Biogeographic history of Pterocarya (Juglandaceae) inferred from phylogenomic and fossil data
Journal of Systematics and Evolution,
Год журнала:
2024,
Номер
62(6), С. 1165 - 1176
Опубликована: Фев. 22, 2024
Abstract
Pterocarya
(Juglandaceae)
is
disjunctly
distributed
in
East
Asia
and
the
Caucasus
region
today,
but
its
fossils
are
widely
Northern
Hemisphere.
We
first
inferred
phylogeny
with
time
estimation
of
under
node‐dating
(ND)
based
on
plastomes
all
eight
extant
species
tip‐dating
(TD)
69
morphological
characters
19
extinct
species,
respectively.
compared
biogeographical
reconstructions
timetrees
from
ND
TD,
respectively,
then
compiled
83
fossil
records
599
current
occurrences
for
predicting
potential
distributions
past
future.
The
most
recent
comment
ancestor
at
40.46
Ma
(95%
highest
posterior
density
[HPD]:
28.04–54.86)
TD
26.81
HPD:
23.03–33.12)
ND.
distribution
was
attributed
to
one
dispersal
vicariant
event
without
fossils,
as
many
six
dispersal,
vicariant,
11
local
extinction
events
when
considering
fossils.
migrated
between
North
America
via
Bering
Land
Bridge
during
early
Oligocene
Miocene
periods.
With
closure
Turgai
Strait,
dispersed
Europe
through
Miocene.
analyses
indicated
that
preferred
warm
temperate
regions
across
Hemisphere
since
Oligocene,
drastic
temperature
decline
caused
high
latitudes.
Except
fraxinifolia
stenoptera
,
suitable
habitats
this
genus
predicted
contract
by
2070
due
climate
change.
Язык: Английский
RAD‐seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian–North American disjunct clade Benthamidia of Cornus (Cornaceae)
Journal of Systematics and Evolution,
Год журнала:
2023,
Номер
62(1), С. 1 - 19
Опубликована: Дек. 13, 2023
Abstract
The
big‐bracted
dogwood
clade
Benthamidia
of
Cornus
is
a
typical
example
the
well‐known
eastern
Asia
(EA)
and
North
America
(NA)
floristic
disjunction,
with
greater
species
diversity
in
EA
than
NA.
lineage
provides
an
opportunity
to
explore
factors
contributing
plant
unevenness
between
NA
test
hypotheses
on
origin
disjunct
distribution
from
phylogenetic
perspective.
We
generated
RAD‐seq
data,
conducted
phylogenomic
biogeographic
analyses
for
sampling
all
(9)
subspecies
(10)
currently
recognized
floras.
also
assessed
delineation
calculated
evaluate
Finally,
we
examined
variation
diversification
rates
ecological
niches
phylogeny
potential
causes
underlying
observed
pattern.
Our
results
revealed
relationships
congruent
previous
studies
suggested
trans‐Beringian
ancestral
mid‐Oligocene,
dispersal
Mexico
United
States
mid‐Miocene,
early
SW
China.
confirmed
rate
clade.
Species
delimitation
analysis
17
,
including
subspecies.
By
integrating
molecular
data
morphology,
proposed
retain
without
changing
their
ranks.
increased
as
intrinsic
factor
explaining
region
driven
mainly
by
isolation
partially
niche
divergence.
Язык: Английский
Evolutionary origins of the eastern North American–Mesoamerican floristic disjunction: Current status and future prospects
American Journal of Botany,
Год журнала:
2023,
Номер
110(3)
Опубликована: Фев. 16, 2023
Biogeographic
disjunction
patterns,
where
multiple
taxa
are
shared
between
isolated
geographic
areas,
represent
excellent
systems
for
investigating
the
historical
assembly
of
modern
biotas
and
fundamental
biological
processes
such
as
speciation,
diversification,
niche
evolution,
evolutionary
responses
to
climate
change.
Studies
on
plant
genera
disjunct
across
northern
hemisphere,
particularly
eastern
North
America
(ENA)
Asia
(EAS),
have
yielded
tremendous
insight
geologic
history
rich
temperate
floras.
However,
one
most
prevalent
patterns
involving
ENA
forests
has
been
largely
overlooked:
that
cloud
Mesoamerica
(MAM),
with
examples
including
Acer
saccharum,
Liquidambar
styraciflua,
Cercis
canadensis,
Fagus
grandifolia,
Epifagus
virginiana.
Despite
remarkable
nature
this
pattern,
which
recognized
over
75
years,
there
few
recent
efforts
empirically
examine
its
ecological
origins.
Here
I
synthesize
previous
systematic,
paleobotanical,
phylogenetic,
phylogeographic
studies
establish
what
is
known
about
pattern
provide
a
roadmap
future
research.
argue
evolution
fossil
record
Mexican
flora
more
broadly,
represents
key
missing
piece
in
broader
puzzle
hemisphere
biogeography.
also
suggest
ENA-MAM
an
system
examining
questions
how
traits
life
strategies
mediate
change
predicting
broadleaf
will
respond
ongoing
climatic
pressures
Anthropocene.
Язык: Английский
The diversity of epixylic bryophytes in relation to dead wood properties and forest management in New Brunswick, Canada
Forest Ecology and Management,
Год журнала:
2024,
Номер
554, С. 121646 - 121646
Опубликована: Янв. 11, 2024
Язык: Английский
Data‐driven guidelines for phylogenomic analyses using SNP data
Applications in Plant Sciences,
Год журнала:
2024,
Номер
12(6)
Опубликована: Авг. 9, 2024
Abstract
Premise
There
is
a
general
lack
of
consensus
on
the
best
practices
for
filtering
single‐nucleotide
polymorphisms
(SNPs)
and
whether
it
better
to
use
SNPs
or
include
flanking
regions
(full
“locus”)
in
phylogenomic
analyses
subsequent
comparative
methods.
Methods
Using
genotyping‐by‐sequencing
data
from
22
Glycine
species,
we
assessed
effects
SNP
vs.
locus
usage
retention
stringency.
We
compared
branch
length,
node
support,
divergence
time
estimation
across
16
datasets
with
varying
amounts
missing
total
size.
Results
Our
results
revealed
five
aspects
that
may
be
generally
applicable:
(1)
tree
topology
largely
congruent
analyses;
(2)
strictly
(e.g.,
90–100%)
reduces
support
can
alter
some
inferred
relationships;
(3)
absolute
lengths
vary
by
two
orders
magnitude
between
datasets;
(4)
type
length
variation
have
little
effect
estimation;
(5)
phylograms
ancestral
states
rates
morphological
evolution.
Discussion
does
not
phylogenetic
inference
significantly,
unless
researchers
want
need
lengths.
recommend
against
using
excessive
thresholds
reduce
risk
producing
inconsistent
topologies
generating
low
support.
Язык: Английский
Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand
Biology,
Год журнала:
2023,
Номер
12(3), С. 484 - 484
Опубликована: Март 21, 2023
Unique
and
biodiverse,
mangrove
ecosystems
provide
humans
with
benefits
contribute
to
coastal
protection.
Rhizophora
mucronata,
a
member
of
the
Rhizophoraceae
family,
is
prevalent
in
forests
Thailand.
R.
mucronata's
population
structure
genetic
diversity
have
received
scant
attention.
Here,
we
sequenced
entire
genome
mucronata
using
10×
Genomics
technology
obtained
an
assembly
size
219
Mb
N50
length
542,540
bases.
Using
2857
single
nucleotide
polymorphism
(SNP)
markers,
this
study
investigated
80
accessions
from
The
was
moderate
(I
=
0.573,
Ho
0.619,
He
0.391).
Two
subpopulations
were
observed
confirmed
both
principal
component
analysis
(PCA).
Analysis
molecular
variance
(AMOVA)
showed
that
there
more
variation
within
populations
than
between
them.
Mean
pairwise
differentiation
(FST
0.09)
not
much
difference
populations.
Intriguingly,
predominant
clustering
pattern
did
correspond
Gulf
Thailand
Andaman
Sea,
which
are
separated
by
Malay
Peninsula.
Several
factors
could
influenced
pattern,
such
as
hybridization
anthropogenic
factors.
This
research
will
important
information
for
future
conservation
management
Язык: Английский
Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Сен. 6, 2023
Abstract
Premise
In
phylogenomic
analyses,
no
consensus
exists
on
whether
using
single
nucleotide
polymorphisms
(SNPs)
or
including
flanking
regions
(full
‘locus’)
is
best,
nor
how
strictly
missing
data
should
be
filtered.
Moreover,
empirical
evidence
SNP-only
trees
are
suitable
for
downstream
phylogenetic
comparative
methods
such
as
divergence
time
estimation
and
ancestral
state
reconstructions
lacking.
Methods
Using
GBS
from
22
taxa
of
Glycine
,
we
addressed
the
effects
SNP
vs.
locus
usage
filtering
stringency
inference
methods.
We
compared
branch
length,
node
support,
across
eight
datasets
with
varying
amounts
total
size.
Results
Our
results
reveal
five
aspects
usage:
1
.
tree
topology
largely
congruent
regardless
type
parameters;
2
too
reduces
confidence
in
some
relationships;
3
absolute
lengths
vary
by
two
orders
magnitude
between
datasets;
4
length
variation
have
little
effect
estimation;
5
phylograms
significantly
alter
states.
Discussion
When
conducting
analyses
recommend
not
to
filter
minimize
risk
misleading
topologies,
low
inaccurate
times.
Язык: Английский
The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae
Molecular Biology and Evolution,
Год журнала:
2024,
Номер
41(8)
Опубликована: Авг. 1, 2024
Abstract
Selaginellaceae,
originated
in
the
Carboniferous
and
survived
Permian–Triassic
mass
extinction,
is
largest
family
of
lycophyte,
which
sister
to
other
tracheophytes.
It
stands
out
from
tracheophytes
by
exhibiting
extraordinary
habitat
diversity
lacking
polyploidization.
The
organelle
genome-based
phylogenies
confirmed
monophyly
Selaginella,
with
six
or
seven
subgenera
grouped
into
two
superclades,
but
phylogenetic
positions
enigmatic
Selaginella
sanguinolenta
clade
remained
problematic.
Here,
we
conducted
a
phylogenomic
study
on
Selaginellaceae
utilizing
large-scale
nuclear
gene
data
RNA-seq
elucidate
phylogeny
explore
causes
incongruence
S.
clade.
Our
analyses
resolved
three
different
clade,
were
supported
sorted
sets,
respectively.
results
flow
test,
species
network
inference,
plastome-based
congruently
suggested
probable
hybrid
origin
involving
each
common
ancestor
superclades
Selaginellaceae.
hypothesis
corroborated
evidence
rhizophore
morphology
spore
micromorphology.
chromosome
observation
Ks
distributions
further
hybridization
accompanied
Divergence
time
estimation
based
independent
datasets
sets
plastid
genome
inferred
that
allopolyploidization
occurred
Early
Triassic.
To
our
best
knowledge,
Mesozoic
reported
here
represents
earliest
record
revealed
unique
triad
for
hybrid-originated
group
comprehensive
proposed
retaining
both
parental
alleles
through
conversion.
Язык: Английский
The Diversity of Epixylic Bryophytes in Relation to Dead Wood Properties and Forest Management in New Brunswick, Canada
Опубликована: Янв. 1, 2023
Rotting
wood
is
widely
recognized
as
an
important
feature
for
bryophyte
diversity
in
forest
ecosystems
but
management
practices,
that
focused
on
high
yields,
led
to
widespread
reductions
the
quantity
and
quality
of
woody
debris.
As
a
results,
many
epixylic
specialists
are
now
uncommon
or
threatened
throughout
much
their
former
ranges.
How
debris
required
maintain
desirable
biodiversity,
which
qualities
do
this
most
effectively
still
be
answered.
To
answered
it,
we
focus
two
datasets
from
mid-rotation
mature
plantations
same
landscape
better
understand
community
trajectories,
using
space-for-time
substitution
account
influence
stand
age.
Mid-rotation
showed
more
similarity
terms
liverwort
richness
untreated
hydrophytic
mosses
than
plantation.
We
speculate
discrepancy
between
plantation
due
drained
soils
longer
duration
intensive
reducing
abundance
coarse
(CWD).
Our
results
revealed
clear
positive
relationship
total
CWD
surface
area
diversity.
therefore
offer
preliminary
recommendation
land
managers
ensure
minimum
178
m2
per
hectare
managed
stands
support
at
levels
comparable
those
minimally-managed
stands.
More
case
xeric
sites,
where
threshold
maximum
near
detected
these
Because
canopy
composition
humidity
had
also
significant
composition,
further
study
likely
needed
calibrate
adjust
different
type,
soil
moisture,
fertility
regimes
should
analyzed
regards
system
manage
occurs.
Язык: Английский