bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Авг. 15, 2022
Abstract
The
genus
Lonicera
L.
is
widely
distributed
and
well-known
for
its
high
species
richness
morphological
diversity.
Previous
studies
have
suggested
that
many
sections
of
are
not
monophyletic
phylogenetic
relationships
within
the
still
poorly
known.
In
this
study,
we
sampled
37
accessions
,
covering
four
subgenus
Chamaecerasus
plus
six
outgroup
taxa
to
recover
main
clades
based
on
sequences
nuclear
loci
generated
by
target
enrichment
cpDNA
from
genome
skimming.
We
found
extensive
cytonuclear
discordance
across
subgenus.
Both
plastid
analyses
supported
sister
.
Within
Isika
Niatoon
were
polyphyletic.
Based
chloroplast
phylogenies
propose
merge
korolkowii
into
section
Coeloxylosteum
caerulea
Nintooa.
addition,
estimated
originated
in
late
Miocene
(19.84
Ma).
stem
age
Nintooa
was
be
17.97
Ma
(95%
HPD:
13.31-
22.89).
16.35
9.33-
45.15).
Ancestral
area
reconstruction
indicate
Qinghai
Tibet
Plateau
(QTP)
Asia,
with
subsequent
dispersal
other
areas.
aridification
Asian
interior
possibly
promoted
rapid
radiation
region,
uplift
QTP
appears
triggered
recent
diversification
adjacent
regions.
Overall,
study
provides
new
insights
taxonomically
complex
lineages
at
level
process
speciation.
Annals of Botany,
Год журнала:
2024,
Номер
133(5-6), С. 697 - 710
Опубликована: Янв. 17, 2024
Abstract
Background
and
Aims
The
staghorn
fern
genus
Platycerium
is
one
of
the
most
commonly
grown
ornamental
ferns,
it
evolved
to
occupy
a
typical
pantropical
intercontinental
disjunction.
However,
species-level
relationships
in
have
not
been
well
resolved,
spatiotemporal
evolutionary
history
also
needs
be
explored.
Methods
Plastomes
all
18
species
were
newly
sequenced.
Using
plastome
data,
we
reconstructed
phylogenetic
among
Polypodiaceae
members
with
focus
on
species,
further
conducted
molecular
dating
biogeographical
analyses
genus.
Key
Results
present
yielded
robustly
supported
hypothesis
Platycerium.
Molecular
results
showed
that
split
from
its
sister
Hovenkampia
~35.2
million
years
ago
(Ma)
near
Eocene–Oligocene
boundary
began
diverge
~26.3
Ma
during
late
Oligocene,
while
multiple
speciation
events
within
occurred
middle
Miocene.
Biogeographical
analysis
suggested
originated
tropical
Africa
then
dispersed
eastward
southeast
Asia–Australasia
westward
neotropical
areas.
Conclusions
Our
using
plastid
phylogenomic
approach
improved
our
understanding
global
climate
changes
both
Late
Oligocene
Warming
cooling
following
mid-Miocene
Climate
Optimum
may
promoted
Platycerium,
transoceanic
long-distance
dispersal
plausible
explanation
for
distribution
today.
study
investigating
provides
case
only
formation
disjunction
this
but
‘out
Africa’
origin
plant
lineages.
PLoS ONE,
Год журнала:
2025,
Номер
20(2), С. e0314919 - e0314919
Опубликована: Фев. 14, 2025
Sinopodophyllum
hexandrum
(
S.
)
is
an
endangered
traditional
Chinese
medicine
as
abundant
podophyllotoxin
with
powerful
anticancer
activity.
In
this
study,
the
rootstalks
of
from
different
geographical
locations
in
China
[S1
(Gansu)
and
S2
(Shaanxi)]
were
used
research
materials
to
clone
key
gene
pluviatolide
O-methyltransferase
3
ShOMT3
biosynthetic
pathway.
Subsequently,
bioinformatics
analysis
its
encoded
protein
was
subjected
using
various
software
including
ProtParam,
DeepTMHMM,
SubLoc,
Signal-P
5.0,
Swiss-model.
The
results
revealed
that
CDS
region
1119
bp
long,
encoding
372
amino
acids.
theoretical
molecular
weight
41.32784
kD,
isoelectric
point
(pI)
5.27.
instability
coefficient
46.05,
aliphatic
index
93.58,
grand
average
hydropathicity
(GRAVY)
0.037,
indicating
it
unstable
hydrophobic
protein.
does
not
contain
transmembrane
domains
or
signal
peptides,
a
non-secreted
Secondary
structure
prediction
suggests
consists
alpha
helices,
random
coils,
extended
strands,
beta-turns.
Tertiary
functions
monomer.
phylogenetic
tree,
has
highest
homology
Podophyllum
peltatum
P.
).
successful
cloning
provide
basis
excellent
genetic
resources
for
regulatory
mechanism
pathway
breeding
.
American Journal of Botany,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 17, 2025
Abstract
Premise
Biotic
disjunctions
have
attracted
scientific
attention
for
the
past
200
years.
Despite
being
represented
in
many
familiar
plants
(such
as
bald
cypress,
flowering
dogwood,
sweetgum,
partridgeberry,
etc.),
eastern
North
American
(ENA)–Mexican
(M)
disjunction
remains
poorly
understood.
Major
outstanding
questions
include
divergence
times
of
taxa
exhibiting
and
environmental/geological
processes
that
may
underlie
disjunction.
Symphyotrichum
Nees
(Asteraceae),
one
most
diverse
genera
USA,
displays
several
examples
disjunct
ENA–M
taxa.
Methods
We
generated
target
capture
data
using
Angiosperms353
baitset
first
well‐sampled
phylogenomic
hypothesis
its
close
relatives.
Focusing
on
S
.
subgenus
Virgulus
,
we
used
MCMC
TREE
to
perform
time
estimation
R
package
BioGeoBEARS
infer
ancestral
regions
biogeographic
transitions
between
America
Mexico.
Finally,
niche
reconstruction
method
Utremi
test
a
role
historical
aridification
generating
Results
Our
molecular
suggest
recent
radiation
at
Plio‐Pleistocene
boundary
(~2.5
mya),
with
early
connections
Mexico
lineages
closed
off
shortly
after
were
followed
by
vicariance
across
this
region.
Except
some
present‐day
broadly
distributed
species,
there
is
complete
lack
movement
ENA
M
~0.5
mya.
Conclusions
A
reconstructed
distribution
suitable
habitat
Pleistocene
climatic
models
corroborates
results
from
modeling
confirms
glacial
cycles
are
more
likely
be
associated
breakup
connections.
Proceedings of the Royal Society B Biological Sciences,
Год журнала:
2023,
Номер
290(2003)
Опубликована: Июль 26, 2023
Demonstrating
the
process
of
transregional
biogeography
and
mechanisms
underlying
evolutionary
radiations
is
crucial
to
understanding
biological
evolution.
Here,
we
use
Hydrangeeae
(Hydrangeaceae),
a
tribe
with
unique
disjunct
distribution
complex
trait
variations,
using
solid
phylogenetic
framework,
investigate
how
geographical
climatic
factors
interact
functional
traits
trigger
plant
radiations.
We
constructed
first
highly
supported
dated
framework
79
protein-coding
genes
obtained
from
81
plastomes,
representing
63
species
all
major
clades,
found
that
most
extant
originated
asynchronous
diversification
two
lineages
undergoing
repeated
expansion
retraction,
at
middle
high
latitudes
Northern
Hemisphere
between
East
Asia
North
America,
during
Eocene
Pleistocene
(driven
by
geologic
dynamics).
In
accordance
these
drivers,
interactions
flora
central-eastern
China
Japan
occurred
frequently
after
Late
Tertiary.
resource
limitation
range
fragmentation
probably
accelerated
Hydrangeeae,
which
supports
resource-use
hypothesis.
Our
study
sheds
light
on
radiation
assembly
within
Asia,
Asian-North
American
disjunction,
through
integration
phylogenomic
biogeographic
data
ecological
data.
Journal of Systematics and Evolution,
Год журнала:
2024,
Номер
63(1), С. 99 - 114
Опубликована: Ноя. 11, 2024
Abstract
Panax
(Araliaceae)
is
a
small
genus
containing
several
well
known
medicinally
important
species.
It
has
disjunct
distribution
between
Eastern
Asia
and
North
America,
with
most
species
from
eastern
Asia,
especially
the
Himalayan‐Hengduan
Mountains
(HHM).
This
study
used
genomic
target
enrichment
method
to
obtain
358
nuclear
ortholog
loci
complete
plastome
sequences
59
accessions
representing
all
18
of
genus.
Divergence
time
estimation
biogeographic
analyses
suggest
that
was
probably
widely
distributed
America
during
middle
Eocene.
During
late
Eocene
Oligocene
may
have
experienced
extensive
extinctions
global
climate
cooling.
survived
diverged
early
in
mountains
Southwest
China
tropical
Indochina,
where
some
taxa
migrated
northwestward
HHM,
eastward
central
China,
then
onward
toward
Japan
America.
Gene
flow
identified
as
main
contributor
phylogenetic
discordance
(33.46%)
within
.
We
hypothesize
common
ancestors
P.
ginseng
+
japonicus
quinquefolius
clade
had
allopolyploidization,
which
increased
adaptability
cooler
drier
environments.
Miocene,
dispersals
occurred
region
HHM
contiguous
areas,
suggesting
acted
refugium
also
served
secondary
diversification
center
for
Our
findings
highlight
interplay
orographic
uplift
climatic
changes
greatly
contributed
diversity
Journal of Systematics and Evolution,
Год журнала:
2023,
Номер
62(3), С. 333 - 357
Опубликована: Окт. 10, 2023
Abstract
The
discontinuous
geographic
distribution
pattern
of
plants
in
the
north
temperate
zone
has
been
a
focus
biogeographic
research,
especially
concerning
mechanisms
behind
formation
such
and
spatial
temporal
evolution
this
intermittent
pattern.
Hypotheses
boreotropical
origin,
land
bridge
migration,
out‐of‐Tibet
have
proposed
to
explain
Lonicera
shows
typical
Europe–Asia–North
America
distribution,
which
makes
for
good
case
study
investigate
above
three
hypotheses.
In
study,
we
inferred
phylogeny
based
on
plastid
genomes
nuclear
data
set
with
broad
taxon
sampling,
covering
83
species
representing
two
subgenera
four
sections.
Both
phylogenetic
analyses
found
section
Isika
polyphyletic,
while
sections
Nintooa
,
Isoxylosteum
Coelxylosteum
were
monophyletic
subgenus
Chamaecerasus
.
Based
chloroplast
phylogeny,
suggest
transferring
maximowiczii
tangutica
into
Reconstruction
ancestral
areas
suggests
that
originated
Qinghai–Tibetan
Plateau
(QTP)
and/or
Asia,
subsequently
dispersed
other
regions.
aridification
Asian
interior
may
facilitated
rapid
radiation
region.
At
same
time,
uplifts
Tibetan
appear
triggered
spread
recent
diversification
genus
QTP
adjacent
areas.
Overall,
our
results
deepen
understanding
evolutionary
history
American Journal of Botany,
Год журнала:
2023,
Номер
110(11)
Опубликована: Ноя. 1, 2023
Abstract
Premise
Glacial/interglacial
cycles
and
topographic
complexity
are
both
considered
to
have
shaped
today's
diverse
phylogeographic
patterns
of
taxa
from
unglaciated
eastern
North
America
(ENA).
However,
few
studies
focused
on
the
phylogeography
population
dynamics
wide‐ranging
ENA
herbaceous
species
occurring
in
forest
understory
habitat.
We
examined
pattern
evolutionary
history
Podophyllum
peltatum
L.,
a
widely
distributed
herb
inhabiting
deciduous
forests
ENA.
Methods
Using
chloroplast
DNA
(cpDNA)
sequences
nuclear
microsatellite
loci,
we
investigated
structure
genetic
diversity
species.
Molecular
dating,
demographic
analyses,
ecological
niche
modeling
were
also
performed
illustrate
patterns.
Results
Our
cpDNA
results
identified
three
main
groups
that
largely
congruent
with
boundaries
along
Appalachian
Mountains
Mississippi
River,
two
major
geographic
barriers
Populations
located
east
Appalachians
central
exhibited
relatively
higher
levels
diversity.
Extant
lineages
may
diverged
during
late
Miocene,
range
expansions
different
happened
Pleistocene
glacial/interglacial
cycles.
Conclusions
findings
indicate
started
facilitate
divergence
P.
before
Pleistocene.
Persistence
multiple
refugia,
including
areas
around
Quaternary
glacial
period,
subsequent
under
hospitable
climatic
condition,
especially
westward
expansion,
likely
responsible
for
species’
contemporary
pattern.