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Yangel Bin Laden
In a pilot study, the Department of Forestry and Parks Service (DoFPS) used environmental deoxyribonucleic acid (eDNA) technology to identify 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 the DNA reference database of Bhutanese species to fully exploit eDNA technology.
eDNA offers a more cost-effective alternative to traditional methods such as camera traps for biodiversity monitoring. By analyzing DNA collected from environmental samples, 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 to May 2022, focused on the Mandechu River, which runs for about 45 km from Berti in the upper reaches to Poncal in the lower reaches. Sampling sites included the main channel of the Mandechu River, its tributaries and backwaters. The study area was selected because of its high biodiversity as indicated by existing species databases.
Despite advances in technology, the eDNA approach still faces challenges because reference databases are incomplete. DoFPS cross-checks the collected DNA against multiple reference databases, including the National Center for Biotechnology Information and the European Molecular Biology Laboratory. The process is similar to checking a new word against a dictionary to confirm its existence.
Tshering Dorji, a former lecturer in the School of Natural Resources who uses eDNA to study macroinvertebrates, reports similar difficulties.
His research involved DNA barcoding of 350 samples from 30 rivers along the Punasanchu Basin. While 23 samples were exact matches to the Barcode of Life Data System (BOLD), only seven were identified as unique species and only five reached species level identification. The remaining two samples were morphospecies, meaning he could not identify them at the species level.
The Environmental DNA for Biodiversity Monitoring in Bhutan report outlines key limitations and areas for improvement. Some of the key recommendations include the establishment of a comprehensive DNA reference database for Bhutan’s species, strengthening the infrastructure and resources for independent environmental DNA analysis, and providing specialized training for officials conducting environmental DNA surveys.
This preliminary study found a wide variety of species, including 16 carnivores, 10 ungulates, three 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 macaque fish, among others.
Between April and May 3, 2022, 48 eDNA samples were collected from 20 locations.
Research shows that eDNA metabarcoding of stream water is an effective method for detecting rare and endangered species. This study supports these findings, finding extremely rare aquatic, semi-aquatic and terrestrial species among fish, amphibians, mammals and birds. For many of these species, this is the first documented detection using stream water samples and metabarcoding.
Although the limitations of the reference database affected species identification, the study utilized operational taxonomic units (OTUs) to estimate overall biodiversity. In the Royal Manas National Park and Remgang Forest District, eDNA analysis identified a total of 671 OTUs, of which 75 were classified at the species level, 185 at the genus level, 90 at the family level, 46 at the order level, and 2 at the class level.
“Our approach not only identifies distinct taxa, but also captures some of the variation within species,” the report states. “Going forward, it will be critical to improve and expand our reference database. This will greatly enhance species identification and could potentially match the accuracy seen in regions with large reference datasets.”
The pilot study was supported by the World Wildlife Fund (USA and Bhutan).
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