Animals,
Год журнала:
2023,
Номер
13(8), С. 1285 - 1285
Опубликована: Апрель 8, 2023
Leatherback
turtles
migrate
long
distances
between
nesting
beaches
and
distant
foraging
areas
worldwide.
This
study
analyzes
the
genetic
diversity,
life
history
stage,
spatiotemporal
distribution,
associated
threats
of
a
aggregation
in
Southwest
Atlantic
Ocean.
A
total
242
leatherbacks
stranded
or
bycaught
by
artisanal
fisheries
were
recorded
from
1997
to
2021
Uruguay,
with
sizes
ranging
110.0
170.0
cm
carapace
lengths,
indicating
that
is
composed
large
juveniles
adults.
Results
Bayesian
mixed-stock
analysis
show
come
primarily
West
African
rookeries,
based
on
mitochondrial
DNA
sequences
obtained
59
representing
seven
haplotypes,
including
novel
one
(Dc1.7).
The
main
threat
identified
area
bycatch
but
most
carcasses
observed
badly
decomposed.
There
was
significant
seasonal
interannual
variability
strandings
likely
availability
prey
intensity
fishing
effort.
Taken
together,
these
findings
reinforce
importance
South
American
for
need
determine
regional
habitat
use
migratory
routes
across
broader
region,
order
develop
effective
conservation
measures
mitigate
both
at
areas.
ABSTRACT
Terrestrial
vertebrates
are
experiencing
worldwide
population
declines
and
species
extinctions.
To
effectively
conserve
remaining
populations
species,
rapid,
cost‐effective,
scalable
methods
needed
to
complement
longstanding
monitoring
methods.
Increasingly,
environmental
DNA
(eDNA)‐based
approaches
being
used
for
terrestrial
vertebrate
biomonitoring
within
a
range
of
environments.
However,
as
we
move
eDNA
onto
land,
presented
with
new
set
challenges.
This
necessitates
the
development
“best‐practice”
sample
collection
guidelines
systems
purpose
detecting
vertebrates.
address
these
needs,
conducted
systematic
literature
review
143
peer‐reviewed
papers
applying
(excluding
Lissamphibia)
that
were
published
between
2012
2023.
We
summarize
use
biomonitoring,
focusing
on
study
design
field
techniques.
Over
decade
observe
steady
growth
in
annual
number
publications,
3
33
The
majority
reviewed
studies
targeted
mammals
temperate
forest
regions.
While
an
equal
focused
metabarcoding
approach
assess
community
taxon
composition
and/or
species‐specific
detection
methods,
novel
uses
increasingly
published.
These
include
animal
behavior
genetics.
record
three
types
sampling
strategies,
eight
different
substrate
types,
seven
preservation
suggesting
there
is
no
“one
size
fits
all”
eDNA‐based
methodology
when
With
multitude
aims,
across
environments,
target
organisms
ecologies,
standardization
extremely
challenging.
table
known
factors
influencing
Furthermore,
identify
five
key
considerations
be
addressed
targeting
aim
guiding
decision
making.
Nature Ecology & Evolution,
Год журнала:
2023,
Номер
7(6), С. 873 - 888
Опубликована: Май 15, 2023
The
field
of
environmental
DNA
(eDNA)
is
advancing
rapidly,
yet
human
eDNA
applications
remain
underutilized
and
underconsidered.
Broader
adoption
analysis
will
produce
many
well-recognized
benefits
for
pathogen
surveillance,
biodiversity
monitoring,
endangered
invasive
species
detection,
population
genetics.
Here
we
show
that
deep-sequencing-based
approaches
capture
genomic
information
from
humans
(Homo
sapiens)
just
as
readily
the
intended
target
species.
We
term
this
phenomenon
genetic
bycatch
(HGB).
Additionally,
high-quality
could
be
intentionally
recovered
substrates
(water,
sand
air),
holding
promise
beneficial
medical,
forensic
applications.
However,
also
raises
ethical
dilemmas,
consent,
privacy
surveillance
to
data
ownership,
requiring
further
consideration
potentially
novel
regulation.
present
evidence
detectable
'wildlife'
samples
bycatch,
demonstrate
identifiable
can
human-focused
sampling
discuss
translational
implications
such
findings.
Endangered Species Research,
Год журнала:
2023,
Номер
52, С. 303 - 341
Опубликована: Сен. 20, 2023
Sea
turtles
are
an
iconic
group
of
marine
megafauna
that
have
been
exposed
to
multiple
anthropogenic
threats
across
their
different
life
stages,
especially
in
the
past
decades.
This
has
resulted
population
declines,
and
consequently
many
sea
turtle
populations
now
classified
as
threatened
or
endangered
globally.
Although
some
worldwide
showing
early
signs
recovery,
still
face
fundamental
threats.
is
problematic
since
important
ecological
roles.
To
encourage
informed
conservation
planning
direct
future
research,
we
surveyed
experts
identify
key
contemporary
(climate
change,
take,
fisheries,
pollution,
disease,
predation,
coastal
development)
faced
by
turtles.
Using
survey
results
current
literature,
also
outline
knowledge
gaps
our
understanding
impact
these
how
targeted
often
involving
emerging
technologies,
could
close
those
gaps.
Molecular Ecology,
Год журнала:
2023,
Номер
32(15), С. 4118 - 4132
Опубликована: Май 30, 2023
Abstract
Advancements
in
environmental
DNA
(eDNA)
approaches
have
allowed
for
rapid
and
efficient
species
detections
diverse
environments.
Although
most
eDNA
research
is
focused
on
leveraging
genetic
diversity
to
identify
taxa,
some
recent
studies
explored
the
potential
these
detect
within‐species
variation,
allowing
population
assessments
abundance
estimates
from
samples.
However,
we
currently
lack
a
framework
outlining
key
considerations
specific
generating,
analysing
applying
data
two
purposes.
Here,
discuss
how
various
markers
differ
with
regard
information
detectability
samples
analysis
of
differs
common
tissue‐based
analyses.
We
then
outline
it
may
be
possible
obtain
absolute
by
detecting
intraspecific
variation
mixtures
under
multiple
scenarios.
also
major
causes
contributing
allele
detection
frequency
errors
data,
their
consequences
population‐level
analyses
bioinformatic
remove
erroneous
sequences.
This
review
summarizes
advances
required
harness
full
eDNA‐based
inform
questions
ecology,
evolutionary
biology
conservation
management.
Scientific Reports,
Год журнала:
2023,
Номер
13(1)
Опубликована: Фев. 14, 2023
Animal
conservation
relies
on
assessing
the
distribution
and
habitat
use
of
species,
but
for
endangered/elusive
animals
this
can
prove
difficult.
The
Monk
Seal,
Monachus
monachus,
is
one
world's
most
endangered
species
pinniped,
only
endemic
to
Mediterranean
Sea.
During
recent
decades,
direct
observations
have
been
few
scattered,
making
it
difficult
determine
its
away
from
Aegean
Sea
(core
area
post-decline
relict
population).
This
study
environmental
DNA
(eDNA)
analysis
detect
presence
Seal
in
135
samples
collected
120
locations
central/western
Sea,
spanning
about
1500
km
longitudinally
1000
latitudinally.
A
recently
described
species-specific
qPCR
assay
was
used
marine-water
samples,
mostly
during
2021
by
a
Citizen
Science
(CS)
project.
Positive
detections
occurred
throughout
longitudinal
range,
including
westernmost
surveyed
(Balearic
archipelago).
positive
indicated
six
"hotspots",
overlapping
with
historical
sites,
suggesting
that
habitat-specific
characteristics
play
fundamental
role.
We
applied
single-season
occupancy
models
correct
detection
probability
assess
importance
site-specific
characteristics.
distance
small
islets
protected
(or
access-restricted)
areas
correlated
negatively
probability.
novel
molecular
approach,
here
first
time
an
extensive
CS
study,
proved
potential
as
tool
monitoring
species.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 2, 2024
ABSTRACT
Metagenomics
has
enabled
the
rapid,
unbiased
detection
of
microbes
across
diverse
sample
types,
leading
to
exciting
discoveries
in
infectious
disease,
microbiome,
and
viral
research.
However,
analysis
metagenomic
data
is
often
complex
computationally
resource-intensive.
CZ
ID
a
free,
cloud-based
genomic
platform
that
enables
researchers
detect
using
data,
identify
antimicrobial
resistance
genes,
generate
consensus
genomes.
With
ID,
can
upload
raw
sequencing
find
matches
NCBI
databases,
get
per-sample
taxon
metrics,
perform
variety
analyses
visualizations.
The
intuitive
interface
interactive
visualizations
make
exploring
interpreting
results
simple.
Here,
we
describe
expansion
with
new
long
read
mNGS
pipeline
accepts
Oxford
Nanopore
generated
(
czid.org
).
We
report
benchmarking
standard
mock
microbial
community
dataset
against
Kraken2,
widely
used
tool
for
analysis.
evaluated
ability
this
divergent
viruses
simulated
datasets.
also
assessed
limit
spiked-in
virus
cell
line
as
proxy
clinical
samples.
Lastly,
detected
known
novel
previously
characterized
disease
vector
(mosquitoes)
We
used
non-invasive
real-time
genomic
approaches
to
monitor
one
of
the
last
surviving
populations
critically
endangered
kākāpō
(
Strigops
habroptilus
).
first
established
an
environmental
DNA
metabarcoding
protocol
identify
distribution
and
other
vertebrate
species
in
a
highly
localized
manner
using
soil
samples.
Harnessing
nanopore
sequencing
high-quality
reference
genome,
we
then
extracted
species-specific
from
soil.
combined
long
read-based
haplotype
phasing
with
known
individual
variation
population
presence
individuals,
confirmed
these
genomically
informed
predictions
through
detailed
metadata
on
distributions.
This
study
shows
that
identification
is
feasible
DNA,
important
implications
for
future
efforts
application
genomics
conservation
rare
species,
potentially
expanding
research
monitoring
inferring
fitness
parameters
such
as
diversity
inbreeding.
Environmental DNA,
Год журнала:
2023,
Номер
5(5), С. 1048 - 1064
Опубликована: Авг. 9, 2023
Abstract
Molecular
techniques
using
DNA
retrieved
from
community
or
environmental
samples,
in
particular
(eDNA),
are
becoming
increasingly
popular
for
detecting
individual
species,
assessing
biodiversity,
and
quantifying
ecological
indices.
More
recently,
eDNA
has
also
been
proposed
as
a
template
population
genetics,
several
studies
have
already
tested
the
feasibility
of
this
approach,
mostly
looking
at
vertebrate
species.
Their
results
along
with
general
opportunities
offered
by
these
types
“community‐based”
such
possibility
to
target
multiple
species
same
time,
generated
great
enthusiasm
expectations
genetics.
However,
not
every
aspect
genetics
can
be
addressed
eDNA‐based
data
some
inherent
limitations
may
challenge
its
conclusions.
Here,
we
firstly
review
state
current
knowledge
samples
Then,
focusing
on
eDNA,
summarize
but
detail
four
main
use
population‐level
inferences,
namely,
(1)
difficulty
retrieve
species‐specific
dataset,
(2)
potential
lack
correlation
between
observed
true
allelic
frequencies,
(3)
loss
information
multi‐locus
genotyping
linkage
loci,
(4)
uncertainty
about
individuals
contributing
sampled
pool
(e.g.,
number,
life‐stage,
sex).
Some
might
overcome
development
new
technologies
models
that
account
specificities
eDNA.
Others,
however,
inherent,
their
effect
inferences
must
thoroughly
evaluated.
The
gaining
insights
into
genetic
diversity
structure
is
appealing
scientists,
conservation
managers,
other
practitioners.
Yet,
avoid
false
incorrect
it
imperative
known
considered
alongside
advantages.