bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 4, 2023
Abstract
Adaptive
radiations
are
characterized
by
rapid
ecological
diversification
and
speciation
events,
leading
to
fuzzy
species
boundaries
between
ecologically
differentiated
species.
therefore
key
systems
for
understanding
how
formed
maintained,
including
the
role
of
de
novo
mutations
vs.
pre-existing
variation
in
adaptation
genome-wide
consequences
hybridization
events.
For
example,
adaptive
introgression,
where
beneficial
alleles
transferred
lineages
through
hybridization,
may
fuel
facilitate
new
environments.
In
this
study,
we
employed
whole-genome
resequencing
data
investigate
evolutionary
origin
hummingbird-pollinated
flowers
characterize
patterns
phylogenetic
discordance
introgression
Penstemon
subgenus
Dasanthera
,
a
small
diverse
radiation
plants.
We
found
that
magenta
hummingbird-adapted
have
apparently
evolved
twice
from
ancestral
blue-violet
bee-pollinated
within
radiation.
These
shifts
flower
color
accompanied
variety
inactivating
anthocyanin
pathway
enzyme,
suggesting
independent
loss-of-function
underlie
parallel
evolution
trait.
Although
were
heterogenous
across
genome,
strong
effect
gene
density
suggests
that,
general,
natural
selection
opposes
maintains
genetic
differentiation
gene-rich
genomic
regions.
Our
results
highlight
importance
both
mutation
as
sources
change
indicate
driving
radiations.
Nature,
Год журнала:
2024,
Номер
628(8009), С. 811 - 817
Опубликована: Апрель 17, 2024
Abstract
Hybridization
allows
adaptations
to
be
shared
among
lineages
and
may
trigger
the
evolution
of
new
species
1,2
.
However,
convincing
examples
homoploid
hybrid
speciation
remain
rare
because
it
is
challenging
demonstrate
that
hybridization
was
crucial
in
generating
reproductive
isolation
3
Here
we
combine
population
genomic
analysis
with
quantitative
trait
locus
mapping
species-specific
traits
examine
a
case
Heliconius
butterflies.
We
show
elevatus
sympatric
both
parents
has
persisted
as
an
independently
evolving
lineage
for
at
least
180,000
years.
This
despite
pervasive
ongoing
gene
flow
one
parent,
pardalinus
,
which
homogenizes
99%
their
genomes.
The
remaining
1%
introgressed
from
other
melpomene
scattered
widely
across
H.
genome
islands
divergence
These
contain
multiple
are
under
disruptive
selection,
including
colour
pattern,
wing
shape,
host
plant
preference,
sex
pheromones
mate
choice.
Collectively,
these
place
on
its
own
adaptive
peak
permit
coexistence
parents.
Our
results
driven
by
introgression
ecological
traits,
possible
multilocus
genetic
architecture.
PLoS Biology,
Год журнала:
2023,
Номер
21(9), С. e3002294 - e3002294
Опубликована: Сен. 28, 2023
In
the
formation
of
species,
adaptation
by
natural
selection
generates
distinct
combinations
traits
that
function
well
together.
The
maintenance
adaptive
trait
in
face
gene
flow
depends
on
strength
and
nature
acting
underlying
genetic
loci.
Floral
pollination
syndromes
exemplify
evolution
for
particular
pollinators.
North
American
wildflower
genus
Penstemon
displays
remarkable
floral
syndrome
convergence,
with
at
least
20
separate
lineages
have
evolved
from
ancestral
bee
(wide
blue-purple
flowers
present
a
landing
platform
bees
small
amounts
nectar)
to
hummingbird
(bright
red
narrowly
tubular
offering
copious
nectar).
Related
taxa
differ
offer
an
attractive
opportunity
examine
genomic
basis
complex
divergence.
this
study,
we
characterized
divergence
among
229
individuals
species
includes
both
syndromes.
Field
plants
are
easily
classified
into
based
phenotypic
differences
hybrids
displaying
intermediate
rare.
Despite
unambiguous
differences,
genome-wide
differentiation
between
is
minimal.
Hummingbird-adapted
populations
more
genetically
similar
nearby
bee-adapted
than
geographically
distant
hummingbird-adapted
populations,
terms
dXY.
However,
number
loci
strongly
differentiated
species.
These
approximately
"species-diagnostic
loci,"
which
appear
nearly
fixed
syndromes,
sprinkled
throughout
genome
high
recombination
regions.
Several
map
closely
previously
established
quantitative
(QTLs).
striking
difference
diagnostic
as
whole
suggests
strong
maintain
traits,
but
sufficient
homogenize
background.
A
surprisingly
alleles
confer
form
identity
complex.
Evolution Letters,
Год журнала:
2024,
Номер
8(4), С. 575 - 586
Опубликована: Апрель 23, 2024
Abstract
Chromosomal
rearrangements
can
lead
to
the
coupling
of
reproductive
barriers,
but
whether
and
how
they
contribute
completion
speciation
remains
unclear.
Marine
snails
genus
Littorina
repeatedly
form
hybrid
zones
between
populations
segregating
for
multiple
inversion
arrangements,
providing
opportunities
study
their
barrier
effects.
Here,
we
analyzed
2
adjacent
transects
across
ecotypes
fabalis
(“large”
“dwarf”)
adapted
different
wave
exposure
conditions
on
a
Swedish
island.
Applying
whole-genome
sequencing,
found
12
putative
inversions
9
17
chromosomes.
Nine
reached
near
differential
fixation
ecotypes,
all
were
in
strong
linkage
disequilibrium.
These
cover
20%
genome
carry
93%
divergent
single
nucleotide
polymorphisms
(SNPs).
Bimodal
both
indicated
that
maintain
genetic
phenotypic
integrity
following
contact.
The
bimodality
reflects
clines
extension
effect
whole
genome.
Demographic
inference
suggests
arose
during
period
allopatry
has
been
maintained
>
1,000
generations
after
secondary
Overall,
this
shows
chromosomal
contributes
isolation.
Notably,
overlap
with
inverted
genomic
regions
associated
ecotype
differences
closely
related
species
(Littorina
saxatilis),
suggesting
same
regions,
similar
structural
variants,
evolution
distinct
species.
Molecular Biology and Evolution,
Год журнала:
2024,
Номер
41(1)
Опубликована: Янв. 1, 2024
Abstract
Adaptive
radiations
are
characterized
by
rapid
ecological
diversification
and
speciation
events,
leading
to
fuzzy
species
boundaries
between
ecologically
differentiated
species.
therefore
key
systems
for
understanding
how
formed
maintained,
including
the
role
of
de
novo
mutations
versus
preexisting
variation
in
adaptation
genome-wide
consequences
hybridization
events.
For
example,
adaptive
introgression,
where
beneficial
alleles
transferred
lineages
through
hybridization,
may
fuel
facilitate
new
environments.
In
this
study,
we
employed
whole-genome
resequencing
data
investigate
evolutionary
origin
hummingbird-pollinated
flowers
characterize
patterns
phylogenetic
discordance
introgression
Penstemon
subgenus
Dasanthera,
a
small
diverse
radiation
plants.
We
found
that
magenta
hummingbird-adapted
have
apparently
evolved
twice
from
ancestral
blue-violet
bee-pollinated
within
radiation.
These
shifts
flower
color
accompanied
variety
inactivating
anthocyanin
pathway
enzyme,
suggesting
independent
loss-of-function
underlie
parallel
evolution
trait.
Although
were
heterogenous
across
genome,
strong
effect
gene
density
suggests
that,
general,
natural
selection
opposes
maintains
genetic
differentiation
gene-rich
genomic
regions.
Our
results
highlight
importance
both
mutation
as
sources
change
indicate
driving
radiations.
Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 21, 2025
ABSTRACT
Cultivation
of
crops
close
to
their
wild
relatives
may
jeopardise
the
integrity
genetic
resources.
Detecting
cultivars
among
plants
is
necessary
characterise
crop‐wild
gene
flow,
but
can
be
challenging
if
and
are
phenotypically
highly
similar.
Genomics
tools
used
instead,
selection
diagnostic
loci
for
cultivar
identification
difficult
cultivated
genepools
closely
related.
In
Ethiopia,
Arabica
coffee
resistant
berry
disease
(CBD)
occur
near
Coffea
arabica
local
landraces.
However,
abundance
distribution
these
across
sites
remains
unclear.
Here,
we
present
a
new
module
SMAP
package
called
relatedness
pairwise
relationships
between
individuals
based
on
haplotype
calls
identify
that
distinguish
(sets
of)
from
each
other.
Next,
estimate
relative
CBD‐resistant
60
Ethiopian
using
genome‐wide
fingerprinting
approach.
We
confirm
presence
in
around
75%
with
high
agreement
field
survey
our
DNA
At
least
20
out
supposedly
C.
contain
signatures
genepool.
Overall,
conclude
widespread
sites.
The
development
opens
opportunities
assess
other
regions
Ethiopia
apply
similar
screenings
crops.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 19, 2025
Abstract
Understanding
how
evolution
proceeds
from
molecules
to
organisms
interactions
requires
integrative
studies
spanning
biological
levels.
Linking
phenotypes
with
associated
genes
and
fitness
illuminates
adaptive
walks
move
between
peaks.
Floral
can
confer
rapid
reproductive
isolation,
often
converging
in
association
pollinator
guilds.
Within
the
monkeyflowers
(
Mimulus
sect.
Erythranthe
),
yellow
flowers
within
red
hummingbird-pollinated
species
have
arisen
at
least
twice,
suggesting
possible
shifts.
We
compare
two
yellow-flowered
forms
of
M.
cardinalis
verbenaceus
their
counterparts
floral
phenotypes,
biochemistry,
transcriptomic
genomic
variation,
interactions.
find
convergence
ongoing
both
morphs,
consistent
changes
traits
large
effect
(floral
pigments,
gene
expression),
resulting
strong
preference
for
by
bumblebees.
Shifts
scent
emission
opening
size
also
favor
bee
adaptation,
smaller-effect
steps
hummingbird
pollination.
By
examining
intraspecific,
incipient
shifts
related
species,
we
elucidate
early
stages,
revealing
convergent
mutations
color)
may
drive
attraction,
followed
smaller
mechanical
fit
reward
access.
Thus,
impact
isolation
speciation
via
evolution.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 1, 2023
ABSTRACT
Understanding
how
evolution
proceeds
from
molecules
to
organisms
interactions
is
critical
for
evolutionary
biology
and
requires
integrative
studies
that
span
biological
levels.
By
linking
phenotypic
changes
with
associated
genes
fitness
implications,
we
gain
insight
on
the
repeatability
of
adaptive
walks
move
between
peaks,
which
remains
poorly
understood
at
intermediate
stages,
e.g.
potential
valleys.
Floral
trait
can
proceed
rapidly,
confer
reproductive
isolation,
provides
numerous
examples
convergent
pollinator
guilds.
Within
monkeyflowers
(
Mimulus
sect.
Erythranthe
),
intraspecific
shifts
yellow
flowers
within
red
hummingbird-pollinated
species
have
arisen
least
twice
may
represent
incipient
optima
adaptation.
Here,
compare
two
natural
yellow-flowered
forms
M.
cardinalis
verbenaceus
their
conspecifics
in
floral
phenotypes,
biochemistry,
transcriptomic
genomic
variation,
pollinators.
We
find
morphs
both
species,
consistent
traits
large
effect
(floral
pigments
gene
expression),
result
strong
preference
by
bumblebees.
Shifts
additional
(scent
emissions
opening
size)
are
also
bee
pollination,
smaller-effect
steps
an
ongoing
walk
hummingbird
pollination.
examining
variation
representing
related
this
work
elucidates
early
stages
highlighting
mutations
color)
drive
attraction,
preceding
smaller
controlling
fit
reward
access.
This
integrates
phenotypic,
biochemical,
genomic,
behavioral
evidence
shed
light
repeated
new
impact
isolation
speciation
via
evolution.
G3 Genes Genomes Genetics,
Год журнала:
2023,
Номер
14(3)
Опубликована: Дек. 29, 2023
Penstemon
is
the
most
speciose
flowering
plant
genus
endemic
to
North
America.
species'
diverse
morphology
and
adaptation
various
environments
have
made
them
a
valuable
model
system
for
studying
evolution.
Here,
we
report
first
full
reference
genome
assembly
annotation
davidsonii.
Using
PacBio
long-read
sequencing
Hi-C
scaffolding
technology,
constructed
de
novo
of
437,568,744
bases,
with
contig
N50
40
Mb
L50
5.
The
includes
18,199
gene
models,
both
transcriptome
contain
over
95%
complete
eudicot
BUSCOs.
This
will
serve
as
evolutionary
history
genetic
diversity
genus.
