A team of researchers led by the University of Illinois Urbana-Champaign has developed a new DNA-collection method that allows scientists to capture genetic information from wildlife without disturbing the animals or putting their own lives into jeopardy. The experts tested this protocol on elephant dung and managed to collect enough DNA to sequence the whole genomes not only of the elephants, but also of the microbes, plants, and other organisms associated to them.
“We combined existing methodologies in such a way that we are now able to use noninvasive samples to generate genome-scale data,” said study lead author Alida de Flamingh, a postdoctoral researcher in Genetics and Ecology at Illinois. “This allows us to assess wildlife populations without having to dart, capture, or immobilize animals.”
According to study co-author Alfred Roca, a professor of Animal Sciences at the same university, collecting DNA from animal dung is not something new. “Elephant fecal samples have been used for decades to study the genetics of elephants,” he said. “But this relies on very cumbersome methods, often involving chemicals that in some cases may be dangerous. The collections are bulky, they’re hard to ship and they have to be refrigerated, making the whole process very costly.”
Now, the researchers tested a less expensive alternative: using small data-collection cards that have previously been treated to prevent the samples from degrading, allowing to store them for months without refrigeration.
First, the scientists collected and analyzed samples from zoo elephants to determine how long after defecation the fecal samples would still yield viable genomic data. The analysis revealed that even after 72 hours, the samples could be reliably used for genomic sequencing. In a next step, the team tested this procedure on samples collected from wild African savanna elephants. The sequencing led to treasure trove of information.
“I was surprised. I thought we might get some elephant DNA from the cards, but I was thinking on the order of two percent. However, on average, more than 12 percent of the DNA was attributed to the elephant,” Roca reported.
Since this was achieved without using costly and time-consuming laboratory methods that target only elephant DNA, each sample yielded a vast amount of information not only about the elephants, but also the microbial composition of their guts, their habitat, and diet.
“It’s really beneficial to get an idea of everything that’s in there because now you can start asking questions, not only about elephant genomes but also about things like their health, their diet and whether there are pathogens or parasites present,” de Flamingh explained.
According to the researchers, when it comes to elephant genomes, the results are comparable with – or even better than – those obtained from blood samples. “You can explore the connectivity of different elephant populations, the level of genetic diversity, the level of inbreeding and relatedness among elephants. And I would say there are lots of reasons you don’t want to have to collect blood samples from wild elephants,” Roca said.
“It’s possible to do what you could do with blood, but it goes beyond that. You now can do analyses that you couldn’t do before with blood DNA, which only provides information about the elephant’s genome,” de Flamingh concluded.
The study is published in the journal Frontiers in Genetics.
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