Advances in systems analysis, software engineering, and high performance computing book series,
Journal Year:
2024,
Volume and Issue:
unknown, P. 215 - 226
Published: March 29, 2024
Artificial
Intelligence
(AI)
emerges
as
a
potent
ally
in
augmenting
environmental
monitoring
and
fortifying
conservation
efforts.
Now
we
have
seen
escalating
challenges
the
need
for
sustainable
practices.
This
paper
outlines
innovative
applications
transformative
potential
of
AI
managing
complexities
ecological
preservation
monitoring.
facilitates
real-time
processing
interpretation
voluminous
data.
It
helps
informed
decision-making
strategic
planning
initiatives.
The
employment
AI-driven
models
technologies
such
machine
learning
algorithms,
computer
vision
sensor
networks
has
proven
instrumental
biodiversity.
plays
pivotal
role
enabling
precision
by
facilitating
identification
prioritization
critical
areas
requiring
immediate
intervention.
contributes
to
development
smart
adaptive
systems
capable
autonomously
tracking
analysing
disturbances
human
encroachments.
Molecular Ecology Resources,
Journal Year:
2021,
Volume and Issue:
21(7), P. 2565 - 2579
Published: May 18, 2021
Abstract
Bioinformatic
analysis
of
eDNA
metabarcoding
data
is
a
crucial
step
toward
rigorously
assessing
biodiversity.
Many
programs
are
now
available
for
each
the
required
analyses,
but
their
relative
abilities
at
providing
fast
and
accurate
species
lists
have
seldom
been
evaluated.
We
used
simulated
mock
communities
real
fish
to
evaluate
performance
13
bioinformatic
pipelines
retrieve
occurrence
read
abundance
using
12S
mt
rRNA
gene
marker.
four
indices
compare
outputs
program
with
samples:
sensitivity,
F‐measure,
root‐mean‐square
error
(RMSE)
on
abundances,
execution
time.
found
marked
differences
among
only
taxonomic
assignment
step,
both
in
terms
F‐measure
RMSE.
Running
time
was
highly
different
between
step.
The
fastest
best
were
assembled
into
pipeline.
compared
this
pipeline
constructed
from
existing
toolboxes
(OBITools,
Barque,
QIIME
2).
Our
Barque
obtained
all
appear
be
better
alternatives
analysing
when
complete
reference
database
available.
Analysis
also
indicated
only.
This
study
reveals
major
during
choice
algorithm
can
significant
impact
diversity
estimates
should
made
according
objectives
study.
Ecology and Evolution,
Journal Year:
2021,
Volume and Issue:
11(22), P. 15766 - 15779
Published: Oct. 22, 2021
Abstract
Environmental
DNA
(eDNA)
metabarcoding
is
an
increasingly
popular
tool
for
measuring
and
cataloguing
biodiversity.
Because
the
environments
substrates
in
which
preserved
differ
considerably,
eDNA
research
often
requires
bespoke
approaches
to
generating
data.
Here,
we
explore
how
two
experimental
choices
study
design—the
number
of
PCR
replicates
depth
sequencing
replicates—influence
composition
consistency
taxa
recovered
from
extracts.
We
perform
24
each
six
soil
samples
using
most
common
metabarcodes
Fungi
Viridiplantae
(ITS1
ITS2),
sequence
replicate
average
~84,000
reads.
find
that
are
broadly
consistent
relative
abundance
dominant
taxa,
but
low
unique
one
or
a
few
replicates.
Taxa
observed
out
make
up
21–29%
total
detected.
also
observe
rarefaction
influences
alpha
diversity
beta
estimates.
Read
sampling
local
contribution
diversity,
placement
ordinations,
dispersion
ordinations.
Our
results
suggest
that,
because
drive
some
estimates,
read
depths
may
be
sufficient
many
biological
applications
metabarcoding.
However,
rare
stochastically,
never
fully
recover
true
amplifiable
extract.
Rare
outliers
lead
differences
at
different
depths.
conclude
researchers
should
consider
complexity
unevenness
community
when
choosing
analytical
approaches,
depths,
filtering
thresholds
arrive
stable
Estuaries and Coasts,
Journal Year:
2022,
Volume and Issue:
45(7), P. 2254 - 2273
Published: June 25, 2022
Abstract
Environmental
DNA
(eDNA)
detection
methods
can
complement
traditional
biomonitoring
to
yield
new
ecological
insights
in
aquatic
systems.
However,
the
conceptual
and
methodological
frameworks
for
eDNA
interpretation
were
developed
primarily
freshwater
environments
have
not
been
well
established
estuaries
marine
that
are
by
nature
dynamic,
turbid,
hydrologically
complex.
context
species
life
history
critical
successful
application
of
methods,
challenges
associated
with
subject
a
symposium
held
at
University
California
Davis
on
January
29,
2020
(
https://marinescience.ucdavis.edu/engagement/past-events/edna
).
Here,
we
elaborate
upon
topics
addressed
evaluate
monitoring
biodiversity
studies
estuaries.
We
first
provide
concise
overview
science
then
examine
San
Francisco
Estuary
(SFE)
as
case
study
illustrate
how
programs
regional
guidance
future
potential
applications.
Additionally,
offer
recommendations
enhancing
communication
between
scientists
natural
resource
managers,
which
is
essential
integrating
into
existing
programs.
Our
intent
create
accessible
those
outside
field
eDNA,
especially
without
oversimplifying
or
advantages
these
methods.
Methods in Ecology and Evolution,
Journal Year:
2022,
Volume and Issue:
14(2), P. 415 - 430
Published: April 12, 2022
Abstract
Several
studies
have
shown
the
potential
of
eDNA‐based
proxies
for
plant
identification,
but
little
is
known
about
their
spatial
and
temporal
resolution.
This
limits
its
use
biodiversity
assessments
monitoring
vegetation
responses
to
environmental
changes.
Here
we
calibrate
signals
detected
with
soil
eDNA
surveys
by
comparing
a
standard
visual
above‐ground
survey.
Our
approach
compares
in
an
old‐growth
boreal
forest
southern
Norway,
surveyed
100
permanent
1‐m
2
plots
seven
times
over
30‐year
period,
single
metabarcoding‐based
survey
from
samples
collected
at
same
year
last
On
average,
60%
10%
vascular
plants
bryophytes
recorded
across
all
were
eDNA.
Taxa
more
representative
local
taxa
pool
than
specific
plot,
corresponded
those
period
although
most
closely
matched
current
composition.
Soil
abundant
better
rare
ones
both
unrecorded
detected.
study
highlights
broad
scales.
The
method's
ability
detect
makes
it
suitable
assessment
composition
area
broad‐scale
diversity
assessments.
American Journal of Botany,
Journal Year:
2023,
Volume and Issue:
110(2)
Published: Jan. 12, 2023
Over
the
past
quarter
century,
environmental
DNA
(eDNA)
has
been
ascendant
as
a
tool
to
detect,
measure,
and
monitor
biodiversity
(species
communities),
means
of
elucidating
biological
interaction
networks,
window
into
understanding
patterns
biodiversity.
However,
only
recently
potential
eDNA
realized
in
botanical
world.
Here
we
synthesize
state
applications
systems
with
emphases
on
aquatic,
ancient,
contemporary
sediment,
airborne
systems,
focusing
both
single-species
approaches
multispecies
community
metabarcoding.
Further,
describe
how
abiotic
biotic
factors,
taxonomic
resolution,
primer
choice,
spatiotemporal
scales,
relative
abundance
influence
utilization
interpretation
results.
Lastly,
explore
several
areas
opportunities
for
further
development
tools
plants,
advancing
our
knowledge
efficacy,
utility,
cost-effectiveness,
ultimately
facilitating
increased
adoption
analyses
systems.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: May 23, 2024
Abstract
Anthropogenically
forced
changes
in
global
freshwater
biodiversity
demand
more
efficient
monitoring
approaches.
Consequently,
environmental
DNA
(eDNA)
analysis
is
enabling
ecosystem-scale
assessment,
yet
the
appropriate
spatio-temporal
resolution
of
robust
assessment
remains
ambiguous.
Here,
using
intensive,
eDNA
sampling
across
space
(five
rivers
Europe
and
North
America,
with
an
upper
range
20–35
km
between
samples),
time
(19
timepoints
2017
2018)
conditions
(river
flow,
pH,
conductivity,
temperature
rainfall),
we
characterise
at
which
information
on
diversity
animal
kingdom
can
be
gathered
from
eDNA.
In
space,
beta
was
mainly
dictated
by
turnover,
a
scale
tens
kilometres,
highlighting
that
measures
are
not
confounded
upstream.
Fish
communities
showed
nested
assemblages
along
some
rivers,
coinciding
habitat
use.
Across
time,
seasonal
life
history
events,
including
salmon
eel
migration,
were
detected.
Finally,
effects
taxon-specific,
reflecting
filtering
rather
than
molecules.
We
conclude
riverine
metabarcoding
measure
scales
relevant
to
species
community
ecology,
demonstrating
its
utility
delivering
insights
into
river
ecology
during
change.
Aquatic Conservation Marine and Freshwater Ecosystems,
Journal Year:
2025,
Volume and Issue:
35(2)
Published: Feb. 1, 2025
ABSTRACT
Molecular
traces
are
increasingly
being
applied
to
assess
the
presence
of
species
and
communities.
Studies
on
environmental
DNA
(eDNA)
have,
a
large
extent,
become
common
practice
in
detection,
but
less
studies
have
compared
biodiversity
estimations
with
more
temporary
RNA
(eRNA).
This
study
compares
metabarcoding
results
from
pond
water
obtained
both
molecule
types
by
sequencing
V4
region
18S
rRNA
marker.
Water
was
collected
two
depths,
20
80
cm,
filtered
sequentially
through
filter
porosities,
0.45
0.22
μm.
Each
cut
half
before
fixation
either
96%
ETOH
or
RNAlater.
The
showed
no
differences
between
fixatives
for
molecule.
Overall,
estimates
eDNA
significantly
overperformed
eRNA,
likely
due
higher
concentrations
terrestrial
sources.
Comparisons
depths
variation
only,
increasing
levels
found
at
upper
layer.
Both
pore
sizes
captured
distinctive
compositions
taxa,
where
about
30%
diversity
uniquely
identified
second,
finer
filter.
Taken
together,
these
findings
imply
that
choice
molecular
marker,
depth
size
affects
pond.
Environmental DNA,
Journal Year:
2021,
Volume and Issue:
4(1), P. 117 - 134
Published: June 1, 2021
Abstract
Large
rivers
and
their
estuaries
are
structurally
complex
comprise
a
diversity
of
habitats
supporting
rich
biodiversity.
As
result,
identifying
monitoring
fish
communities
using
traditional
methods
in
such
systems
may
often
be
logistically
challenging.
Using
the
mitochondrial
DNA
12S
MiFish
primers,
we
performed
an
eDNA
metabarcoding
analysis
to
assess
effect
spatial
environmental
factors
on
variation
community
structure
along
most
St.
Lawrence
River/Estuary/Gulf
(Québec
Canada),
transect
spanning
1300
km
across
from
fluviatile
non‐tidal
section
marine
environment.
A
total
129
species
were
identified
including
freshwater
species.
For
sectors,
80
compared
with
85
previously
reported
based
conventional
sampling.
also
revealed
similar
River.
Furthermore,
our
study
improved
current
knowledge
about
brackish
sections
by
describing
transition
between
association
drastic
shift
conditions
observed
end
fluvial
estuary
beginning
middle
(brackish)
estuary.
Altogether,
this
exemplifies
how
is
powerful
tool
document
shifts
large
temperate
lotic
ecosystems.
Environmental DNA,
Journal Year:
2021,
Volume and Issue:
3(5), P. 1007 - 1022
Published: June 23, 2021
Abstract
Protecting
freshwater
biodiversity
is
considered
an
ultimate
challenge
but
depends
on
reliable
surveys
of
species
distribution
and
abundance
which
eDNA
metabarcoding
(environmental
DNA
metabarcoding)
may
offer.
To
do
so,
a
better
understanding
the
sources
temporal
variation
among
data
transformation
in
studies
needed.
Here,
we
show
that
based
relative
critical
to
suitable
analyses
Hellinger
performed
slightly
than
other
methods.
Furthermore,
site
localities
significantly
explain
variation,
while
no
explained
by
time
sampling.
This
indicates
communities
vary
more
spatially
temporally
within
dendritic
system
composed
small
rivers.
We
then
further
documented
community
structure
St.
Charles
River
(Québec
City,
Canada)
six
its
tributaries.
revealed
existence
eight
explaining
82.1%
read
this
river
network.
Moreover,
environmental
variables
sites
53.0%
reads,
sampling
events
variation.
Altogether,
supports
claim
powerful
tool
document
monitor
fish
watersheds
systems.
Environmental DNA,
Journal Year:
2022,
Volume and Issue:
4(5), P. 987 - 999
Published: May 21, 2022
Abstract
Plant–animal
interactions
(PAI)
represent
major
channels
of
energy
transfer
through
ecosystems,
where
both
positive
and
antagonistic
simultaneously
contribute
to
ecosystem
functioning.
Monitoring
PAI
therefore
increases
the
understanding
environmental
health,
integrity,
functioning,
studying
complex
accurate,
cost‐effective
sampling
can
aid
in
management
detrimental
anthropogenic
impacts.
Environmental
DNA
(eDNA)‐based
monitoring
represents
an
increasingly
common,
nondestructive
approach
for
biodiversity
monitoring,
which
could
help
elucidate
PAI.
Here,
we
aim
provide
overall
discussion
on
potential
using
eDNA
study
We
assessed
existing
literature
this
subject
from
2009
2021
a
freely
accessible
web
search
tool.
The
was
conducted
by
keywords
involving
PAI,
including
species‐specific
metabarcoding
approaches,
recovering
43
studies.
summarized
advantages
current
limitations
such
outline
research
priorities
improve
future
eDNA‐based
methods
analysis.
Among
studies
identified
measure
as
pollination,
herbivory,
mutualistic,
parasitic
relationships,
they
have
often
higher
taxonomic
diversity
several
direct
comparisons
with
DNA‐based
gut/bulk
conventional
survey
methods.
Research
needs
include
following:
better
influencing
factors
detection
involved
(e.g.,
degradation,
origin,
types),
methodological
standardization
(sampling
primer
development),
more
inclusive
sequence
reference
databases.
If
these
are
addressed,
it
will
significant
impact
enable
eDNA.
In
future,
implementation
particularly
benefit
scalability
biomonitoring
surveys
that
imperative
health
assessments.