American Journal of Botany,
Год журнала:
2024,
Номер
111(8)
Опубликована: Авг. 1, 2024
Abstract
Premise
Hybridization
is
recognized
as
an
important
mechanism
in
fern
speciation,
with
many
allopolyploids
known
among
congeners,
well
evidence
of
ancient
genome
duplications.
Several
contemporary
instances
deep
(intergeneric)
hybridization
have
been
noted,
invariably
resulting
sterile
progeny.
We
chose
the
christelloid
lineage
family
Thelypteridaceae,
for
its
high
frequency
both
intra‐
and
intergeneric
hybrids,
to
investigate
recent
hybrid
speciation
between
deeply
diverged
lineages.
also
seek
understand
ecological
evolutionary
outcomes
lineages
across
landscape.
Methods
By
phasing
captured
reads
within
a
phylogenomic
data
set
GoFlag
408
nuclear
loci
using
HybPhaser,
we
investigated
candidate
hybrids
identify
parental
estimated
divergence
ages
by
inferring
dated
phylogeny
fossil
calibrations
treePL.
niche
conservatism
one
confirmed
allotetraploid
diploid
progenitors
centroid,
overlap,
unfilling,
expansion
(COUE)
framework.
Results
provide
at
least
six
clade
estimate
up
45
million
years
progenitors.
The
quantification
analysis
showed
moderate
overlap
allopolyploid
species
progenitors,
significant
from
progenitor
other.
Conclusions
examples
provided
here
highlight
overlooked
role
that
allopolyploidization
following
may
play
diversification
range
expansions.
Applying
this
approach
other
taxa
reveal
similar
pattern
highly
successful
novel
Molecular Phylogenetics and Evolution,
Год журнала:
2024,
Номер
199, С. 108161 - 108161
Опубликована: Июль 28, 2024
The
Salicaceae
includes
approximately
54
genera
and
over
1,400
species
with
a
cosmopolitan
distribution.
Members
of
the
family
are
well-known
for
their
diverse
secondary
plant
metabolites,
they
play
crucial
roles
in
tropical
temperate
forest
ecosystems.
Phylogenetic
reconstruction
has
been
historically
challenging
due
to
limitations
molecular
markers
extensive
history
hybridization
polyploidy
within
family.
Our
study
employs
whole-genome
sequencing
74
generate
an
phylogeny
Salicaceae.
We
generated
two
RAD-Seq
enriched
sequence
datasets
extracted
additional
gene
sets
corresponding
universal
Angiosperms353
Salicaceae-specific
targeted-capture
arrays.
reconstructed
maximum
likelihood-based
phylogenies
using
supermatrix
coalescent-based
supertree
approaches.
fossil-calibrated
estimates
that
originated
around
128
million
years
ago
unravels
complex
taxonomic
relationships
findings
confirm
non-monophyly
subgenus
Salix
s.l.
further
support
merging
subgenera
Chamaetia
Vetrix,
both
which
exhibit
intricate
patterns
among
different
sections.
Overall,
our
not
only
enhances
understanding
evolution
Salicaceae,
but
also
provides
valuable
insights
into
Plants,
Год журнала:
2024,
Номер
13(5), С. 612 - 612
Опубликована: Фев. 23, 2024
Erigeron
represents
the
third
largest
genus
on
Juan
Fernández
Islands,
with
six
endemic
species,
five
of
which
occur
exclusively
younger
Alejandro
Selkirk
Island
one
species
both
islands.
While
its
continental
sister
is
unknown,
Islands
appears
to
be
monophyletic
and
most
likely
evolved
from
South
American
progenitor
species.
We
characterized
complete
chloroplast
genomes
including
accessions
E.
fernandezia
each
Robinson
Crusoe
purposes
elucidating
molecular
evolution
phylogenetic
relationships.
found
highly
conserved
in
size,
gene
order
contents,
further
identified
several
mutation
hotspot
regions.
In
addition,
we
two
positively
selected
genes
(ccsA
ndhF)
among
The
plastome
sequences
confirmed
monophyly
islands
corroborated
previous
relationships
New
findings
current
study
include
(1)
major
lineages,
turricola–E.
luteoviridis
fernandezia–E.
ingae–E.
rupicola,
(2)
non-monophyly
occurring
islands,
(3)
alpine
ingae
complex.
American Journal of Botany,
Год журнала:
2024,
Номер
111(3)
Опубликована: Март 1, 2024
Abstract
Premise
The
western
North
American
fern
genus
Pentagramma
(Pteridaceae)
is
characterized
by
complex
patterns
of
ploidy
variation,
an
understanding
which
critical
to
comprehending
both
the
evolutionary
processes
within
and
its
current
diversity.
Methods
We
undertook
a
cytogeographic
study
across
range
genus,
using
combination
chromosome
counts
flow
cytometry
infer
level.
Bioclimatic
variables
elevation
were
used
compare
niches.
Results
found
that
diploids
tetraploids
are
common
widespread,
triploids
rare
sporadic;
in
contrast
with
genome
size
inferences
earlier
studies,
no
hexaploids
found.
Diploids
show
different
geographic
ranges:
only
northernmost
portion
(Washington,
Oregon,
British
Columbia)
Sierra
Nevada
California.
Diploid,
triploid,
tetraploid
cytotypes
co‐occur
relatively
few
localities:
southern
(San
Diego
County,
California)
desert
Southwest
(Arizona)
parts
range,
along
Pacific
Coast
Conclusions
Tetraploids
occupy
wider
bioclimatic
niche
than
P.
triangularis
at
genus‐wide
scale.
It
unknown
whether
due
their
expansion
upon
diploid
niche,
if
have
contracted
competition
or
changing
abiotic
conditions,
this
occupancy
multiple
origins
tetraploids.
Applications in Plant Sciences,
Год журнала:
2024,
Номер
12(4)
Опубликована: Апрель 22, 2024
Phylogenetic
inference
of
polyploid
species
is
the
first
step
towards
understanding
their
patterns
diversification.
In
this
paper,
we
review
challenges
and
limitations
inferring
relationships
plants
using
traditional
phylogenetic
sequencing
approaches,
as
well
mischaracterization
tree
from
single
or
multiple
gene
trees.
We
provide
a
roadmap
to
infer
interspecific
among
lineages
by
comparing
evaluating
application
current
phylogenetic,
phylogenomic,
transcriptomic,
whole-genome
approaches
different
platforms.
For
reconstruction,
assess
following
criteria:
(1)
amount
prior
information
tools
required
capture
genetic
region(s)
interest;
(2)
probability
recovering
homeologs
for
species;
(3)
time
efficiency
downstream
data
analysis.
Moreover,
discuss
bioinformatic
pipelines
that
can
reconstruct
networks
relationships.
summary,
although
phylogenomic
have
improved
our
reticulate
in
polyploid-rich
genera,
difficulties
reliable
orthologous
genes
sorting
all
homeologous
copies
allopolyploids
remain
challenge.
future,
assembled
long-read
will
assist
recovery
identification
copies,
which
be
particularly
useful
reconstructing
independent
origins
polyploids.
American Journal of Botany,
Год журнала:
2024,
Номер
111(8)
Опубликована: Авг. 1, 2024
Abstract
Premise
Hybridization
is
recognized
as
an
important
mechanism
in
fern
speciation,
with
many
allopolyploids
known
among
congeners,
well
evidence
of
ancient
genome
duplications.
Several
contemporary
instances
deep
(intergeneric)
hybridization
have
been
noted,
invariably
resulting
sterile
progeny.
We
chose
the
christelloid
lineage
family
Thelypteridaceae,
for
its
high
frequency
both
intra‐
and
intergeneric
hybrids,
to
investigate
recent
hybrid
speciation
between
deeply
diverged
lineages.
also
seek
understand
ecological
evolutionary
outcomes
lineages
across
landscape.
Methods
By
phasing
captured
reads
within
a
phylogenomic
data
set
GoFlag
408
nuclear
loci
using
HybPhaser,
we
investigated
candidate
hybrids
identify
parental
estimated
divergence
ages
by
inferring
dated
phylogeny
fossil
calibrations
treePL.
niche
conservatism
one
confirmed
allotetraploid
diploid
progenitors
centroid,
overlap,
unfilling,
expansion
(COUE)
framework.
Results
provide
at
least
six
clade
estimate
up
45
million
years
progenitors.
The
quantification
analysis
showed
moderate
overlap
allopolyploid
species
progenitors,
significant
from
progenitor
other.
Conclusions
examples
provided
here
highlight
overlooked
role
that
allopolyploidization
following
may
play
diversification
range
expansions.
Applying
this
approach
other
taxa
reveal
similar
pattern
highly
successful
novel
