In
the
past
decade,
advances
in
genome
sequencing
have
allowed
researchers
to
uncover
history
of
hybridization
diverse
groups
species,
including
our
own.
Although
field
has
made
impressive
progress
documenting
extent
natural
hybridization,
both
historical
and
recent,
there
are
still
many
unanswered
questions
about
its
genetic
evolutionary
consequences.
Recent
work
suggested
that
outcomes
may
be
part
predictable,
but
open
nature
selection
on
hybrids
biological
variables
shape
such
hampered
this
area.
We
synthesize
what
is
known
mechanisms
drive
changes
ancestry
after
highlight
major
unresolved
questions,
discuss
their
implications
for
predictability
evolution
hybridization.
The Plant Journal,
Год журнала:
2023,
Номер
114(4), С. 743 - 766
Опубликована: Фев. 13, 2023
Hybridization
has
long
been
recognized
as
a
fundamental
evolutionary
process
in
plants
but,
until
recently,
our
understanding
of
its
phylogenetic
distribution
and
biological
significance
across
deep
scales
largely
obscure.
Over
the
past
decade,
genomic
phylogenomic
datasets
have
revealed,
perhaps
not
surprisingly,
that
hybridization,
often
associated
with
polyploidy,
common
throughout
history
plants,
particularly
various
lineages
flowering
plants.
However,
studies
also
highlighted
challenges
disentangling
signals
ancient
hybridization
from
other
sources
conflict
(in
particular,
incomplete
lineage
sorting).
Here,
we
provide
critical
review
vascular
outlining
well-documented
cases
plant
phylogeny,
well
unique
to
documenting
versus
recent
hybridization.
We
definition
for
which,
knowledge,
explicitly
attempted
before.
Further
extent
reticulation
should
remain
an
important
research
focus,
especially
because
published
examples
likely
represent
tip
iceberg
terms
total
future
increasingly
explore
macroevolutionary
this
process,
impact
on
trajectories
(e.g.
how
does
influence
trait
evolution
or
generation
biodiversity
over
time
scales?),
life
ecological
factors
shape,
shaped,
frequency
geologic
phylogeny.
Finally,
consider
implications
ubiquitous
conceptualize,
analyze,
classify
Networks,
opposed
bifurcating
trees,
more
accurate
representations
many
cases,
although
ability
infer,
visualize,
use
networks
comparative
analyses
is
highly
limited.
Developing
improved
methods
generation,
visualization,
represents
direction
biology.
Current
classification
systems
do
generally
allow
recognition
reticulate
lineages,
classifications
themselves
are
based
evidence
chloroplast
genome.
Updating
better
reflect
nuclear
phylogenies,
considering
whether
recognize
systems,
will
challenge
systematics
community.
Nature Ecology & Evolution,
Год журнала:
2024,
Номер
8(4), С. 777 - 790
Опубликована: Фев. 21, 2024
Chromosomes
are
a
central
unit
of
genome
organization.
One-tenth
all
described
species
on
Earth
butterflies
and
moths,
the
Lepidoptera,
which
generally
possess
31
chromosomes.
However,
some
display
dramatic
variation
in
chromosome
number.
Here
we
analyse
210
chromosomally
complete
lepidopteran
genomes
show
that
chromosomes
extant
lepidopterans
derived
from
32
ancestral
linkage
groups,
term
Merian
elements.
elements
have
remained
largely
intact
through
250
million
years
evolution
diversification.
Against
this
stable
background,
eight
lineages
undergone
extensive
reorganization
either
numerous
fissions
or
combination
fusion
fission
events.
Outside
these
lineages,
fusions
rare
rarer
still.
Fusions
often
involve
small,
repeat-rich
sex-linked
element.
Our
results
reveal
constraints
architecture
Lepidoptera
provide
deeper
understanding
chromosomal
rearrangements
eukaryotic
evolution.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Май 14, 2023
Abstract
Chromosomes
are
a
central
unit
of
genome
organisation.
One
tenth
all
described
species
on
Earth
Lepidoptera,
butterflies
and
moths,
these
generally
possess
31
holocentric
chromosomes.
However,
subset
lepidopteran
display
dramatic
variation
in
chromosome
counts.
By
analysing
210
chromosomally-complete
genomes,
the
largest
analysis
eukaryotic
chromosomal-level
reference
genomes
to
date,
we
show
that
diverse
karyotypes
extant
derived
from
32
ancestral
linkage
groups,
which
term
Merian
elements.
elements
have
remained
largely
intact
across
250
million
years
evolution
diversification.
Against
this
stable
background,
identify
eight
independent
lineages
evaded
constraint
undergone
extensive
reorganisation
-
either
by
numerous
fissions
or
combination
fusion
fission
events.
Outside
lineages,
fusions
rare
rarer
still.
Fusions
tend
involve
small,
repeat-rich
and/or
Z
chromosome.
Together,
our
results
reveal
constraints
architecture
Lepidoptera
enable
deeper
understanding
importance
chromosomal
rearrangements
shaping
genomes.
Nature Genetics,
Год журнала:
2024,
Номер
56(4), С. 710 - 720
Опубликована: Март 15, 2024
Abstract
Polyploidy
(genome
duplication)
is
a
pivotal
force
in
evolution.
However,
the
interactions
between
parental
genomes
polyploid
nucleus,
frequently
involving
subgenome
dominance,
are
poorly
understood.
Here
we
showcase
analyses
of
bamboo
system
(Poaceae:
Bambusoideae)
comprising
series
lineages
from
diploid
(herbaceous)
to
tetraploid
and
hexaploid
(woody),
with
11
chromosome-level
de
novo
genome
assemblies
476
transcriptome
samples.
We
find
that
woody
subgenomes
exhibit
stunning
karyotype
stability,
parallel
dominance
two
clades
gradual
shift
clade.
Allopolyploidization
have
shaped
evolution
tree-like
lignified
culms,
rapid
growth
synchronous
flowering
characteristic
bamboos
as
large
grasses.
Our
work
provides
insights
into
remarkable
system,
including
its
dependence
on
genomic
context
ability
switch
which
dominant
over
evolutionary
time.
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.
Molecular Biology and Evolution,
Год журнала:
2019,
Номер
37(4), С. 1100 - 1113
Опубликована: Дек. 6, 2019
The
adaptive
radiation
of
cichlid
fishes
in
East
African
Lake
Malawi
encompasses
over
500
species
that
are
believed
to
have
evolved
within
the
last
800,000
years
from
a
common
founder
population.
It
has
been
proposed
hybridization
between
ancestral
lineages
can
provide
genetic
raw
material
fuel
such
exceptionally
high
diversification
rates,
and
evidence
for
this
recently
presented
Victoria
region
superflock.
Here,
we
report
genomes
also
show
two
split
3-4
Ma,
today
represented
by
cichlids
riverine
Astatotilapia
sp.
"ruaha
blue."
ancestries
present
large
blocks
several
kilobases,
but
there
is
little
variation
pattern
species,
suggesting
large-scale
mosaic
structure
was
largely
established
prior
radiation.
Nevertheless,
tens
thousands
polymorphic
variants
apparently
derived
interspersed
genomes.
These
loci
striking
excess
differentiation
across
ecological
subgroups
assemblage,
parental
alleles
sort
differentially
into
benthic
pelagic
lineages,
consistent
with
strong
differential
selection
on
these
during
divergence.
Furthermore,
enriched
genes
involved
immune
response
vision,
including
opsin
previously
identified
as
important
speciation.
Our
results
reinforce
role
explosive
demonstrating
its
significance
one
largest
recent
vertebrate
radiations.
Frontiers in Genetics,
Год журнала:
2020,
Номер
11
Опубликована: Июль 28, 2020
It
has
long
been
recognized
that
hybridization
and
polyploidy
are
prominent
processes
in
plant
evolution.
Although
classically
as
significant
speciation
adaptation,
recognition
of
the
importance
interspecific
gene
flow
dramatically
increased
during
genomics
era,
concomitant
with
an
unending
flood
empirical
examples,
or
without
genome
doubling.
Interspecific
is
thus
increasingly
thought
to
lead
evolutionary
innovation
diversification,
via
adaptive
introgression,
homoploid
hybrid
allopolyploid
speciation.
Less
well
understood,
however,
suite
genetic
genomic
mechanisms
set
motion
by
merger
differentiated
genomes,
temporal
scale
over
which
recombinational
complexity
mediated
might
be
expressed
exposed
natural
selection.
We
focus
on
these
issues
here,
considering
types
molecular
saltational
event
between
two
diverged
species,
either
doubling,
how
various
can
contribute
novel
phenotypes.
Genetic
include
infusion
new
alleles
genesis
structural
variation
including
translocations
inversions,
homoeologous
exchanges,
transposable
element
mobilization
insertional
effects,
presence-absence
copy
number
variation.
Polyploidy
generates
massive
transcriptomic
regulatory
alteration,
presumably
disrupted
stoichiometries
factors,
small
RNAs
other
interactions
cascade
from
single-gene
expression
change
up
through
entire
networks
transformed
modules.
highlight
both
combinatorial
possibilities
range
scales
such
generated,
selection
drift.
Molecular Biology and Evolution,
Год журнала:
2020,
Номер
37(9), С. 2568 - 2583
Опубликована: Апрель 23, 2020
Abstract
Hybridization
between
invasive
and
native
species
has
raised
global
concern,
given
the
dramatic
increase
in
range
shifts
pest
outbreaks
due
to
anthropogenic
dispersal.
Nevertheless,
secondary
contact
sister
lineages
of
local
provides
a
natural
laboratory
understand
factors
that
determine
introgression
maintenance
or
loss
barriers.
Here,
we
characterize
early
evolutionary
outcomes
following
Helicoverpa
armigera
H.
zea
Brazil.
We
carried
out
whole-genome
resequencing
moths
from
Brazil
two
temporal
samples:
during
outbreak
2013
2017.
There
is
evidence
for
burst
hybridization
widespread
into
coinciding
with
expansion
2013.
However,
armigera,
admixture
proportion
length
introgressed
blocks
were
significantly
reduced
2017,
suggesting
selection
against
admixture.
In
contrast
genome-wide
pattern,
there
was
striking
adaptive
single
region
zea,
including
an
insecticide
resistance
allele
increased
frequency
over
time.
summary,
despite
extensive
gene
flow
after
contact,
boundaries
are
largely
maintained
except
containing
insecticide-resistant
locus.
document
worst-case
scenario
species,
which
now
instead
one,
acquired
pyrethroid
insecticides
through
introgression.