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.
Alida de Flaming, a postdoctoral researcher at the University of Illinois, Urbana-Champaign, who led the work with the U.S. First, Professor of Zoology 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.
“the elephant stool samples They have been used for decades to study the genetics of elephants. “But this relies on very cumbersome methods, often involving chemicals that can be dangerous in some cases. The kits are bulky, difficult to ship and must 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 the U.S. anthropology professor.
“Ancient DNA can be problematic because the samples degrade and may result in very low levels of DNA for the target species,” de Flamming said. Obtaining genomic data from dung can similarly be challenging, with lower concentrations of elephant DNA than is available from blood samples. “I thought this seemed like an excellent opportunity to test whether the same methodologies could 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 they could produce droppings. 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 Rudi van Aarde, an 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 sequence data The cards were obtained through genetic databases, and the team finds 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 the DNA is attributed to the elephant.”
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 start asking questions, not just about the elephants’ 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.”
de Flaming is a postdoctoral researcher and Malhey and Roca are professors at the Carl R. Woese of Genomic Biology at the University of Illinois.
The combination of non-invasive fecal DNA methods enables whole genome and metagenome analyzes of wildlife biology, Frontiers in genetics (2023). DOI: 10.3389/fgene.2022.1021004
University of Illinois at Urbana-Champaign
the quote: Team Simplifies DNA Collection and Analysis for Wildlife Conservation (2023, January 12), Retrieved January 12, 2023 from https://phys.org/news/2023-01-team-dna-analysis-wildlife.html
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