A new approach to collecting DNA allows scientists to capture genetic information from wildlife without disturbing the animals or putting their safety at risk. Tested on elephant dung, the protocol yielded enough DNA to sequence the complete genome of not only elephants but also their associated microbes, plants, parasites and other organisms — at a fraction of the cost of current methods.
The researchers report their findings in the journal Frontiers in genetics.
“We have combined existing methodologies in such a way that we can now use non-invasive samples to generate genome-wide data,” he said. Alida de Flaminga postdoctoral researcher at the University of Illinois at Urbana-Champaign who led work with the U. of I. animal science professor Alfred Roca. “This allows us to assess wildlife populations without having to throw, capture or immobilize the animals.”
Rocca said collecting DNA from elephant dung is nothing new.
“Elephant poop samples have been used for decades to study elephant genome,” he said. But this relies on very cumbersome methods, often involving chemicals that can be dangerous in some cases. The kits are huge, difficult to ship and have to be refrigerated, which makes the whole process very expensive.”
De Flamingh tested a relatively inexpensive alternative: using postcard-sized data collection cards that had been processed to prevent samples from deteriorating. Previous research has shown that once samples are smeared onto cardstock, they can be stored for several months without refrigeration.
The inspiration for the study came from de Vlaming’s work with Yu. anthropologistProfessor and co-author of the study Rayban Malhiwhose lab focuses on ancient DNA.
“Ancient DNA can be problematic because the samples degrade and may result in very low levels of DNA for the target species,” said de Vlaming. Obtaining genomic data from dung can similarly be difficult, with lower concentrations of elephant DNA than is available from blood samples. “I think this is an excellent opportunity to test whether the same methodologies can be applied to non-invasive samples to generate the same type of data.”
The team first collected samples from the zoo’s elephants in experiments designed to determine how long after defecation the droppings could yield applicable genomic data. The Jacksonville Zoo and Gardens in Florida and the Dallas Zoo allowed the team to collect samples from African savannah elephants. The researchers retrieved the samples immediately after defecation and 24, 48 and 72 hours later.
Their tests revealed that even a three-day-old dung produced enough DNA for genetic studies of elephants.
The researchers then tested their approach on samples collected from wild African savannah elephants. Study collaborator and co-author Rudy Van Ardean emeritus professor of zoology and entomology at the University of Pretoria, South Africa, and colleagues used the cards to collect elephant dung samples after identifying a geographically and ecologically diverse group of wild areas across southern Africa.
By running the sequence data obtained from the cards through genetic databases, the team found a treasure trove of information in the dung.
“I was surprised,” said Roca. “I thought we might get some elephant DNA from the cards, but I was thinking on the order of 2%. However, on average more than 12% of elephant DNA has been attributed to.”
The researchers said this was achieved without using laboratory methods that target only elephant DNA, which is an expensive and time-consuming procedure. As a result, each sample provided an enormous amount of data about the elephant, the microbial composition of its gut, its habitat and its diet. Researchers have even discovered the DNA of butterflies and other arthropods that interact with dung after it is deposited.
“It’s really helpful to get an idea of everything there because now you can ask questions, not just about elephant genomes but also about things like their health and diet and whether there are pathogens or parasites,” de Flamming said.
When it comes to elephant genomes, Roca said, the results are similar to those obtained with blood samples.
“You can explore the interdependence of different elephant groups, the level of genetic diversity, the level of inbreeding and the relationship between elephants,” he said. “And I would say there are a lot of reasons why you wouldn’t want to collect blood samples from wild elephants.”
“It’s possible to do what you can do with blood, but it goes beyond that,” said de Flaming. “You can now do analyzes that you couldn’t do before with blood DNA, which only provides information about the elephant genome.”