Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data
Genome Biology and Evolution,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 3, 2025
Abstract
The
nocturnal
aye-aye,
Daubentonia
madagascariensis,
is
one
of
the
most
elusive
lemurs
on
island
Madagascar.
timing
its
activity
and
arboreal
lifestyle
has
generally
made
it
difficult
to
obtain
accurate
assessments
population
size
using
traditional
census
methods.
Therefore,
alternative
estimates
provided
by
genetic
inference
are
essential
for
yielding
much
needed
information
conservation
measures
enabling
ecological
evolutionary
studies
this
species.
Here,
we
utilize
genomic
data
from
17
individuals—including
5
newly
sequenced,
high-coverage
genomes—to
estimate
history.
Essential
estimation
recently
published
annotations
aye-aye
genome
which
allow
variation
at
putatively
neutral
regions
be
included
in
procedures,
subject
selective
constraints,
or
linkage
such
sites,
excluded
owing
biasing
effects
selection
demographic
inference.
By
comparing
a
variety
tools
develop
well-supported
model
history,
find
strong
support
two
demes,
separating
northern
Madagascar
rest
island.
Additionally,
that
experienced
severe
reductions
size.
first
occurred
rapidly,
approximately
3,000
5,000
years
ago,
likely
corresponded
with
arrival
humans
second
over
past
few
decades
related
substantial
habitat
loss,
suggesting
species
still
undergoing
decline
remains
great
risk
extinction.
Language: Английский
Estimating the distribution of fitness effects in aye-ayes (Daubentonia madagascariensis), accounting for population history as well as mutation and recombination rate heterogeneity
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 3, 2025
ABSTRACT
The
distribution
of
fitness
effects
(DFE)
characterizes
the
range
selection
coefficients
from
which
new
mutations
are
sampled,
and
thus
holds
a
fundamentally
important
role
in
evolutionary
genomics.
To
date,
DFE
inference
primates
has
been
largely
restricted
to
haplorrhines,
with
limited
data
availability
leaving
other
suborder
primates,
strepsirrhines,
under-explored.
advance
our
understanding
population
genetics
this
taxonomic
group,
we
here
map
exonic
divergence
aye-ayes
(
Daubentonia
madagascariensis
)
–
only
extant
member
Daubentoniidae
family
Strepsirrhini
suborder.
We
further
infer
highly-endangered
species,
utilizing
recently
published
high-quality
annotated
reference
genome,
well-supported
model
demographic
history,
as
well
both
direct
indirect
estimates
underlying
mutation
recombination
rates.
inferred
is
generally
characterized
by
greater
proportion
deleterious
relative
humans,
providing
evidence
larger
long-term
effective
size.
In
addition
however,
immune-related
sensory-related
genes
were
found
be
amongst
most
rapidly
evolving
aye-aye
genome.
Language: Английский
Temporal challenges in detecting balancing selection from population genomic data
G3 Genes Genomes Genetics,
Journal Year:
2024,
Volume and Issue:
14(6)
Published: March 29, 2024
Abstract
The
role
of
balancing
selection
in
maintaining
genetic
variation
remains
an
open
question
population
genetics.
Recent
years
have
seen
numerous
studies
identifying
candidate
loci
potentially
experiencing
selection,
most
predominantly
human
populations.
There
are
however
alternative
evolutionary
processes
that
may
leave
similar
patterns
variation,
thereby
confounding
inference,
and
the
expected
signatures
additionally
change
a
temporal
fashion.
Here
we
use
forward-in-time
simulations
to
quantify
statistical
power
detect
using
both
site
frequency
spectrum-
linkage
disequilibrium-based
methods
under
variety
evolutionarily
realistic
null
models.
We
find
whilst
spectrum-based
little
immediately
after
balanced
mutation
begins
segregating,
increases
with
time
since
introduction
allele.
Conversely,
considerable
allele
is
young,
dissipates
rapidly
as
increases.
Taken
together,
this
suggests
effective
at
detecting
long-term
(>25N
generations
allele)
over
much
shorter
timescales
(<1N
generations),
leaving
large
frame
which
current
action
selection.
Finally,
investigate
extent
mimic
these
patterns,
demonstrate
need
for
caution
attempting
distinguish
from
those
neutral
(e.g.
structure
admixture)
well
selective
partial
sweeps).
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
Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: April 16, 2024
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