Leveraging graphical model techniques to study evolution on phylogenetic networks
Philosophical Transactions of the Royal Society B Biological Sciences,
Journal Year:
2025,
Volume and Issue:
380(1919)
Published: Feb. 13, 2025
The
evolution
of
molecular
and
phenotypic
traits
is
commonly
modelled
using
Markov
processes
along
a
phylogeny.
This
phylogeny
can
be
tree,
or
network
if
it
includes
reticulations,
representing
events
such
as
hybridization
admixture.
Computing
the
likelihood
data
observed
at
leaves
costly
size
complexity
grows.
Efficient
algorithms
exist
for
trees,
but
cannot
applied
to
networks.
We
show
that
vast
array
models
trait
phylogenetic
networks
reformulated
graphical
models,
which
efficient
belief
propagation
exist.
provide
brief
review
on
general
then
focus
linear
Gaussian
continuous
traits.
how
techniques
exact
approximate
(but
more
scalable)
gradient
calculations,
prove
novel
results
parameter
inference
some
models.
highlight
possible
fruitful
interactions
between
methods.
For
example,
approaches
have
potential
greatly
reduce
computational
costs
phylogenies
with
reticulations.
Language: Английский
A Literature Review of Stochastic Modeling for Phylogenetic Comparative Analysis in Trait Evolution
Mathematics,
Journal Year:
2025,
Volume and Issue:
13(3), P. 361 - 361
Published: Jan. 23, 2025
Evolutionary
inferences
from
phylogenetic
trees
can
be
modeled
stochastically
using
a
range
of
mathematical
frameworks.
Among
these,
stochastic
differential
equations
(SDEs)
provide
particularly
flexible
and
powerful
approach
to
capturing
the
continuous-time
dynamics
evolutionary
processes.
This
review
summarizes
advances
in
modeling
for
trait
evolution
along
tree,
with
focus
on
(SDEs),
Gaussian
non-Gaussian
processes,
time
series
models
that
expressed
as
special
cases
general
frameworks,
depending
questions
being
addressed
or
types
data
analyzed.
We
explore
current
developments
future
research
directions
comparative
analysis
evolution.
Language: Английский
Reconstructing semi-directed level-1 networks using few quarnets
Journal of Computer and System Sciences,
Journal Year:
2025,
Volume and Issue:
unknown, P. 103655 - 103655
Published: March 1, 2025
Language: Английский
TINNiK: inference of the tree of blobs of a species network under the coalescent model
Algorithms for Molecular Biology,
Journal Year:
2024,
Volume and Issue:
19(1)
Published: Nov. 5, 2024
The
tree
of
blobs
a
species
network
shows
only
the
tree-like
aspects
relationships
taxa
on
network,
omitting
information
substructures
where
hybridization
or
other
types
lateral
transfer
genetic
occur.
By
isolating
such
regions
inference
can
serve
as
starting
point
for
more
detailed
investigation,
indicate
limit
what
may
be
inferrable
without
additional
assumptions.
Building
our
theoretical
work
identifiability
from
gene
quartet
distributions
under
Network
Multispecies
Coalescent
model,
we
develop
an
algorithm,
TINNiK,
statistically
consistent
inference.
We
provide
examples
its
application
to
both
simulated
and
empirical
datasets,
utilizing
implementation
in
MSCquartets
2.0
R
package.
Language: Английский