DNA From Dung CERC Researchers Develop Non-Invasive Techniques For Studying Wild Animal Populations
Scientists from the Center for Environmental Research and Conservation (CERC), a member of the Earth Institute at Columbia University, have developed non-invasive collection, extraction, and amplification protocols providing high quality DNA from an animal’s dung. The DNA is targeted from cells sloughed from the gut lining. Their research techniques, publishing in the Journal of Heredity, will enable a broad application of genetic analysis, particularly with regard to endangered, elusive, or aggressive species.
Genetic study on many species is both a difficult and stressful process, as the purest collection technique is to draw a blood sample or collect a piece of tissue. For wild animals, this requires that they are captured and handled. Drs. Prithiviraj Fernando and Don J. Melnick of CERC have developed inexpensive and reliable techniques that amplify mitochondrial and nuclear DNA from an animal’s dung. Their new protocols have proven to overcome previous barriers to non-invasive sampling, including contamination, low quality, and degradation of DNA.
How and from what ancestors a species evolved over millions of years, changes in geographic distribution, and behavioral characteristics, are among the insights held in each individual’s DNA. The ability to identify individuals genetically (genotyping) enables researchers to obtain information relevant to management and conservation, such as estimating population size, sex ratios, reproductive success and dispersal. “The advantages of using dung for genetic studies are tremendous. All animals defecate regularly, it is easy to find and collect, and storage and transport require little technology or expense,” said Fernando. The study compared the genetic results from both blood and dung samples of 20 Asian elephants to identify any differences in reliability between the two sources. Extracted DNA from both sources was amplified by PCR (Polymerase Chain Reaction) for a number of nuclear loci multiple times. A minor level of error was seen in the DNA extractions between the blood and dung, however, when two extractions from dung were coupled with a single amplification from each, the error was eliminated.
The age and location of the dung is a factor as environmental variables such as temperature, humidity, and exposure to sun can allow bacterial activity to degrade the DNA. The researchers recommend that the dung be 24 hours old or less, but they have extracted good DNA from dung as old as a few weeks.
“The advances we have made in these methods will greatly enhance the use of genetics to collect population data on animals we will never see with our own eyes, including the most endangered large mammal in the world, the Javan rhino,” said Melnick, who is also the executive director of CERC.
Studies in the CERC lab have found that non-invasive DNA extraction from dung works on other mammals, including rhinos, apes, monkeys, and canids, as well as other groups of vertebrates such as birds, reptiles and amphibians. The researchers suggest that it will work for most, if not all, animal species, however, since the DNA is derived from cells sloughed during gut passage, the quantity of DNA obtained may vary with the individual’s diet and digestive system. Each species will need to be assessed to determine the optimum quantity of dung needed.
This spring, the researchers will work in Sri Lanka, Java, and Vietnam to collect dung from elephants, rhinos, and other endangered species, in order to obtain information that can be used for their conservation and management.
Center for Environmental
Research and Conservation
A consortium of five leading science and education institutions—Columbia University, the American Museum of Natural History, The New York Botanical Garden, the Wildlife Conservation Society, and Wildlife Trust—the Center for Environmental Research and Conservation employs a wide array of resources to train the next generation of environmental leaders charged with conserving Earth’s biological diversity.
The Earth Institute at Columbia University is among the world’s leading academic centers for the integrated study of Earth, its environment, and society. The Earth Institute builds upon excellence in the core disciplines—earth sciences, biological sciences, engineering sciences, social sciences and health sciences—and stresses cross-disciplinary approaches to complex problems. Through its research training and global partnerships, it mobilizes science and technology to advance sustainable development, while placing special emphasis on the needs of the world’s poor.