Team streamlines DNA collection and analysis for wildlife conservation
University of Illinois at Urbana-Champaign, Phys.org
January 12, 2023
See link https://phys.org/news/2023-01-team-dna-analysis-wildlife.html
A new DNA-collection approach allows scientists to capture genetic
information from wildlife without disturbing the animals or putting their
own safety in jeopardy. The protocol, tested on elephant dung, yielded
enough DNA to sequence whole genomes not only of the elephants but also of
the associated microbes, plants, parasites and other organisms—at a
fraction of the cost of current approaches.
The researchers report their findings in the journal Frontiers in Genetics.
"We combined existing methodologies in such a way that we are now able to
use noninvasive samples to generate genome-scale data," said Alida de
Flamingh, a postdoctoral researcher at the University of Illinois
Urbana-Champaign who led the work with U. of I. animal sciences professor
Alfred Roca. "This allows us to assess wildlife populations without having
to dart, capture or immobilize animals."
Collecting DNA from elephant dung is not new, Roca said.
"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."
De Flamingh tested a relatively inexpensive alternative: using
postcard-sized data-collection cards that have been treated to prevent the
samples from degrading. Previous research has shown that once samples are
smeared on the cards, they can be stored for months without refrigeration.
The inspiration for the study came from de Flamingh's work with U. of I.
anthropology professor and study co-author Ripan Malhi, whose laboratory
focuses on ancient DNA.
"Ancient DNA can be problematic because samples are degraded and may yield
very low levels of target species DNA," de Flamingh said. Obtaining genomic
data from dung can be similarly challenging, with lower elephant DNA
concentrations than are available from blood samples. "I thought, this
sounds like an excellent opportunity to test whether the same methodologies
can be applied to noninvasive samples to generate the same type of data."
The team first collected samples from zoo elephants in experiments designed
to determine how long after defecation the dung would yield viable genomic
data. The Jacksonville Zoo and Gardens in Florida and the Dallas Zoological
Gardens allowed the team to collect samples from their African savanna
elephants. The researchers retrieved the samples immediately after
defecation and 24, 48 and 72 hours later.
Their tests revealed that even three-day-old dung yielded enough DNA for
genomic studies of the elephants.
The researchers next tested their approach on samples collected from wild
African savanna elephants. Study collaborator and co-author Rudi van Aarde,
a professor emeritus of zoology and entomology at the University of
Pretoria, South Africa, and his colleagues used the cards to collect
elephant dung samples after identifying a geographically and ecologically
diverse set of wild areas across South Africa.
By running the sequence data obtained from the cards through genomic
databases, the team found a treasure trove of information in the dung.
"I was surprised," Roca said. "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 was attributed to the elephant."
This was achieved without using laboratory methods that target only
elephant DNA, a costly and time-consuming procedure, the researchers said.
As a result, each sample yielded a vast amount of data about the elephant,
the microbial composition of its gut, its habitat and diet. The researchers
even detected the DNA of butterflies and other arthropods that interact
with the dung after it is deposited.
"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 said.
When it comes to the elephant genomes, the results are comparable to those
obtained via blood samples, Roca said.
"You can explore the connectivity of different elephant populations, the
level of genetic diversity, the level of inbreeding and relatedness among
elephants," he said. "And I would say there are lots of reasons you don't
want to have to collect blood samples from wild elephants."
"It's possible to do what you could do with blood, but it goes beyond
that," de Flamingh said. "You now can do analyses that you couldn't do
before with blood DNA, which only provides information about the elephant's
De Flamingh is a postdoctoral researcher and Malhi and Roca are professors
at the Carl R. Woese Institute for Genomic Biology at the University of