Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data
Applications in Plant Sciences,
Год журнала:
2024,
Номер
12(2)
Опубликована: Март 1, 2024
Abstract
Premise
Digitized
biodiversity
data
offer
extensive
information;
however,
obtaining
and
processing
can
be
daunting.
Complexities
arise
during
cleaning,
such
as
identifying
removing
problematic
records.
To
address
these
issues,
we
created
the
R
package
Geographic
And
Taxonomic
Occurrence
R‐based
Scrubbing
(gatoRs).
Methods
Results
The
gatoRs
workflow
includes
functions
that
streamline
downloading
records
from
Global
Biodiversity
Information
Facility
(GBIF)
Integrated
Biocollections
(iDigBio).
We
also
to
clean
downloaded
specimen
Unlike
previous
packages,
accounts
for
differences
in
download
structure
between
GBIF
iDigBio
allows
user
control
via
interactive
cleaning
steps.
Conclusions
Our
pipeline
enables
scientific
community
process
efficiently
is
accessible
coding
novice.
anticipate
will
useful
both
established
beginning
users.
Furthermore,
expect
our
facilitate
introduction
of
biodiversity‐related
concepts
into
classroom
use
herbarium
specimens.
Язык: Английский
Complete Chloroplast Genome Analysis of Casearia kurzii: Gene Loss at the IR Boundary and Monophyletic Evolution Within Casearia
Plants,
Год журнала:
2025,
Номер
14(9), С. 1356 - 1356
Опубликована: Апрель 30, 2025
Genomic
analysis
is
crucial
for
understanding
the
evolutionary
history,
phylogenetic
relationships,
and
effective
conservation
of
plant
species.
Casearia
kurzii
an
important
medicinal
genus
Casearia,
but
its
complete
chloroplast
genome
has
not
previously
been
reported,
limiting
genetic
studies
efforts.
In
this
study,
we
assembled
annotated
C.
using
Illumina
sequencing
technology
conducted
a
comparative
genomics
with
14
closely
related
species
to
clarify
position
within
Casearia.
The
was
157,998
bp,
showing
typical
quadripartite
structure.
Key
findings
included:
(1)
loss
rpl22
gene
at
IR
boundary;
(2)
identification
60
simple
sequence
repeats
(SSRs)
(3)
discovery
five
candidate
molecular
markers
species-level
identification.
Phylogenetic
revealed
that
formed
strongly
supported
monophyletic
clade
(100%
bootstrap
support)
velutina,
decandra,
glomerata,
originated
approximately
15.8
million
years
ago.
This
study
provides
tools
accurate
species,
laying
foundation
exploring
adaptive
evolution
advancing
research.
Язык: Английский
Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae)
Ecology and Evolution,
Год журнала:
2023,
Номер
13(1)
Опубликована: Янв. 1, 2023
Abstract
Using
the
genus
Casearia
,
we
assessed
status
of
nested
singletons:
individual
specimens
corresponding
to
accepted
species
but
in
molecular
trees
appearing
within
clades
closely
related
species.
Normally,
such
cases
would
be
left
undecided,
while
on
other
hand,
timely
taxonomic
decisions
are
required.
We
argue
that
morphological,
chorological,
and
ecological
data
can
informative
illuminate
patterns
speciation.
Their
use
provide
a
first
step
testing
taxon
concepts
at
level.
focused
five
singletons
.
employed
PCA
cluster
analysis
assess
phenotypic
differentiation.
geocoordinates,
calculated
niche
space
differentiation
based
19
bioclim
variables,
by
means
equivalency
similarity
tests
generated
dot
maps.
found
were
morphologically
distinctive
two
(
selloana
C.
manausensis
),
relatively
zizyphoides
mariquitensis
partially
overlapping
last
case
grandiflora
).
For
was
broadly
overlapping,
it
one
narrowly
no
observed.
Niche
overlap,
showed
patterns.
Given
these
data,
interpret
as
presumably
well‐distinguished
taxa,
their
narrow
distribution
ranges
suggesting
recently
emerging
lineages.
The
three
not
clearcut.
Morphological
suggest
particularly
conspecific
with
arborea
differences
intriguing.
Our
approach
reject
notion
potential
synonymy
phylogenetic
placement
for
least
cases.
also
shows
complete
lack
which
support
synonymy.
Язык: Английский
Patterns in the genetic structure of 49 lowland rain forest tree species co‐distributed on opposite sides of the northern Andes
Biotropica,
Год журнала:
2024,
Номер
56(2)
Опубликована: Фев. 22, 2024
Abstract
The
Andes
are
a
major
dispersal
barrier
for
lowland
rain
forest
plants
and
animals,
yet
hundreds
of
tree
species
distributed
on
both
sides
the
northern
Andes,
raising
questions
about
how
influenced
their
biogeographic
histories
population
genetic
structure.
To
explore
these
questions,
we
generated
standardized
datasets
thousands
SNPs
from
paired
populations
49
co‐distributed
in
communities
located
Panama
Amazonian
Ecuador
calculated
diversity
(
π
)
absolute
divergence
d
XY
within
between
populations,
respectively.
We
predicted
(1)
higher
ancestral
source
region
(east
or
west
Andes)
each
taxon
(2)
correlation
statistics
with
attributes,
including
elevational
range
life‐history
strategy.
found
that
was
putative
regions,
possibly
reflecting
founder
events
during
colonization.
little
support
relationship
attributes
except
limits
exhibited
,
implying
older
times.
One
possible
explanation
this
pattern
is
through
mountain
passes
declined
importance
relative
to
via
alternative
routes
as
experienced
uplift.
no
difference
mean
Central
America
Amazon.
Overall,
our
results
suggest
across
has
left
enduring
signatures
structure
widespread
trees.
outline
additional
hypotheses
be
tested
species‐specific
case
studies.
Язык: Английский
Extended phylogenetic analysis and morphology of the Iresine cassiniiformis – I. hartmanii alliance (Amaranthaceae) reveals two further geographically distinct species
Botanical Sciences,
Год журнала:
2024,
Номер
103(1)
Опубликована: Дек. 19, 2024
Background:
Shrubs
recognized
as
I.
hartmanii
were
known
from
the
northern
Mexican
deserts,
whereas
cassiniiformis
is
considered
to
occur
throughout
highlands.
Morphologically
similar
individuals
reported
under
both
names
also
south
beyond
Isthmus
of
Tehuantepec
Guatemala.
Question:
Are
and
distinct
species,
or
do
they
represent
widespread
taxa
exhibiting
clinal
variation
due
adaptation
along
a
gradient
spanning
desert
evergreen
tropical
forest?
Taxon:
Amaranthaceae,
Iresine.
Study
site:
Mexico
Central
America.
Method:
Field
herbarium
work,
molecular
phylogenetics,
morphology,
palynology,
distribution
mapping.
Results:
Plastid
nuclear
phylogenetic
trees
suggest
complex
speciation
scenario
in
Iresine,
revealing
new
lineages
mountains
Chiapas,
Oaxaca
Guatemala
that
differ
by
morphological
characters.
Iresine
appears
monophyletic
occurs
Trans-Mexican
Volcanic
Belt
comprises
core
clade
confined
deserts.
Specimens
morphologically
intermediate
cassiniiformis,
part
species
nrITS,
directly
zone,
either
representing
ancestral
types
introgression
cassiniiformis.
Conclusion:
Our
results
underscore
importance
an
integrative
taxonomy
approach
including
phylogenetics
morphology
with
dense
sampling
putative
geographical
range
order
arrive
at
explicit
hypotheses
on
limits.
Here
this
supports
description
naming
two
species.
Язык: Английский
A new species of Casearia Jacq. (Salicaceae) from Central Panama and insights into its phylogenetic position within the genus
PhytoKeys,
Год журнала:
2023,
Номер
236, С. 97 - 112
Опубликована: Дек. 6, 2023
We
describe
here
a
new
species
of
Casearia
from
Panama
based
on
both
morphological
and
molecular
data.
Caseariaisthmicasp.
nov.
is
restricted
to
the
mid-elevation
cloud
forests
Central
presents
similarities
with
two
more
widespread
species,
C.sanchezii
high
elevation
areas
El
Salvador
Mexico
C.tremula
Caribbean,
America,
Northern
South
America.
Caseariaisthmica
differs
in
presenting
pedunculated
congested
inflorescences
up
20
flowers,
as
well
flowers
12
stamens
pubescent
style.
Phylogenetic
analysis
selected
plastid
(petD,
trnK-matK,
rpl16
rps4-trnLF)
nuclear
(GBSSI
ITS)
markers
shows
that
belongs
subclade
B3
Casearia,
lineage
encompasses
Caribbean.
Results
were
congruent
allowed
broader
understanding
this
taxon,
especially
regarding
its
relationships
other
Casearia.
Язык: Английский