Abstract
Background
Diversifying
animal
cultivation
demands
efficient
genotyping
for
enabling
genomic
selection,
but
non-model
species
lack
solutions.
The
aim
of
this
study
was
to
optimize
a
genotyping-by-sequencing
(GBS)
double-digest
RAD-sequencing
(ddRAD)
pipeline.
Bovine
data
used
automate
the
bioinformatic
analysis.
application
optimization
demonstrated
on
European
whitefish
data.
Results
DdRAD
generation
designed
reliable
estimation
relatedness
and
is
scalable
up
384
samples.
GBS
sequencing
yielded
approximately
one
million
reads
each
around
100
assessed
Optimizing
various
strategies
create
de-novo
reference
genome
variant
calling
(mock
reference)
showed
that
using
three
samples
outperformed
other
building
with
single
or
very
large
number
Adjustments
most
pipeline
tuning
parameters
had
limited
impact
high-quality
data,
except
identity
criterion
merging
mock
clusters.
For
species,
over
15k
variants
based
were
obtained
comparable
results
ones
called
an
existing
genome.
Repeatability
analysis
high
concordance
replicates,
particularly
in
bovine
while
repeatability
did
not
exceed
earlier
observations.
Conclusions
proposed
cost-effective
ddRAD
strategy,
coupled
bioinformatics
workflow,
enables
broad
adoption
across
diverse
farmed
species.
While
beneficial,
obligatory.
integration
Snakemake
streamlines
usage
computer
clusters
supports
customization.
This
user-friendly
solution
facilitates
both
model
Aquatic Conservation Marine and Freshwater Ecosystems,
Год журнала:
2023,
Номер
33(12), С. 1460 - 1476
Опубликована: Сен. 19, 2023
Abstract
Extinctions
occur
naturally
in
all
environments,
but
rates
have
accelerated
rapidly
during
the
Anthropocene,
especially
fresh
water.
Despite
supporting
many
fish
species
of
conservation
importance,
there
has
never
been
a
formal
assessment
their
extinction
risks
Britain,
which
impeded
inclusion
relevant
legislation
and
policy.
This
study
therefore
used
International
Union
for
Conservation
Nature
(IUCN)
Red
List
Threatened
Species™
Categories
Criteria
to
conduct
first
systematic
threats
facing
native
freshwater
diadromous
fishes
Britain.
In
addition,
national
assessments
were
produced
England,
Scotland
Wales,
reflecting
level
at
environmental
policy
decisions
are
taken
Seven
categorized
as
being
threatened
with
regional
level,
European
eel
Anguilla
anguilla
allis
shad
Alosa
alosa
classified
Critically
Endangered,
Atlantic
salmon
Salmo
salar
,
vendace
Coregonus
albula
whitefish
lavaretus
Arctic
charr
Salvelinus
alpinus
twaite
fallax
Vulnerable.
burbot
Lota
lota
was
Regionally
Extinct,
ferox
trout
Data
Deficient,
25
Least
Concern.
sturgeon
Acipenser
sturio
houting
oxyrinchus
although
probably
native,
qualified
only
vagrants
water,
so
Not
Applicable.
The
provide
objective
baselines
against
future
changes
can
be
determined,
key
evidence
base
support
management
habitats
It
is
recommended
that
repeated
every
10
years,
would
enable
status,
effectiveness
policies
where
targeted
interventions
may
required
examined
using
Index.
Abstract
Objectives
European
whitefish
(
Coregonus
lavaretus
L
.)
is
a
freshwater
salmonid
that
inhabits
cold
regions
of
central
and
north
Europe
Siberia.
It
an
important
aquaculture
species
in
Finland,
selectively
bred
since
1999.
The
breeding
programme
has
applied
genomic
selection
uses
SNP
markers
phenotypic
data
to
improve
traits
such
as
growth,
product
quality,
fish
health.
Salmonids
are
known
for
chromosomal
rearrangements,
the
current
C.
reference
genome
based
on
individual
from
Switzerland
may
deviate
Finnish
one.
Therefore,
we
have
assembled
whitefish.
This
allows
us
better
assess
genetic
basis
enhance
accuracy
selection.
Data
description
was
sequenced
using
combination
Illumina
PacBio
technologies
wtbg2
HiRise
software.
assembly
size
2.94
Gb
comprises
6,706
scaffolds
with
scaffold
N50
1.36
Mb.
Evolutionary Applications,
Год журнала:
2021,
Номер
14(10), С. 2470 - 2489
Опубликована: Июнь 11, 2021
Identifying
the
molecular
mechanisms
facilitating
adaptation
to
new
environments
is
a
key
question
in
evolutionary
biology,
especially
face
of
current
rapid
and
human-induced
changes.
Translocations
have
become
an
important
tool
for
species
conservation,
but
attendant
small
population
sizes
ecological
pressures
might
affect
phenotypic
genotypic
variation
trajectories
dramatically
unknown
ways.
In
Scotland,
European
whitefish
(
Scottish Geographical Journal,
Год журнала:
2023,
Номер
139(3-4), С. 445 - 465
Опубликована: Июль 18, 2023
Ice
coverage
not
only
affects
the
climate
and
landscape
of
geographical
regions
but
has
impacted
species
composition,
fragmentation
isolation
populations,
colonisation
routes
post-glaciation.
Major
advancements
in
generating
genetic
data
applying
sophisticated
analyses
to
accurately
model
demographic
history
animal
plant
allowed
evolutionary
biologists
novel
insights.
Meanwhile,
physical
geographers
have
made
major
reconstructing
glacial
history.
However,
information
flow
between
geographic
fields
on
this
topic
remains
limited;
consequently,
studies
contemporary
biodiversity
tend
be
vague
about
role
history,
while
is
rarely
leveraged
when
discussing
historical
glaciation.
In
review,
we
bring
together
current
knowledge
changing
patterns
ice
British
Isles
from
maximum
extent
British-Irish
sheet
(BIIS)
ca.
27
ka
through
end
large-scale
at
start
Holocene
period
11.5
ka.
We
do
so
then
highlight
how
glaciation
affected
composition
during
time
subsequent
temperate
flora
fauna
variation
seen
them.
International Journal of Limnology,
Год журнала:
2024,
Номер
60, С. 5 - 5
Опубликована: Янв. 1, 2024
Over
the
past
centuries,
coregonines
have
been
exposed
to
a
range
of
stressors
that
led
extinctions,
extirpations,
and
speciation
reversals.
Given
some
populations
remain
at
risk
fishery
managers
begun
restoring
where
they
extirpated,
we
reviewed
primary
gray
literature
describe
diversity
coregonine
restoration
or
conservation
actions
previously
used.
Although
stocking
hatchery-reared
fish
has
commonly
used
for
supplementing
existing
fisheries,
considered
efforts
only
with
specifically
goals.
Likewise,
conservation-driven
translocation
were
not
widespread,
except
in
United
Kingdom
creation
refuge
supplement
distribution
declining
stocks.
Habitat
occurred
more
broadly
included
improving
spawning
habitat,
connectivity,
nutrient
concentrations.
harvest
regulations
are
regulate
found
fewer
examples
protected
areas
outright
closures.
Finally,
interactions
invasive
species
can
be
considerable
stressor,
yet
relatively
few
control
undertaken
direct
benefit
coregonines.
In
conclusion,
our
review
prior
Coregonid
symposia
revealed
limited
emphasis
on
relative
traditional
approaches
(
e.g.
,
supplementation
stock
assessment)
studying
life
history
genetics.
Ideally,
by
providing
this
broad
strategies,
future
management
will
from
learning
about
greater
potential
could
locally
applied.
Evolution Letters,
Год журнала:
2024,
Номер
8(5), С. 706 - 718
Опубликована: Июнь 19, 2024
Reciprocal
effects
of
adaptive
radiations
on
the
evolution
interspecific
interactions,
like
parasitism,
remain
barely
explored.
We
test
whether
recent
European
whitefish
(
Journal of Evolutionary Biology,
Год журнала:
2021,
Номер
34(12), С. 1954 - 1969
Опубликована: Окт. 17, 2021
Pleistocene
glaciations
dramatically
affected
species
distribution
in
regions
that
were
impacted
by
ice
cover
and
subsequent
postglacial
range
expansion
contemporary
biodiversity
complex
ways.
The
European
whitefish,
Coregonus
lavaretus,
is
a
widely
distributed
salmonid
fish
on
mainland
Europe,
but
Britain
it
has
only
seven
native
populations,
all
of
which
are
found
the
western
extremes
island.
origins
colonization
routes
into
unknown
likely
contributed
to
genetic
patterns
regional
uniqueness.
Here,
we
used
up
25,751
genome-wide
polymorphic
loci
reconstruct
history
discern
demographic
evolutionary
forces
underpinning
divergence
between
British
populations.
Overall,
lower
diversity
Scottish
populations
high
differentiation
(FST
=
0.433-0.712)
from
English/Welsh
other
Differentiation
was
elevated
rather
than
particular
genomic
regions.
Demographic
modelling
supported
Scotland
northern
refugia
separate
route
for
southern
refugia,
with
these
two
groups
having
been
separated
more
ca.
50
Ky.
We
cyto-nuclear
discordance
at
scale,
clustering
closely
Baltic
population
mtDNA
analysis
not
nuclear
data,
Norwegian
Alpine
displaying
same
haplotype
being
distantly
related
tree.
These
findings
suggest
neutral
processes,
primarily
drift
regionally
distinct
pre-glacial
histories,
important
drivers
whitefish.
This
sheds
new
light
establishment
freshwater
fauna
after
last
glacial
maximum.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Окт. 4, 2023
Abstract
Background
Diversifying
animal
cultivation
demands
efficient
genotyping
for
enabling
genomic
selection,
but
non-model
species
lack
solutions.
The
aim
of
this
study
was
to
optimize
a
genotyping-by-sequencing
(GBS)
double-digest
RAD-sequencing
(ddRAD)
pipeline.
Bovine
data
used
automate
the
bioinformatic
analysis.
application
optimization
demonstrated
on
European
whitefish
data.
Results
DdRAD
generation
designed
reliable
estimation
relatedness
and
is
scalable
up
384
samples.
GBS
sequencing
yielded
approximately
one
million
reads
each
around
100
assessed
Optimizing
various
strategies
create
de-novo
reference
genome
variant
calling
(mock
reference)
showed
that
using
three
samples
outperformed
other
building
with
single
or
very
large
number
Adjustments
most
pipeline
tuning
parameters
had
limited
impact
high-quality
data,
except
identity
criterion
merging
mock
clusters.
For
species,
over
15k
variants
based
were
obtained
comparable
results
ones
called
an
existing
genome.
Repeatability
analysis
high
concordance
replicates,
particularly
in
bovine
while
repeatability
did
not
exceed
earlier
observations.
Conclusions
proposed
cost-effective
ddRAD
strategy,
coupled
bioinformatics
workflow,
enables
broad
adoption
across
diverse
farmed
species.
While
beneficial,
obligatory.
integration
Snakemake
streamlines
usage
computer
clusters
supports
customization.
This
user-friendly
solution
facilitates
both
model
Research Square (Research Square),
Год журнала:
2024,
Номер
unknown
Опубликована: Фев. 16, 2024
Abstract
Background
Diversifying
animal
cultivation
demands
efficient
genotyping
for
enabling
genomic
selection,
but
non-model
species
lack
solutions.
The
aim
of
this
study
was
to
optimize
a
genotyping-by-sequencing
(GBS)
double-digest
RAD-sequencing
(ddRAD)
pipeline.
Bovine
data
used
automate
the
bioinformatic
analysis.
application
optimization
demonstrated
on
European
whitefish
data.
Results
DdRAD
generation
designed
reliable
estimation
relatedness
and
is
scalable
up
384
samples.
GBS
sequencing
yielded
approximately
one
million
reads
each
around
100
assessed
Optimizing
various
strategies
create
de-novo
reference
genome
variant
calling
(mock
reference)
showed
that
using
three
samples
outperformed
other
building
with
single
or
very
large
number
Adjustments
most
pipeline
tuning
parameters
had
limited
impact
high-quality
data,
except
identity
criterion
merging
mock
clusters.
For
species,
over
15k
variants
based
were
obtained
comparable
results
ones
called
an
existing
genome.
Repeatability
analysis
high
concordance
replicates,
particularly
in
bovine
while
repeatability
did
not
exceed
earlier
observations.
Conclusions
proposed
cost-effective
ddRAD
strategy,
coupled
bioinformatics
workflow,
enables
broad
adoption
across
diverse
farmed
species.
While
beneficial,
obligatory.
integration
Snakemake
streamlines
usage
computer
clusters
supports
customization.
This
user-friendly
solution
facilitates
both
model
