A Javan rhino death news in the last two years were spread on the media in 2018 and 2019. This is a shocking due to the fact that it only takes one year after the death of Samson back in April 2018; we lost another one – a juvenile male rhino, Manggala in April 2019. Manggala’s death was found first by the Rhino Health Unit (RHU) team that was doing their regular trajectory activity in order to collect fecal samples for the Javan rhino DNA analysis. What is trajectory? Trajectory method is an intensive Javan rhino monitoring method where the team in the field will follow the Javan rhino individual target to collect its fecal samples. According RHU team supervisor, Drh. Zulfiqri, Wildlife Health Monitoring Specialist WWF Indonesia – Ujung Kulon Program, the initial individual target that they are trying to follow was not Manggala, but Dipati, an adult male Javan rhino that were caught several times in the camera trap of that grid, however they haven’t got a chance to find Dipati, they found Manggala’s body in the wallow instead.
The Javan rhino DNA analysis an Ujung Kulon National Park (UKNP) program that collaborated with WWF Indonesia that projected as the species division of WWF Indonesia – Ujung Kulon’s main program. It became the main program due to its significance genetic data that can inform us the kinship of the Javan rhino within the population. In addition, Javan rhino only has a single and small population in Ujung Kulon National Park. With the vulnerability of the UKNP’s carrying capacity that has been identified, certainly it is a huge risk to keep the Javan rhino population in one population pocket. The second habitat discourse still becomes the best solution in the Javan rhino conservation, however, the Javan rhino individual genetic profile also will help on the individual selection that will be translocated to the second population pocket. The Javan rhino genetic profile mapping will also answer the level of inbreeding that occurred in the assumed Javan rhino population due to its small population, the inbreeding risk is high.
A collaborated research of UKNP, Eijkmann Institute, Yayasan Badak Indonesia (YABI), and WWF Indonesia – Ujung Kulon Program in 2014 was conducted to collect random fecal samples to assess the Javan rhino population size. From the research, there were 49 fecal samples that collected randomly. Through a DNA analysis approach, the team identified 19 different individuals that produce 2 halotypes (a genotype characteristic that inherited by one of the parents) that showed that all 19 individuals are from two maternal lines. This is truly concerning among the Javan rhino conservationists since how low the diversity of the Javan rhino genetic in its developing generation. This becomes the baseline of how significance the genetic study because there are so many things that can be unraveled using the genetic analysis approach.
For years, UKNP and WWF Indonesia – Ujung Kulon Program were trying to formulate target and main purpose of the Javan rhino DNA analysis which finally realized by collaborating with Institute for Research and Community Services of Biological Resources Research Center and Biotechnology Bogor Agriculture University (Lembaga Penelitian dan Pengabdian Masyarakat Pusat Penelitian Sumberdaya Hayati dan Bioteknologi Institut Pertanian Bogor/LPPM IPB) in 2017 for the Javan rhino genetic analysis. The main purpose of this research is to collect Javan rhino individual DNA profile data that can be mapped and used as the policy rationale on the individual selection for the second population. This collaboration is a unique one because the frame work of the sampling in the field will determine the result that obtained in the laboratory.
Fecal sample is only one of the various biological samples that can be used for Javan rhino genetic analysis such as blood, tissue, skin, muscle, and bone samples. Ideally the samples that usually used is blood samples, however because the Javan rhino blood sampling is considered invasive since the Javan rhino is prone to stress. The effort of the Javan rhino blood sampling is also known to be huge because it needs a collaboration and understanding of the multi stakeholders regarding the procedure and side effect that may have occurred from the blood sampling that needs anesthesia before the collection. Fecal sampling is considered to be a non invasive method and the most ideal one at this moment. Every month, fecal samples will be collected by the RHU team using trajectory method. Trajectory method will reduce the possibility of random fecal sampling that can deteriorate the sample processing in the laboratory. Each month, the RHU team will review and decide together with the UKNP Agency of the selected individual target for fecal sampling.
In the laboratory, the fecal sample will be processed into the DNA extraction. DNA extraction is method to extract the DNA from the cell, including the nucleus cell. The, we will obtain only the DNA to be tested. The Javan rhino fecal sample is still contains undigestible food plant, thus it needs an optimal method to extract the Javan rhino DNA only without the interference of other food plant DNA. This is different with the blood samples where its extraction protocol has been standardized since it is considered to be clearer from the contaminant. The extracted DNA will be assessed qualitatively and quantitatively to see the purity and the concentration of the DNA. The indicator of a good extracted DNA can be seen from the visible and clear DNA band during the electrophoresis visualization or show no visible other DNA band such as protein. After the DNA is extracted, the DNA will be amplified enzymatic using the PCR (Polymerase Chain Reaction). The enzymatic reaction is a reaction that involves enzymatic work using polymerase enzyme. Similar to DNA extraction, PCR process also needs an optimal protocol which can made the sample processing longer than usual. In addition, the proper genetic marker also will determine the Javan rhino DNA analysis process. What is the genetic marker? Genetic marker is an individual identification based on its genetic characteristic (genotype). The nucleus DNA marker comprises microsatellite and functional DNA. In the population with the low DNA diversity, microsatellite is highly functional to differentiate one individual to another.
At this moment, the microsatellite usage in the Javan rhino population is not yet used profusely. This resulted of the Javan rhino microsatellite isolation is still using the Vietnam Javan rhino. The difficulties on developing the Javan rhino microsatellite is due to the samples that used for the developing it is suggested to be from blood samples, which until now has never been done yet.
DNA analysis to get DNA profile is an innovative approach for the Javan rhino conservation effort. Through this approach, the Javan rhino kinship can be identified and mapped, thus it will reduce the inbreeding that will produce individuals with good DNA survival rate. Through DNA approach, we can also monitor the Javan rhino individuals that have good genetic quality that can help for the second population program in the future.
In practical, DNA analysis is certainly facing a lot of constrains. However, it is a developing and promising approach for the Javan rhino conservation. Hopefully, using this molecular approach, the future of the Javan rhino conservation can be conducted better by working together with the government and partners.