Molecular Ecology,
Год журнала:
2024,
Номер
33(18)
Опубликована: Авг. 19, 2024
Abstract
Genome‐wide
technologies
open
up
new
possibilities
to
clarify
questions
on
genetic
structure
and
phylogeographic
history
of
taxa
previously
studied
with
microsatellite
loci
mitochondrial
sequences.
Here,
we
used
736
individual
red
deer
(
Cervus
elaphus
)
samples
genotyped
at
35,701
single
nucleotide
polymorphism
(SNPs)
assess
the
population
species
throughout
Europe.
The
results
identified
28
populations,
higher
degrees
distinction
in
peripheral
compared
mainland
populations.
Iberian
show
high
differentiation,
lineages
Western
Central
Iberia
maintaining
their
distinctiveness,
which
supports
separate
refugial
ranges
within
along
little
recent
connection
between
remaining
European
Norwegian
exhibited
lowest
variability
largest
allele
frequency
differences
from
compatible
a
bottlenecks
drift
during
post‐glacial
colonization
southern
refugia.
Scottish
populations
showed
distance
but
levels
diversity.
Hybrid
zones
were
found
Eastern
Europe
as
well
Pyrenees,
where
France
are
close
contact
deer.
Anthropogenic
restocking
has
promoted
Pyrenean
zone,
admixture
events
Isle
Rum
Netherlands,
least
partly
two
main
central‐eastern
Our
analysis
enabled
detailed
resolution
large
mammal
widely
distributed
contributes
resolving
evolutionary
history,
can
also
inform
conservation
management
policies.
Tree Genetics & Genomes,
Год журнала:
2025,
Номер
21(1)
Опубликована: Фев. 1, 2025
Abstract
Thuja
plicata
is
a
conifer
tree
that
valued
for
its
cultural,
ecological
and
wood
quality
features
in
natural
range
western
North
America
used
Europe
as
an
exotic
timber
species.
It
increasingly
mixed
species
forests
the
UK
are
managed
using
regeneration,
raising
questions
about
genetic
diversity
of
both
adult
trees
offspring
these
stands.
We
studied
population
structure
four
woodlands
adults
naturally
regenerated
T.
.
discovered
194,154
Single
Nucleotide
Polymorphisms
(SNPs)
Genotyping-by-Sequencing
(GBS)
retained
655
SNPs
across
598
genome
sequence
scaffolds
analysis.
The
majority
included
only
one
SNP,
suggesting
that;
selected
were
widely
distributed
within
genome.
found
many
monomorphic
sites,
most
which
restricted
to
single
woodland,
indicative
differentiation
among
woodlands.
three
ancestral
populations
(K
=
3)
low
levels
admixture
indicating
starting
materials
largely
from
populations.
Estimates
heterozygosity
(H
o
)
nucleotide
(π)
(overall
H
0.174,
π
0.00226)
all
sites
but
slightly
higher
juveniles
at
two
sites.
Our
genotyping
methods
results
on
standing
this
important
provide
insight
into
ability
planted
face
environmental
shifts
disease
threats.
Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 11, 2025
ABSTRACT
The
bestRAD
technique
is
a
reduced
genome
representation
approach
with
high‐capacity
sample
multiplexing
and
physical
isolation
of
biotin‐labelled
target
DNA
fragments
using
streptavidin
beads,
which
should
reduce
total
cost
genotyping
errors.
While
we
here
formalise
the
relevance
this
within
HTS
landscape,
our
foremost
aim
was
to
improve
its
replicability,
validity,
transparency.
We
first
optimised
molecular
laboratory
protocol
shared
associated
protocols
(e.g.,
final
detailed
methodologies,
quality
control,
best
practices)
under
FAIR
principles.
Using
84
worldwide
individual
samples
Oriental
fruit
fly,
Bactrocera
dorsalis
,
major
invasive
pest,
revealed
low
rate
PCR
duplicates,
robustness
quantity,
high
genotype
call
rate,
insignificant
error
nuclear
mitochondrial
representativeness,
level
genetic
information.
This
in‐depth
data
assessment,
along
handling
time
by
an
estimated
one‐third
relative
parent
RAD‐Seq
version,
demonstrates
that
excellent
compromise
between
quality.
generated
high‐quality
genomic
resources
for
B.
also
share
details
recommendations
can
be
readily
used
in
any
applied
all
organisms,
even
without
published
sequence.
Botanical Journal of the Linnean Society,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 14, 2025
Abstract
Hybridization
is
a
key
driver
of
evolutionary
processes
and
speciation.
Advances
in
sequencing
technology
provide
unprecedented
opportunity
to
study
discriminating
phenotypic
characters
at
the
molecular
level
identify
candidate
loci
associated
with
speciation
process.
Salix
chlorolepis
rare
threatened
endemic
shrub
species
restricted
upper
slopes
Mount
Albert
(Canada)
proposed
hybridize
S.
brachycarpa,
locally
abundant
geographically
widespread
congener.
We
aimed
characterize
rangewide
genetic
variation
chlorolepis,
establish
whether
it
actually
hybridizes
assess
leaf
pilosity
an
indicative
variable
trait
related
introgressive
hybridization.
Using
single
nucleotide
polymorphism
data,
we
inferred
patterns
structure
diversity.
tested
for
associations
environmental
distance,
taxonomic
identity,
or
variability
hair
density
using
populations
genomics
approaches
multilocus
(partial
Mantel
tests
generalized
dissimilarity
models)
single-locus
(latent
factor
mixed
model,
pRDA,
PCAdapt,
OutFLANK)
levels.
Although
common
ancestry
persists
within
fine-scale
spatial
reflects
its
fragmented
distribution.
Interspecific
admixture
sympatry
zones
corroborates
existence
Leaf
important
explaining
genotype
between
two
taxa.
flagged
nine
that
are
both
strongly
phenotype
divergent
selection
The
such
‘impermeable’
introgression
ensures
maintenance
interspecific
barrier
clear
differentiation
species.
Such
genomic
heterogeneity
alleviates
assimilation
risk
by
more
congener
despite
ongoing
introgression.
Genetic Resources and Crop Evolution,
Год журнала:
2024,
Номер
71(7), С. 3193 - 3203
Опубликована: Янв. 31, 2024
Abstract
Turkey
oak
(
Quercus
cerris
L.)
is
one
of
the
most
ecologically
and
economically
significant
deciduous
tree
species
in
Central
Southeast
European
regions.
The
has
long
been
known
to
exhibit
high
levels
genetic
phenotypic
variation.
Recent
climate
response
predictions
for
suggest
a
distribution
extension
Europe
under
change.
Since
relative
drought-tolerant
behaviour,
it
regarded
as
potential
alternative
other
forest
during
forestry
adaptation
efforts,
not
only
its
native
regions
but
also
Western
Europe.
For
this
reason,
survey
existing
variability,
resources,
adaptability
great
significance.
Next-generation
sequencing
approaches,
such
ddRAD-seq
(Double
digest
restriction-site
associated
DNA
sequencing),
allow
attainment
high-resolution
genome-wide
single
nucleotide
polymorphisms
(SNPs).
This
study
provides
first
highly
variable
SNP
data
generated
by
ddRAD-seq.
dataset
comprises
17
607
de
novo
26
059
reference
mapped
SNPs
88
individuals
from
eight
populations,
two
Bulgaria,
Kosovo,
five
Hungary.
Reference
mapping
was
carried
out
using
cork
oak’s
suber
genome.
obtained
markers
are
suitable
investigating
selection
local
inferring
diversity,
differentiation,
population
structure.
accessible
at:
https://doi.org/10.5281/zenodo.8091252
Animal Conservation,
Год журнала:
2024,
Номер
unknown
Опубликована: Июль 20, 2024
Abstract
Over
the
past
decade,
development
of
genetic
and
genomic
tools
for
conservation
management
has
come
forward
in
leaps
bounds.
Once
considered
a
‘nice
to
have’,
data
are
fast
becoming
an
essential
tool
informing
managing
translocations.
However,
due
complexity
field,
easily
using
decision‐making
monitoring
remains
beyond
reach
most
managers
biologists.
In
May
2020,
we
launched
Threatened
Species
Initiative
(TSI),
programme
designed
generate
resources
Australia's
threatened
species.
Critical
project
is
not
only
generation
reference
genomes
population
but
online
toolkit
managers.
The
‘one
stop
shop’
from
collecting
samples,
generating
analysing
data,
interpretable
report.
A
series
workflows
pipelines
have
been
developed,
including
TSI
Biodiversity
Portal,
that
uses
point
click
web
interfaces
transfer
raw
sequence
assemble
genomes,
transcriptomes
soon
genetics
decisions.
Here
present
how
current
works
provide
case
study
examples
it
being
used
inform
translocations
