Evolutionary Applications,
Journal Year:
2023,
Volume and Issue:
16(9), P. 1619 - 1636
Published: Sept. 1, 2023
Abstract
Lumpfish,
Cyclopterus
lumpus
,
have
historically
been
harvested
throughout
Atlantic
Canada
and
are
increasingly
in
demand
as
a
solution
to
controlling
sea
lice
salmon
farms—a
process
which
involves
both
the
domestication
transfer
of
lumpfish
between
geographic
regions.
At
present,
little
is
known
regarding
population
structure
diversity
wild
Canada,
limiting
attempts
assess
potential
impacts
escaped
individuals
from
pens
on
currently
at‐risk
populations.
Here,
we
characterize
spatial
genomic‐environmental
associations
populations
Northwest
using
70K
SNP
array
data
whole‐genome
re‐sequencing
(WGS).
broad
scales,
our
results
reveal
large
environmentally
associated
genetic
break
southern
(Gulf
Maine
Bay
Fundy)
northern
(Newfoundland
Gulf
St.
Lawrence),
linked
variation
ocean
temperature
ice
cover.
finer
evidence
was
also
evident
distinct
coastal
group
Newfoundland
significant
isolation
by
distance
across
region.
Both
consistent
environmental
elevated
genome‐wide
F
ST
values
among
these
three
regional
groups
supports
their
biological
relevance.
This
study
represents
first
extensive
description
revealing
fine
scale
genomic
diversity.
Our
will
facilitate
commercial
use
cleaner
fish
aquaculture,
identification
escapees,
delineation
conservation
units
this
species
Canada.
Nature Ecology & Evolution,
Journal Year:
2022,
Volume and Issue:
6(4), P. 469 - 481
Published: Feb. 17, 2022
Abstract
Supergenes
are
sets
of
genes
that
inherited
as
a
single
marker
and
encode
complex
phenotypes
through
their
joint
action.
They
identified
in
an
increasing
number
organisms,
yet
origins
evolution
remain
enigmatic.
In
Atlantic
cod,
four
megabase-scale
supergenes
have
been
linked
to
migratory
lifestyle
environmental
adaptations.
Here
we
investigate
the
origin
maintenance
these
analysis
whole-genome-sequencing
data,
including
new
long-read-based
genome
assembly
for
non-migratory
cod
individual.
We
corroborate
finding
chromosomal
inversions
underlie
all
supergenes,
show
they
originated
at
different
times
between
0.40
1.66
million
years
ago.
reveal
gene
flux
supergene
haplotypes
where
stationary
co-occur
conclude
this
is
driven
by
conversion,
on
basis
increase
GC
content
exchanged
sites.
Additionally,
find
evidence
double
crossover
haplotypes,
leading
exchange
~275
kilobase
fragment
with
potentially
involved
adaptation
low
salinity
Baltic
Sea.
Our
results
suggest
can
be
maintained
over
long
timescales
same
way
hybridizing
species,
selective
purging
introduced
genetic
variation.
Journal of Evolutionary Biology,
Journal Year:
2023,
Volume and Issue:
36(12), P. 1761 - 1782
Published: Nov. 9, 2023
Abstract
Inversions
are
structural
mutations
that
reverse
the
sequence
of
a
chromosome
segment
and
reduce
effective
rate
recombination
in
heterozygous
state.
They
play
major
role
adaptation,
as
well
other
evolutionary
processes
such
speciation.
Although
inversions
have
been
studied
since
1920s,
they
remain
difficult
to
investigate
because
reduced
conferred
by
them
strengthens
effects
drift
hitchhiking,
which
turn
can
obscure
signatures
selection.
Nonetheless,
numerous
found
be
under
Given
recent
advances
population
genetic
theory
empirical
study,
here
we
review
how
different
mechanisms
selection
affect
evolution
inversions.
A
key
difference
between
mutations,
single
nucleotide
variants,
is
fitness
an
inversion
may
affected
larger
number
frequently
interacting
processes.
This
considerably
complicates
analysis
causes
underlying
We
discuss
extent
these
disentangled,
approach.
often
roles
adaptation
speciation,
but
direct
their
obscured
characteristic
makes
so
unique
(reduced
arrangements).
In
this
review,
examine
impact
evolution,
weaving
together
both
theoretical
studies.
emphasize
most
patterns
overdetermined
(i.e.
caused
multiple
processes),
highlight
new
technologies
provide
path
forward
towards
disentangling
mechanisms.
Molecular Ecology,
Journal Year:
2020,
Volume and Issue:
29(24), P. 4765 - 4782
Published: Aug. 17, 2020
Abstract
Copy
number
variants
(CNVs)
are
a
major
component
of
genotypic
and
phenotypic
variation
in
genomes.
To
date,
our
knowledge
evolution
has
largely
been
acquired
by
means
single
nucleotide
polymorphism
(SNPs)
analyses.
Until
recently,
the
adaptive
role
structural
(SVs)
particularly
that
CNVs
overlooked
wild
populations,
partly
due
to
their
challenging
identification.
Here,
we
document
usefulness
Rapture,
derived
reduced‐representation
shotgun
sequencing
approach,
detect
investigate
copy
alongside
SNPs
American
lobster
(
Homarus
americanus
)
populations.
We
conducted
comparative
study
examine
potential
local
adaptation
1,141
lobsters
from
21
sampling
sites
within
southern
Gulf
St.
Lawrence,
which
experiences
highest
yearly
thermal
variance
Canadian
marine
coastal
waters.
Our
results
demonstrated
account
for
higher
genetic
differentiation
than
SNP
markers.
Contrary
SNPs,
no
significant
genetic–environment
association
was
found,
48
CNV
candidates
were
significantly
associated
with
annual
sea
surface
temperature,
leading
clustering
locations
despite
geographic
separation.
Altogether,
provide
strong
empirical
case
putatively
contribute
species
unveil
stronger
spatial
signal
population
structure
SNPs.
provides
nonmodel
highlights
importance
considering
enhance
understanding
ecological
evolutionary
processes
shaping
structure.
Evolution Letters,
Journal Year:
2020,
Volume and Issue:
4(5), P. 430 - 443
Published: Aug. 27, 2020
The
study
of
local
adaptation
in
the
presence
ongoing
gene
flow
is
natural
selection
action,
revealing
functional
genetic
diversity
most
relevant
to
contemporary
pressures.
In
addition
individual
genes,
genome-wide
architecture
can
itself
evolve
enable
adaptation.
Distributed
across
a
steep
thermal
gradient
along
east
coast
North
America,
Atlantic
silversides
(Menidia
menidia)
exhibit
an
extraordinary
degree
suite
traits,
and
capacity
for
rapid
from
standing
variation,
but
we
know
little
about
patterns
genomic
variation
species
range
that
this
remarkable
adaptability.
Here,
use
low-coverage,
whole-transcriptome
sequencing
sampled
environmental
cline
show
marked
signatures
divergent
neutral
differentiation.
1371
km
southern
section
its
distribution
have
very
low
differentiation
(median
FST
=
0.006
1.9
million
variants),
consistent
with
historical
connectivity
observations
recent
migrants.
Yet
almost
14,000
single
nucleotide
polymorphisms
(SNPs)
are
nearly
fixed
(FST
>
0.95)
alternate
alleles.
Highly
differentiated
SNPs
cluster
into
four
tight
linkage
disequilibrium
(LD)
blocks
span
hundreds
genes
several
megabases.
Variants
these
LD
disproportionately
nonsynonymous
concentrated
enriched
multiple
functions
related
known
adaptations
silversides,
including
lipid
storage,
metabolic
rate,
spawning
behavior.
Elevated
levels
absolute
divergence
demographic
modeling
suggest
maintaining
under
flow.
These
findings
represent
extreme
case
heterogeneity
genome,
highlight
how
shapes
continuous
populations.
Locally
adapted
alleles
may
be
common
features
populations
distributed
gradients,
will
likely
key
conserving
future
responses
change.
Proceedings of the National Academy of Sciences,
Journal Year:
2022,
Volume and Issue:
119(8)
Published: Feb. 14, 2022
Life
on
Earth
has
been
characterized
by
recurring
cycles
of
ecological
stasis
and
disruption,
relating
biological
eras
to
geological
climatic
transitions
through
the
history
our
planet.
Due
increasing
degree
abruption
caused
human
influences
many
advocate
that
we
now
have
entered
era
Anthropocene,
or
"the
age
man."
Considering
ongoing
mass
extinction
ecosystem
reshuffling
observed
worldwide,
a
better
understanding
drivers
will
be
requisite
for
identifying
routes
intervention
mitigation.
Ecosystem
stability
may
rely
one
few
keystone
species,
loss
such
species
could
potentially
detrimental
effects.
The
Atlantic
cod
(Gadus
morhua)
historically
highly
abundant
is
considered
in
ecosystems
northern
Ocean.
Collapses
stocks
both
sides
reported
effects
include
vast
reshuffling.
By
whole-genome
resequencing
demonstrate
stabilizing
selection
maintains
three
extensive
"supergenes"
cod,
linking
these
genes
persistence
stasis.
Genomic
inference
historic
effective
population
sizes
shows
continued
declines
North
Sea-Skagerrak-Kattegat
system
past
millennia,
consistent
with
an
early
onset
marine
Anthropocene
industrialization
commercialization
fisheries
throughout
medieval
period.
Philosophical Transactions of the Royal Society B Biological Sciences,
Journal Year:
2022,
Volume and Issue:
377(1856)
Published: June 13, 2022
Local
adaptation
leads
to
differences
between
populations
within
a
species.
In
many
systems,
similar
environmental
contrasts
occur
repeatedly,
sometimes
driving
parallel
phenotypic
evolution.
Understanding
the
genomic
basis
of
local
and
evolution
is
major
goal
evolutionary
genomics.
It
now
known
that
by
preventing
break-up
favourable
combinations
alleles
across
multiple
loci,
genetic
architectures
reduce
recombination,
like
chromosomal
inversions,
can
make
an
important
contribution
adaptation.
However,
little
about
whether
inversions
also
contribute
disproportionately
Our
aim
here
highlight
this
knowledge
gap,
showcase
existing
studies,
illustrate
with
without
using
simple
models.
We
predict
generating
stronger
effective
selection,
speed
up
adaptive
process
or
enable
where
it
would
be
impossible
otherwise,
but
highly
dependent
on
spatial
setting.
further
empirical
work
needed,
in
particular
cover
broader
taxonomic
range
understand
relative
importance
compared
regions
inversions.
This
article
part
theme
issue
‘Genomic
architecture
supergenes:
causes
consequences’.
Genes,
Journal Year:
2023,
Volume and Issue:
14(4), P. 876 - 876
Published: April 7, 2023
The
blue
mussel
Mytilus
chilensis
is
an
endemic
and
key
socioeconomic
species
inhabiting
the
southern
coast
of
Chile.
This
bivalve
supports
a
booming
aquaculture
industry,
which
entirely
relies
on
artificially
collected
seeds
from
natural
beds
that
are
translocated
to
diverse
physical–chemical
ocean
farming
conditions.
Furthermore,
production
threatened
by
broad
range
microorganisms,
pollution,
environmental
stressors
eventually
impact
its
survival
growth.
Herein,
understanding
genomic
basis
local
adaption
pivotal
developing
sustainable
shellfish
aquaculture.
We
present
high-quality
reference
genome
M.
chilensis,
first
chromosome-level
for
Mytilidae
member
in
South
America.
assembled
size
was
1.93
Gb,
with
contig
N50
134
Mb.
Through
Hi-C
proximity
ligation,
11,868
contigs
were
clustered,
ordered,
into
14
chromosomes
congruence
karyological
evidence.
comprises
34,530
genes
4795
non-coding
RNAs.
A
total
57%
contains
repetitive
sequences
predominancy
LTR-retrotransposons
unknown
elements.
Comparative
analysis
coruscus
conducted,
revealing
genic
rearrangements
distributed
whole
genome.
Notably,
transposable
Steamer-like
elements
associated
horizontal
transmissible
cancer
explored
genomes,
suggesting
putative
relationships
at
chromosome
level
Bivalvia.
Genome
expression
also
showing
differences
between
two
ecologically
different
populations.
evidence
suggests
adaptation
physiological
plasticity
can
be
analyzed
develop
production.
provides
molecular
knowledge
complex.
Journal of Heredity,
Journal Year:
2020,
Volume and Issue:
111(4), P. 319 - 332
Published: June 1, 2020
Genetic
and
genomic
architectures
of
traits
under
selection
are
key
factors
influencing
evolutionary
responses.
Yet,
knowledge
their
impacts
has
been
limited
by
a
widespread
assumption
that
most
controlled
unlinked
polygenic
architectures.
Recent
advances
in
genome
sequencing
eco-evolutionary
modeling
unlocking
the
potential
for
integrating
information
into
predictions
population
responses
to
environmental
change.
Using
simulations,
we
demonstrate
hypothetical
single-locus
control
life
history
trait
produces
highly
variable
unpredictable
harvesting-induced
evolution
relative
classically
applied
multilocus
model.
Single-locus
complex
is
thought
be
uncommon,
yet
blocks
linked
genes,
such
as
those
associated
with
some
types
structural
variation,
have
emerged
taxonomically
phenomena.
Inheritance
resembles
single
loci,
thus
enabling
single-locus-like
adaptation.
number
effect
sizes,
degree
linkage
among
them
all
occur
along
continuum.
We
review
how
often
associated,
directly
or
indirectly,
expected
from
anthropogenic
stressors
likely
play
large
role
adaptation
disturbance.
suggest
using
models
explore
extremes
uncertainties
when
architecture
unknown,
refining
parameters
becomes
available,
explicitly
incorporating
loci
possible.
By
overestimating
complexity
(e.g.,
independent
loci)
selection,
risk
underestimating
nonlinearity)
dynamics.
Ecology and Evolution,
Journal Year:
2020,
Volume and Issue:
10(2), P. 638 - 653
Published: Jan. 1, 2020
Abstract
Genomic
architecture
and
standing
variation
can
play
a
key
role
in
ecological
adaptation
contribute
to
the
predictability
of
evolution.
In
Atlantic
cod
(
Gadus
morhua
),
four
large
chromosomal
rearrangements
have
been
associated
with
gradients
migratory
behavior
regional
analyses.
However,
degree
parallelism,
extent
independent
inheritance,
functional
distinctiveness
these
remain
poorly
understood.
Here,
we
use
12K
single
nucleotide
polymorphism
(SNP)
array
demonstrate
extensive
individual
rearrangement
genotype
within
populations
across
species
range,
suggesting
that
local
fine‐scale
is
enabled
by
inheritance.
Our
results
significant
association
migration
phenotype
environmental
range.
Individual
exhibit
modularity,
but
also
contain
loci
showing
multiple
associations.
Clustering
genetic
distance
trees
reduced
differentiation
range
are
consistent
shared
as
source
contemporary
adaptive
diversity
cod.
Conversely,
find
haplotypes
LG12
LG1
rearranged
region
diverged
Atlantic,
despite
Exchange
structurally
variable
genomic
regions,
well
selective
pressures,
has
likely
facilitated
stocks.
highlight
importance
enabling
marine
species.