Easy‐to‐use R functions to separate reduced‐representation genomic datasets into sex‐linked and autosomal loci, and conduct sex assignment
Molecular Ecology Resources,
Год журнала:
2023,
Номер
unknown
Опубликована: Авг. 1, 2023
Identifying
sex-linked
markers
in
genomic
datasets
is
important
because
their
presence
supposedly
neutral
autosomal
can
result
incorrect
estimates
of
genetic
diversity,
population
structure
and
parentage.
However,
detecting
loci
be
challenging,
available
scripts
neglect
some
categories
variation.
Here,
we
present
new
R
functions
to
(1)
identify
separate
ZW
XY
sex
determination
systems
(2)
infer
the
individuals
based
on
these
loci.
We
tested
data
for
two
bird
one
mammal
species
compared
biological
inferences
made
before
after
removing
using
our
function.
found
that
function
identified
with
≥98.8%
accuracy
an
average
87.8%.
showed
standard
filters,
such
as
low
read
depth
call
rate,
failed
remove
up
54.7%
This
led
(i)
overestimation
FIS
by
24%,
number
private
alleles
8%;
(ii)
wrongly
inferring
significant
differences
heterozygosity;
(iii)
obscuring
(iv)
~11%
fewer
correct
parentages.
discuss
how
failure
lead
(e.g.
sex-biased
dispersal
cryptic
structure)
misleading
management
recommendations.
For
reduced-representation
at
least
15
known-sex
each
sex,
offer
convenient
resources
remaining
(freely
https://github.com/drobledoruiz/conservation_genomics).
Язык: Английский
Reproductive characteristics, population genetics, and pairwise kinship inform strategic recovery of a plant species in a fragmented landscape
Conservation Science and Practice,
Год журнала:
2023,
Номер
5(4)
Опубликована: Фев. 22, 2023
Abstract
Population
genetics
and
understanding
of
mating
systems
provide
fundamental
information
for
conservation
planning.
Pairing
these
methods
is
a
powerful
tool
in
the
study
threatened
species,
however,
they
are
rarely
applied
concert.
We
examined
system
used
molecular
to
measure
pairwise
kinship
potential
inbreeding
Hibbertia
spanantha
,
critically
endangered
long‐lived
shrub
endemic
Sydney
Basin,
Australia,
as
model
planning
species
highly
fragmented
populations.
In
situ
hand
pollination
experiments
demonstrated
that
preferentially
outcrossing,
with
limited
ability
self‐pollinate
(either
autogamously
or
geitonogamously).
Although
population
confirmed
high
levels
clonality,
there
currently
enough
heterozygosity
successful
open
pollination,
primarily
through
buzz
by
Sweat
Bees
(
Lasioglossum
[Chilalictus
]).
High
clonality
one
may
be
cause
reduced
fitness,
identified
because
our
outcrossing
treatment
produced
significantly
more
seeds
greater
viability
seed
mass
than
treatments.
Differences
weight
filled
(viable)
were
between
populations,
although
not
treatments,
where
clonal
dominance
swamping
pollinator
foraging
activities.
Identification
system,
reproductive
capacity,
impacts
fragmentation
on
genetic
health
provides
robust
basis
strategic
this
including
establishment
an
ex
rescue
augmentation.
These
easily
applicable
particularly
relevant
other
plant
small
populations
those
occurring
systems.
Язык: Английский
Genetic diversity assessment of Helichrysum arenarium (Asteraceae) for the genetic restoration of declining populations
Ecology and Evolution,
Год журнала:
2024,
Номер
14(2)
Опубликована: Фев. 1, 2024
(L.)
Moench
(Asteraceae)
is
a
self-compatible,
insect-pollinated
herb
occurring
in
sand
grasslands,
and
declining
endangered
many
parts
of
its
European
distribution
range.
A
recovery
plan
Язык: Английский
Maternal effects and inbreeding depression in post‐translocation progeny of Campanula glomerata
Plant Biology,
Год журнала:
2024,
Номер
26(3), С. 427 - 436
Опубликована: Март 1, 2024
Evaluation
of
plant
translocation
success
based
on
fitness-related
quantitative
traits
combined
with
molecular
markers
may
contribute
to
a
finer
assessment
inbreeding,
selective
and
rescue
processes,
which
might
have
long-term
consequences
for
population
dynamics
viability.
We
investigated
fitness
(seed
germination,
seedling
viability,
juvenile
growth
mortality)
15
microsatellite
loci
the
first
post-translocation
seed
progeny
from
two
translocated
populations
Campanula
glomerata,
an
insect-pollinated,
self-incompatible
perennial
herb.
examined
whether
heterosis
through
admixture,
site
maternal
transplant
source
origin
lineage
affect
quality
in
controlled
cultivation
conditions.
Flower
production
germination
transplants
was
higher
one
sites,
be
related
differences
soil
vegetation
composition
cover.
Strong
effects
were
found
size,
largest
producing
progeny.
The
rosette
diameter
maintained
across
whole
period
measured.
There
inbreeding
depression
(rather
than
heterosis)
biparental
at
early
stage,
also
expressed
mortality.
Our
findings
highlight
that
origin,
especially
when
sources
consisted
small,
fragmented
remnants,
value
generations.
If
persist,
they
global
genetic
diversity
patterns
long
term.
Further
admixture
next
generations
buffer
or
lead
outbreeding
depression.
Язык: Английский
Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex-assignment
Authorea (Authorea),
Год журнала:
2022,
Номер
unknown
Опубликована: Дек. 2, 2022
Identifying
sex-linked
markers
in
genomic
datasets
is
important,
because
their
analyses
can
reveal
sex-specific
biology,
and
presence
supposedly
neutral
autosomal
result
incorrect
estimates
of
genetic
diversity,
population
structure
parentage.
But
detecting
loci
be
challenging,
available
scripts
neglect
some
categories
variation.
Here,
we
present
new
R
functions
to
(1)
identify
separate
ZW
XY
sex
determination
systems
(2)
infer
the
individuals
based
on
these
loci.
Two
additional
are
presented,
(3)
remove
with
artefactually
high
heterozygosity,
(4)
produce
input
files
for
parentage
analysis.
We
test
data
two
sexually-monomorphic
bird
species,
including
one
a
neo-sex
chromosome
system,
by
comparing
biological
inferences
made
before
after
removing
using
our
function.
found
that
standard
filters,
such
as
low
read
depth
call
rate,
failed
up
28.7%
This
led
(i)
overestimation
FIS
≤
9%,
number
private
alleles
8%;
(ii)
wrongly
inferring
significant
sex-differences
(iii)
obscuring
structure,
(iv)
~11%
fewer
correct
parentages.
discuss
how
failure
lead
(e.g.,
sex-biased
dispersal
cryptic
structure)
misleading
management
recommendations.
For
reduced-representation
at
least
15
known-sex
each
sex,
offer
convenient,
easy-to-use
resources
avoid
this,
remaining
individuals.
Язык: Английский
Assessing spatial mating patterns in translocated populations of Campanula glomerata
Global Ecology and Conservation,
Год журнала:
2023,
Номер
46, С. e02548 - e02548
Опубликована: Июнь 19, 2023
Plant
translocations
represent
a
solution
for
rescuing
nonviable
populations
and
recreating
population
networks.
An
essential
criterion
translocation
success
is
genetic
diversity
enhancement
or
maintenance
in
post-translocation
generations.
Genetic
mixing,
i.e.
individual
relatedness
spatial
structure,
also
needs
to
be
considered.
We
investigated
the
processes
involved
patterns
of
first
generation
(recruits
seed
progeny)
translocated
insect-pollinated,
self-incompatible
herb
Campanula
glomerata.
combined
direct
indirect
estimates
contemporary
mating
gene
dispersal
using
15
microsatellite
loci
estimate
clonal
extent,
reconstruct
sibship
parentage
pollen
distances.
representative
natural
seed-source
populations.
Combining
sources
enhanced
effective
number
breeders
(Ne
=
102–175).
Clonal
propagation
was
only
marginal.
Pollen
occurred
at
short
distances
within
(up
18
m),
favouring
fine-scale
structure
(SGS).
This
means
that
diversity,
random
high
admixture
levels
are
ascribed
mixed
arrangement
transplants.
Stronger
SGS
might
lead
biparental
inbreeding
reduced
set
due
lack
compatible
neighbours,
impact
long-term
sustainability.
Increasing
seed-dispersal
among
sites
mediated
by
grazing
livestock
used
grassland
management.
Some
long-distance
flow
events
(0.68–2.35
km)
between
were
detected,
suggesting
potential
creating
large
restore
connectivity
flow.
Язык: Английский