Animal Genetics,
Journal Year:
2024,
Volume and Issue:
55(3), P. 319 - 327
Published: Feb. 7, 2024
Abstract
With
the
advent
of
next‐generation
sequencing,
an
increasing
number
cases
de
novo
variants
in
domestic
animals
have
been
reported
scientific
literature
primarily
associated
with
clinically
severe
phenotypes.
The
emergence
new
at
each
generation
is
a
crucial
aspect
understanding
pathology
early‐onset
diseases
and
can
provide
valuable
insights
into
similar
humans.
aim
collecting
deleterious
animals,
we
searched
compiled
reports
on
42
31
genes
animals.
No
clear
disease‐associated
phenotype
has
established
humans
for
three
these
(
NUMB
,
ANKRD28
KCNG1
).
For
remaining
28
genes,
strong
similarity
between
animal
human
phenotypes
was
recognized
from
available
information
OMIM
OMIA,
revealing
importance
comparative
studies
supporting
use
as
natural
models
diseases,
line
One
Health
approach.
EMBO Reports,
Journal Year:
2023,
Volume and Issue:
24(10)
Published: Aug. 24, 2023
Abstract
Owing
to
advances
in
genome
sequencing,
stability
has
become
one
of
the
most
scrutinized
cellular
traits
across
Tree
Life.
Despite
its
centrality
all
things
biological,
mutation
rate
(per
nucleotide
site
per
generation)
ranges
over
three
orders
magnitude
among
species
and
several‐fold
within
individual
phylogenetic
lineages.
Within
major
organismal
groups,
rates
scale
negatively
with
effective
population
size
a
amount
functional
DNA
genome.
This
relationship
is
parsimoniously
explained
by
drift‐barrier
hypothesis,
which
postulates
that
natural
selection
typically
operates
reduce
until
further
improvement
thwarted
power
random
genetic
drift.
this
constraint,
molecular
mechanisms
underlying
replication
fidelity
repair
are
free
wander,
provided
performance
entire
system
maintained
at
prevailing
level.
The
evolutionary
flexibility
bears
on
resolution
several
prior
conundrums
population‐genetic
analysis
raises
challenges
for
future
applications
these
areas.
Genome Research,
Journal Year:
2023,
Volume and Issue:
33(4), P. 587 - 598
Published: April 1, 2023
The
rates
of
mutation,
recombination,
and
transposition
are
core
parameters
in
models
evolution.
They
impact
genetic
diversity,
responses
to
ongoing
selection,
levels
load.
However,
even
for
key
evolutionary
model
species
such
as
Drosophila
melanogaster
simulans,
few
estimates
these
available,
we
have
little
idea
how
vary
between
individuals,
sexes,
or
populations.
Knowledge
this
variation
is
fundamental
parameterizing
genome
Here,
provide
direct
their
a
West
African
European
population
D.
simulans
Across
89
flies,
observe
58
single-nucleotide
mutations,
286
crossovers,
transposable
element
(TE)
insertions.
Compared
the
melanogaster,
find
has
lower
mutation
rate
(1.67
×
10-9
site-1
gen-1
vs.
4.86
gen-1)
(8.99
10-5
copy-1
23.36
gen-1),
but
higher
recombination
(3.44
cM/Mb
2.06
cM/Mb).
similar
significantly
lower,
not
different,
rate.
Overall,
paternal-derived
mutations
more
frequent
than
maternal
ones
both
species.
Our
study
quantifies
among
different
populations
our
will
benefit
future
studies
genetics.
Molecular Biology and Evolution,
Journal Year:
2025,
Volume and Issue:
42(3)
Published: March 1, 2025
Given
the
many
levels
of
biological
variation
in
mutation
rates
observed
to
date
primates-spanning
from
species
individuals
genomic
regions-future
steps
our
understanding
rate
evolution
will
not
only
be
aided
by
a
greater
breadth
coverage
across
primate
clade
but
also
depth
as
afforded
an
evaluation
multiple
trios
within
individual
species.
In
order
help
bridge
these
gaps,
we
here
present
analysis
representing
one
most
basal
splits
on
tree
(aye-ayes),
combining
whole-genome
sequencing
seven
parent-offspring
three-generation
pedigree
with
novel
computational
pipeline
that
takes
advantage
recently
developed
pan-genome
graphs,
thereby
circumventing
application
(highly
subjective)
quality
metrics
has
previously
been
shown
result
notable
differences
detection
de
novo
mutations
and
ultimately
estimates
rates.
This
deep
sampling
enabled
both
detailed
picture
parental
age
effects
sex
dependency
rates,
which
compare
studied
primates,
provided
unique
insights
into
nature
genetic
endangered
primates
planet.
Mutations
fuel
evolution
while
also
causing
diseases
like
cancer.
Epigenome-targeted
DNA
repair
can
help
organisms
protect
important
genomic
regions
from
mutation.
However,
the
adaptive
value,
mechanistic
diversity,
and
of
epigenome-targeted
systems
across
tree
life
remain
unresolved.
Here,
we
investigated
histone
reader
domains
fused
to
protein
MSH6
(MutS
Homolog
6)
over
4,000
eukaryotes.
We
uncovered
a
paradigmatic
example
convergent
evolution:
has
independently
acquired
distinct
domains;
PWWP
(metazoa)
Tudor
(plants),
previously
shown
target
modifications
in
active
genes
humans
(H3K36me3)
Arabidopsis
(H3K4me1).
Conservation
shows
signatures
natural
selection,
particularly
for
amino
acids
that
bind
specific
modifications.
Species
have
gained
or
retained
readers
tend
larger
genome
sizes,
especially
marked
by
significantly
more
introns
genic
regions.
These
patterns
support
previous
theoretical
predictions
about
co-evolution
architectures
mutation
rate
heterogeneity.
The
implications
evolution,
health,
mutational
origins
genetic
diversity
life.
Molecular Biology and Evolution,
Journal Year:
2025,
Volume and Issue:
42(1)
Published: Jan. 1, 2025
Abstract
The
rate
at
which
mutations
arise
is
a
fundamental
parameter
of
biology.
Despite
progress
in
measuring
germline
mutation
rates
across
diverse
taxa,
such
estimates
are
missing
for
much
Earth's
biodiversity.
Here,
we
present
the
first
estimate
from
phylum
Mollusca.
We
sequenced
three
pedigreed
families
white
abalone
Haliotis
sorenseni,
long-lived,
large-bodied,
and
critically
endangered
mollusk,
estimated
de
novo
8.60
×
10−9
single
nucleotide
per
site
generation.
This
similar
to
measured
vertebrates
with
comparable
generation
times
longevity
abalone,
higher
than
faster-reproducing
invertebrates.
spectrum
also
that
seen
vertebrate
species,
although
an
excess
rare
C
>
A
polymorphisms
wild
individuals
suggests
modifier
allele
or
environmental
exposure
may
have
once
increased
rates.
use
our
infer
baseline
effective
population
sizes
(Ne)
multiple
Pacific
find
persisted
over
most
their
evolutionary
history
as
large
stable
populations,
contrast
extreme
fluctuations
recent
small
census
day.
then
timing
pattern
evolution
genus
Haliotis,
was
previously
unknown
due
few
fossil
calibrations.
Our
findings
important
step
toward
understanding
they
establish
key
conservation
genomics
research
mollusks.
Genome Biology and Evolution,
Journal Year:
2024,
Volume and Issue:
16(3)
Published: March 1, 2024
Abstract
Background
selection
describes
the
reduction
in
neutral
diversity
caused
by
against
deleterious
alleles
at
other
loci.
It
is
typically
assumed
that
purging
of
affects
linked
variants,
and
indeed
simulations
only
treat
a
genomic
window.
However,
background
unlinked
loci
also
depresses
diversity.
In
agreement
with
previous
analytical
approximations,
our
human-like
genome
realistically
high
genome-wide
mutation
rate,
effects
exceed
those
selection.
reduces
genetic
factor
independent
census
population
size.
Outside
genic
regions,
strength
increases
mean
coefficient,
contradicting
theory
but
theory.
Neutral
within
regions
fairly
Deleterious
load
among
haploid
individuals
underdispersed,
indicating
nonindependent
evolution
mutations.
Empirical
evidence
for
underdispersion
was
previously
interpreted
as
global
epistasis,
we
recover
it
from
non-epistatic
model.
Annual Review of Biomedical Data Science,
Journal Year:
2024,
Volume and Issue:
7(1), P. 83 - 105
Published: April 26, 2024
Novel
sequencing
technologies
are
making
it
increasingly
possible
to
measure
the
mutation
rates
of
somatic
cell
lineages.
Accurate
germline
rate
measurement
have
also
been
available
for
a
decade,
assess
how
this
fundamental
evolutionary
parameter
varies
across
tree
life.
Here,
we
review
some
classical
theories
about
and
evolution
that
were
formulated
using
principles
population
genetics
biology
aging
cancer.
We
find
measurements,
while
still
limited
in
phylogenetic
diversity,
seem
consistent
with
theory
selection
preserve
soma
is
proportional
life
span.
However,
make
conflicting
predictions
regarding
which
species
should
most
accurate
DNA
repair.
Resolving
conflict
will
require
carefully
measuring
scale
time
division
achieving
better
understanding
pleiotropy
among
types.
Animal
genomes
exhibit
a
remarkable
variation
in
size,
but
the
evolutionary
forces
responsible
for
such
are
still
debated.
As
effective
population
size
(N
e
)
reflects
intensity
of
genetic
drift,
it
is
expected
to
be
key
determinant
fixation
rate
nearly-neutral
mutations.
Accordingly,
Mutational
Hazard
Hypothesis
postulates
lineages
with
low
N
have
bigger
genome
sizes
due
accumulation
slightly
deleterious
transposable
elements
(TEs),
and
those
high
maintain
streamlined
as
consequence
more
selection
against
TEs.
However,
existence
both
empirical
confirmation
refutation
using
different
methods
scales
precludes
its
general
validation.
Using
high-quality
public
data,
we
estimated
TE
content
non-synonymous
synonymous
substitutions
(dN/dS)
proxy
807
species
including
vertebrates,
molluscs
insects.
After
collecting
available
life-history
traits,
tested
associations
among
proxies,
while
accounting
phylogenetic
non-independence.
Our
results
confirm
TEs
major
drivers
variation,
endorse
traits
dN/dS
reliable
proxies
.
do
not
find
any
evidence
increased
drift
result
an
across
animals.
Within
closely
related
clades,
only
few
isolated
weak
emerge
fishes
birds.
outline
scenario
where
dynamics
vary
according
lineage-specific
patterns,
lending
no
support
predominant
force
driving
long-term
evolution
Systematic Biology,
Journal Year:
2023,
Volume and Issue:
72(6), P. 1357 - 1369
Published: Sept. 12, 2023
The
evolutionary
implications
and
frequency
of
hybridization
introgression
are
increasingly
being
recognized
across
the
tree
life.
To
detect
from
multi-locus
genome-wide
sequence
data,
a
popular
class
methods
based
on
summary
statistics
subsets
3
or
4
taxa.
However,
these
often
carry
assumption
constant
substitution
rate
lineages
genes,
which
is
commonly
violated
in
many
groups.
In
this
work,
we
quantify
effects
variation
D
test
(also
known
as
ABBA-BABA
test),
D3
test,
HyDe.
All
tests
used
widely
range
taxonomic
groups,
part
because
they
very
fast
to
compute.
We
consider
species
lineages,
their
lineage-by-gene
interaction,
gene-tree
edges.
simulated
networks
according
birth-death-hybridization
process,
so
capture
realistic
phylogenies.
For
all
tested,
found
marked
increase
false
discovery
reticulation
(type-1
error
rate)
when
there
lineages.
was
most
sensitive,
with
around
80%
type-1
error,
such
that
appears
more
sensitive
departure
clock
than
presence
reticulation.
tests,
power
events
decreased
number
increased,
indicating
multiple
can
obscure
one
another
if
occur
within
small
subset
Our
study
highlights
need
using
site-based
statistics,
points
advantages
do
not
require
assumptions
rates
genes.