A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model
Published: Nov. 11, 2024
The
aye-aye
(
Language: Английский
Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Sept. 22, 2024
The
demographic
history
of
a
population,
and
the
distribution
fitness
effects
(DFE)
newly
arising
mutations
in
functional
genomic
regions,
are
fundamental
factors
dictating
both
genetic
variation
evolutionary
trajectories.
Although
DFE
inference
has
been
performed
extensively
humans,
these
approaches
have
generally
either
limited
to
simple
models
involving
single
or,
where
complex
population
inferred,
without
accounting
for
potentially
confounding
selection
at
linked
sites.
Taking
advantage
coding-sparse
nature
genome,
we
propose
2-step
approach
which
coalescent
simulations
first
used
infer
multi-population
model,
utilizing
large
non-functional
regions
that
likely
free
from
background
selection.
We
then
use
forward-in-time
perform
conditional
on
demography
inferred
expected
estimation
procedure.
Throughout,
recombination
mutation
rate
maps
were
account
underlying
empirical
heterogeneity
across
human
genome.
Importantly,
within
this
framework
it
is
possible
utilize
fit
multiple
aspects
data,
scheme
represents
generalized
such
large-scale
species
with
genomes.
Language: Английский
iHDSel software: The Price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: June 3, 2024
A
large
number
of
methods
have
been
developed
and
continue
to
be
for
detecting
the
signatures
selective
sweeps
in
genomes.
Significant
advances
made,
including
combination
different
statistical
strategies
incorporation
artificial
intelligence
(machine
learning)
methods.
Despite
these
advances,
several
common
problems
persist,
such
as
unknown
null
distribution
statistics
used,
necessitating
simulations
resampling
assign
significance
statistics.
Additionally,
it
is
not
always
clear
how
deviations
from
specific
assumptions
each
method
might
affect
results.
In
this
work,
allelic
classes
haplotypes
are
used
along
with
informational
interpretation
Price
equation
design
a
statistic
known
that
can
detect
genomic
patterns
caused
by
sweeps.
The
consists
Jeffreys
divergence,
also
population
stability
index,
applied
two
samples.
Results
simulated
data
show
optimal
performance
divergent
selection.
Analysis
real
SARS-CoV-2
genome
shows
some
sites
playing
key
roles
virus's
fitness
immune
escape
capability
detected
method.
new
statistic,
called
JHAC,
incorporated
into
iHDSel
software
available
at
https://acraaj.webs.uvigo.es/iHDSel.html.
Language: Английский
Long-term balancing selection maintains cryptic color polymorphism in frogs
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 18, 2024
Color
polymorphism
can
influence
the
evolutionary
fate
of
cryptic
species
because
it
increases
populations'
chances
survival
in
heterogenous
or
variable
environments.
Yet,
little
is
known
about
molecular
and
mechanisms
underlying
persistence
color
polymorphisms,
impact
these
polymorphisms
have
on
macro-evolutionary
dynamics
lineages.
Here,
we
examine
history
most
widespread
anurans,
involving
green
brown
morphs.
Using
an
order-scale
comparative
analysis,
show
that
morphs
co-exist
within
over
long
periods
time
polymorphic
lineages
switch
habitat
more
frequently
greater
diversification
rates
than
other
groups.
We
then
identify
locus
responsible
for
green/brown
a
group
African
grass
frogs,
demonstrate
this
genomic
region
evolving
under
long-term
balancing
selection,
resulting
trans-specific
polymorphism.
These
results
provide
micro-evolutionary
mechanism
observed
at
scale.
This
study
highlights
importance
ecology
evolution
provides
framework
future
research
genetic
architecture
selective
forces
traits.
Language: Английский
iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2
Biology Methods and Protocols,
Journal Year:
2024,
Volume and Issue:
9(1)
Published: Jan. 1, 2024
Abstract
A
large
number
of
methods
have
been
developed
and
continue
to
evolve
for
detecting
the
signatures
selective
sweeps
in
genomes.
Significant
advances
made,
including
combination
different
statistical
strategies
incorporation
artificial
intelligence
(machine
learning)
methods.
Despite
these
advances,
several
common
problems
persist,
such
as
unknown
null
distribution
statistics
used,
necessitating
simulations
resampling
assign
significance
statistics.
Additionally,
it
is
not
always
clear
how
deviations
from
specific
assumptions
each
method
might
affect
results.
In
this
work,
allelic
classes
haplotypes
are
used
along
with
informational
interpretation
Price
equation
design
a
statistic
known
that
can
detect
genomic
patterns
caused
by
sweeps.
The
consists
Jeffreys
divergence,
also
population
stability
index,
applied
two
samples.
Results
simulated
data
show
optimal
performance
divergent
selection.
Analysis
real
severe
acute
respiratory
syndrome
coronavirus
2
genome
shows
some
sites
playing
key
roles
virus’s
fitness
immune
escape
capability
detected
method.
new
statistic,
called
JHAC,
incorporated
into
iHDSel
(informed
HacDivSel)
software
available
at
https://acraaj.webs.uvigo.es/iHDSel.html.
Language: Английский
Computational Genomics and Its Applications to Anthropological Questions
American Journal of Physical Anthropology,
Journal Year:
2024,
Volume and Issue:
186(S78)
Published: Dec. 1, 2024
ABSTRACT
The
advent
of
affordable
genome
sequencing
and
the
development
new
computational
tools
have
established
a
era
genomic
knowledge.
Sequenced
human
genomes
number
in
tens
thousands,
including
thousands
ancient
genomes.
abundance
data
has
been
met
with
analysis
that
can
be
used
to
understand
populations'
demographic
evolutionary
histories.
Thus,
variety
methods
now
exist
leveraged
answer
anthropological
questions.
This
includes
novel
likelihood
Bayesian
methods,
machine
learning
techniques,
vast
array
population
simulators.
These
provide
powerful
insights
gained
from
datasets,
although
they
are
generally
inaccessible
those
less
experience.
Here,
we
outline
theoretical
workings
behind
genomics
limitations
other
considerations
when
applying
these
examples
how
already
applied
We
hope
this
review
will
empower
anthropologists
utilize
their
own
research.
Language: Английский