Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA)
Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 6, 2025
ABSTRACT
The
advance
of
environmental
DNA
(
eDNA
)
has
enabled
rapid
and
non‐invasive
species
detection
in
aquatic
environments.
While
most
studies
focus
on
detection,
recent
works
explored
using
concentration
to
quantify
abundance.
However,
the
differential
individual
contribution
samples
could
easily
obscure
concentration‐species
abundance
relationship.
We
propose
number
segregating
sites
as
a
proxy
for
estimating
Segregating
reflect
genetic
diversity
population,
which
is
less
sensitive
than
concentration.
examined
relationship
between
silico,
vitro,
situ
experiments,
two
brackish
goby
species,
Acanthogobius
hasta
Tridentiger
bifasciatus
.
Analyses
simulated
vitro
data
with
mixed
from
known
individuals
showed
strong
correlation
R
2
>
0.9;
p
<
0.01).
In
we
analysed
collected
mesocosm.
results
further
validated
that
=
0.70,
0.01)
was
not
affected
by
biotic
factors,
including
body
size
feeding
behaviour
0.05).
cross‐validation
test
also
predicted
bias
variability
Overall,
among
compared
This
advancement
can
significantly
enhance
proficiency
Язык: Английский
A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light, and temperature
Environmental DNA,
Год журнала:
2024,
Номер
6(4)
Опубликована: Июль 1, 2024
Abstract
Environmental
DNA
(eDNA)
degradation
influences
the
effectiveness
of
eDNA‐based
biodiversity
monitoring,
but
factors
that
determine
rate
decay
eDNA
in
terrestrial
environments
are
poorly
understood.
We
assessed
persistence
vertebrate
from
a
mock
community
created
with
soil
zoo
enclosures
holding
10
target
species
different
taxonomic
classes
(reptiles,
birds,
and
mammals)
biomass
(little
penguin
giraffe).
examined
detection
rates
resulting
metabarcoding,
as
well
relative
concentrations
via
qPCR,
samples
over
eight
time
points
(0–12
weeks),
during
exposure
to
three
ambient
temperatures
(10,
25,
40°C)
levels
ultraviolet
B
(UV‐B)
radiation
(0%,
50%,
100%
intensity).
recorded
considerable
variation
detectability
between
species,
independent
temperature,
UV‐B
effects.
Quantitative
polymerase
chain
reaction
(PCR)
indicated
for
all
temperature
UV
treatments,
although
it
was
still
possible
detect
some
after
12
weeks.
Degradation
were
lowest
high
presumably
due
reducing
bacterial
metabolism.
The
investigated
did
not
influence
decay.
Our
results
indicate
can
persist
under
range
longer
than
expected.
Sheltered
sites
minimal
radiation,
which
have
previously
been
considered
ideal
collection,
may
be
optimal
cases
microbial
A
better
understanding
is
needed
enhance
accuracy
metabarcoding
surveying
communities.
Язык: Английский
Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations
Frontiers in Conservation Science,
Год журнала:
2025,
Номер
5
Опубликована: Янв. 2, 2025
Introduction
Rewilding,
the
facilitation
of
self-sustaining
and
resilient
ecosystems
by
restoring
natural
processes,
is
an
increasingly
popular
conservation
approach
potential
solution
to
biodiversity
climate
crises.
Outcomes
rewilding
can
be
unpredictable,
monitoring
essential
determine
whether
are
recovering.
Metabarcoding,
particularly
environmental
DNA
(eDNA),
revolutionizing
could
play
important
role
in
understanding
impacts
but
has
mostly
been
applied
within
aquatic
systems.
Methods
This
systematic
review
focuses
on
applications
eDNA
metabarcoding
terrestrial
monitoring,
with
additional
insights
from
bulk
ingested
DNA.
We
examine
publication
trends,
choice
sampling
substrate
focal
taxa,
investigate
how
well
performs
compared
other
methods
(e.g.
camera
trapping).
Results
Terrestrial
represented
a
small
proportion
total
papers,
forests
most
studied
system,
soil
water
substrates,
vertebrates
targeted
taxa.
Most
studies
focused
measuring
species
richness,
few
included
analyzes
functional
diversity.
Greater
richness
was
found
when
using
multiple
took
this
approach.
Metabarcoding
did
not
consistently
outperform
terms
number
vertebrate
taxa
detected,
likely
influenced
marker,
habitat.
Discussion
Our
findings
indicate
that
metabarcoding,
eDNA,
key
rewilding,
further
ground-
truthing
needed
establish
appropriate
experimental
pipelines
for
target
system
interest.
Systematic
Review
Registration
https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0
,
identifier
38w9q.
Язык: Английский
From Water to Land: A Review on the Applications of Environmental DNA and Invertebrate‐Derived DNA for Monitoring Terrestrial and Semi‐Aquatic Mammals
Mammal Review,
Год журнала:
2025,
Номер
unknown
Опубликована: Май 5, 2025
ABSTRACT
Terrestrial
and
semi‐aquatic
mammals
are
facing
increasing
threats
globally,
highlighting
the
need
for
reliable
data
on
species'
occurrence,
distribution,
abundance
effective
conservation
efforts.
However,
obtaining
robust
information
over
broad
spatial
temporal
scales
remains
a
significant
challenge.
Environmental
DNA
(eDNA)
invertebrate‐derived
(iDNA)
applications
have
emerged
as
powerful
surveying
methods,
with
potential
to
revolutionise
ecological
monitoring
by
improving
species
detections
providing
better
insights
into
mammalian
distribution
diversity.
While
eDNA
relies
genetic
material
shed
their
surroundings,
iDNA
leverages
from
invertebrates
that
interact
mammals.
Both
approaches
offer
cost‐effective
means
obtain
records
community
diversity
metrics.
This
review
explores
global
of
e/iDNA
terrestrial
By
comprehensive
overview
applications,
sampling
design,
challenges,
prospects,
this
serves
guide
researchers
conservationists
seeking
use
evaluating
current
state
identifies
challenges
milestones
be
addressed
these
methods
become
practical
method
scale.
It
highlights
further
research
enhance
sensitivity
reliability
detections,
standardisation
methodologies,
validation
through
comparison
traditional
methods.
sheds
light
valuable
tools
aiding
mammal
inspiring
future
advancements
in
field.
Язык: Английский
Metazoan diversity in Chilean hypersaline lakes unveiled by environmental DNA
Frontiers in Ecology and Evolution,
Год журнала:
2025,
Номер
13
Опубликована: Янв. 31, 2025
Saline
and
hypersaline
wetlands
are
biodiversity
hotspots
for
metazoans
such
as
aquatic
invertebrates
wading
birds.
However,
the
survival
of
these
habitats
their
biota
is
increasingly
threatened
by
a
combination
pressures
from
climate
change
extractive
processes.
With
goal
improving
conservation
efforts
in
ecosystems,
this
study
tests
use
eDNA
methods
metazoan
biomonitoring.
We
employed
multi-assay
approach
utilizing
three
genetic
markers—12S
rRNA,
18S
COI
—to
analyze
sediment
water.
Samples
were
collected
lakes
Northern
Chile:
Salar
de
Atacama
(Laguna
Puilar),
Pujsa,
Tara.
outputs
also
compared
with
results
generated
macroinvertebrate
assessments
using
kick-nets.
Our
analyses
revealed
total
21
22
taxa
across
water,
respectively.
The
highest
diversity
was
found
Tara
(15
within
13
water).
design
detected
range
resident
different
status,
spanning
rotifers
to
endangered
snails,
amphipods
flamingos.
Macroinvertebrate
data
via
kick-net
surveys
further
validated
most
biodiverse
system.
Compared
net-based
assessments,
analysis
allowed
more
refined
taxonomic
assignments
copepods
ostracods,
while
certain
Ephydridae
or
Hirudinea
not
through
molecular
tests.
Overall,
provides
evidence
that
an
effective
tool
elucidate
fine
scale
assemblages
can
refine
lakes.
Язык: Английский
A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture‐Based DNA Metabarcoding
Ecology and Evolution,
Год журнала:
2025,
Номер
15(4)
Опубликована: Апрель 1, 2025
ABSTRACT
Pollen
identification
(ID)
and
quantification
is
important
in
many
fields,
including
pollination
ecology
agricultural
sciences,
efforts
to
explore
optimal
molecular
methods
for
identifying
low
concentrations
of
DNA
from
plant
mixtures
are
increasing,
but
quantifying
mixture
proportions
remains
challenging.
Traditional
pollen
ID
using
microscopy
time‐consuming,
requires
expertise
has
limited
accuracy
throughput.
Molecular
barcoding
approaches
being
explored
offer
improved
The
common
approach,
amplicon
sequencing,
employs
PCR
amplification
isolate
barcodes,
introduces
significant
bias,
impairing
downstream
quantification.
We
apply
a
novel
hybrid
capture
approach
artificial
improve
upon
current
taxon
methods.
method
randomly
fragments
uses
RNA
baits
which
allows
duplicate
removal,
reducing
bias.
Four
reference
databases
were
used
A
restricted
matK
database
containing
only
species
yielded
sequence
highly
correlated
with
input
proportions,
demonstrating
the
potential
usefulness
metabarcoding
mixtures.
Identification
power
was
further
tested
two
libraries
constructed
publicly
available
sequences:
plastid
barcode
RefSeq
complete
chloroplast
references.
Single
barcode‐based
did
not
consistently
resolve
or
genus
level.
performed
better
qualitatively
had
coverage
(relative
here)
introduced
issues.
At
family
level,
both
comparable
qualitative
results,
quantitatively.
Whilst
developed
here
tremendous
potential,
choice
expansion
one
most
factors
allowing
quantitative
full
set
genomic
regions
screened
by
this
method.
Язык: Английский
Estimation of Species Abundance Based on the Number of Segregating Sites using Environmental DNA (eDNA)
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 20, 2024
Abstract
The
advance
of
environmental
DNA
(eDNA)
has
enabled
rapid
and
non-invasive
species
detection
in
aquatic
environments.
Although
most
studies
focus
on
detections,
some
recent
explored
the
potential
using
eDNA
concentration
to
quantify
abundance.
However,
differential
individual
contribution
samples
could
easily
obscure
concentration-species
abundance
relationship.
We
propose
number
segregating
sites
as
a
proxy
for
estimating
Since
reflects
genetic
diversity
population,
which
is
less
sensitive
than
concentration.
examined
relationship
between
silico,
vitro,
situ
two
brackish
goby
species,
Acanthogobius
hasta
Tridentiger
bifasciatus
.
Analyses
simulated
data
vitro
with
mixed
from
known
individuals
showed
strong
correlation
(R
2
>
0.9;
P
<
0.01).
Results
experiment
further
validated
=
0.70,
0.01),
such
was
not
affected
by
biotic
factors,
including
body
size
feeding
behavior
(P
0.05).
cross-validation
test
also
that
predicted
bias
variability
Overall,
correlates
stronger
provides
better
estimate
This
advancement
can
significantly
enhance
quantitative
capabilities
technology.
Язык: Английский
Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes
eLife,
Год журнала:
2024,
Номер
12
Опубликована: Март 15, 2024
Ancient
environmental
DNA
(aeDNA)
from
lake
sediments
has
yielded
remarkable
insights
for
the
reconstruction
of
past
ecosystems,
including
suggestions
late
survival
extinct
species.
However,
translocation
and
lateral
inflow
in
can
potentially
distort
stratigraphic
signal
DNA.
Using
three
different
approaches
on
two
short
sediment
cores
Yamal
peninsula,
West
Siberia,
with
ages
spanning
only
hundreds
years,
we
detect
identified
mitochondrial
genomes
multiple
mammoth
woolly
rhinoceros
individuals—both
species
that
have
been
thousands
years
mainland.
The
occurrence
clearly
identifiable
aeDNA
Pleistocene
megafauna
(e.g.
>400
K
reads
one
core)
throughout
these
subsurface
cores,
along
specificities
sedimentology
dating,
confirm
processes
acting
regional
scales,
such
as
extensive
permafrost
thawing,
influence
record
should
be
accounted
paleoecology.
Язык: Английский
Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes
eLife,
Год журнала:
2023,
Номер
12
Опубликована: Сен. 1, 2023
Ancient
environmental
DNA
(aeDNA)
from
lake
sediments
has
yielded
remarkable
insights
for
the
reconstruction
of
past
ecosystems,
including
suggestions
late
survival
extinct
species.
However,
translocation
and
lateral
inflow
in
can
potentially
distort
stratigraphic
signal
DNA.
Using
three
different
approaches
on
two
short
sediment
cores
Yamal
peninsula,
West
Siberia,
with
ages
spanning
only
hundreds
years,
we
detect
identified
mitochondrial
genomes
multiple
mammoth
woolly
rhinoceros
individuals-both
species
that
have
been
thousands
years
mainland.
The
occurrence
clearly
identifiable
aeDNA
Pleistocene
megafauna
(e.g.
>400
K
reads
one
core)
throughout
these
subsurface
cores,
along
specificities
sedimentology
dating,
confirm
processes
acting
regional
scales,
such
as
extensive
permafrost
thawing,
influence
record
should
be
accounted
paleoecology.
Язык: Английский
tombRaider– improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 26, 2024
ABSTRACT
Environmental
DNA
metabarcoding
has
revolutionized
ecological
surveys
of
natural
systems.
By
amplifying
and
sequencing
small
gene
fragments
from
environmental
samples
containing
complex
mixtures,
scientists
are
now
capable
exploring
biodiversity
patterns
across
the
tree
life
in
a
time-efficient
cost-effective
manner.
However,
accuracy
species
haplotype
identification
can
be
compromised
by
sequence
artefacts
pseudogenes.
Despite
various
strategies
developed
over
years,
effective
removal
remains
challenging
inconsistent
data
reporting
standards
hinder
reproducibility
eDNA
experiments.
To
address
these
issues,
we
introduce
tombRaider
,
an
open-source
command
line
software
program
(
https://github.com/gjeunen/tombRaider
)
R
package
https://github.com/gjeunen/tombRaider_R
to
remove
pseudogenes
post
clustering
denoising.
features
modular
algorithm
evaluating
multiple
criteria,
including
similarity,
co-occurrence
patterns,
taxonomic
assignment,
presence
stop
codons.
We
validated
using
published
sets,
mock
invertebrate
communities,
air
zoo,
salmon
haplotypes
aquatic
eDNA.
Our
results
demonstrate
that
effectively
removed
higher
proportion
while
retaining
authentic
sequences,
thus
enhancing
reliability
eDNA-derived
diversity
metrics.
This
user-friendly
not
only
improves
quality
studies,
but
also
contributes
standardised
practices,
aspect
currently
lacking
this
emerging
research
field.
Язык: Английский