Philosophical Transactions of the Royal Society B Biological Sciences,
Journal Year:
2020,
Volume and Issue:
375(1808), P. 20190602 - 20190602
Published: Aug. 9, 2020
Across
the
tree
of
life,
hosts
have
evolved
mechanisms
to
control
and
mediate
interactions
with
symbiotic
partners.
We
suggest
that
evolution
physical
structures
allow
spatially
separate
symbionts,
termed
compartmentalization,
is
a
common
mechanism
used
by
hosts.
Such
compartmentalization
allows
to:
(i)
isolate
symbionts
their
reproduction;
(ii)
reward
cooperative
punish
or
stop
non-cooperative
symbionts;
(iii)
reduce
direct
conflict
among
different
strains
in
single
host.
Compartmentalization
has
allowed
increase
benefits
they
obtain
from
partners
across
diversity
interactions,
including
legumes
rhizobia,
plants
fungi,
squid
Vibrio
,
insects
nutrient
provisioning
bacteria,
insects,
human
microbiome.
In
cases
where
not
evolved,
we
ask
why
not.
argue
when
interact
competitive
hierarchy,
engage
partnerships
which
are
less
costly,
likely
evolve.
conclude
key
understanding
cooperation.
This
article
part
theme
issue
‘The
role
microbiome
host
evolution’.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Journal Year:
2020,
Volume and Issue:
70(7), P. 3956 - 4042
Published: July 1, 2020
We
here
present
annotated
lists
of
names
Candidatus
taxa
prokaryotes
with
ranks
between
subspecies
and
class,
proposed
the
mid-1990s,
when
provisional
status
was
first
established,
end
2018.
Where
necessary,
corrected
are
that
comply
current
provisions
International
Code
Nomenclature
Prokaryotes
its
Orthography
appendix.
These
lists,
as
well
updated
newly
published
additions
corrections
to
be
periodically
in
Journal
Systematic
Evolutionary
Microbiology,
may
serve
basis
for
valid
publication
if
proposals
expand
type
material
naming
also
include
gene
sequences
yet-uncultivated
is
accepted
by
Committee
on
Systematics
Prokaryotes.
F1000Research,
Journal Year:
2017,
Volume and Issue:
6, P. 1287 - 1287
Published: July 31, 2017
The
goal
of
many
genome
sequencing
projects
is
to
provide
a
complete
representation
target
(or
genomes)
as
underpinning
data
for
further
analyses.
However,
it
can
be
problematic
identify
which
sequences
in
an
assembly
truly
derive
from
the
genome(s)
and
are
derived
associated
microbiome
or
contaminant
organisms.
We
present
BlobTools,
modular
command-line
solution
visualisation,
quality
control
taxonomic
partitioning
datasets.
Using
guanine+cytosine
content
sequences,
read
coverage
libraries
taxonomy
sequence
similarity
matches,
BlobTools
assist
primary
data,
leading
improved
assemblies,
screening
final
assemblies
potential
contaminants.
Through
simulated
paired-end
dataset,s
containing
mixture
metazoan
bacterial
taxa,
we
illustrate
main
workflow
suggest
useful
parameters
low-complexity
metagenome
assemblies.
Molecular Ecology,
Journal Year:
2016,
Volume and Issue:
26(8), P. 2212 - 2236
Published: Dec. 20, 2016
The
study
of
reproductive
isolation
and
species
barriers
frequently
focuses
on
mitochondrial
genomes
has
produced
two
alternative
almost
diametrically
opposed
narratives.
On
one
hand,
mtDNA
may
be
at
the
forefront
speciation
events,
with
co-evolved
mitonuclear
interactions
responsible
for
some
earliest
genetic
incompatibilities
arising
among
isolated
populations.
other
there
are
numerous
cases
introgression
across
boundaries
even
when
nuclear
gene
flow
is
restricted.
We
argue
that
these
seemingly
contradictory
patterns
can
result
from
a
single
underlying
cause.
Specifically,
accumulation
deleterious
mutations
in
creates
problem
evolutionary
solutions.
In
cases,
compensatory
or
epistatic
changes
genome
ameliorate
effects
mutations,
thereby
establishing
coadapted
genotypes
within
populations
forming
basis
between
Alternatively,
high
mutation
loads
rescued
by
replacement
more
fit,
foreign
haplotype.
Coupled
many
nonadaptive
mechanisms
preferentially
affect
cytoplasmic
genomes,
this
form
adaptive
contribute
to
widespread
discordance
genealogies.
Here,
we
review
recent
advances
related
incompatibilities,
including
potential
cointrogression
interacting
genes.
also
address
an
emerging
controversy
over
classic
assumption
selection
inefficient
discuss
lead
lineages
down
paths
response
accumulation.
Molecular Ecology,
Journal Year:
2017,
Volume and Issue:
26(11), P. 2905 - 2921
Published: March 10, 2017
Abstract
Ecological
specialization
to
restricted
diet
niches
is
driven
by
obligate,
and
often
maternally
inherited,
symbionts
in
many
arthropod
lineages.
These
heritable
typically
form
evolutionarily
stable
associations
with
arthropods
that
can
last
for
millions
of
years.
Ticks
were
recently
found
harbour
such
an
obligate
symbiont,
Coxiella
‐
LE
,
synthesizes
B
vitamins
cofactors
not
obtained
sufficient
quantities
from
blood
diet.
In
this
study,
the
examination
81
tick
species
shows
some
symbioses
are
ancient
acquisition
followed
codiversification
as
observed
ticks
belonging
Rhipicephalus
genus.
However,
other
characterized
low
evolutionary
stability
frequent
host
shifts
extinction
events.
Further
revealed
presence
nine
genera
inherited
bacteria
ticks.
Although
these
primarily
thought
be
facultative,
their
distribution
among
rather
suggests
at
least
four
may
have
independently
replaced
likely
represent
alternative
symbionts.
Phylogenetic
evidence
otherwise
indicates
cocladogenesis
globally
rare
most
originate
via
horizontal
transfer
existing
symbiont
between
unrelated
species.
As
a
result,
structure
communities
fixed
across
phylogeny.
Most
importantly,
commonly
reach
high
levels
diversity
up
six
coexisting
within
We
further
conjecture
interactions
pivotal
drivers
community
both
