Decoding the wildlife crime scene: DNA barcoding to the rescue of the globally threatened Philippine Duck

An isolated cluster of more than 7,000 islands, the Philippines is a popular tourist destination in Southeast Asia with pretty beaches and welcoming people.  But it is also a mega biodiversity hotspot.  Despite being smaller than its more famous counterparts like Madagascar and the Amazon rainforest, it has a higher level of endemism.  Approximately, 33 percent of its plants, 75 percent of its amphibians, 70 percent of its reptiles, and 44 percent of its birds are found nowhere in the world.  Every year new species are discovered even after more than 75% of its original habitat has been lost due to the intensification of anthropogenic pressures.

The Philippine Duck, Anas luzonica Fraser, 1839, is the only dabbling duck species endemic to the Philippines.  One can find it in both freshwater and saltwater habitats, including mangroves, open sea and watercourses inside forests.  It feeds on fish, shrimps, insects, rice and young vegetation.  The population has declined sharply in the last few decades due to overhunting and habitat destruction, mainly clearing of mangroves for shrimp farms, conversion of wetlands for aquaculture and pollution of wetlands due to pesticide-laden runoff from surrounding rice fields.

Photographs of stuffed specimens that came from a batch of 46 individuals confiscated from Pantabangan, Nueva Ecija.  DNA was extracted from tissue samples of these individuals.  Photos by Ronniel Pedales.

From 10,000-100,000 individuals in 1993 to fewer than 10,000 by 2002 and the number has dropped to fewer than 5,000 according to the current estimates.  Considered as one of the most globally threatened Anatidae species, it is listed as Vulnerable by IUCN and is legally protected in five sites of the Philippines.  Even after these conservation measures, this alarming trend is continuing, with local extinctions and near-disappearances reported at several significant sites.  Morphological features can be confusing for its identification, especially when it is easy to traffic as domestic meat.  Ardea Licuanan, Mariano Roy Duya, Perry Ong and Ian Fontanilla at the University of Philippines, Diliman were motivated by this challenge to generate DNA barcodes for the Philippine duck to assist in accurate and quick identification, which they published in the May 2017 issue of the Journal of Threatened Taxa*.

But first, let us get familiar with the concept of DNA barcoding. Just like we barcode products in supermarkets, which can be scanned to get a particular product’s details instantly, similarly DNA barcoding facilitates species identification without relying on its morphological features.  A DNA barcode is a standardised short DNA sequence that can be recovered and characterised for species identification while DNA barcoding is the technique for analysing it.  We can say that DNA barcode is the taxonomic GPS. Just sequence a DNA barcode of an unidentified specimen and voila, it is identified without knowing anything about it beforehand.  It is a rapid and cost-efficient technique that aids biodiversity inventory and makes information accessible to the scientific community, decision-makers and managers.  It is especially very helpful in identifying species of conservation significance that are illegally hunted, highly valued in traditional medicine and unsustainably harvested.  The most commonly used marker in animals is the mitochondrial cytochrome c oxidase 1 gene or CO1 sequence because nearly all organisms carry a version of it in their mitochondria.  It is short enough to be sequenced quickly and economically, and long enough for detecting variations among species.

The team extracted CO1 sequences from adult Philippine Duck individuals that were confiscated by agents of the Philippine National Police and the Department of Environment and Natural Resources from Pantabangtan, Nueva Ecija, and came up with some interesting results.  They successfully generated 46 CO1 DNA barcodes with three unique COI DNA sequences.  The DNA barcode could differentiate the Philippine Duck from 25 other <em>Anas</em> species, but it failed to do so between hybridising species.  Now, this is where it gets complicated.  Though thought to be an unusual event in nature, hybridization is quite common among Anas species, i.e., different species can sometimes mate with each other and produce fertile offspring.  It is known to cause decreased genetic divergence between two species such that genetically they are difficult to distinguish.  They also assessed the population genetic structure of the samples and found a reduced genetic fitness, an indication of bottleneck event likely to happen. Will the Philippine Duck end up like the Brow-antlered Deer of India or locally called Sangai?

The Sangai is endemic to Keibul Lamjao National Park of Manipur.  Even though it made an extraordinary comeback from the brink of extinction, the bottleneck has led to decreased genetic diversity among its individuals.  Another more popular example from India is of the Asiatic Lion, found only in the Gir Forest National Park, Gujarat.  If we compare DNA fingerprints of its individuals, they are as similar as identical twins in humans.  Both of the species exist as a single isolated population in India and their alarmingly low levels of genetic diversity pose a high risk of extinction.  It would be interesting to see how hybridization and declining genetic fitness of Philippine Duck will affect its survival and how reliable DNA barcoding will be for its conservation.  As the samples were from just one locality, extensive sampling is required from all over the Philippines to see if the other populations show the similar decline in genetic fitness.

With DNA barcodes of the Philippine Duck now available, it is expected to enable timely identification of confiscated specimen and control its illegal trade.  The results of the population genetic analysis point to the need for stricter and more effective conservation policies as the declining population trend shows that the present measures are not working.  Special focus is required on community-based conservation as the human activities are the likely cause of the declining population of the duck.  Hence, policies and conservation initiatives should take into account the interests of local communities and their dependence on the natural resources.  Also, as responsible tourists and citizens of this planet, we can help by making eco-friendly and sustainable choices and informing others of the same.

Even though a majority of the scientific community has accepted DNA barcoding as a revolutionary new technique for species identification and inventory, there is also a growing opposition to it, especially among taxonomists.  There are technical, political and ethical issues associated with it but DNA barcoding is here to stay.  However, integration of DNA barcode with morphological data of an organism makes more sense for a reliable species identification than to consider either of them alone for the job, given both of them have their own limitations.

Reference

* Licuanan, A.M., M.R.M. Duya, P.S. Ong & I.K.C. Fontanilla (2017). DNA barcoding, population genetics, and phylogenetics of the illegally hunted Philippine Duck Anas luzonica (Aves: Anseriformes: Anatidae). Journal of Threatened Taxa 9(5): 10141–10150; https://doi.org/10.11609/jott.2253.9.5.10141-10150