bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Dec. 21, 2023
A
bstract
Methods
for
rapidly
inferring
the
evolutionary
history
of
species
or
populations
with
genome-wide
data
are
progressing,
but
computational
constraints
still
limit
our
abilities
in
this
area.
We
developed
an
alignment-free
method
to
infer
phylogenies
and
implemented
it
Python
package
T
opic
C
ontml
.
The
uses
probabilistic
topic
modeling
(specifically,
Latent
Dirichlet
Allocation
LDA)
extract
‘topic’
frequencies
from
k
-mers,
which
derived
multilocus
DNA
sequences.
These
extracted
then
serve
as
input
program
PHYLIP
package,
is
used
generate
a
tree.
evaluated
performance
on
simulated
datasets
gaps
three
biological
datasets:
(1)
14
sequence
loci
two
Australian
bird
distributed
across
nine
populations,
(2)
5162
80
mammal
species,
(3)
raw,
unaligned,
non-orthologous
P
ac
B
io
sequences
12
species.
Our
empirical
results
suggest
that
efficient
statistically
robust.
also
assessed
uncertainty
estimated
relationships
among
clades
using
bootstrap
procedure.
Proceedings of the National Academy of Sciences,
Journal Year:
2024,
Volume and Issue:
121(29)
Published: July 8, 2024
Large
volumes
of
liquid
water
transiently
existed
on
the
surface
Mars
more
than
3
billion
years
ago.
Much
this
is
hypothesized
to
have
been
sequestered
in
subsurface
or
lost
space.
We
use
rock
physics
models
and
Bayesian
inversion
...
Proceedings of the National Academy of Sciences,
Journal Year:
2024,
Volume and Issue:
121(29)
Published: July 8, 2024
Large
volumes
of
liquid
water
transiently
existed
on
the
surface
Mars
more
than
3
billion
years
ago.
Much
this
is
hypothesized
to
have
been
sequestered
in
subsurface
or
lost
space.
We
use
rock
physics
models
and
Bayesian
inversion
...
Biological Journal of the Linnean Society,
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 25, 2024
Abstract
The
use
of
genetic
data
to
reconstruct
systematic
relationships
has
revolutionized
our
understanding
avian
evolution.
Morphology-based
classifications
were
often
in
conflict
because
different
opinions
among
scholars
about
the
relative
importance
certain
phenotypes.
considerable
morphological
variation
observed
birds
was
codified
into
phylogenetic
characters
by
Livezey
and
Zusi
(2006)
who
also
scored
them
for
150
extinct
extant
taxa.
Herein
we
have
evaluated
signal
1860
these
mapping
a
molecular
phylogeny
including
102
taxa
that
represent
all
(with
underlying
assumption
this
tree
topology
is
good
estimate
evolutionary
birds).
fit
with
mean
consistency
index
(CI)
0.38.
Muscle
are
most
homoplasious
(CI
0.32),
while
related
integument,
feathers,
intestinal,
respiratory,
syrinx,
urogenital,
nervous,
reproductive
organs
show
considerably
better
(mean
CI
0.49).
We
explored
what
may
unambiguously
support
basal
clades
well-supported
data.
found
only
few
(e.g.
Galloanserae,
Procellariimorphae)
being
supported
unambiguous
apomorphies,
many
well-established
Pelecaniformes,
Charadriiformes,
Accipitriformes,
Coraciiformes)
lack
such
entirely.
