Cladistics

Cladistics (2016) 1–5

10.1111/cla.12180

Homology and synapomorphy-symplesiomorphy—neither

synonymous nor equivalent but different perspectives on the same
phenomenon
Stefan Richter*
Allgemeine & Spezielle Zoologie, Institut f€
ur Biowissenschaften, Universit€
at Rostock, Universit€
atsplatz 2, Rostock 18055, Germany
Accepted 20 September 2016

Abstract

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or
equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the
one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time
with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to
that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. corre-
spondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primi-
tive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of
speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to
the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig’s terms synapomorphy and
symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an
unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those
characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however,
is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).
© The Willi Hennig Society 2016.

Since Patterson (1982) suggested the synonymy of
synapomorphy and homology, the relationships
between the concepts of homology and synapomor-
phy/symplesiomorphy have been discussed.1 The two
*Corresponding author.
E-mail address: stefan.richter@uni-rostock.de
1
Williams and Ebach (2012) noted a semantic difficulty in apply-
ing theses terms. Indeed, the terms synapomorphy and symple-
siomorphy do not pertain to general statements but refer to a special
character state that might be either a synapomorphy or a symple-
siomorphy in reference to a certain taxon. Homology refers to a gen-
eral relationship between structures. If two structures are
homologous, they should be called homologues. This implies that
the actual question is whether synapomorphy and homologue are
synonymous. However, this semantic inconsistency—I don’t see that
it is more than that—goes back to Patterson (1982) and beyond. In
my view, the use of the term homology (pl. homologies) for corre-
sponding structures is well established.
mutually exclusive opinions were recently defended
(Nixon and Carpenter, 2012a; Nixon & Carpenter
2012b, Brower and de Pinna, 2012, 2014; Nixon and
Carpenter, 2013; Farris, 2012, 2013, 2014a,b; Williams
and Ebach, 2012; Assis, 2013; Platnick 2013).
The two views are exemplified here by four quotes,
two for each of the two opinions:
Homology is not synonymous with synapomorphy: it includes
symplesiomorphy, and Hennig clearly included both ple-
siomorphy and synapomorphy as types of homology. (Nixon
and Carpenter, 2012a: 160)
Hennig (1966) recognized symplesiomorphies as homologies,
and that view is logically correct under the concept of homol-
ogy (homogeny) prevalent among evolutionists since 1870.
(Farris, 2014b: 555)
While secondary losses (reversals) are often synapomorphies,
symplesiomorphies (“absent” or otherwise) have no

© The Willi Hennig Society 2016

2 Stefan Richter / Cladistics 0 (2016) 1–5
evidentiary import to cladistic hypotheses of relationship.
Thus, we argue that identifying symplesiomorphic character
states as ‘homologous’ is conceptually vacuous, because they
are either synapomorphies (homologues) of more inclusive
taxa, or complementary absences that unite no group.
(Brower and de Pinna, 2014: 330)
Thus we maintain and reinforce our preference for the con-
ceptual, if not terminological, equivalence of homology and
synapomorphy in cladistics. (Brower and de Pinna, 2014: 335)
I start my argumentation with what could be called
the standard procedure of numerical cladistic analysis
(e.g. Farris, 1983; Meier, 1992; Nixon and Carpenter,
1993; Richter, 2005). The first step is the establishment
of a character matrix with characters and character
states. Here, I deal only with binary characters which
might be absent/present characters or both states rep-
resenting different conditions of the same organ/struc-
ture (neomorphic and transformational characters
sensu Sereno, 2007). It will be shown that distinguish-
ing between the two kinds of characters is very impor-
tant. I start with a binary character where neither of
the two states refers to the absence of an organ or
structure.
First, it is very important to distinguish character/
character states from the actual “thing” which is
described, the “organ” or “structure” (recently we
have introduced the term morpheme to replace these
less precise terms; Richter and Wirkner, 2014; G€ opel
and Richter, 2016). Character states, however, are by
definition the evolutionary units (historical individuals
sensu Grant and Kluge, 2004) and differ fundamen-
tally from the organ/structure (see also Hennig, 1966).
The delineation of character states and characters is
part of a process that finally results in a character
matrix. Here, I use as an example the arthropod
ommatidium, with either a crystalline cone made of
four semper cells (state 0) or a crystalline cone made
of two semper cells (state 1). Whereas the character
states represent the evolutionary units, each semper
cell could well be independently recognized as a “struc-
ture” as well as the entire ommatidium, respectively.
As a result of the character analysis, character state
identity (Brower and Schawaroch, 1996) will be estab-
lished by using the same scores (0, 1) for the same
character state in different terminals; for example, we
identify in some species a crystalline cone made of four
cells, and in others made of two cells. For the decision
whether the (never completely identical) structure
indeed refers to the same character state, it has been
suggested first referring to the topographic identity,
and then using the “standard test criteria for recogniz-
ing homology” (Brower and Schawaroch, 1996: 267). I
have suggested the correspondences should outweigh
the non-correspondences in a “1st step of testing
homology hypotheses” (Richter, 2005). What is identi-
fied by passing the 1st test has been often called
“primary homology” (Farris et al., 1970; de Pinna,
1991) although the more general term “hypothesis on
homology” has also been suggested (Nixon and Car-
penter, 2012a). De Pinna (1991) defined “primary
homology” as “conjecture of homology” and “sec-
ondary homology” as “supported phylogenetic homol-
ogy”. Because de Pinna (1991) equated phylogenetic
homology with synapomorphy (following Patterson,
1982), for him secondary homology is supported
synapomorphy. One should keep in mind, however,
that the identification of character state identity refers
to both, synapomorphies and symplesiomorphies, in
the same way. At this stage, a certain state might rep-
resent one or the other, so we do not know yet
whether (for example) the crystalline cone made of
four or the one made of two cone cells represents the
symplesiomorphy.
The “2nd step of testing homology hypotheses” is
the congruence analysis in which all character state
transformations are tested against each other in the
most parsimonious topology. Certain character state
transformations might now be considered as homo-
plastic (i.e. not congruent with the most parsimonious
topology), while others might be corroborated (i.e. the
transformation from one character state to another of
a certain character appears only once on the topol-
ogy). Because the resulting topology is an unrooted
network, no direction of transformation (e.g. 0–1 or
1–0) is implied. Only the rooting of the topology trans-
forms those ‘homologies’ (or homologues) into
synapomorphies or symplesiomorphies; which of the
two states represents the symplesiomorphic and which
the synapomorphic one depends exclusively on the
rooting in the next step (see also Farris, 2014b).
This implies that between this kind of homology
supported by a congruence test and both synapomor-
phy and symplesiomorphy exactly the same relation-
ship exists. I do not see any possibility to exclude
symplesiomorphy from this relationship. In this
respect, I agree with Nixon and Carpenter (2012a,b)
and Farris (2012, 2013, 2014b). Brower and de Pinna
(2014: 330) are correct in so far that in cases where
both states represent the presence of a thing (i.e. a
structure or organ), the symplesiomorphic state would
refer to a synapomorphy of a more inclusive taxon.
However, this does not make them synonymous
because these terms are relative terms and always need
an exact reference to a certain taxon (see footnote 1).
Ax (1984) used the term synapomorphy only referring
to sister groups. This has been adopted by some
authors (particularly from Germany) but is different
from Hennig’s original approach that used synapo-
morphy for characters (states) shared by two or more
taxa (see also Richter 2016). In any case, the terms
(syn)apomorphy and (sym)plesiomorphy refer directly
to the real historical process of speciation and
 Stefan Richter / Cladistics 0 (2016) 1–5
character transformation (phylogenesis) and were first
created by Hennig for distinguishing “ancestral” from
“derived” species or groups as concepts of his “devia-
tion rule” (Hennig, 1950, 1953; see Richter and Meier,
1994) whereas the “concept of homology has no rela-
tion to the direction of transformation between the
various characters [states] that come all from one ini-
tial character [state] of the common ancestor” (Hennig,
1984: 38; my translation).
This shows that synapomorphy and symplesiomor-
phy are neither synonymous nor equivalent to
homology but synapomorphy/symplesiomorphy and
homology refer to the same phenomenon (correspon-
dence through common origin) but from a different
perspective.
Or in Hennig’s (1953: 16) words (my translation):
Homologies are not only the true synapomorphies but also the
symplesiomorphies. The concepts of synapomorphy and
homology, therefore, do not coincide. Of course, the homology
criteria form the starting point of any systematic work which
uses morphological methods. Only correspondences in homolo-
gous characters can be compared. But not all homologies are
important for systematics: symplesiomorphies are not.2
One might want to argue, however, that the term
homology (supported by a congruence test) can then
be applied in any unrooted network but in my view
this is only then true when indeed both character
states refer to the presence of a morpheme.
Homology and absence
This leads to the second part of the recent debate,
referring to the problem of “absence”. Character state
identity might indeed have different implications if one
character state refers to a certain structure/organ and
the other to its absence (a/p characters or neomorphic
characters; see also Pleijel, 1995; Richter, 2005; Sereno,
2007).
Interestingly enough, already in 1950, Hennig only
considered ‘Merkmals€ ubereinstimmungen’ (character
correspondences) to be potentially homologous.
Hennig’s view remains very clear in his succeeding
publications:
In general we speak only of the homology of organs but a
‘character’ may also be the absence of an organ. [. . .] It is
completely unequivocal to say that the absence of wings in
2
“Homologien sind ja nicht nur die echten Synapomorphien, son-
dern auch die Symplesiomorphien. Die Begriffe Synapomorphie und
Homologie decken sich also nicht. Nat€
urlich stehen die Kriterien der
Homologie am Anfange der systematischen Arbeit, soweit sie mor-
phologische Methoden benutzt. Verglichen werden k€ onnen u €ber-
€
haupt nur Ubereinstimmungen in homologen Merkmalen. Aber
nicht alle Homologien sind f€ ur die L€osung einer systematischen
Frage von Bedeutung: die Symplesiomorphien sind es nicht.”
3
the Anoplura and Mallophaga is a synapomorphous charac-
ter, whereas in the Collembola, Protura, etc. it is a symple-
siomorphous character. (Hennig, 1966: 95)
The term homology applies in principle only to structures
that are present (positive characters). A ‘character [state]’,
however, is also (by definition) the absence of a structure. For
the purposes of phylogenetic systematics it is important to
distinguish whether a ‘negative character’ is the result of the
reduction of a particular structure or to the result of its pri-
mary absence. The common concept of homology ignores this
important aspect. It is therefore clear that either the meaning
of the term homology needs to be extended, or other terms/
concepts need to be added. (Hennig, 1984: 38; my translation)
For Hennig (1966: 95), the discrepancy between the
concepts “organ” (structure) and “character” was
obvious. Hennig was a systematist, primarily interested
in the classification of organisms. For him, dealing
with “differential” or “corresponding” characters was
a natural thing but it was also Hennig who recognized
that “the true method of phylogenetic systematics is
not to determine the degree of morphological corre-
spondence, or distinguish between ‘essential’ and
‘nonessential’ characters, but to seek out synapomor-
phous correspondences” (Hennig, 1966: 146). And, of
course, the absence of wings might indeed be an
important “differential” character (but not an organ
or structure) for insect classification but for Hennig it
was much more important to distinguish whether (or
when) the absence of wings is symplesiomorphic or
synapomorphic. The applicability of the concept of
homology was not in the focus of Hennig’s interest
(particularly not in his earlier contributions).
If we now go back to what has been called “homol-
ogy” (supported by a congruence test) referring to an
unrooted topology, in my view the argumentation above
makes it necessary to replace this term here. The non-
directional character state transformation in an
unrooted topology refers in the same way to what will
be after rooting synapomorphy and symplesiomorphy
but in the case of “absence” not to homology. There is
no homology relationship between something which
does exist and something which does not exist. In an
unrooted topology it is also open whether the absence
state will turn out as synapomorphy or as symple-
siomorphy after rooting. For this phenomenon regard-
ing unrooted topologies, I suggest “synmorphy” as a
new term, which easily could also refer to a/p charac-
ters. In a rooted cladogram, however, synapomorphy
and symplesiomorphy are necessary and sufficient terms
for the characterization of the character states.
So far we have dealt with the character states of a
cladistic analysis and have shown that the term homol-
ogy is not needed in this context. It can easily be
replaced by three steps of (i) identification of character
4 Stefan Richter / Cladistics 0 (2016) 1–5
state identity, (ii) identification of “synmorphy” by a
congruence analysis, and (iii) identification of symple-
siomorphic and synapomorphic character states by
rooting the topology.
Homology and transformation series
Different characters [states] that are to be regarded as trans-
formation stages of the same original character [state] are
generally called homologous. (Hennig, 1966: 93)
In deciding whether different [italics in the original] characters
[states] of several kinds are to be regarded as homologous
[ . . . ] it is a question of determining whether they can be
regarded as transformation conditions of a character that was
present in a different condition, which did not have to be the
stem species of only the compared species. But in deciding
whether corresponding [italics in the original] characters
[states] of several species are regarded as synapomorphies,
convergencies, [ . . . ] we must determine whether the same
character [state] was already present in a stem species that is
common only to the bearers of the identical characters
[states]. (Hennig, 1966: 120)
The first step in finding synapomorphous correspondences is
to identify, among different species (or species groups), those
corresponding or divergent characters [states] that belong to
one and the same phylogenetic transformations series. This is
the problem of homology of characters [states] in a broadened
sense. (Hennig, 1966: 146)
These three quotes show at first the difficulties of
Hennig’s application of the term character. In all
cases, we would replace character by character state
(as I have done above). What is mostly called charac-
ter today, Hennig called “transformation series”
(although not consistently). Hennig’s character concept
is clearly a historical one that necessarily implies the
transformation from one character state to another,
i.e. from the plesiomorphic state to the apomorphic
state, which therefore refers to both character states
(plesiomorphic and apomorphic) as historical individu-
als (Grant and Kluge, 2004). The three quotes also
show that Hennig applied the term homology for iden-
tifying or delineating “transformation series”. The sec-
ond quote also shows that Hennig was clear when he
intended to talk about homology and when about
synapomorphy, symplesiomorphy or convergence. The
recognition of what has been called taxic and transfor-
mational homology becomes meaningless when we fol-
low Hennig’s terminology (see Farris, 2014a and
Brower, 2015 for more details).
‘Hennig (1966: 94) also recognized that what
Remane (1952) called “principal criteria of homology”
are indeed also only auxiliary criteria “because the real
principal criterion—the belonging of the character
state to a certain phylogenetic transformation series—
cannot be directly determined” (see also Richter 2016).
This means that character state transformation is not
directly epistemically accessible (see Rieppel, 2006). In
many cases, however, the topographic identity might
help to identify the character to which the character
states belong (see Brower and Schawaroch, 1996).
In the quotes above, Hennig clearly speaks only about
character states that refer to something which is present,
but obviously characters (transformation series) might
also include character states that refer to the absence of
a structure/organ. When Sereno (2007: 573ff) distin-
guished between “neomorphic characters” and “trans-
formational characters” he suggested that the
neomorphic characters should comprise only two states,
absence and presence of a certain “new” structure/or-
gan, whereas the transformational characters should
not include the state “absent”. One might argue that the
absence of wings in fleas and lice obviously belongs to
the same phylogenetic transformation series as its pres-
ence in other Pterygota. This argument might be even
plausible for the absence of wings in “apterygote hexa-
pods” but what about crustaceans and other arthropods
—or even sponges? In those cases, can one really argue
that the absence of wings belongs to the same transfor-
mation series? As discussed before, in both cases (i.e.
between all species of fleas, and between “apterygote
hexapods” and sponges), “the absence of wings”, does
not represent a homology either because there are no
correspondences to consider. The absence of wings in
fleas, however, most probably does represent a synapo-
morphy and the absence of wings in “apterygote hexa-
pods” might indeed represent a symplesiomorphy.
The absence of wings in sponges, however, in my view
does not represent a shared symplesiomorphy with
“apterygote hexapods”. There is nothing which would
refer to wings in sponges which could give an argument
for putting them in the same transformation series with
absence and presence of wings in hexapods. However,
what is the difference between sponges and “apterygote
hexapods” in terms of the absence of wings? One could
argue that only in the hexapods does a reference system3
exist which allows finding the homologous position
(compare with Hennig, 1984: 38), i.e. the three-segmen-
ted thorax, something which is not the case in sponges.
In crustaceans, it would be clearly possible to identify
the first, second and third segment posterior of the max-
illary/labial segment which correspond to the thoracic
segments in hexapods but is this sufficient for identify-
ing the same reference system; at least there is no three-
segmented thorax? In other words, should crustaceans
be scored as “absent” or as “inapplicable” for the char-
acter wings?
3
Topographic identity is certainly the most important kind of ref-
erence system although one should be aware that other kinds might
exist, such as if we compare different seta types: Do they belong to a
transformation series determined by their position on the body or do
all types of setae belong in one transformation series independent of
their position (see Keiler & Richter 2011 for an example)?
 Stefan Richter / Cladistics 0 (2016) 1–5
In my view, the solution to the problem is that we
have to consider an encaptic system of neomorphic
characters. If just the “wings” were to be considered as
an isolated neomorphic character, then indeed aptery-
gote hexapods, crustaceans and sponges would share
the same symplesiomorphic state, “absence of wings”;
however, I think this kind of scoring would not be cor-
rect. We need to include another more inclusive neo-
morphic character, the “three-segmented thorax”
(present only in hexapods). Then crustaceans and
sponges are to be scored as inapplicable for the less
inclusive character “wings at meso- and metathorax”,
and only apterygote insects, fleas and lice should be
scored as “absent”. Instead of the character “three-seg-
mented thorax” we could also use “segmented trunk” as
neomorphic character (present in all hexapods and crus-
taceans). Crustaceans (as apterygote hexapods) could
then be scored as “absent” for a second neomorphic
character, “wings at second and third post-labial/maxil-
lary segment”. In any of these cases, sponges are to be
scored as inapplicable for the character “wings”. When
a certain taxon has to be scored as “absent” or when as
“inapplicable” for a certain neomorphic character
depends on the entire (encaptic) system of all neomor-
phic characters.
Obviously, the solution is complex and different
options are possible. This clearly shows that the delin-
eation of transformation series (i.e. characters) remains
of primary importance in morphological cladistics (see
Sereno, 2007; Richter and Wirkner, 2014).
Acknowledgements
I am grateful to Torben G€ opel and George D. F.
(Buz) Wilson for discussion and comments on the
manuscript. I also thank participants of the Hennig
XXXIV meeting in New York City for discussion,
where these ideas were first presented. James M. Car-
penter, Andrew V. Z. Brower and an anonymous
reviewer provided critical but helpful reviews—needless
to say that all errors and shortcomings are mine.
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