Download Cladistic analyses of molecular characters

Contributions
Cladistic
analyses of molecular characters:
The
71
Zoology,
to
SPB Academic
(1/3)
93-100
(2002)
The
Hague
Publishing bv,
and the
good, the bad
ugly
Maximilian+J. Telford
Museum
University
email:
of Zoology, Department of Zoology, Downing Street, Cambridge
Keywords: molecular synapomorphy, phylogeny,
rare
Abstract
heritable
that
racter.
molecular
is
a traditional
Taxa
that
an
other than
point
they
out
problems
are
that molecular
treat
derived
specific
to other taxa
as more
and illustrate
a
treated
characters
are
which
in
molecular
closely
genomic change, RGC, Metazoa, cladistics
susceptible
as
Herein,
to the
The
same
morphological
towards
a
from the Metazoa.
genetic
ods of
Contents
ing.
Mitochondrial
acoel
in
gene
the EF1
94
apparent
Mitochondrial genetic
Indels
codes
order in
alpha
gene
94
birds
95
and the position
of the
flatworms
gene
fusions
with
96
due to
secondary
loss
of
a
novel domain combinations
aligned
approach
and
a
genetic codes:
96
the
-
the
in the
gene
signatures:
Conclusions
that is
Rather,
complemen-
heritable characteristics
variety
of characters
way that
same
a
deal
amino acids
or
this
not
of the
used
is
cladist would
morphological character. In such molecular
cladistic
studies,
character
(synapomorphies)
sharing
taxa
closely related
lacking
this
novel
a
to each other than
As
character.
in
derived
or
inferred
are
they
to
be
are
more
to taxa
morphology-based
plesiomorphy)
close
be
cannot
as
indicator of
an
relationship.
tics used to date have been covered in
Rokas and
by
Holland
touched
on
some
of their
97
the
taken
an
excellent
who also
(2000),
echinoderms
hemichordates
the priapulids
does
appreciated
manner.
treats
and
-
steadily improv-
of nucleotides
sequences
in the
customary
review
Mitochondrial
are
phylogenetics
Examples of the diverse molecular characteris-
charac-
Polarity
Hox
increasingly
ever
cladistics, the sharing of a primitive character
(sym95
Introns
Apparent homoplasy
Molecular
faster and meth-
95
Contradictory stories from
and
accumulating
93
and
steady expansion
phylogenetics.
One strand of molecular
becoming
use
real
the
seen
phylogenetic analysis
impressive
Introduction
years have
data are
genome
Homoplasy:
15
past
of the field of molecular
tary
ter:
UK;
cha-
characters
characters.
polarity
any
same
related to each
these problems (and point
general solution) using examples
the
morphological
without these
of homoplasy and uncertain
characters
be
can
cladist would
share
in
emerging discipline
characteristic
(synapomorphies) are recognized
I
3EJ,
Introduction
cladistics
Molecular
way
CB2
[email protected]
dicyemid
examine in
more
shortcomings.
detail the
mesozoans
98
using Molecular Synapomorphies
99
Rare
Acknowledgments
99
References
99
Genomic
Holland).
some
I will
suffer
Changes
show
from
the
-
1
want
potential pitfalls
RGCs
(referred
-
assessment
as
by
that, perhaps unsurprisingly,
same
problems
as
morphological characters, lies in
homology
to
Rokas and
morpho-
logical characteristics but that their strength,
tive to
to
when
the
rela-
ease
of molecular characters.
of
94
M.J.
real and
Homoplasy:
1 would like to
distinction between real and apparent
a
ho-
moplasy. Homoplasy entails the parallel evolution
of a
character state in
particular
through
eages
sion. In truth, because most
in
arise
ters
unrelated lin-
two
parallelism
convergence,
type, it is highly unlikely that
but
fact
pheno-
in
moplasy. The homoplasy problem arises because
we
can
rarely know enough about
character (for
molecular
tic bristle
example
developmental basis for
on
fly’s leg)
a
morphological
a
investigate
cannot
we
phological analyses generally have
identity.
rely
to
the
diagnos-
every
ascertain
to
on
Mor-
overall
strength of phylogenetic signal within the totality
of the data
the
set
to
reveal
homoplasy in (hopefully)
minority of characters.
Traditional molecular
analysis of molecular characters
genetic code,
a
of the
genome
significant
It
event.
the
hundreds (or in the
of
case
of
specificity
the anticodon of
or
a
small
hugely
for
happen suddenly,
cannot
example by changing
synthetase
that of the
even
eukaryotic mitochondrion, is
a
tRNA,
tRNA
a
tens
as
or
nuclear genome many
a
thousands) of amino acids would be swapped and
this would affect almost every
be lethal. The
protein and would
likely mechanism for
more
change is, rather, the gradual,
apparent ho-
to
Changing
certainly
mor-
appear identical
leading
unrelated
a
independently
character could arise
in
are
to
truly identical
a
lineages. Characters only
separate
fashion
to alterations
developmental pathways and finally
phological
rever-
morphological charac-
involving genotypic changes leading
in
or
immensely complicated
an
Cladistic
Mitochondrial genetic codes
apparent
For the purposes of this discussion
make
-
Telford
certain
codon followed
Castresana et
al.,
its
by
in
gradual reintroduction
complete loss of
its
Even
1998).
happen
guise (see
the
so,
clearly immensely complex and
potential
less
to
likely, there
can
be
of 19 others (or
likely,
equally
happened,
there is
only
change would
a
from
to
changes
that
allowing
I
codon)
If all
stop codon).
even
to
reassign-
reassigned
the incumbent amino acid (or stop
same
unlikely
seems
64 codons with the
are
and each
change
e.g.
process is
often. To make convergent codon
ment even
and
reassignment
new
a
any
were
change has
a
in 1280 chance that the
in two
occur
independent lin-
phylogenetic efforts suffer
eages.
from the
with
opposite problem; it is usually
certainty
character
-
a
that
one
is
easy
with
dealing
to
know
Considering the unlikeliness
reassignment,
particular amino acid
at
a
particular
are
within
position
due
the low
to
for
protein,
a
diversity
of
However,
example.
potential character
multiple
is
or
amino
20
prevalent because,
independent
a
I
or
specific position in
in 20 chance,
two
1
a
ment of
two
codons
The
that the novel state
ought
identical.
synapomorphies'
of molecular
great strength
to be that
they avoid
both of these
Being molecularly based it is
identity between characters
easy
to
genotypic
See
layers,
“What
You
Is
and
What
moreover, because these characters
order of
tween
complexity
nucleotides
should not be
are
various
a
than
or
simple
species
problem. What
surprising
cases
we
a
higher
be-
homoplasy
find, however,
homoplasy af-
fecting these molecular characters and
of these below.
of
substitutions
of real
(Telford
et
and the
al., 2000).
reassignments
are seen:
In
the codon
reassigned from coding for Lysine
from
1 discuss
include UAA and UAG codons
STOP
to
being
Glutamine
-
You Get”
amino acids, real
echinoderms
independently reassigned from
development-
are
of the
coding for Asparagine and AUA reassigned
convergence
in
al
one
problems.
morphological cha-
racters with their hidden
eukaryotic
Perhaps
Methionine to Isoleucine. Other clear instances of
to be certain of
in different
with molecular characters, unlike
in the
flatworms
same
AAA has been
will be
nuclei.
even
in 4
both taxa the
respectively,
of this within
striking examples is the convergent reassign-
changes
taxa, there is
surprising
instances
rhabditophoran
at
convergent codon
to discover that there
states
acids) real homoplasy
given
it is
mitochondria and
most
(4 nucleotides
of
identical
an
some
the
nuclear genomes of
ciliates and the green
diplomonads,
several
alga Acetabularia acetabu-
lum and UGA reassigned from STOP
to
Tryptophan
five separate times in the mitochondria of various
eukaryotic
groups
(Knight
Fortunately, thanks
netic information,
we are
example,
are
eration of mitochondrial
sources
of
not mislead into
that the echinoderms and the
for
worms,
al., 2001).
et
to other
phylogebelieving
rhabditophoran
sister-groups,
flat-
but consid-
genetic codes highlights
Contributions
71
Zoology,
to
the need to understand how
it
to use
changes
ever
as
in
a
molecular
certain
changes
are
95
trait evolves if one is
a
equal; due
not
are
for whatever
or
2002
-
synapomorphy. Clearly
genetic code
constraint
(1/3)
more
likely
adaptive
all
what-
to
reasons,
than others.
to occur
discussed above instead
vertebrate code with
of the
sence
the
Rhabditophora.
result, Berney
Mitochondrial gene order in birds
is
arrangements
event. There
in
the
are
circular
which
also,
13
the face of it,
on
2
proteins,
ferent ways.
the
Despite
genome,
in 2*10 52 dif-
vanishingly
small
prob-
ability of independent adoption of any specific novel
it
arrangement,
ment
of three
contiguous
and Glutamic
drial control
occasions
al.,
has been shown that
region has occurred
at
on
1994). Of
from
least 4 separate
inversions of sections of
genomes have also been
and Palmer,
ment
to the mitochon-
the evolution of birds (Mindell
1998). Parallel
chloroplast
rearrange-
(Proline-tRNA, ND6,
genes
acid-tRNA) relative
during
a
course,
position A
to
et
plant
reported (Hoot
shifting
position
a
B
single frag-
has
et
In
al.
direct contradiction of this
found
(2000)
alpha
rhabditophoran
flatworms and
thors
Based
Once
able
the
again,
gene shared
on
an
a
short
by
one
acoel,
group
these
au-
Rhabditophora.
it turns
that wider
out
sampling
again
was
showed
importance of understanding the evolution
the character.
the
Littlewood
region of
same
cies
of acoel and
peptide motif.
of
in fact derived
are
resolve this contradiction and
to
peptide
Convoluta
this observation
that the acoels
suggested
from within the
and 22 tRN As
rRNAs,
theoretically be arranged
can
unlikely
an
mitochondrial
metazoan
gene
in-
The ab-
derived from within
not
are
motif in the EFI
roscoffensis.
Convergent evolution of novel mitochondrial
other animals.
rhabditophoran novelties demonstrates
that the acocls
clearly
sharing the standard
most
EF1
et
al.
alpha from
3
further spe-
found that all three
On
of
(2001) sequenced
the other hand,
lacked
the
menagerie of
a
other metazoans (molluscs, annelids, nematodes and
chordates) did have the character
mation. This
persuasive of
phoran
or
a
close
approxi-
particular character, although initially
a
link between acoels and rhabdito-
flatworms, proved
unreliable due
ho-
to
moplasy.
much
a
higher likelihood of convergence than suggested
by the probability quoted above, but the tendency
for repeated evolution of
ment
might also point
a
particular novel
to an
some
dense
prior knowledge
of bird
sampling and through
phylogcny.
assumption that parallel changes
gene order
caused
us
are
hugely unlikely
to reconstruct
an
in
An
a
priori
mitochondrial
could
incorrect
easily have
phylogcny.
In
the
example
cally
be
must
(3-thymosin
tide in the
be
gene
and the position
of the
acoel flatworms
triplicated
years.
other
flatworms, the
plete
gut,
the two
Although,
acoels lack
a
groups share
a
in
lot
showed
are
of contro-
coelom and
no
not
com-
other obvious
suggest
unrelated and Telford et al.
that the acoels do
with
common
features. Ribosomal RNA
phylogenies
two groups
and
we
one
On
as
the
a
have two
con-
of which
logi-
the
(2000)
share the rhabdito-
phoran flatworm mitochondrial
genetic code changes
hand, the
one
single
short
pep-
of metazoans, has been shown to
serially
arthropods (Manuel
seemingly
et
linked in nematodes and
al., 2000). This unusual char-
gives
Hypothesis'
strong
a
the
to
support
that postulates
clade of
moulting animals including nematodes and arthropods. On the other hand, the Glutamyl
The acoel flatworms have caused
recent
homoplastic.
majority
aminoacyl
versy in
below,
gene, which exists
Ecdysozoa
EF1alpha
I describe
molecular characters,
tradictory
acter
Indels in the
stories from gene
fusions
arrange-
underlying constraint.
Importantly, this constraint could only be inferred
through sufficiently
Contradictory
genes
in
and the
are
found
including
which
the yeast
plant Arabidopsis and also
to
tein in both
This
synthetases,
most taxa
ces
and
tRNA
be fused into
a
and
are
Prolyl
separate
Saccharomyin
nematodes,
single, bifunctional
pro-
arthropods and vertebrates (Bcrthonneau
Mirande,
finding
2000 and
seems
to
unpublished
Ecdysozoa Hypothesis, flies
to the vertebrates than
observations).
suggest that, contrary
they
are
are
more
closely
to
the
related
to the nematodes.
96
M.J.
Clearly
one
of these
two
characters must be homoand nematodes
plastic. Perhaps arthropods
deed ecdysozoan
nematodes have reverted to
the
for
RNA
two
in which
sister-groups,
if the
coelomate vertebrates
either is
the
to the
and
convergently.
On
or
has been
then
correct
share
not
closely related
than
todes,
then
unique domain combinations.
lost in
secondarily
What
find is
we
taxa is needed
from
worms
one
of these
characters is
look
for all
the
Meanwhile,
homoplastic.
be the result of very
rare
of them must indeed
point is made that,
seem
the face of it to
on
genetic
events,
have occurred
one
or
other
convergently.
mains
a
number of domain
large
combinations of
in
two
out
pairs of protein
three metazoans
by
by humans and flies. If
humans and worms,
by
and worms, and
Introns
Should this
12
destroy
We
shared
our
3
we
we
look for
find
shared
Ecdysozoa
Perhaps less suiprising than the previous examples,
Hypothesis?
it
without closer examination of these results.
is
becoming
or
presence
absence of
synapomorphy
(but
by
is not
no means
when
tors of
and
than
and
The
molecular
some cases
less reliable
thought (Krzywinski
Wada et al.,
a
readily
phylogenetic relationship
have been
as
using the
adequately sampled,
are
prove
that
reliable. In
always
all)
lost and hence
intron
an
becomes clear that introns
edly
clear
increasingly
as
it
probably not,
is
elegans
certainly
model
a
rapidly
in
the
a
very
species
It is
laboratory.
indica-
small and constant cell number and has
once
mode
of
Examination
2002).
and
development
an
genome associated with these
of the genes
an
Apparent homoplasy
due
to
secondary
loss
of
other taxa,
in
has evolved
atypical
its
of the
joining
mains
only
in
a
supports
(unpublished
is
Tyrosine
a
the
the
and
choanoflagellates.
in the
do-
found
This
presumed link between
Metazoa. This
work led
collaboration with Rob Russell and
Aloy, EMBL, Heidelberg)
to
look for novel
combinations of protein domains in the
sequenced
Kinase
combination
comprising the Metazoa and their
choanoflagellates
Patrick
the
and
single protein
sister-group;
observation
the
EGF
in the clade
possible
us
(2001) have demonstrated that the
genomes of
human,
fly
completely
and
nematode
hope that unique domain combinations might
it
a
has been
order
to
make up for in
lacks
in
brainpower.
The
we
of C.
are
can
see
elegans
derived. The
genes
(derived)
reveals
homologs
it
has
are
new
genes,
for
probably evolved in
hardwiring what the
worm
upon
that the genes and the
of this is that many of its
to have been
secondarily lost and
analyses
I
formative
present,
unreliable because
and,
reasonably
at
of character
be
ge-
highly unusual and highly
this fact makes the
distribution
ex-
chemoreception which,
were
significance
likely
lost
the other hand, it
point of these observations is that,
reflection,
nome
on
large number of
postulated,
a
atypical
genome
evolving;
and,
those associated with
ample
Caroll
fast
are
several of its Hox genes
a
character: Novel domain combinations
King and
most
has
lifestyle constraints.
various oddities. Of its
genes with clear
in
reproduce
small,
very
Besansky, 2002;
not
derived animal. C.
selected to
repeat-
might
least
at
problem here lies with Caenorhabditis ele-
which is
gans,
none
by flies
by humans and flies.
confidence in the
think
by
flies and worms,
all combinations of three domains then
shared
we
do-
find 20 shared
we
humans and worms, 29 shared
and 276 shared
mentioned. If
of the
and absent in the out-groups
com-
humans and absent
and the out-groups
present
nema-
might share certain
to flies and
common
to discover
two
the exclusion of
to
then flies and humans
binations
is
to
worms
Hypothesis is correct, which
and humans
arthropods
nematodes,
and
out-groups (fungi and plants).
or
If the older, Coelomate
sampling of sister
although both characters
might expect flies
we
in humans
links flies
Ecdysozoa Hypoth-
Ecdysozoa Hypothesis
unique combinations of protein domains
some
seen
test the
to
If the
(see above).
vertebrates. Further
which
analysis of molecular characters
provide characters
esis
(3-thymosin is either convergent
worms
Cladistic
and
pseudocoelomate
of
triplication
in flies and
more
state
arthropods
or
coelomate
are
either
case
primitive, unfused
a
synthetases
vertebrates have fused their genes
the other hand,
are
in-
-
Telford
presented above unin-
states
we
observe
explained by the secondary
the
could
loss of
Contributions
to
of these
many
Zoology, 71 (1/3)
in the
characters
2002
-
97
of
ancestry
the
nematode.
What
we
in all of these
see
true of
equally
two factors
cases
and this is
-
morphological characters
important in order
are
by homoplasy, real
it is
desirable to
not
to be fooled
apparent. First and foremost,
or
sample widely. Only through
that certain
code
a
sam-
can
we
changes in mitochondrial genetic
sampling of the
Metazoa
stand where and when these code
in this clade.
can
under-
we
changes occurred
one
are
expect
a
certain
character
unrelated lineages or,
genome,
The
be
to
evolve
to
in the
as
case
highlights
when
performing such studies;
further
be assessed in both
is
generally preferable
sent
to be
of
or
to
genes
unless
in
elegans
ele-
taxa in
character that
a
derived
a
can
it is present in the
cause
ancient
impossible
certain character is absent in
pointed
by Rokas
out
of evidence is not the
The
inability
clone
to
a
genome
and Holland
same as
a
warm
the
likely
can
is absent in
to
see
we
are
the
more
considering,
the
a
a
same
rea-
derived cha-
frog. The
use
of
which character state
see
bloodedness) is primitive and which
derived is
procedure known
a
This is
simply
an
as
out-
argument from
parsimony because, in this example, if warm bloodedness
were
the
primitive
once
it
state
would have to
and then been lost
frogs
and
once
pretation requires
in lizards;
twice;
once
the alternative inter-
that it has evolved
just
once
in
mammals.
Character
is
polarity
just
important
as
molecular characters and below I
when
give
two
a
prove
because,
(2000),
three
bloodedness should be
it
We
primitive character be-
primitive. Following
or warm
sequenced
to
to the rabbit
frog which, being
than the
early diverging frog
(cold
a
the other
ab-
secondary loss (cases
dealing with completely
is often all but
is
racter because
using
genomes, it
lineage
assume
soning,
commonplace) and further-
are
peculiar
on
state
as
seem
any of these
to
bloodedness,
Warm
derived character
a
in determin-
help
of the rabbit
quadru-
the ancestor
and the horse and absent in the lizard.
in
to
particular.
hand, is
have evolved
that is coded
one
relationship
group comparison.
important consideration
particularly susceptible
more,
the
is in fact
all
by
even
of horses. This character cannot
(therefore)
Molecular characters
present.
missing
of the C.
primitive and
a
might
repeatedly
lost genes of C.
secondarily
gcins
a
we
lost?
secondarily
of the
case
primitive
we
underlying molecular reasons why
any
character that is shared
peds: rabbits, lizards, frogs and
must understand the charac-
ter and its evolution. We should ask whether there
bloodedness
warm
horse.
that the five toed foot is
Secondly, and hopefully this follows
from the first,
the
Considering first the five-toed foot; this
a
ing
happen relatively frequently, and only through
broad
on
is that
-
pling many lineages within the eukaryotes
see
five-toed foot with the lizard and
with
examples
of when this has been
problematic.
as
absence
evidence of absence.
certain DNA sequence does
Mitochondrial genetic codes: The echinoderms and
hemichordates
not demonstrate it
does
exist.
not
The hemichordates,
long thought
Polarity
to
be
more
dates than to the third
As
emphasised above, only the sharing of derived
characters
is informative
relationships.
Shared primitive
place
those
larger
clade of all
absolutely
taxa that have
clear
to anyone
between
about which
simply
them within
(or had
and
those characters. To make this
distics there follows
lationship
phylogenetic
characters
that possess
species
sequently lost)
regarding
we
an
a
know
not
well
sub-
point
versed in cla-
example. Consider the
rabbit,
a
the
horse
and
a
only that the rabbit shares
a
name
closely
group
this close
the
and
sister-group
Degnan,
position
1999; Halanych,
above has been cited in
a
the chor-
of deuterostomes;
phylogenies
the
deny
the hemichordates
of the echinoderms
in mitochondrial
changes
to
were
relationship between chordates and hemi-
chordates and instead
as
suggests,
related
echinoderms. Recent molecular
idea of
re-
lizard
their
as
1996).
genetic
support
(Bromham
One
of this alternative
hemichordate/echinoderm clade:
assignment
of the
code discussed
the
re-
in echinoderms of the codon AUA from
coding for Methionine (Met)
to
coding
for Isoleu-
98
MJ.
cine (He) has
been shown to
recently
heinichordates (Castresana
that this character (AUA
ously interpreted
as
al.,
et
Upon closer inspection,
He) is
of the
that it is
Bilateria,
parsimonious
equally
ther AUA
Met,
=
one
Knowing
AUA
or
follows: (i) if AUA
Bilateria this
is
the
requires
Met is
=
assume
He
=
state. Each of these solutions
close
a
show
readily
can
to
clear
not
that AUA also codes for He in the Cnidaria,
out-group
that ei-
primitive
changes
2
as
primitive within the
requires the change
AUA
He
=
its
AUA
to
What had not been considered,
In
the
absence of
molog
of this
like
be
chozoan Hox
primitive
evolution of AUA
convergent
Met
twice;
in
once
the chordates and
protostomes (Telford
of the character AUA
derms and
in hemichordates has
viding
To
(see
update this story, it
also
that
above)
dclius
et
the
acoels,
character AUA
follow
be
=
AUA
Met
is
parsimoniously
morphy linking
co-
these two
groups.
increasingly likely
flatworms
branching bilaterians (Jon1999).
in
that,
Met
=
al.,
et
the
suggests
=
If this
basally
that
It would
primitive.
that the character AUA
most
the
been conclu-
acoelomorph
then the observation
true,
in
once
=
the
interpreted
as
a
synapo-
hemichordates and echinoderms.
fact
being derived,) then
in
the
dicyemids
are
peptide
that the
the
gene
signatures;
dicyemid
mesozoans
and,
and
sozoan
deuterostomian
metazoan status of
genes
one or
act
can
as
more
a
is taken,
approach
properly considered is the
the
dicyemid
mesozoan.
shown that certain
of
specific Hox
peptides
genes
were
polarity
of
case
It
had
a
has
Hox
been
not
been
gene of
previously
found in the homeoboxes
associated with each of
also
shared
by the
the Hox
genes
closely
possible
to
1999). Kobayashi
that
a
Hox
contained
one
of the
Lox5 gene that is
clade.
et
al
(1999)
found in
gene
From this
a
were
et
al.,
able to show
dicyemid
mesozoan
peptides characteristic of the
specific
to
the
lophotrochozoan
they deduced that the
mesozoan
by
arose
related Hox
out-group.
mesozoan
gives limited support for
from within the
When
identify
this
certain
ter
is
the derivation of
mesozoans
polarity of the charac-
emphasise the significance of this approach,
can
consider the
within the
worms
share
are
approach
established (Telford, 2000).
To
one
This
gene.
Lophotrochozoa but this result only
becomes credible when the
a
relationship
The
protostomes.
of the
priapulid
priapulids clearly
Ubx/abdA- like gene with other
protostomes
Lox2 and Lox4 in the
priapulid
gene is
lophotrochozoan clade)
one
most
looks
similar
for
to
arthropod Ubx
gene,
priapulids share only
residue with the
Hypothesis, the
the
synapomorphic
amino acids within this
finds that the
arthropods, all
a
‘signa-
however,
group
comparison
of protostomes,
as
or
other amino acids
the
By contrast,
being present
specific
same
to
one
single derived
being either primitive, i.e., interpreted through
the three great clades of bilaterian: deuterostomes,
eedysozoans and lophotrochozoans (de Rosa
The
dispute.
derived amino acids within the Lox5 gene that
ture’
Another instance where the
not in
was
of the
proxy
it is
meta-
crown-groups).
mesozoans
because
Fortunately,
duplication,
When
gene.
priapulids
meso-
(although it does exclude them from the ecdy-
but, consistent with the Ecdysozoa
The
primitive
simply
(called
Hox
the
zoans
then
He could indeed
in
was
zoan
He in echino-
=
not
linking
seems
al., 2002; Ruiz-Trillo
branching
AUA
shared derived character pro-
a
additional evidence
indeed the earliest
are
is
to be
requires
to
al., 2000). In short, the
et
occurrence
sively shown
He
=
equally parsimo-
(the ecdysozoan and deutero-
of the LOX5
shows
possible
like, ecdysozoan-
can
character states both
discovery
ho-
a
states
primitive. If this lophotro-
signature
state for this character
the
the
considered
the
was
possessing
out-group
lophotrochozoan-like)
or
niously
stomian
within the Bialteria this
an
character (deuterostome
Met to AUA
is
by
(Telford, 2000).
of this gene, each of the three
Met at base of the Bilateria and the reversal AUA
He
suggested
however,
polarity of these Hox signatures
=
He in the echinoderms, (ii) if AUA
metazoan
simple morphology.
=
=
analysis of molecular characters
derived from within this clade rather than be-
was
parsimoni-
most
derived character.
a
Cladistic
-
ing the basally branching
1998).
however, it is
=
in
co-occur
Telford
the
out-
in the ancestor
priapulid.
comparisons offer
over-
whelming support (from polarised residues) for the
notion that both
to
be basal
Platyhelminthes (previously thought
bilaterians) and Brachiopoda (previously
widely believed
are
in fact
to
be related
to
the
deuterostomes)
lophotrochozoans (Telford,
2000).
Contributions
71
Zoology,
to
(1/3)
2002
-
99
Conclusions
The theme
linking all of these potential problems
1-alpha
sequences
do not
Acoela.
Mol. Biol.
Evol.
Bromham
stome
with molecular
characters is the
need
a
how
they evolve. In particular,
sider the potential
is
vital
to
con-
that
homoplasy
Rosa
plesiomorphy
of
also
are
synapomorphy
versus
easily overlooked
as
sym-
seen.
of
not want
that molecular
reliable.
On
give the impression
synapomorphies
the contrary, I
very valuable
their great
do is
to
of
source
essentially
are
believe that
un-
Hoot
are
RA.
ease
of
certaining homology between features of DNA, and
of
differing complexity that
be
can
of features
used,
JD.
J.
only
a
Jenner
Zool.
superiority of molecular
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