Lost frogs rediscovered with environmental DNA

Date:
September 8, 2020
Source:
Cornell University
Summary:
Scientists have detected signs of a frog listed extinct and not
seen since 1968, using an innovative technique to locate declining
and missing species in two regions of Brazil.



FULL STORY ========================================================================== Scientists have detected signs of a frog listed extinct and not seen
since 1968, using an innovative technique to locate declining and missing species in two regions of Brazil.


==========================================================================
The frog, Megaelosia bocainensis, was among seven total species --
including four other declining species, and two that had disappeared
locally for many years -- that were detected. The findings appeared in
a paper, "Lost and Found: Frogs in a Biodiversity Hotspot Rediscovered
with Environmental DNA," published in August in Molecular Ecology.

Megaelosia bocainensis. A disappeared species from Parque Nacional da
Serra da Bocaina, Brazil, known only from this museum specimen collected
in 1968, and detected by eDNA surveys. In the study, the researchers
collected and screened environmental DNA (eDNA) in the biodiverse Atlantic Coastal Forest and Cerrado grasslands of Brazil.

The eDNA technique offers a way to survey that can confirm the presence
of species undetected by traditional methods, providing a tool for
conservation scientists to evaluate the presence of threatened species, especially those with low population densities and those not seen
in years.

After careful research to identify species at various levels of threat in
these regions of Brazil, the researchers used the eDNA method to search
for 30 target amphibian species in six localities where the frogs were
known to previously live.

"Little bits of DNA in the environment don't tell us about how many
individuals there are or whether those individuals are healthy, but
it does tell us that the species is still present," said senior author
Kelly Zamudio, the Goldwin Smith Professor of Ecology and Evolutionary
Biology in the College of Arts and Sciences.



========================================================================== "This is one more kind of survey data, and for species that are declining
or locally disappeared, it not only means they are there, but there's
now the potential to study them in more detail," she said, noting that
for many species, very little is known.

Around the world, conservationists have been challenged to keep pace
with declining and disappearing amphibians. At the same time, living
organisms leave DNA traces in the soil, water and air. Now, scientists
are increasingly using highly sensitive sampling techniques to detect
eDNA for conservation purposes.

In the study, the researchers targeted 13 frog species that have totally disappeared and are presumed extinct; 12 frogs that have disappeared
locally but are still found in other parts of their range; and five
species that were once very abundant and are still there but hard to find.

The researchers hiked into the sampling sites carrying battery packs,
a shoebox-sized peristaltic pump and backpacks of sterile tubing. They
used the pump and tubing to draw up to 60 liters of stream or pond water through a capsule fitted with a filter for capturing DNA. A buffer was
then applied to stabilize and preserve the DNA on the filter.

Back in the lab, the researchers extracted the DNA, genetically sequenced
it, weeded out genetic material from humans, pigs, chickens and other
organisms until they could isolate all the frog DNA.



==========================================================================
"Now you've got a subset of genetic sequences that we know only belong
to frogs, and then it's step by step, going finer and finer, until you
get to the genus and species you are looking for," Zamudio said.

Identifying M. bocainensis required clever detective work: The species disappeared long ago, and there were no tissues from which to extract DNA
for comparison with the eDNA. But the researchers did have the sequences
for all the sister species in the genus Megaelosia and they knew the
ranges of the sister species and M. bocainensis.

"We know there's a Megaelosia there," Zamudio said, "we just don't know
which one it is, but the only one that has ever been reported there historically is the one that went missing. Do we believe it? That's how
far the analysis can take us." Zamudio added that samples from nearby
areas may be worth collecting for more signs of M. bocainensis.

Carla Martins Lopes, a researcher at Sa~o Paulo State University in
Brazil, is the paper's first author.

The Brazilian National Council for Scientific and Technological
Development and the Sa~o Paulo Research Foundation funded the study.


========================================================================== Story Source: Materials provided by Cornell_University. Original written
by Krishna Ramanujan. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Carla Martins Lopes, De'lio Bae^ta, Alice Valentini, Mariana
Lu'cio Lyra,
Ariadne Fares Sabbag, Joa~o Luiz Gasparini, Tony Dejean, Ce'lio
Fernando Basptista Haddad, Kelly Raquel Zamudio. Lost and found:
Frogs in a biodiversity hotspot rediscovered with environmental
DNA. Molecular Ecology, 2020; DOI: 10.1111/mec.15594 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/09/200908131127.htm

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