Bulletin of the Society of Systematic Biologists,
Год журнала:
2023,
Номер
2(1), С. 1 - 35
Опубликована: Дек. 8, 2023
Biologists
and
philosophers
of
science
have
been
unable
to
fully
resolve
the
decades-long
controversy
as
what
kind
unit
living
biodiversity
should
receive
valued
label
“species”:
reproductive
communities
(among
sexual
organisms),
genealogical
groups,
or
clusters
organisms
that
share
traits.
Among
these
choices,
which
represent
a
spectrum
from
process
history
observable
outcome
(respectively),
latter
(more
operationalist)
concepts
are
not
viable.
Species
must
embody
imply
cohesive
integrating
processes
such
interbreeding
shared
ecological
pressures
if
they
sufficient
power
bear
burden
we
give
them:
predict
explain
traits
across
genome
among
organisms.
This
commitment
is
needed
whether
biologists
use
species
taxonomic
containers
synthesize
data,
minimal
phylogenetic
units,
actors
in
evolutionary
diversification.
These
varied
uses
can
be
satisfied
via
concept
community,
but
strict
Biological
Concept
(BSC).
Its
two
drawbacks
focus
on
contemporary
restriction
intrinsic
factors.
Current
compatibility
may
future
matings,
it
does
well
genes
already
have.
The
alive
today
were
shaped
by
isolating
factors
past,
those
present,
whatever
extent
differ.
most
broadly-useful
therefore
see
retrospectively,
past.
As
well,
BSC’s
exclusion
extrinsic
renders
each
its
units
incomplete
explanation
synthesis.
Reproductive
nature
isolated
just
(genetic)
differences,
also
purely
(e.g.,
geographic)
Such
real,
natural
entities
whose
integrated
self-reinforcing
constrained
descent
aligned
distribution
many
Retrospective
Community
(RRCC),
formalized
mathematically
multispecies
coalescent
models,
justifies
traditional
practice
taxonomists
using
morphological
data
seek
echoes
past
cohesion.
However,
naturally
deserve
ranked
species,
demes
populations,
vexing
question.
There
no
natural,
discrete
broadly
informative
rank
applies
universally,
perhaps
even
usually.
To
justified,
justified
for
asexual
sexuals.
presence
absence
sex
one
example
variability
confront.
Because
vary
clades,
useful
broadly-applicable
cannot
specify
detailed
mechanisms.
Nor
perfectly
align
named
taxonomy
with
evolution,
because
structured
match
taxonomy’s
partition
boxes.
Taxonomic
approximate,
only
units.
Settling
retrospection,
letting
go
meaning
rank,
accepting
approximation
allow
biology
turn
far
more
daunting
task:
listening
world
understand
interacting
built
distinction
identity,
emerging
out
into
present
day.
Frontiers in Marine Science,
Год журнала:
2023,
Номер
10
Опубликована: Июнь 8, 2023
As
the
global
ocean
continues
to
experience
consequences
of
an
increase
in
frequency
and
intensity
heat
waves,
trend
is
expected
persist
into
21st
century,
with
a
projected
tripling
waves
by
2040.
This
phenomenon
poses
significant
threat
marine
ecosystems
survival
organisms,
including
ecologically
economically
vital
bivalves.
Bivalves
are
vulnerable
harm
from
stress
at
various
levels
biological
organization,
their
growth
can
be
negatively
impacted
high
temperatures,
potentially
leading
mass
mortalities
posing
ecosystem
quality
food
security.
In
light
these
concerns,
this
review
aims
provide
comprehensive
examination
effects
on
It
summarizes
physiological
biochemical
changes
that
bivalves
undergo
response
extreme
events
offers
overview
strategies
they
employ
mitigate
impacts.
A
better
understanding
underlying
mechanisms
bivalve
responses
crucial
order
fully
appreciate
impact
organisms.
synthesizes
current
knowledge
highlights
importance
further
research
area.
By
providing
during
use
its
impact,
support
development
more
effective
approaches
minimize
PLoS Genetics,
Год журнала:
2024,
Номер
20(1), С. e1011110 - e1011110
Опубликована: Янв. 18, 2024
In
the
presence
of
recombination,
evolutionary
relationships
between
a
set
sampled
genomes
cannot
be
described
by
single
genealogical
tree.
Instead,
are
related
complex,
interwoven
collection
genealogies
formalized
in
structure
called
an
ancestral
recombination
graph
(ARG).
An
ARG
extensively
encodes
ancestry
genome(s)
and
thus
is
replete
with
valuable
information
for
addressing
diverse
questions
biology.
Despite
its
potential
utility,
technological
methodological
limitations,
along
lack
approachable
literature,
have
severely
restricted
awareness
application
ARGs
evolution
research.
Excitingly,
recent
progress
reconstruction
simulation
made
ARG-based
approaches
feasible
many
systems.
this
review,
we
provide
accessible
introduction
exploration
ARGs,
survey
breakthroughs,
describe
to
further
existing
goals
open
avenues
inquiry
that
were
previously
inaccessible
genomics.
Through
discussion,
aim
more
widely
disseminate
promise
genomics
encourage
broader
development
adoption
inference.
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2024,
Номер
16(12), С. a041445 - a041445
Опубликована: Март 4, 2024
Joshua
V.
Peñalba1,
Anna
Runemark2,
Joana
I.
Meier3,4,
Pooja
Singh5,6,
Guinevere
O.U.
Wogan7,
Rosa
Sánchez-Guillén8,
James
Mallet9,
Sina
J.
Rometsch10,11,
Mitra
Menon12,
Ole
Seehausen5,6,
Jonna
Kulmuni13,14,16
and
Ricardo
Pereira15,16
1Museum
für
Naturkunde,
Leibniz
Institute
for
Evolution
Biodiversity
Science,
Center
Integrative
Discovery,
10115
Berlin,
Germany
2Department
of
Biology,
Lund
University,
22632
Lund,
Sweden
3Tree
Life,
Wellcome
Sanger
Institute,
Hinxton,
Cambridgeshire
CB10
1SA,
United
Kingdom
4Department
Zoology,
University
Cambridge,
CB2
3EJ,
5Department
Aquatic
Ecology,
Ecology
Evolution,
Bern,
3012
Switzerland
6Center
&
Biogeochemistry,
Swiss
Federal
Science
Technology
(EAWAG),
CH-8600
Kastanienbaum,
7Department
Oklahoma
State
Stillwater,
74078,
USA
8Red
de
Biología
Evolutiva,
INECOL,
Xalapa,
Veracruz,
CP
91073,
Mexico
9Organismal
Evolutionary
Harvard
Massachusetts
02138,
10Department
Yale
New
Haven,
Connecticut
06511,
11Yale
Biospheric
Studies,
12Department
California
Davis,
95616,
13Department
Population
Ecosystem
Dynamics,
Amsterdam,
1098
XH
The
Netherlands
14Organismal
Biology
Research
Programme,
Helsinki,
Biocenter
3,
Finland
15Department
Museum
Natural
History
Stuttgart,
Stuttgart
70191,
Correspondence:
ricardojn.pereira{at}gmail.com
↵16
These
authors
contributed
equally
to
this
work.
Plant Communications,
Год журнала:
2023,
Номер
4(5), С. 100599 - 100599
Опубликована: Апрель 12, 2023
Studies
of
plants
have
been
instrumental
for
revealing
how
new
species
originate.
For
several
decades,
botanical
research
has
complemented
and,
in
some
cases,
challenged
concepts
on
speciation
developed
via
the
study
other
organisms
while
also
additional
ways
which
can
form.
Now,
ability
to
sequence
genomes
at
an
unprecedented
pace
and
scale
allowed
biologists
settle
decades-long
debates
tackle
emerging
challenges
research.
Here,
we
review
these
recent
genome-enabled
developments
plant
speciation.
We
discuss
complications
related
identification
reproductive
isolation
(RI)
loci
using
analyses
landscape
genomic
divergence
highlight
important
role
that
structural
variants
speciation,
as
increasingly
revealed
by
sequencing
technologies.
Further,
genomics
advanced
what
know
routes
formation,
like
hybridization
or
whole-genome
duplication,
casting
doubt
others,
population
bottlenecks
genetic
drift.
While
fast-track
genes
mutations
confer
RI,
emphasize
follow-up
molecular
field
experiments
remain
critical.
Nonetheless,
clarified
outsized
ancient
rather
than
mutations,
particularly
early
during
conclude
highlighting
promising
avenues
future
study.
These
include
expanding
so
far
about
epigenetic
changes
broadening
scope
taxonomic
breadth
studies,
synthesizing
information
from
extensive
data
already
generated
community.
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2023,
Номер
16(3), С. a041446 - a041446
Опубликована: Дек. 5, 2023
Emma
L.
Berdan1,2,
Thomas
G.
Aubier3,4,
Salvatore
Cozzolino5,
Rui
Faria6,7,
Jeffrey
Feder8,
Mabel
D.
Giménez9,10,
Mathieu
Joron11,
Jeremy
B.
Searle12
and
Claire
Mérot13
1Department
of
Marine
Sciences,
Gothenburg
University,
40530,
Sweden
2Bioinformatics
Core,
Department
Biostatistics,
Harvard
T.H.
Chan
School
Public
Health,
Medical
School,
Boston,
Massachusetts
02115,
USA
3Laboratoire
Évolution
&
Diversité
Biologique,
Université
Paul
Sabatier
Toulouse
III,
UMR
5174,
CNRS/IRD,
31077
Toulouse,
France
4Department
Biology,
University
North
Carolina
at
Chapel
Hill,
27599,
5Department
Naples
Federico
II,
Complesso
Universitario
di
Monte
S.
Angelo,
80126
Napoli,
Italia
6CIBIO,
Centro
de
Investigação
em
Biodiversidade
e
Recursos
Genéticos,
InBIO,
Laboratório
Associado,
Universidade
do
Porto,
Vairão,
Portugal
7BIOPOLIS
Program
in
Genomics,
Biodiversity
Land
Planning,
CIBIO,
4485-661
8Department
Biological
Notre
Dame,
Indiana
46556,
9Consejo
Nacional
Investigaciones
Científicas
y
Técnicas
(CONICET),
Instituto
Genética
Humana
Misiones
(IGeHM),
Parque
la
Salud
Provincia
"Dr.
Ramón
Madariaga,"
N3300KAZ
Posadas,
Misiones,
Argentina
10Facultad
Ciencias
Exactas,
Químicas
Naturales,
Universidad
N3300LQH
11Centre
d'Ecologie
Fonctionnelle
et
Evolutive,
Montpellier,
CNRS,
EPHE,
IRD,
12Department
Ecology
Evolutionary
Cornell
Ithaca,
New
York
14853,
13CNRS,
6553
Ecobio,
OSUR,
Rennes,
35000
Correspondence:
claire.merot{at}gmail.com;
emma.berdan{at}gmail.com
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2023,
Номер
16(9), С. a041440 - a041440
Опубликована: Дек. 27, 2023
Ecologically
mediated
selection
against
hybrids,
caused
by
hybrid
phenotypes
fitting
poorly
into
available
niches,
is
typically
viewed
as
distinct
from
epistatic
Dobzhansky-Muller
incompatibilities.
Here,
we
show
how
transgressive
in
hybrids
manifests
incompatibility.
After
outlining
our
logic,
summarize
current
approaches
for
studying
ecology-based
on
hybrids.
We
then
quantitatively
review
QTL-mapping
studies
and
find
traits
differing
between
parent
taxa
are
polygenic.
Next,
describe
verbal
models
of
translate
to
phenotypic
genetic
fitness
landscapes,
highlighting
emerging
detecting
polygenic
Finally,
a
synthesis
published
data,
report
that
trait
transgression-and
thus
possibly
extrinsic
incompatibility
hybrids-escalates
with
the
divergence
parents.
discuss
conceptual
implications
conclude
ecological
basis
will
facilitate
new
discoveries
about
mechanisms
speciation.
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2023,
Номер
15(10), С. a041607 - a041607
Опубликована: Сен. 11, 2023
Radka
Reifová1,
S.
Lorena
Ament-Velásquez2,
Yann
Bourgeois3,
Jenn
Coughlan4,
Jonna
Kulmuni5,6,
Agnieszka
P.
Lipinska7,8,
Genta
Okude9,
Laurie
Stevison10,
Kohta
Yoshida9
and
Jun
Kitano9
1Department
of
Zoology,
Faculty
Science,
Charles
University,
128
00
Prague,
Czech
Republic
2Department
Stockholm
106
91
Stockholm,
Sweden
3DIADE,
University
Montpellier,
CIRAD,
IRD,
34090
France
4Department
Ecology
&
Evolutionary
Biology,
Yale
New
Haven,
Connecticut
06520,
USA
5Institute
for
Biodiversity
Ecosystem
Dynamics,
Department
Population
Amsterdam,
1012
The
Netherlands
6Organismal
Biology
Research
Programme,
Helsinki,
00100
Finland
7Department
Algal
Development
Evolution,
Max
Planck
Institute
72076
Tuebingen,
Germany
8CNRS,
UMR
8227,
Integrative
Marine
Models,
Sorbonne
Université,
Station
Biologique
de
Roscoff,
29680
9Department
Genomics
National
Genetics,
Mishima,
Shizuoka
411-8540,
Japan
10Department
Biological
Sciences,
Auburn
Auburn,
Alabama
36849,
Correspondence:
radka.reifova{at}natur.cuni.cz;
jkitano{at}nig.ac.jp
Molecular Ecology Resources,
Год журнала:
2024,
Номер
24(4)
Опубликована: Фев. 28, 2024
Abstract
Characterizing
the
processes
underlying
reproductive
isolation
between
diverging
lineages
is
central
to
understanding
speciation.
Here,
we
present
RIDGE—Reproductive
Isolation
Detection
using
Genomic
polymorphisms—a
tool
tailored
for
quantifying
gene
flow
barrier
proportion
and
identifying
relevant
genomic
regions.
RIDGE
relies
on
an
Approximate
Bayesian
Computation
with
a
model‐averaging
approach
accommodate
diverse
scenarios
of
lineage
divergence.
It
captures
heterogeneity
in
effective
migration
rate
along
genome
while
accounting
variation
linked
selection
recombination.
The
detection
test
numerous
summary
statistics
compute
Bayes
factor,
offering
robust
statistical
framework
that
facilitates
cross‐species
comparisons.
Simulations
revealed
RIDGE's
efficiency
capturing
signals
ongoing
migration.
Model
averaging
proved
particularly
valuable
high
model
uncertainty
where
no
or
homogeneity
can
be
wrongly
assumed,
typically
recent
divergence
times
<0.1
2
N
e
generations.
Applying
four
published
crow
data
sets,
first
validated
our
by
well‐known
large
region
associated
mate
choice
patterns.
Second,
identified
significant
overlap
outlier
loci
traditional
scans,
results
suggest
substantial
portion
previously
outliers
are
likely
false
positives.
Outlier
allele
differentiation,
relative
measures
count
shared
polymorphisms
fixed
differences.
Our
analyses
also
highlight
value
incorporating
multiple
including
newly
developed
ones
useful
challenging
conditions.
Proceedings of the National Academy of Sciences,
Год журнала:
2022,
Номер
119(30)
Опубликована: Июль 18, 2022
Microbial
communities
are
found
throughout
the
biosphere,
from
human
guts
to
glaciers,
soil
activated
sludge.
Understanding
statistical
properties
of
such
diverse
can
pave
way
elucidate
common
mechanisms
...Multiple
ecological
forces
act
together
shape
composition
microbial
communities.
Phyloecology
approaches—which
combine
phylogenetic
relationships
between
species
with
community
ecology—have
potential
disentangle
but
often
...