Molecular Phylogenetics and Evolution,
Год журнала:
2021,
Номер
159, С. 107110 - 107110
Опубликована: Фев. 18, 2021
In
this
study,
we
analyzed
313
plastid
genomes
(plastomes)
of
Poaceae
with
a
focus
on
expanding
our
current
knowledge
relationships
among
the
subfamily
Pooideae,
which
represented
over
half
dataset
(164
representatives).
total,
47
plastomes
were
sequenced
and
assembled
for
study.
This
is
largest
study
its
kind
to
include
plastome-level
data,
not
only
increase
sampling
at
both
taxonomic
molecular
levels
aim
resolving
complex
reticulate
relationships,
but
also
analyze
effects
alignment
gaps
in
large-scale
analyses,
as
well
explore
divergences
an
expanded
set
14
accepted
grass
fossils
more
accurate
calibrations
dating.
Incorporating
broad
systematic
assessments
Pooideae
taxa
conducted
by
authors
within
last
five
years,
produced
robust
phylogenomic
reconstruction
subfamily,
included
all
two
supergeneric
(Calothecinae
Duthieeae).
We
further
explored
how
including
plastome
analyses
oftentimes
can
produce
incorrect
or
misinterpretations
Pooideae.
presented
itself
consistently
changing
specific
nodes
different
stripping
thresholds
(percentage-based
removal
per
column).
Our
summary
recommendation
genomic
datasets
strip
columns
pairwise
identity
reduce
errant
signal
from
poly
A/T
bias.
To
do
used
"mask
alignment"
tool
Geneious
software.
Finally,
determined
overall
divergence
age
roughly
84.8
Mya,
line
with,
slightly
older
than
most
recent
estimates.
Journal of Systematics and Evolution,
Год журнала:
2018,
Номер
56(5), С. 405 - 429
Опубликована: Янв. 18, 2018
Abstract
Continental‐scale
assembly
of
floras
results
from
past
and
present
in
situ
diversification
association
with
several
external
processes.
Among
these
processes
are
the
making
breaking
connections
among
landmasses.
Connections
landmasses
constantly
flux
as
climates
landscapes
along
connection
corridors,
so
that
or
land
bridges,
may
either
facilitate
restrict
migration
at
a
given
time.
Across
changing
landscape‐level
organismal
factors
include
dispersal
potential
vectors
propagules,
competition,
predation,
distributions
altered
by
pathogens.
Assembly
flora
is,
therefore,
outcome
complex,
interacting,
temporally‐varying
render
simplistic
explanations
unlikely.
In
case
North
America,
continent
experienced
ephemeral
adjacent
regions
via
five
bridges
over
last
100
Ma
different
times
under
specific
landscape
morphologies,
including
edaphic
characteristics.
Here,
I
emphasize
earliest
connections,
Beringia,
which
probably
comprised
an
initially‐incomplete
bridge
during
Cretaceous
Paleocene
resulting
compression,
fragmentation,
rotation
Asian‐North
American
sub‐blocks
America
began
moving
westward
northern
portion
Mid‐Atlantic
Ridge.
During
same
time,
additional
was
added
to
Beringia
accretion
terranes
subduction
edge
Pacific
Plate
beneath
American‐Asian
Plates
Eocene
form
Aleutian
Islands.
Other
between
were
Atlantic,
Antilles,
Central
Magellan
bridge.
American Journal of Botany,
Год журнала:
2019,
Номер
106(4), С. 573 - 597
Опубликована: Апрель 1, 2019
Premise
of
the
Study
A
key
question
in
evolutionary
biology
is
why
some
clades
are
more
successful
by
being
widespread
geographically,
biome
diverse,
or
species‐rich.
To
extend
understanding
how
shifts
area,
biomes,
and
pollinators
impact
diversification
plants,
we
examined
relationships
these
to
across
mega‐genus
Salvia
.
Methods
chronogram
was
developed
from
a
supermatrix
anchored
hybrid
enrichment
genomic
data
targeted
sequence
for
over
500
nearly
1000
species.
Ancestral
areas
biomes
were
reconstructed
using
BioGeo
BEARS
Pollinator
guilds
scored,
ancestral
determined,
pollinator
identified,
rates
switches
compared.
Key
Results
well‐resolved
phylogenetic
backbone
updated
subgeneric
designations
presented.
originated
Southwest
Asia
Oligocene
subsequently
dispersed
worldwide.
Biome
frequent
likely
lineage
utilizing
broadleaf
and/or
coniferous
forests
arid
shrublands.
None
four
species
correlated
biomes.
Shifts
pollination
system
not
shifts,
except
one
hummingbird
shift
that
precedes
major
near
crown
New
World
subgen.
Calosphace
Multiple
reversals
back
bee
occurred
within
this
clade.
Conclusions
diversified
extensively
different
continents,
with
both
bird
pollinators.
The
lack
tight
correlation
biome,
most
documented
points
other
important
drivers
speciation
Journal of Systematics and Evolution,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 3, 2025
Abstract
When
and
how
disjunct
distributions
of
biological
taxa
arose
has
long
attracted
interest
in
biogeography,
yet
the
East
Asian–Tethyan
disjunction
is
understudied.
Cupressus
(Cupressaceae)
shows
this
disjunction,
with
10
species
Asia
three
Mediterranean
region.
Here
we
used
target‐capture
sequencing
obtained
1991
single‐copy
nuclear
genes,
plus
complete
plastomes,
to
infer
evolutionary
history
.
Our
phylogenomic
reconstruction
resolved
four
well
supported
clades
,
but
revealed
significant
phylogenetic
conflicts,
inter‐lineage
gene
flow,
incomplete
lineage
sorting
tree
estimation
error
all
making
important
contributions.
The
Chengiana
clade
most
likely
originated
by
hybridization
between
ancestors
Himalayan–Hengduan
Mountains
subtropical
clades,
whereas
orogenic
climatic
changes
may
have
facilitated
flow
within
clade.
Molecular
dating
suggested
that
recent
common
ancestor
appeared
around
middle
Eocene
period
then
became
continuously
distributed
across
Eurasia.
when
diverged,
been
driven
Eocene/Oligocene
declines
global
temperature,
reinforced
ecogeographic
barrier
created
uplift
Qinghai–Tibet
Plateau.
Niche
shifts
clade,
signatures
selection
genes
for
drought
salt
tolerance,
probably
indicate
adaptation
local
conditions.
Overall,
our
study
in‐depth
analyses
are
powerful
tools
deciphering
complex
origin
organisms,
especially
gymnosperms.
Botanical Journal of the Linnean Society,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 17, 2025
Abstract
Heterotrophic
plants
are
among
the
most
recalcitrant
from
a
systematics
perspective
because
of
reduced
morphological
and
genomic
features,
often
extreme
substitution
rate
heterogeneity.
The
orchid
subtribe
Calypsoinae
exemplifies
this,
containing
several
lineages
that
have
lost
leaves
photosynthesis.
In
particular,
relationships
leafy
Asian
Oreorchis
leafless
American
Corallorhiza
been
contentious.
Here
we
used
nuclear
sequence
capture
to
resolve
within
addressed
monophyly
Oreorchis,
for
which
previous
studies
highlighted
conflicting
patterns
or
paraphyly,
depending
on
data
analysed.
Nuclear
analyses
provided
strong
support
monophyletic
paraphyletic
latter
with
two
strongly
supported
clades.
As
in
studies,
plastid
recovered
assemblages
both
genera.
Topology
tests
using
rejected
constrained
topologies,
further
revealing
cytonuclear
conflict.
Network-based
revealed
lack
evidence
hybridization,
suggesting
incomplete
lineage
sorting
associated
biological
historical
factors
driven
intergenomic
Additionally,
found
loci
identified
as
putatively
holomycotrophic
species
functionally
enriched
organellar
functions.
study
provides
case
resurrection
Kitigorchis
sister
Corallorhiza,
species,
erythrochrysea
indica,
highlights
challenges
phylogenetics
mycoheterotrophs.
Arctic Science,
Год журнала:
2016,
Номер
3(3), С. 585 - 617
Опубликована: Дек. 23, 2016
The
Beringian
Coevolution
Project
(BCP),
a
field
program
underway
in
the
high
northern
latitudes
since
1999,
has
focused
on
building
key
scientific
infrastructure
for
integrated
specimen-based
studies
mammals
and
their
associated
parasites.
BCP
contributed
new
insights
across
temporal
spatial
scales
into
how
ancient
climate
environmental
change
have
shaped
faunas,
emphasizing
processes
of
assembly,
persistence,
diversification
vast
region.
collections
also
represent
baseline
records
biotic
diversity
from
at
time
accelerated
change.
These
specimens
data
form
an
unmatched
resource
identifying
hidden
diversity,
interpreting
past
responses
to
oscillations,
documenting
contemporary
conditions,
anticipating
outcomes
complex
biological
systems
regime
ecological
perturbation.
Because
its
dual
focus
hosts
parasites,
record
provides
foundation
comparative
analyses
that
can
document
effects
dynamic
geographic
distribution,
transmission
dynamics,
emergence
pathogens.
By
using
specific
examples
carnivores,
eulipotyphlans,
lagomorphs,
rodents,
ungulates,
we
demonstrate
broad,
provide
permanent
informs
policy
decisions
regarding
human
impact
effect
natural
populations.
Journal of Systematics and Evolution,
Год журнала:
2018,
Номер
56(4), С. 297 - 308
Опубликована: Июнь 25, 2018
Abstract
Vitis
L.
(the
grape
genus)
is
the
economically
most
important
fruit
crop,
as
source
of
grapes
and
wine.
Phylogenetic
relationships
within
genus
have
been
highly
controversial.
Herein,
we
employ
sequence
data
from
whole
plastomes
to
attempt
enhance
phylogenetic
resolution.
The
results
support
New
World
subgenus
monophyletic.
Within
clade,
V.
californica
sister
remaining
.
Furthermore,
,
a
Eurasian
clade
robustly
supported
clade.
vinifera
ssp.
sylvestris
core
Asian
Several
widespread
species
in
North
America
are
found
be
non‐monophyletic
plastome
tree,
for
example,
broadly
defined
cinerea
aestivalis
each
needs
split
into
several
species.
non‐monophyly
some
may
also
due
common
occurrences
hybridizations
American
classification
by
Munson
nine
series
discussed
based
on
results.
Analyses
divergence
times
lineage
diversification
rapid
radiation
beginning
Neogene.
Frontiers in Plant Science,
Год журнала:
2019,
Номер
10
Опубликована: Дек. 20, 2019
Rubus
(Rosaceae)
comprises
more
than
500
species
with
additional
commercially
cultivated
raspberries
and
blackberries.
The
most
recent
(>
100
years
old)
global
taxonomic
treatment
of
the
genus
defined
12
subgenera;
two
subgenera
were
subsequently
described
some
rearranged.
Intra-
interspecific
ploidy
levels
hybridization
make
phylogenetic
estimation
challenging.
Our
objectives
to
estimate
phylogeny
94
taxonomically
geographically
diverse
three
cultivars
using
chloroplast
DNA
sequences
target
capture
approximately
1,000
low
copy
nuclear
genes;
divergence
times
between
major
clades;
examine
historical
biogeography
diversification.
Target
sequencing
identified
eight
groups
within
Rubus.
Subgenus
Orobatus
Subg.
Anoplobatus
monophyletic,
while
other
recognized
para-
or
polyphyletic.
Multiple
events
likely
occurred
across
at
subgeneric
levels,
e.g.,
(blackberries)
×
Idaeobatus
(raspberries)
Cylactis
(Arctic
berries)
hybrids.
raspberry
heritage
known
blackberry
hybrids
was
confirmed.
common
ancestor
distributed
in
North
America.
distribution
during
Miocene
(about
20
Ma)
from
America
into
Asia
Europe
Bering
land
bridge
southward
crossing
Panamanian
Isthmus.
diversified
greatly
Miocene.
taxonomy
does
not
reflect
relationships
revision
is
warranted.
migrated
towards
Asia,
Europe,
Central
South
early
then
diversified.
Ancestors
may
have
Oceania
by
long
distance
bird
dispersal.
This
presents
a
roadmap
for
further
systematics
research.
In
conclusion,
dataset
provides
high
resolution
though
it
also
gave
evidence
gene
tree/species
tree
cytonuclear
discordance.
Discordance
be
due
incomplete
lineage
sorting,
rather
lack
signal.
study
illustrates
importance
multiple
methods
when
examining
complex
utility
software
programs
that
signal
conflict
datasets.