Yangyel Lhaden
In a pilot study, the Department of Forests and Park Services (DoFPS) employed environmental deoxyribonucleic acid (eDNA) technology to identify a remarkable 201 unique vertebrate taxa in Bhutan, of which 134 were identified at the species level.
Despite the impressive results, the study highlights the urgent need to expand Bhutan’s species DNA reference database to fully leverage eDNA technology.
eDNA is revolutionising biodiversity monitoring by offering a more cost-effective alternative to traditional methods such as camera traps. By analysing DNA collected from environmental samples—ranging from feces and mucus to shed skin, hair, and carcasses—scientists can identify species without direct observation. In this study, water samples were used to detect the presence of various organisms.
The pilot study, conducted from April 2022 to May 2022, focused on the Mangde Chhu River, spanning approximately 45 kilometres from Berti in the upper stretch to Pangkhar in the lower stretch. Sampling sites included the main channel of Mangde Chhu, its tributaries, and stagnant water bodies. The study area was selected due to its high biological diversity, as indicated by existing species databases.
Despite the technological advancements, the eDNA method faced challenges due to an incomplete reference database. The DoFPS crosschecked the collected DNA against several reference databases, including the National Centre for Biotechnology Information and the European Molecular Biology Laboratory. This process is akin to checking a new word against a dictionary to confirm its existence.
A former lecturer at the College of Natural Resources, Tshering Dorji, who studied macroinvertebrates using eDNA, reported similar difficulties.
His research involved DNA barcoding of 350 specimens from 30 streams along the Punatsangchhu basin. While 23 specimens matched perfectly with the Barcode of Life Data System (BOLD), only seven were identified as unique species, and just five reached species-level identification. The remaining two were morphospecies, indicating that he could not identify them at the species level.
The eDNA for biodiversity monitoring in Bhutan report outlines critical limitations and areas for improvement. Some of the key recommendations include building a comprehensive DNA reference database for Bhutanese species, enhancing infrastructure and resources for independent eDNA analysis, and providing specialised training for officials conducting eDNA surveys.
The pilot study detected a diverse range of species, including 16 carnivores, 10 ungulates, 3 primates, 11 rodents, and 15 bats. Interestingly, 33 of the identified species are listed on the IUCN Red List, including the critically endangered white-bellied heron and the endangered Golden Mahseer, among others.
Forty eight eDNA samples were collected from 20 sites from April 2022 to May 3, 2022.
Studies suggest that eDNA metabarcoding of stream water is an effective method for detecting rare and threatened species. This study supports those findings, having identified exceptionally rare aquatic, semi-aquatic, and terrestrial species across fish, amphibians, mammals, and birds. For many of these species, this represents the first documented detection using stream water samples and metabarcoding.
Although the reference database limitations impacted species identification, the study utilised Operational Taxonomic Units (OTUs) to estimate overall biodiversity. In the Royal Manas National Park and Zhemgang Forest Division, eDNA analysis identified a total of 671 OTUs, with 75 classified to the species level, 185 to the genus level, 90 to the family level, 46 to the order level, and 2 to the class level.
“Our method not only identifies different taxonomic groups but also captures some variation within species,” the report states. “Looking ahead, improving, and expanding our reference databases is essential. This will greatly enhance species identification and could achieve the accuracy seen in areas with extensive reference datasets.”
The pilot study was supported by the World Wildlife Fund (the US and Bhutan).