PLoS ONE,
Journal Year:
2014,
Volume and Issue:
9(11), P. e112843 - e112843
Published: Nov. 11, 2014
The
use
of
phylogenetic
information
in
community
ecology
and
conservation
has
grown
recent
years.
Two
key
issues
for
phylogenetics
studies,
however,
are
(i)
low
terminal
resolution
(ii)
arbitrarily
defined
species
pools.We
used
three
DNA
barcodes
(plastid
regions
rbcL,
matK,
trnH-psbA)
to
infer
a
phylogeny
527
native
naturalized
trees
Puerto
Rico,
representing
the
vast
majority
entire
tree
flora
island
(89%).
We
maximum
likelihood
(ML)
approach
with
without
constraint
that
enforced
monophyly
recognized
plant
orders.
Based
on
50%
consensus
trees,
ML
analyses
improved
relative
comparable
generated
Phylomatic
(proportion
internal
nodes
resolved:
constrained
=
74%,
unconstrained
68%,
52%).
quantified
composition
15
protected
forests
Rico
using
phylogenies.
found
some
evidence
communities
areas
high
water
stress
were
relatively
phylogenetically
clustered.
Reducing
scale
at
which
pool
was
(from
soil
types)
changed
our
results
depending
(ML
vs.
Phylomatic)
used.
Overall,
increased
provided
by
revealed
additional
patterns
not
observed
less-resolved
phylogeny.With
barcode
presented
here
(based
an
island-wide
pool),
we
show
more
fully
resolved
increases
power
detect
nonrandom
several
Rican
communities.
Especially
if
combined
functional
traits
geographic
distributions,
this
will
facilitate
stronger
inferences
about
role
historical
processes
governing
assembly
forests,
provide
insight
into
Caribbean
biogeography,
(iii)
aid
incorporating
evolutionary
history
planning.
Ecology Letters,
Journal Year:
2012,
Volume and Issue:
15(8), P. 831 - 840
Published: May 24, 2012
Abstract
The
relative
importance
of
competition
vs.
environmental
filtering
in
the
assembly
communities
is
commonly
inferred
from
their
functional
and
phylogenetic
structure,
on
grounds
that
similar
species
compete
most
strongly
for
resources
are
therefore
less
likely
to
coexist
locally.
This
approach
ignores
possibility
competitive
effects
can
be
determined
by
positions
a
hierarchy
ability.
Using
growth
data,
we
estimated
275
interaction
coefficients
between
tree
French
mountains.
We
show
strengths
mainly
driven
trait
not
or
similarity.
On
basis
this
result,
thus
propose
convergence
local
community
might
due
competition‐sorting
with
different
abilities
only
as
assumed.
then
forest
structure
increasing
plot
age,
which
supports
view.
Ecography,
Journal Year:
2010,
Volume and Issue:
34(4), P. 552 - 565
Published: Dec. 14, 2010
Ecological
and
evolutionary
processes
influence
community
assembly
at
both
local
regional
scales.
Adding
a
phylogenetic
dimension
to
studies
of
species
turnover
allows
tests
the
extent
which
environmental
gradients,
geographic
distance
historical
biogeography
lineages
have
influenced
speciation
dispersal
throughout
region.
We
compare
measures
beta
diversity,
structure
phylobetadiversity
(phylogenetic
among
communities)
in
34
plots
Amazonian
trees
across
white-sand
clay
terra
firme
forests
60
000
square
kilometer
area
Loreto,
Peru.
Dominant
taxa
were
phylogenetically
clustered,
consistent
with
filtering
conserved
traits.
Phylobetadiversity
found
significant
clustering
between
communities
separated
by
distances
B200300
km,
within
recent
watershed
scale
Miocene-aged
clay-soil
near
foothills
Andes.
Although
habitat
type
yielded
statistically
effects
on
turnover,
patterns
we
observed
more
an
effect
specialization
than
limitation.
Our
results
suggest
role
for
broad-scale
biogeographic
processes,
as
well
specialization,
influencing
forests.
PLoS ONE,
Journal Year:
2011,
Volume and Issue:
6(8), P. e23533 - e23533
Published: Aug. 17, 2011
Accurate
knowledge
of
carbon
(C)
content
in
live
wood
is
essential
for
quantifying
tropical
forest
C
stocks,
yet
generic
assumptions
(such
as
biomass
consisting
50%
on
a
weight/weight
basis)
remain
widely
used
despite
being
supported
by
little
chemical
analysis.
Empirical
data
from
stem
cores
59
Panamanian
rainforest
tree
species
demonstrate
that
highly
variable
among
co-occurring
species,
with
an
average
(47.4±2.51%
S.D.)
significantly
lower
than
assumed
values.
Prior
published
values
have
neglected
to
account
volatile
woods.
By
comparing
freeze-
and
oven-dried
samples,
we
show
non-negligible,
excluding
the
fraction
underestimates
2.48±1.28%
(S.D.)
average.
Wood
varied
substantially
(from
41.9-51.6%),
but
was
neither
strongly
phylogenetically
conserved,
nor
correlated
ecological
(i.e.
density,
maximum
height)
or
demographic
traits
relative
growth
rate,
mortality
rate).
Overall,
assuming
fractions
overestimates
stocks
∼3.3-5.3%,
non-trivial
margin
error
leading
4.1-6.8
Mg
ha(-1)
50-ha
dynamics
plot
Barro
Colorado
Island,
Panama.
In
addition
addressing
other
sources
accounting,
such
uncertainties
allometric
models
belowground
biomass,
compilation
use
species-specific
would
improve
both
local
global
estimates
terrestrial
fluxes.
Proceedings of the National Academy of Sciences,
Journal Year:
2011,
Volume and Issue:
108(51), P. 20627 - 20632
Published: Nov. 21, 2011
How
numerous
tree
species
can
coexist
in
diverse
forest
communities
is
a
key
question
community
ecology.
Whereas
neutral
theory
assumes
that
are
adapted
to
common
field
conditions
and
by
chance,
niche
predicts
functionally
different
because
they
specialized
for
niches.
We
integrated
biophysical
principles
into
mathematical
plant
model
determine
whether
how
functional
traits
trade-offs
may
cause
divergence
separation
of
species.
used
this
compare
the
carbon
budget
saplings
across
13
co-occurring
dry-forest
along
gradients
light
water
availability.
found
ranged
strategy,
from
acquisitive
with
high
budgets
at
highest
resource
levels
more
conservative
tolerances
both
shade
drought.
The
crown
leaf
area
index
nitrogen
mass
per
drove
simulated
gradient,
which
was
consistent
observed
distributions
forest.
Stomatal
coordination
avoid
low
potentials
or
hydraulic
failure
caused
but
not
correlated
gradient
trait-based
thus
explains
such
contributes
gradients.
Journal of Ecology,
Journal Year:
2012,
Volume and Issue:
100(3), P. 690 - 701
Published: March 14, 2012
Summary
1.
Niche
theory
proposes
that
species
differences
underlie
both
coexistence
within
communities
and
the
differentiation
in
composition
among
via
limiting
similarity
environmental
filtering.
However,
it
has
been
difficult
to
extend
niche
species‐rich
because
of
empirical
challenge
quantifying
niches
for
many
species.
This
motivated
development
functional
phylogeny‐based
approaches
community
ecology,
which
represent
two
different
means
approximating
attributes.
2.
Here,
we
assess
utility
plant
traits
phylogenetic
relationships
predicting
assembly
processes
using
largest
trait
data
base
date
any
set
communities.
3.
We
measured
17
all
4672
individuals
668
tree
co‐occurring
nine
tropical
rain
forest
plots
French
Guiana.
Trait
variation
was
summarized
into
ordination
axes
reflect
overlap.
4.
also
generated
a
dated
molecular
based
on
DNA
sequencing
plastid
loci
(
rbcL
matK
)
comprising
97%
91%
plots.
5.
found
that,
average,
had
greater
and,
lesser
extent,
than
expected
by
chance.
6.
their
loadings
showed
significant,
albeit
weak,
signal,
suggesting
distance
provides
pertinent
information
overlap
7.
Synthesis
.
provide
most
comprehensive
examination
relative
importance
filtering
structuring
Our
results
confirm
is
overriding
influence
these
systems.
PLoS ONE,
Journal Year:
2013,
Volume and Issue:
8(5), P. e63708 - e63708
Published: May 14, 2013
Understanding
species
distributions
and
the
factors
limiting
them
is
an
important
topic
in
ecology
conservation,
including
nature
reserve
selection
predicting
climate
change
impacts.
While
Species
Distribution
Models
(SDM)
are
main
tool
used
for
these
purposes,
choosing
best
SDM
algorithm
not
straightforward
as
plentiful
can
be
applied
many
different
ways.
mainly
to
gain
insight
1)
overall
distributions,
2)
their
past-present-future
probability
of
occurrence
and/or
3)
understand
ecological
niche
limits
(also
referred
modelling).
The
fact
that
three
aims
may
require
models
outputs
is,
however,
rarely
considered
has
been
evaluated
consistently.
Here
we
use
data
from
a
systematically
sampled
set
occurrences
specifically
test
performance
across
several
commonly
algorithms.
range
distribution
patterns
rare
common
local
widespread.
We
compare
model
fit
(representing
distribution),
accuracy
predictions
at
multiple
spatial
scales,
consistency
environmental
correlations
all
modelling
runs.
As
expected,
choice
determines
outcome.
However,
quality
depends
only
on
algorithm,
but
also
measure
scale
which
it
used.
Although
was
higher
consensus
approach
Maxent,
Maxent
GAM
were
more
consistent
estimating
occurrence,
while
RF
GBM
showed
variables
selection.
Model
outcomes
diverged
narrowly
distributed
than
widespread
species.
suggest
matching
study
with
essential
Models,
provide
suggestions
how
do
this
species’
characteristics
(i.e.
sample
size,
distribution).
Ecography,
Journal Year:
2013,
Volume and Issue:
36(3), P. 264 - 276
Published: Jan. 24, 2013
Tropical
tree
communities
present
one
of
the
most
challenging
systems
for
studying
processes
underlying
community
assembly.
Most
assembly
hypotheses
consider
relative
importance
ecological
similarity
co‐occurring
species.
Quantifying
this
is
a
daunting
and
potentially
impossible
task
in
species‐rich
assemblages.
During
past
decade
tropical
ecologists
have
increasingly
utilized
phylogenetic
trees
functional
traits
to
estimate
species
order
test
mechanistic
hypotheses.
A
large
amount
work
has
resulted
with
many
important
advances
having
been
made
along
way.
That
said,
there
are
still
outstanding
challenges
facing
those
utilizing
trait
approaches
study
Here
I
review
conceptual
background,
major
remaining
phylogenetic‐
trait‐based
ecology
specific
focus
on
trees.
argue
that
both
tremendously
improve
our
understanding
ecology,
but
neither
approach
fully
reached
its
potential
thus
far.
New Phytologist,
Journal Year:
2012,
Volume and Issue:
196(2), P. 497 - 509
Published: Aug. 29, 2012
Summary
Deterministic
niche‐based
processes
have
been
proposed
to
explain
species
relative
abundance
within
communities
but
lead
different
predictions:
habitat
filtering
(
HF
)
predicts
dominant
exhibit
similar
traits
while
niche
differentiation
ND
requires
that
dissimilar
coexist.
Using
a
multiple
trait‐based
approach,
we
evaluated
the
roles
of
and
in
determining
abundances
productive
grasslands.
Four
dimensions
functional
12
co‐occurring
grass
were
identified
using
28
plant
traits.
this
description
niche,
investigated
patterns
similarity
dissimilarity
linked
them
randomly
assembled
six‐species
subjected
fertilization/disturbance
treatments.
Our
results
suggest
jointly
determined
by
acting
on
contrasting
dimensions.
The
effect
decreased
with
increasing
disturbance
decreasing
fertilization.
Dominant
exhibited
whereas
favored
coexistence
rare
dominants
inter‐specific
competition.
This
stabilizing
diversity
was
suggested
negative
relationship
between
over‐yielding
abundance.
We
discuss
importance
considering
independent
better
understand
communities.
Ecology,
Journal Year:
2019,
Volume and Issue:
100(7)
Published: April 24, 2019
We
propose
four
postulates
as
the
minimum
set
of
logical
propositions
necessary
for
a
theory
pulse
dynamics
and
disturbance
in
ecosystems:
(1)
resource
characterizes
magnitude,
rate,
duration
change
caused
by
events,
including
continuing
changes
resources
that
are
result
abiotic
biotic
processes;
(2)
energy
flux
flow
controls
variation
rates
assimilation
across
ecosystems;
(3)
patch
distribution
patches
over
space
time,
resulting
patterns
diversity,
ecosystem
structure,
cross-scale
feedbacks
pulses
(4)
trait
diversity
evolutionary
responses
to
and,
turn,
way
affects
during
after
events.
apply
an
important
class
biomass-altering
disturbances,
derive
seven
generalizations
predict
trajectory,
rate
change,
probability,
diversification
at
scales,
ecological
functional
resilience.
Ultimately,
must
define
variable
combinations
dynamic
stability,
comprising
resistance,
recovery,
adaptation.