Molecular Ecology Resources,
Год журнала:
2021,
Номер
21(4), С. 1318 - 1332
Опубликована: Фев. 5, 2021
Abstract
The
harlequin
ladybird,
Harmonia
axyridis
(Pallas),
is
a
well‐known
model
organism
for
genetic
studies
and
also
well‐studied
natural
enemy
used
pest
control.
It
became
an
invasive
species
after
being
introduced
to
North
America
Europe
as
control
agent.
Though
two
genome
assemblies
this
insect
have
been
previously
reported,
high‐quality
assembly
at
the
chromosome
level
still
not
available.
Here,
we
obtained
new
chromosome‐level
of
H
.
by
combining
various
sequencing
technologies,
namely
Illumina
short
reads,
PacBio
long
10X
Genomics
Hi‐C.
423
Mb
with
scaffold
N50
45.92
Mb.
Using
Hi‐C
data
1,897
scaffolds
were
anchored
eight
chromosomes.
A
total
730,068
repeat
sequences
identified,
making
up
51.2%
assembled
genome.
After
masking
these
sequences,
annotated
22,810
protein‐encoding
genes.
X
Y‐linked
identified
resequencing
male
female
genomes
calculating
coverage
ratios.
Two
gene
families
associated
environmental
adaptation,
odorant
receptor
cytochrome
P450,
analysed
showed
no
obvious
expansion
in
We
successfully
constructed
putative
biosynthesis
pathway
harmonine,
defence
compound
haemolymph
,
which
key
factor
strong
immunity.
helpful
resource
beetle
biology
biology.
Proceedings of the Royal Society B Biological Sciences,
Год журнала:
2019,
Номер
286(1900), С. 20182924 - 20182924
Опубликована: Апрель 3, 2019
Species
delimitation
is
a
major
quest
in
biology
and
essential
for
adequate
management
of
the
organismal
diversity.
A
challenging
example
comprises
fish
species
red
snappers
Western
Atlantic.
Red
have
been
traditionally
recognized
as
two
separate
based
on
morphology:
Lutjanus
campechanus
(northern
snapper)
L.
purpureus
(southern
snapper).
Recent
genetic
studies
using
mitochondrial
markers,
however,
failed
to
delineate
these
nominal
species,
leading
current
lumping
northern
southern
populations
into
single
(
campechanus).
This
decision
carries
broad
implications
conservation
commercially
over-exploited
across
Atlantic
are
currently
listed
vulnerable.
To
address
this
conflict,
we
examine
genome-wide
data
collected
throughout
range
species.
Population
genomics,
phylogenetic
coalescent
analyses
favour
existence
independent
evolutionary
lineages,
result
that
confirms
morphology-based
scenario
agreement
with
conventional
taxonomy.
Despite
finding
evidence
introgression
geographically
neighbouring
South
America,
our
genomic
strongly
support
isolation
differentiation
suggesting
should
be
treated
distinct
taxonomic
entities.
Molecular Biology and Evolution,
Год журнала:
2021,
Номер
unknown
Опубликована: Фев. 10, 2021
Testing
among
competing
demographic
models
of
divergence
has
become
an
important
component
evolutionary
research
in
model
and
non-model
organisms.
However,
the
effect
unaccounted
events
on
choice
parameter
estimation
remains
largely
unexplored.
Using
extensive
simulations,
we
demonstrate
that
under
realistic
scenarios,
failure
to
account
for
population
size
(Ne)
changes
daughter
ancestral
populations
leads
strong
biases
time
estimates
as
well
choice.
We
illustrate
these
issues
reconstructing
recent
history
North
Sea
Baltic
turbots
(Scophthalmus
maximus)
by
testing
16
isolation
with
migration
(IM)
secondary
contact
(SC)
modeling
Ne
effects
linked
selection
barrier
loci.
Failure
resulted
selecting
SC
long
periods
strict
times
preceding
formation
Sea.
In
contrast,
accounting
suggest
(<6
kya)
constant
gene
flow.
further
show
how
interpreting
genomic
landscapes
differentiation
can
help
discerning
models.
For
example,
turbot
data,
islands
signatures
selective
sweeps,
rather
than
old
resisting
introgression.
The
results
have
broad
implications
study
highlighting
potential
unmodeled
inference.
Tested
should
aim
at
representing
scenarios
target
taxa,
extreme
caution
always
be
exercised
when
modeling.
Evolutionary Applications,
Год журнала:
2020,
Номер
13(6), С. 1320 - 1334
Опубликована: Апрель 15, 2020
The
influence
of
species
life
history
traits
and
historical
demography
on
contemporary
connectivity
is
still
poorly
understood.
However,
these
factors
partly
determine
the
evolutionary
responses
to
anthropogenic
landscape
alterations.
Genetic
its
outcomes
depend
a
variety
spatially
dependent
processes,
such
as
population
structure,
local
adaptation,
genetic
admixture,
speciation.
Over
last
years,
genomic
studies
have
been
interrogating
processes
with
increasing
resolution,
revealing
large
diversity
structured
landscapes.
In
parallel,
multispecies
meta-analyses
usually
based
low-genome
coverage
data
provided
fundamental
insights
into
ecological
determinants
connectivity,
key
structure.
comparative
lack
thorough
integration
macro-
micro-evolutionary
scales
fully
realize
their
potential.
Here,
I
present
how
genomics
framework
may
provide
deeper
understanding
process
connectivity.
This
relies
coupling
inference
long-term
demographic
selective
an
assessment
consequences
Standardizing
this
approach
across
several
occupying
same
should
help
understand
spatial
environmental
heterogeneity
has
shaped
patterns
in
different
taxa
contrasted
traits.
will
argue
that
reasonable
amount
genome
sequence
can
be
sufficient
resolve
connect
complex
histories.
Ultimately,
implementing
varied
taxonomic
groups
expected
improve
scientific
guidelines
for
conservation
management
policies.
Nature Communications,
Год журнала:
2021,
Номер
12(1)
Опубликована: Июль 14, 2021
We
lack
a
thorough
understanding
of
the
origin
and
maintenance
standing
genetic
variation
that
enables
rapid
evolutionary
responses
natural
populations.
Whole
genome
sequencing
resurrected
Daphnia
population
shows
in
over
500
genes
follows
an
trajectory
parallels
pronounced
adaptive
evolution
multiple
traits
response
to
predator-driven
selection
its
subsequent
relaxation.
Genetic
carried
by
only
five
founding
individuals
from
regional
genotype
pool
is
shown
suffice
at
enabling
observed
evolution.
Our
results
provide
insight
on
how
populations
can
acquire
genomic
variation,
through
colonization
few
genotypes,
fuels
strong
pressures.
While
these
our
study
involved
hundreds
genes,
we
no
evidence
erosion.
Molecular Ecology,
Год журнала:
2021,
Номер
30(17), С. 4162 - 4172
Опубликована: Июнь 16, 2021
Abstract
Biologists
have
long
been
intrigued
by
apparently
predictable
and
repetitive
evolutionary
trajectories
inferred
across
a
variety
of
lineages
systems.
In
recent
years,
high‐throughput
sequencing
analyses
started
to
transform
our
understanding
such
shifts.
While
researchers
traditionally
categorized
shifts
as
either
“convergent”
or
“parallel,”
based
on
relatedness
the
involved,
emerging
genomic
insights
provide
an
opportunity
better
describe
actual
mechanisms
at
play.
A
synthesis
confirms
that
convergence
is
predominant
driver
evolution
among
species,
whereas
repeated
sorting
standing
variation
major
within
species.
However,
data
reveal
numerous
notable
exceptions
these
expectations,
with
examples
de
novo
mutations
underpinning
convergent
even
very
closely
related
lineages,
while
processes
occurred
deeply
divergent
taxa,
sometimes
via
introgression.
number
found
evidence
for
both
occurring
different
scales
taxa.
We
suggest
relative
importance
versus
depends
interplay
between
gene
flow
populations,
phylogenetic
involved.
Molecular Biology and Evolution,
Год журнала:
2019,
Номер
36(12), С. 2842 - 2853
Опубликована: Авг. 27, 2019
Some
genes
have
repeatedly
been
found
to
control
diverse
adaptations
in
a
wide
variety
of
organisms.
Such
gene
reuse
reveals
not
only
the
diversity
phenotypes
these
unique
but
also
composition
developmental
networks
and
genetic
routes
available
taken
by
organisms
during
adaptation.
However,
causes
remain
unclear.
A
small
number
large-effect
Mendelian
loci
huge
mimetic
butterfly
wing
color
patterns,
reasons
for
their
are
difficult
identify
because
basis
mimicry
has
primarily
studied
two
systems
with
correlated
factors:
female-limited
Batesian
Papilio
swallowtails
(Papilionidae)
non-sex-limited
Müllerian
Heliconius
longwings
(Nymphalidae).
Here,
we
break
correlation
between
phylogenetic
relationship
sex-limited
identifying
controlling
polymorphism
Hypolimnas
misippus
(Nymphalidae)
clytia
(Papilionidae).
The
is
controlled
genome
region
containing
cortex,
classic
P
supergene
numata,
pattern
variation
across
Lepidoptera.
In
contrast,
associated
locus
previously
implicated
patterning.
Thus,
although
many
species
converged
on
cortex
its
neighboring
over
120
My
evolution
polymorphisms
each
evolved
using
different
gene.
Our
results
support
conclusions
that
occurs
mainly
within
∼10
highlight
puzzling
seemingly
complex
polymorphisms.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Янв. 20, 2023
Abstract
Beetles
are
the
most
species-rich
group
of
animals
and
harbor
diverse
karyotypes.
Most
species
have
XY
sex
chromosomes,
but
X0
determination
mechanisms
also
common
in
some
groups.
We
generated
a
whole-chromosome
assembly
beetle
with
neo-sex
chromosome
utilize
eleven
additional
genomes,
to
reconstruct
karyotype
evolution
across
Coleoptera.
identify
ancestral
linkage
groups,
termed
Stevens
elements,
that
share
conserved
set
genes
beetles.
While
X
is
maintained
beetles,
we
find
independent
additions
autosomes
chromosomes.
These
chromosomes
evolve
stereotypical
properties
including
dosage
compensation,
non-random
distribution
sex-biased
expression.
thus
provide
novel
model
gain
better
understanding
forces
driving
evolution.