Authorea (Authorea),
Journal Year:
2023,
Volume and Issue:
unknown
Published: April 15, 2023
1.
Metabarcoding
of
environmental
DNA
(eDNA)
has
recently
improved
our
understanding
biodiversity
patterns
in
marine
and
terrestrial
ecosystems.
However,
the
complexity
these
data
prevents
current
methods
to
extract
analyze
all
relevant
ecological
information
they
contain.
Therefore,
modeling
could
greatly
benefit
from
new
providing
better
dimensionality
reduction
clustering.
2.
Here
we
present
two
deep
learning-based
that
combine
different
types
neural
networks
ordinate
eDNA
samples
visualize
ecosystem
properties
a
two-dimensional
space:
first
is
based
on
variational
autoencoders
(VAEs)
second
metric
learning
(DML).
The
strength
lies
combination
several
inputs:
number
sequences
found
for
each
molecular
operational
taxonomic
unit
(MOTU),
together
with
genetic
sequence
detected
MOTU
within
an
sample.
3.
Using
three
datasets,
show
represent
well
indicators
latent
richness
per
sample,
α-diversity
ꞵ-diversity
between
samples.
We
nonlinear
are
at
extracting
features
datasets
while
avoiding
major
biases
associated
eDNA.
Our
outperform
traditional
dimension
such
as
Principal
Component
Analysis,
t-distributed
Stochastic
Neighbour
Embedding,
Uniform
Manifold
Approximation
Projection
reduction.
4.
results
suggest
provide
more
efficient
way
structure
metabarcoding
data,
thereby
improving
their
interpretation
thus
monitoring.
Marine Ecology Progress Series,
Journal Year:
2023,
Volume and Issue:
731, P. 105 - 127
Published: April 26, 2023
Detailed
knowledge
on
connectivity,
i.e.
the
exchange
of
marine
organisms
among
geographically
separated
populations,
is
essential
for
effective
spatial
planning
strategies
and
design
protected
areas
(MPAs)
in
coastal
ecosystems.
Coastal
waters
around
southern
Africa
are
characterized
by
complex
oceanographic
processes
that
strongly
influence
challenging
management
Here
we
reviewed
connectivity
studies
conducted
across
25°
latitude
both
southeastern
southwestern
sides
based
biophysical
modelling,
ecological
molecular
approaches,
identified
7
corridors
8
barriers
recognized
to
a
variety
vertebrate
invertebrate
taxa
commercial
interest.
These
were
generally
consistent
studies,
species
methodological
reflected
bioregion
breaks.
Nevertheless,
life
history
traits
appear
be
important
understanding
why
some
may
notable
stages
not
others.
Our
review
underlines
value
including
from
different
disciplines
order
have
broad
view
and,
particular,
complementarity
larval-dispersal
models
seascape
genetics
emphasized.
The
this
represent
baselines
critically
assess
existing
MPAs
prioritize
new
efforts
mitigate
human
impacts
PLoS ONE,
Journal Year:
2024,
Volume and Issue:
19(10), P. e0309120 - e0309120
Published: Oct. 16, 2024
The
events
of
the
Cenozoic
era
such
as
mountain
formation
caused
Iran
to
become
one
most
amazing
biodiversity
hotspots
in
world
today.
This
pioneering
study
on
Iranian
snake
biogeography
integrates
historical
and
ecological
analyses.
A
phylogeographic
review
traces
speciation
dispersal,
while
cluster
analysis
with
a
new
checklist
assesses
faunistic
similarities
within
its
surroundings.
Jaccard
Sorenson
indices
generate
similarity
dendrograms,
Indicator
Species
Analysis
pinpoints
regional
key
species,
Endemism
index
calculates
endemism
rates,
enriching
our
knowledge
Iran’s
species
diversity.
Phylogeographic
analyses
identify
four
biogeographical
corridors
for
ingress
into
Iran:
Arabian
region
through
southwestern
Iran,
Western
Asian
mountainous
transition
zone
via
northwestern
Turanian
northeastern
Indus
River
Valley
southeastern
eastern
Iran.
Dendrogram
divides
fauna
three
groups.
first
group
associates
western
Zagros
Khuzestan
Sahara
regions.
second
links
Kopet
Dagh
Turkmen
Steppe
region,
Central
Plateau
Baluchistan
region.
third
connects
northwest
highlands,
Alborz
mountains,
Caspian
Sea
coasts
Mountain
zone.
validates
broad
biogeographic
patterns
ecoregional
associations
indicator
analysis,
providing
finer
resolution.
like
Platyceps
najadum
Hyrcanian
mixed
forests
exemplify
alignment,
mountains
exhibit
unique
faunal
indicators,
indicating
species-level
divergence.
Shared
indicators
among
widespread
ecoregions
reflect
habitat
continuity;
exclusive
emphasize
distinctiveness.
Despite
endemic
prevalence,
they
seldom
act
significant
due
various
factors.
Our
research
confirms
Mountains,
Plain,
Persian
Gulf
diversity
hotspots,
marked
by
higher
richness
compared
other
Marine Ecology,
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 30, 2024
Abstract
Biodiversity
patterns
are
fundamental
in
our
understanding
of
the
distribution
life,
ecosystem
function,
and
conservation.
In
this
concept
analysis,
A
survey
existing
knowledge
on
marine
biodiversity
drivers
across
latitudes,
longitudes,
depths
indicates
that
none
postulated
represent
a
rule.
The
paradigm
latitudinal
gradients
or
bathymetric
diversity
vary
biogeographic
regions
components,
kingdoms,
body
sizes.
same
holds
true
for
hypothesized
longitudinal
cost‐offshore
patterns.
Food
availability
temperature
influence
all
life
forms
appear
to
be
most
relevant
factors
shaping
biodiversity.
However,
these
interact
with
many
other
variables
such
as
spatial
heterogeneity,
ecological
physical
processes
creating
complex
mosaic
limits
any
prediction.
Climate
change,
its
implications
global
primary
productivity
rise,
can
one
major
influences
future
Understanding
emphasizes
need
complete
census
next
decade.
effort
must
use
advanced
technologies,
develop
holistic
approaches
promote
integration
morphological‐
genetic‐based
taxonomy
explore
organisms
size
classes,
at
large
scales
habitat
types,
particularly
open
ocean
deep‐sea
ecosystems.
Without
basic
knowledge,
coupled
identification
observed
patterns,
we
will
unable
fill
gaps
crucial
developing
adequate
conservation
measures
scale.
Molecular Ecology Resources,
Journal Year:
2023,
Volume and Issue:
23(8), P. 1946 - 1958
Published: Sept. 13, 2023
Environmental
DNA
(eDNA)
metabarcoding
provides
an
efficient
approach
for
documenting
biodiversity
patterns
in
marine
and
terrestrial
ecosystems.
The
complexity
of
these
data
prevents
current
methods
from
extracting
analyzing
all
the
relevant
ecological
information
they
contain,
new
may
provide
better
dimensionality
reduction
clustering.
Here
we
present
two
deep
learning-based
that
combine
different
types
neural
networks
(NNs)
to
ordinate
eDNA
samples
visualize
ecosystem
properties
a
two-dimensional
space:
first
is
based
on
variational
autoencoders
second
metric
learning.
strength
our
lies
combination
inputs:
number
sequences
found
each
molecular
operational
taxonomic
unit
(MOTU)
detected
their
corresponding
nucleotide
sequence.
Using
three
datasets,
show
accurately
represent
several
indicators
latent
MOTU
richness
per
sample,
sequence
α-diversity
Jaccard's
β-diversity
between
samples.
We
nonlinear
are
at
features
datasets
while
avoiding
major
biases
associated
with
eDNA.
Our
outperform
traditional
dimension
such
as
Principal
Component
Analysis,
t-distributed
Stochastic
Neighbour
Embedding,
Nonmetric
Multidimensional
Scaling
Uniform
Manifold
Approximation
Projection
reduction.
results
suggest
NNs
more
way
structure
data,
thereby
improving
interpretation
thus
monitoring.
Diversity and Distributions,
Journal Year:
2022,
Volume and Issue:
28(12), P. 2637 - 2647
Published: Aug. 4, 2022
Abstract
Aim
The
Irano‐Anatolian
biodiversity
hotspot
is
among
the
least‐known
hotspots
on
earth.
In
this
study,
we
aim
to
map
richness
and
genetic
divergence
of
lizards
in
its
surrounding
areas
identify
most
important
determinants
patterns.
Location
Iran
Turkey
(Irano‐Anatolian
hotspot).
Methods
Here,
mapped
distribution
211
lizard
species
using
existing
occurrence
data
generated
first
pattern
two
countries
high
diversity
hotspot.
We
also
identified
Results
showed
that
Zagros
Mountains,
Central
Iranian
Plateau
northern
Persian
Gulf
have
highest
richness.
Plateau,
regions
around
Lut
Desert
Jazmourian
Plain
total
Iran.
Alborz
Kopet
Dag
mountains
south
western
parts
average
divergence.
annual
temperature
was
predictor
richness,
change
velocity
influential
determinant
pattern.
Much
our
surprise,
with
are
located
outside
Main
conclusions
This
study
patterns
associated
current
past
climate.
particular,
highlights
legacy
climate
changes
species‐rich
genetically
diverse
So
conservation
efforts
concentrated
inside
may
not
benefit
conservation.
Thus,
future
studies
programs
should
consider
areas.
Environmental DNA,
Journal Year:
2024,
Volume and Issue:
6(5)
Published: Sept. 1, 2024
ABSTRACT
Environmental
DNA
(eDNA)
metabarcoding
surveys
can
support
the
acquisition
of
extensive
biodiversity
data
to
ecosystem
monitoring
and
conservation
actions.
However,
optimization
eDNA
project
design
is
essential
capture
spatio‐temporal
heterogeneity
signals
maximize
diversity
detection.
In
this
study,
we
developed
a
system‐specific
approach
detect
fish
communities
in
kelp
forests,
by
analyzing
fine‐scale
patterns
at
two
sites
along
South
African
coastline,
as
well
testing
effect
biological
replication
pooling
replicates
on
species
At
each
site,
samples
were
collected
stations
shoreline
depth
zones,
was
repeated
time
points
(24
h
apart).
We
detected
113
operational
taxonomic
units
(OTUs)
across
32
families,
but
fewer
than
20%
OTUs
could
be
assigned
species,
indicating
that
barcode
reference
libraries
need
drastically
improved.
significant
differences
small
spatial
scales
(<
600
m)
points,
suggesting
best
site's
patterns,
should
multiple
times
within
least
24
h.
To
~80%
community,
including
some
low
abundance
minimum
four
appear
sufficient.
addition,
higher
number
(76
vs.
65)
found
individual
any
pools.
prior
sequencing
still
valuable
broad‐scale
for
offset
decrease
resolution
with
benefit
accumulating
comprehensive
from
increased
sampling
efforts
over
time.
As
pilot
investigation
into
how
forest‐associated
communities,
study
provides
basis
optimizing
coastal
eDNA‐based
southern
Africa
strengthens
development
long‐term
programs
better
management
Molecular Ecology Resources,
Journal Year:
2023,
Volume and Issue:
unknown
Published: June 8, 2023
Genomic
information
can
aid
in
the
establishment
of
sustainable
management
plans
for
commercially
exploited
marine
fishes,
aiding
long-term
conservation
these
resources.
The
southern
African
hakes
(Merluccius
capensis
and
M.
paradoxus)
are
valuable
demersal
fishes
with
similar
distribution
ranges
but
exhibiting
contrasting
life
histories.
Using
a
comparative
framework
based
on
Pool-Seq
genome-wide
SNP
data,
we
investigated
whether
evolutionary
processes
that
shaped
extant
patterns
diversity
divergence
shared
among
two
congeneric
or
unique
to
each
one.
Our
findings
revealed
paradoxus
show
levels
diversity,
despite
different
census
sizes
life-history
features.
In
addition,
shows
three
highly
structured
geographic
populations
across
Benguela
Current
region
(one
northern
Benguela),
no
consistent
genome-environment
associations
detected.
contrast,
although
population
structure
outlier
analyses
suggested
panmixia
paradoxus,
reconstruction
its
demographic
history
presence
an
Atlantic-Indian
Ocean
subtle
substructuring
pattern.
Therefore,
it
appears
might
be
composed
by
connected
populations,
one
Atlantic
southwest
Indian
Ocean.
reported
low
genomic
as
well
newly
discovered
genetically
distinct
both
hake
species
thus
assist
informing
improving
important
Merluccius.