status of species, sometimes even resulting in their removal from the list of threatened taxa (i.e.…”

A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)

“…This currently limits the number of samples that can be sequenced using this approach. However, shotgun sequencing overcomes the need to select specific vertebrate primers and can simultaneously retrieve prey and predator mitochondrial DNA, predator gut microbiome and gut parasites (Ang et al, 2020;Bon et al, 2012;Paula et al, 2015Paula et al, , 2016Srivathsan et al, 2015Srivathsan et al, , 2016. This maximises the amount of information that can be retrieved within one round of sequencing, without the need to carry out additional lab work as is required for metabarcoding using multiple primers.…”