AMER. ZOOL., 21:47-62 (1981)
The Role of Functional Analysis in Phylogenetic Inference:
Examples from the History of the Xiphosura1
DANIEL C. FISHER
fc
Museum of Paleontology, University of Michigan,
Ann Arbor, Michigan 48109
SYNOPSIS. Conventional cladistic analyses of phylogeny can be interpreted as operating
at the level of phylogenetic trees. They assume that all "evolutionary steps" (transitions
from one character state to the next, along a morphocline) are independent and equal,
and, on that basis, select the cladogram which is consistent with the most parsimonious
trees. Evaluation of the assumptions of independence and equality requires consideration
of hypotheses at the level of scenarios. In some cases, arguments based on functional
analysis can suggest revised interpretations of either homology or polarity. If properly
formulated, these arguments can alter the evaluation of parsimony for trees to the extent
that even the choice of cladogram is affected. The structure of scenario level arguments
is identical to that of arguments operating at tree level. Examples of phylogenetic inference in the context of xiphosurans (horseshoe crabs), using both comparative morphological and functional analysis, illustrate this approach. In different cases, orthodox interpretations of relationship are either challenged or corroborated. Although the
introduction of functional analysis into the process of phylogenetic inference may appear
to compromise the usefulness of the reconstructed phylogeny for testing hypotheses concerning the role of natural selection in evolution, it actually increases the strength of such
tests.
INTRODUCTION
aptation can be made, they can in some
cases assist substantially in choosing among
alternative reconstructions of phylogeny.
These arguments will take a form that, on
one level, has been suggested many times
previously (e.g., Bock, 1977): namely, that
functional morphology can offer important arguments in the context of character
analysis, by suggesting initial interpretations of both homology and polarity, and
by helping to resolve cases of incongruent
apparent synapomorphies. However, my
approach will be unusual in that I will argue that this use of functional morphology
is a natural extension of the best of cladistic methodology. Examples of this approach will be drawn from work on the
phylogeny of horseshoe crabs.
I have chosen to circumvent the issue of
constructing classifications. This decision
is based primarily on constraints of space
and the opinion that classification is less
directly related to the fundamental concerns of evolutionary biology than is phylogenetic inference. In addition, the controversy over methods of classification
seems
less susceptible to objective resolu1
From the Symposium on Functional-Adaptive Anal- tion. This is not to say that the properties
ysis in Systematics presented at the Annual Meeting of
the American Society of Zoologists, 27-30 December, of different methods cannot be investigated empirically (Farris, 1977, 1979, has
at Tampa, Florida.
Of the many difficulties which we might
conceivably face in the context of the controversy alluded to in the title of this symposium, it seems clear that a lack of distinct
alternative interpretations is not one of
them. It has been argued both that explicit
functional analysis must be, and also that it
cannot be, applied to problems of phylogenetic reconstruction. Although these positions would seem to admit no middle
ground, other interpretations are not in
fact prohibited unless we actually accept
one of these extremes. In the following
discussion, I will argue that: (1) all attempts to reconstruct phylogeny involve at
least minimal assumptions that can be construed as pertaining to issues subsumed
under the broad heading of "adaptation";
(2) we may, however, choose to reconstruct
phylogeny without specific evaluation of
arguments concerning adaptation, by
adopting a methodological convention
equivalent to a ceteris paribus clause; and
(3) if testable hypotheses concerning ad-
47
48
DANIEL C. FISHER
SCENARIO,
TREE,
CLADOGRAM,
CLAOOGRAM,
FIG. 1. Correspondence relationships between
cladograms, trees, and scenarios.
done so, for instance, and found phenetic
methods wanting by some of their own
performance criteria), but rather, that any
resolution will require some concensus on
the relative importance of a variety of potential evaluative criteria, all of which will
depend on how we choose to use classifications. It would be rather futile to attempt
to evaluate the relative usefulness of a
hammer and a saw without first having
agreed upon what job was to be performed
with the chosen tool.
PHYLOGENETIC INFERENCE
Since the ideas and procedures basic to
a cladistic approach to phylogenetic inference have been discussed in this symposium and elsewhere (e.g., Hecht et ai,
1977; Cracraft and Eldredge, 1979; Nelson, 1979), I need not belabor them here.
It is important, however, to emphasize the
very useful distinction of three aspects of
the reconstruction of phylogeny (Eldredge, 1979): (1) cladograms (hypotheses
concerning the distribution of synapomorphies among the included taxa, with implications for relative recency of common
ancestry); (2) phylogenetic trees (hypotheses concerning the genealogical history of
the included taxa); and (3) evolutionary
scenarios (hypotheses concerning the historical-ecological context of the evolutionary history of the included taxa). These
three classes of hypotheses involve increasingly specific statements on the phylogenetic relationships of a particular group of
organisms. Furthermore, if we assume that
evolution is a branching (not anastomosing) process, if we deal only with well defined phenons or OTUs, and if we do not
demand that cladograms be exclusively dichotomous, then the correspondence relationships between cladograms, trees, and
scenarios are as mapped in Figure 1. Any
hypothesis at the level of scenarios entail^
a unique hypothesis at the level of tree&r
and any tree entails a unique cladogram.
Working in the other direction, for a finite
number of taxa under consideration, there
is certainly a finite number of possible
cladograms, but whether or not there is
only a finite number of trees derivable
from any one cladogram depends on exactly what information is included in the
tree (Platnick, 1977; Felsenstein, 1978; see
below). In any case, there is an effectively
infinite number of scenarios associated
with any one tree.
Although phylogenetic trees may be defined minimally as statements on the nature of evolutionary relationships between
taxa (ancestor-descendent relationships, or
descendants of a common ancestor, known
or hypothetical), additional information
may be included. For the purposes of this
discussion, 1 will exclude from detailed
consideration trees which specify stratigraphic or temporal data, since this type
of data is not relevant to considering the
role of functional morphology in phylogenetic inference. I will, however, want to
consider trees which specify the character
states associated with their terminal and
interior nodes. Hereafter, I will use the
term "phylogenetic tree" to refer to these
somewhat more complex hypotheses,
which are compounded from trees representing only the topology of relationships
(to be called genealogical trees) and from
trees representing character transformations (character state trees; Farris et al,
1970).
Many phylogenetic systematists have
claimed to be dealing exclusively with hypotheses at the level of cladograms and
have eschewed explicit treatment of trees
on the basis of arguments that trees do not
(always/ever) represent falsifiable hypotheses. Even when trees or scenarios have
been considered justifiable (Eldredge,
1979), it has been argued that the construction (i.e., testing) of cladograms occurs prior to, and is logically independent
HORSESHOE CRAB PHYLOGENY
of, any consideration of hypotheses on the
level of trees. Trees are only to be reconstructed by selecting from the alternatives
that remain, subsequent to, and consequent on, the selection of the single most
Satisfactory (or least unsatisfactory) cladogram, and scenarios similarly follow only
upon the choice of a tree. Given this protocol, it is easy to understand why cladists
have been hesitant to use stratigraphic information (which would consist of statements at tree level) or the results of functional analysis (statements at no less than
scenario level) in the process of testing
competing cladograms. I will suggest, however, that phylogenetic analysis, even when
performed explicitly at the level of cladograms, is not in fact organized as in the
above description.
Character analysis, leading to the recognition of particular synapomorphies, is
based on hypotheses of homology (tested
through morphologic analysis) and hypotheses of polarity (tested primarily by
outgroup comparisons). It is generally
portrayed as preceding the testing of
cladograms, but I believe few workers
would insist that this is the whole story. In
practice, whenever a character incongruity
(the conflict in cladistic implications of different apparent synapomorphies) arises,
we accept the implication that at least one
decision on homology or polarity has been
mistaken, and, using parsimony criteria,
we modify our hypotheses of synapomorphy. A hypothesized synapomorphy is taken as falsifying all cladograms (for the taxa
under consideration) which do not include
the "component" which that synapomorphy defines, or one that is "combinable"
with it (Nelson, 1979). After performing
this operation for all hypothesized synapomorphies, our parsimony criterion allows
us to accept that cladogram which has been
least frequently rejected.
It could be argued that explicit character
analysis is unnecessary—that simply hypothesizing similarities to be synapomorphous and following the cladogram testing
procedure above would result in the same
cladogram selection. While this is entirely
possible, it is also possible, as Eldredge
(1979) has discussed, that such a clado-
49
gram would cluster taxa by symplesiomorphies. In order to reject this possibility, character analysis is required.
Although this explication makes no
mention of trees, the arguments which underlie both character analysis and cladogram selection can be shown to involve
evaluation of the relative parsimony of all
phylogenetic trees that are consistent with
the observed morphologic data. This can
perhaps be most readily appreciated
through consideration of a three-taxon
problem involving cladogram selection.
Associated with the four possible cladograms for three taxa (A, B, and C) are 22
possible genealogical trees (Platnick, 1977).
If we consider only one character with two
states (x and x'), there will be 41 possible
phylogenetic trees (the higher number
arising from the possibility of assigning
either character state to a hypothetical
common ancestor). We will also assume
that A-B-C is a monophyletic group, that
x is the only character state found outside
of A-B-C, and that states are assigned to
the three OTUs as follows: A, x; B, x'; C,
x'. If we consider the hypothesis that x' is
synapomorphous in B and C relative to x
in A, it may seem unnecessary to think of
the consequences of the hypothesis as
being felt at the level of trees, rather than
cladograms. After all, not one of the possible phylogenetic trees associated with
cladograms other than the one showing B
and C as sisters is consistent with such a
hypothesis. Since cladograms are (in a
sense) classes of trees, can we not simply
say that these cladograms have been rejected? The first hint of a problem in such
an approach comes through noting that
even some of the phylogenetic trees associated with the "successful" cladogram are
not consistent with the above hypothesis of
synapomorphy (though this results from
the characters assigned to hypothetical
common ancestors; it is not a necessary
consequence of their topology). More directly to the point is a reminder that a hypothesis of synapomorphy is actually a
compound hypothesis—one of homology
and one of polarity. If these are taken separately, it is clear that their effects cut
across boundaries between the groups of
50
DANIEL C. FISHER
phylogenetic trees associated with particular cladograms. Some, but not all, phylogenetic trees associated with each cladogram are consistent with a given hypothesis
of homology (or polarity). Hypotheses of
homology and polarity thus operate, not
with respect to single cladograms or single
phylogenetic trees, but rather with respect
to classes of phylogenetic trees. These classes
are not the same as the classes of trees consistent with individual cladograms.
The connection with parsimony is clear
if we consider what underlies a given hypothesis of homology, for example. What
we actually observe, in the example above,
is a similarity between x' in B and x' in C,
and between x in A and x in the taxa not
included in A-B-C. We adopt a hypothesis
of homology because we recognize it as
more parsimonious, in terms of the number of evolutionary "steps" required (Camin and Sokal, 1965), to conceive of a given
character state as having arisen once, prior
to the most recent common ancestor of the
taxa showing the similarity, than it would
be to have it arise independently, in the
lineages subsequent to that most recent
common ancestor. This judgement is explicitly a comparison of alternative phylogenetic trees. In general, our evaluation of
similarities and differences consists of asking which phylogenetic trees (necessarily
plural, since we are dealing, at present,
with only one character) account most parsimoniously for the distribution of character states among known taxa. We say
that a hypothesis of synapomorphy falsifies cladograms because all of the phylogenetic trees associated with those cladograms are less parsimonious than some of
the phylogenetic trees associated with the
cladogram that is said to be corroborated.
This general approach to cladistic analysis,
through evaluation of the relative parsimony of trees, is, of course, explicitly developed in numerical cladistic techniques
(though their methods may vary in detail;
e.g., Farris, 1978; Felsenstein, 1979) and
has even been related to the basic principles of phylogenetic systematics by Farris
et al. (1970). Much of it is also implied in
discussions of post-cladogram tree selection (e.g., Platnick, 1977). Yet its implica-
tions for extending methods of phylogenetic analysis appear not to have been
appreciated.
As shown in Figure 1, the correspondence between scenarios and trees is essentially like that between trees and clado-#
grams. If we reject cladograms by rejecting
classes of trees (as less parsimonious than
competitors), might we not reject trees
(and thence cladograms) by rejecting
classes of scenarios (also as less parsimonious
than competitors)? In cladistic analysis using only comparative morphological data
this is effectively prevented by considering
each evolutionary step as independent and
of equal weight in the computation of parsimony. This convention amounts to a ceteris paribus clause which conditions the
evaluation of parsimony on the absence of
significant additional unbalanced constraints on the plausibility of various trees.
Within this approach to cladistic analysis,
the convention has axiomatic status; it is
unfalsifiable by the morphologic data it is
designed to handle. It need not imply that
all other factors are in fact assumed to be
equal—only that we do not understand
enough about their importance and effects
to take them into account. As such, it is a
necessary methodological tool. However,
using it conscientiously demands that we
review those factors under its purview to
determine whether or not their effects remain unresolvable. Along these lines,
Kluge and Farris (1969) have used data on
character variability (because of its hypothesized effects on the rate of character
transformation) to weight the contribution
of different characters to the total evaluation of parsimony. Hecht (1976) has suggested another approach to character
weighting, involving some consideration of
functional morphology, but it operates in
a different fashion from what I will suggest. If functional morphology is to be
used in analysis at the level of cladograms
and trees, I would argue that it must contribute testable hypotheses applicable to all
taxa under consideration, and all characters involved in incompatible hypotheses
of synapomorphy. Hypotheses concerning
adaptation will be used to evaluate the relative parsimony (plausibility) of competing
51
HORSESHOE CRAB PHYLOGENY
classes of scenarios in such a way as to have
an effect at tree level.
Cladistic relationships among xiphosurans
In the following examples, I will conside r only glimpses of a more comprehensive
treatment of relationships among xiphosurans, or horseshoe crabs (Fisher, 1975a,
in preparation), dealing with as few taxa
as possible and considering only those
characters which have the clearest implications for relationships. It will be necessary to present the results of functional
analysis as only sparsely supported assertions. They have been discussed in greater
detail elsewhere (Fisher, 1975a, b, 19776,
1979), but in the present context, their
general plausibility is all that I will try to
defend. Morphological terms and diagrammatic summaries of the morphology
of the species being used are presented in
Figures 2 and 3.
Belinurus koenigianus Woodward-Ewproops danae Meek and Worthen-Pafeo/imulus avitus Dunbar. These three species
are representatives of what are generally
treated as three superfamilies of horsehoe
crabs, the Belinuracea, Euproopacea, and
Limulacea, respectively. These superfamilies are included within the infraorder Limulicina by Eldredge (1974). The conventional interpretation of their relationships
at the level of a genealogical tree is that the
Limulacea were derived from the Euproopacea, which in turn were derived from
the Belinuracea. The only more cautious
statement on their relationships was made
by Eldredge (1974), who argued for a
cladogram which included additional taxa,
but was consistent with this conventional
tree. Using species-level taxa, this interpretation of relationships is shown as the
dashed cladogram of Figure 4A. I will
eventually argue that the solid cladogram
of Figure 4A is a better representation of
their cladistic relationships, but I will do
this in two stages. I will begin by considering only comparative morphological evidence, showing how the conventional use
of this evidence can be understood as operating at the level of trees. I will then consider the applications of functional morphological evidence. In this particular
B
FIG. 2. Morphology of representative xiphosurans;
dorsal aspect on left; partial ventral aspect on right.
A. Limulus polyphemus; Recent. B. Euproops danae;
Carboniferous. Abbreviations: ar, axial ridge; ga, genal angle; ios, interophthalmic spine; mas, marginal
spine of opisthosoma; mvs, moveable spine of opisthosoma; C>7_9, tagma formed of fused opisthosomal
segments 7-9; oa, region occupied by opisthosomal
appendages; ob, occipital band; od, opisthosomal
doublure; Op, opisthosoma; op, opercular pleurite;
or, ophthalmic ridge; pa, region occupied by prosomal appendages; Pr, prosoma; tas, terminal axial
spine; Te, telson.
three-taxon problem, comparative morphological arguments are entirely adequate for distinguishing the best of the
competing cladograms, but functional arguments provide effective corroboration
of certain points.
The most conspicuous character in support of the dashed cladogram in Figure 4A
is the fusion of opisthosomal segments into
one solid tagma, shown in E. danae and P.
avitus. The lines suggestive of opisthosomal segmentation in Figures 2B and 3B
are only topographic indications of the position of segmental boundaries; they are
not functional articulations. B. koenigianus,
in contrast, has opisthosomal segments 7 9 (O7_9) fused, but Oi_6 are freely articulated along both their anterior and posterior boundaries. A similar condition is
seen in other members of the Limulicina,
but even more important is that it is almost
ubiquitous among outgroups, such as the
Pseudoniscina, Synziphosurina, or Aglaspida, and is common among even other
merostomes (for the purposes of this analysis, I accept as unproblematic the higherlevel relationships suggested by Eldredge,
1974, and illustrated in Fig. 4D). Ordinarily, it would simply be said that this pattern
leaves little doubt that, in general, fused
52
DANIEL C. FISHER
FIG. 4. Cladograms representing relationships
among selected xiphosuran taxa; solid lines: cladogram corroborated by this analysis; dashed lines: one
of the cladograms rejected by this analysis. A-C.
Cladograms evaluated in text. D. Relationships
among xiphosuran merostomes; after Eldredge
(1974).
FIG. 3. Diagrammatic sketches of additional taxa
used in examples; dorsal aspect, left; partial ventral
aspect, right; approximately natural size. A. Belinurus
koenigianus; Carboniferous. B. Paleolimulus avitus; ancestor for the synziphosuran and the
Permian. C. Anacontium brevis; Permian. D. Limulitellaaglaspid which did have the derived, mobronni; Triassic.
bile segmented condition. But if this is true
segments are derived with respect to freely
mobile ones. While I agree with this proposition, I understand it as representing a
more complex argument. With respect to
the mobile-fused morphocline, we have
two choices as to polarity. If mobile segments are derived relative to fused ones,
then any two occurrences of these derived,
mobile segments (let us say, once within
synziphosurans and once within aglaspids)
may be either homologous or not homologous. If they are not homologous, then
we are, by definition of homology, dealing
with a phylogenetic tree in which the character in question was not present in the
most recent common ancestor of the synziphosuran and the aglaspid, and was derived independently somewhere along the
lineages leading from that ancestor to each
of them. If, on the other hand, this presumably derived, mobile segmented condition is homologous, then we are dealing
with another class of phylogenetic trees,
namely ones which specify a common
(i.e., if we were to accept any of this class
of phylogenetic trees), then, since that
ancestor is also an ancestor of the limulicines showing the fused condition (within
the constraints of the cladogram accepted
as the higher-level analysis of relationships), there must have been a transformation from the unfused to the fused condition—in other words, a reversal of the
assumed polarity. The only possibilities
left are that the higher-level cladogram is
wrong, or that fusion is a derived condition. We accept this latter hypothesis of
polarity because the phylogenetic trees
with which it is associated account for character evolution without requiring the reversals or convergences required by all
trees associated with other hypotheses of
polarity. This procedure involves the comparison, explicitly or implicitly, of hypotheses at the level of phylogenetic trees.
In order to use the fused condition of
opisthosomal segments in E. danae and P.
avitus as a synapomorphy for resolving the
relationships of these three taxa, two additional points must be covered. First, we
HORSESHOE CRAB PHYLOGENY
53
its associated structures) that was present
in one of its ancestors (at least as recently
as its common ancestor with E. danae), or
else the O7_9 complex in B. koenigianus
and E. danae is convergent. An exactly
analogous set of choices is presented with
respect to the rounded opisthosomal profile. All of the trees represented by these
options involve multiple reversals and/or
convergences. In contrast, if we accept the
synapomorphies declaring B. koenigianus
and E. danae to be sisters, our choice is:
either B. koenigianus has secondarily reverted to a mobile segmented condition, or
P. avitus has independently fused up its
entire opisthosoma. The trees consistent
with either of these alternatives would be
more parsimonious than any of the ones
considered previously. Therefore, I am
led to prefer the only cladogram with
which they are consistent, the solid one in
Figure 4A.
While comparative morphological evidence has proven adequate for cladogram
construction (or testing) in this case, it is
important to consider the contribution
that could have been made by functional
morphology. In xiphosurans, opisthosomal fusion has the consequence of increasing the proportion of body volume
devoted to extrinsic appendage musculature, by reducing the space occupied by
soma of B. koenigianus and E. danae is syn- longitudinal musculature controlling inapomorphic relative to the more triangu- tersegmental posture. Through this effect,
lar profile shown by P. avitus. In addition, opisthosomal fusion is associated with
the fused tagma formed in B. koenigianus more diverse behavioral repertoires and
by O7_9, complete with its single, large, the capacity for higher levels of activity. In
rounded, axial swelling and dorsally di- all known cases of opisthosomal fusion, the
rected spine, is present in E. danae in al- loss of the ability to adjust intersegmental
most identical form (except that in E. posture (potentially important during lodanae the most posterior marginal comotor and righting activities) is counteropisthosomal spine is considerably small- balanced by the greater effectiveness of
er). This condition appears to be synapo- opisthosomal appendages and is allowed
morphic relative to that of P. avitus, where by the development of increased excursion
O7_9 have boundaries that are clearly de- at the prosoma-opisthosoma and opisthomarcated topographically, with no axial soma-telson articulations (in fact, one or
both of these must precede complete fuswelling or single, long spine.
sion). It therefore seems that the fused
We now are left with the problem of condition would always be at a selective
choosing between incongruent apparent advantage relative to mobile opisthosomal
synapomorphies. If the totally fused opis- segments. Accepting these statements conthosoma is accepted as a synapomorphy, cerning the functional significance of opisthen either P. avitus has secondarily lost all thosomal fusion is tantamount to rejecting,
indication of a fused O7_9 tagma (and all
must argue that the opisthosomai segments of B. koenigianus are not secondarily
free. Since they are, in all apparent respects, similar to the free segments of other xiphosuran groups, this hypothesis
*vould require an "extra" reversal for
which there is no independent evidence.
It therefore seems unlikely. Secondly, we
must argue that the fused condition is homologous in E. danae and P. avitus. There
are certainly conspicuous differences between their opisthosomata, but without
particular evidence to the contrary (in the
form of incongruent synapomorphies), it
is certainly most parsimonious to consider
the character homologous. This has been
the choice of all previous workers (Raymond, 1944; StOrmer, 1952, 1955; Eldredge, 1974), and on this basis, the
dashed cladogram would be accepted.
I am aware of no good arguments for
synapomorphies shared by B. koenigianus
and P. avitus that are not also shared by
E. danae. The only other competitor
among dichotomous cladograms for these
three taxa is thus the solid one in Figure
4A, which, although it has never even been
discussed by other workers, has a number
of points to recommend it. Comparative
morphologic analysis (which I now need
not spell out in detail) strongly suggests
that the rounded profile of the opistho-
54
DANIEL C. FISHER
as functionally implausible, those scenarios
which would involve contradictory transformations. Since the ontogenetic development of the fused opisthosoma precedes
any sclerotization (i.e., an individual does
not develop mobile segments which lose
their mobility later in ontogeny), I would
not even expect reversal of this morphocline as an indirect effect of selection for
a paedomorphic condition important in
some other context. Taken together, these
arguments corroborate the hypothesis of
polarity. In this case, however, the parsimony criterion is more broadly based than
the simple counting of evolutionary steps.
Functional analysis also helps to corroborate previous decisions on homology.
While having a strong explanation of the
adaptive significance of fusion would certainly not, by itself, suggest that fusion had
occurred on multiple occasions, it renders
that interpretation more plausible (or less
implausible) when it is suggested on other
grounds. Since the benefits of fusion
would accrue regardless of the particular
tagmatic structure preceding full fusion,
and regardless of the particular means by
which the mobility of segments is restricted, it is particularly easy to explain the differences between the fused opisthosomata
of P. avitus and E. danae as the result of
fusion occuring within the context of differing tagmatic structures. As will be seen
below, no comparable argument is available to suggest that the similarities between
B. koenigianus and E. danae might only be
homeomorphic.
The rounded profile of the opisthosoma
in B. koenigianus and E. danae is an adaptation for precise occlusion with the prosoma during enrollment (Fisher, 1977a).
While there are tentative arguments confirming the polarity suggested above, they
are not strong enough for me to consider
them significant at present. In other
words, the classes of scenarios involving
alternative hypotheses of polarity have
members which appear to be about equally
plausible. However, functional arguments
do have implications for homology here.
What is most important about opisthosomal profile with respect to occlusion with
the prosoma is the precise topography of
the opisthosomal doublure; other aspects
of the morphology of this region are not
constrained by this adaptation. That the
details of the opisthosomal margin should
still be so similar in these two constitutes
an argument that its modification is
mologous. Exactly the same situation obtains with respect to functional analysis of
the O7_9 tagma. It is related to the righting
mechanism of these animals (as an area of
origin for muscles operating the telson,
and as a topographic prominence which
controls the orientation of an individual
when overturned), and although it offers
only tentative arguments for polarity, it is
strongly indicative of homology (again,
since there is a very strong similarity even
between aspects of morphology that are
under relatively weak biomechanical constraint).
In this particular three-taxon problem,
we thus have a case where conventional
cladistic methodology is adequate to resolve character conflict. At certain points
in this reconstruction of relationships,
functional arguments can stand on their
own in support of certain interpretations
of homology or polarity, and they can indicate which of two sets of apparent synapomorphies is more subject to convergence. An even stronger example of this
use of functional analysis could be offered
here, but will instead be dealt with below,
where its application is more critical.
B. koenigianus—E. danae-Anacontium
brevis Raymond-P. avitus. This second example concerns the relationships of Anacontium brevis (known only from its prosoma), relative to the group of three
species discussed above. The only possibility that has been considered previously is
that A. brevis was "closely related" to E.
danae, and the two have always been placed
in the same family (Raymond, 1944;
Stdrmer, 1955). This decision has been
based on the striking similarity of their
ophthalmic ridges, and although it leaves
unspecified their exact relationships at the
level of a tree or cladogram, a cladogram
can be easily derived from it (dashed; Fig.
4B), assuming the validity of the solid
cladogram of Figure 4A. In this case however, comparative morphologic analysis of
HORSESHOE CRAB PHYLOGENY
55
primitive condition. With this interprethis and another character proves inadetation, only the dorsally oriented conquate for choosing between two competing
dition would be indicative of relationcladograms.
ships among these taxa.
On the basis of morphologic analysis the
course of the ophthalmic ridge system of 3) The ventrally oriented condition could
be derived from the dorsally oriented
0 l brevis and E. danae seems synapomorcondition, leading to the opposite of
phous relative to the more narrow, paralthe second possibility—with only the
lel-to-anteriorly-convergent ophthalmic
ventrally oriented condition being inridge system of P. avitus and B. koenigidicative of relationships here.
anus. However, a different light is thrown
on this problem by consideration of the
character alluded to at the end of the last If the approach to this problem is restrictexample. All four of these horseshoe crabs ed to purely morphological analysis, there
(and all others as well) have an occipital is little basis for choosing among these posband along the posterior margin of their sibilities. We might give a slight preference
prosoma. In all of these taxa, the occipital to the first, since the total transformation
band is more or less vertically oriented be- it requires can be accomodated in only two
tween the ophthalmic ridges. However, steps, while both the second and third poslateral to the ophthalmic ridges, its orien- sibility involve one additional step—an initation varies. In E. danae and B. koenigi- tial reversal to the superficially primitive
anns it turns to face ventrally along the condition. However, if this possibility and
posteromedial margin of the genal angle. its implied synapomorphies are accepted,
In P. avitus and A. brevis it faces dorsally we must also accept either convergence in
along the same stretch. In most other be- ophthalmic ridge design by E. danae and
linuraceans and in all other non-limulicine A. brevis, or an independent reversal to the
xiphosurans, it retains its vertical orienta- primitive ophthalmic ridge condition by
tion until it thins out near the tip of the both B. koenigianus and P. avitus. Although
genal angle. Outgroup comparison sug- this latter interpretation might be rejected
gests that the vertical occipital band is on grounds of parsimony, the remaining
primitive, and that both the condition seen classes of phylogenetic trees are equally
in B. koenigianus and E. danae, and that of complex, and thus do not allow us to
P. avitus and A. brevis, are derived with re- choose between cladograms in Figure 4B.
spect to the most primitive state. However, The intuition of most workers might well
what is the polarity of the two "derived" favor the synapomorphy of ophthalmic
conditions relative to each other} This is what ridges, as a more "complex" character than
we need to know if we are to use either of occipital bands, and in doing so, concur
them in the present argument. There are with the orthodox interpretation of relathree possible answers to this question:
tionships. However, there would be little
rigorous basis for such a decision.
1) Both the dorsally oriented and the venA very different result can be obtained
trally oriented condition of the occipital if functional arguments are allowed. The
band could be independently derived ophthalmic ridge system is primarily sigfrom the primitive vertical condition. nificant as a corrugation of the dorsal proThis would make each of them derived somal exoskeleton, stiffening it against dewith respect to the other and allow each formation (particularly during the interval
to be used as a synapomorphy in the after molting and prior to appreciable
present problem (as long as the ho- sclerotization) by muscles originating on it.
mology of multiple occurrences of each Since many of these muscles are associated
condition is assumed).
with the prosomal appendages, the course
2) The dorsally oriented condition could of the ophthalmic ridges bears a close rebe derived from the ventrally oriented lationship to the arrangement and relative
condition, via an intermediate, vertical size of these appendages. The type of
stage, homeomorphic to the overall ophthalmic ridge system seen in P. avitus
56
DANIEL C. FISHER
and B. koenigianus is associated with the
use of the prosomal appendages in: swimming; walking or scuttling along a relatively planar substrate; and burrowing. The
ophthalmic ridge system seen in E. danae
or A. brevis, while not eliminating these activities from the behavioral repertoire,
represents a specialization for clinging to
and walking along relatively narrow, cylindrical substrates, probably represented by
plant axes (Fisher, 1979). This interpretation does not suggest any strong arguments for polarity; it is at least possible that
a transition from one system to the other
could have occurred in either direction.
With regard to homology, there is also no
decisive verdict. Since the ophthalmic
ridge system is tightly constrained by this
adaptation, convergence is certainly a possibility. Yet there is no conspicuous difference between the ophthalmic ridges of A.
brevis and E. danae that would, by itself,
suggest such an interpretation.
Turning to the other character, the
primitive vertical occipital band forms a
relatively blunt trailing edge to the genal
angle during swimming, resulting in significant drag production. Rotating this
band either dorsally or ventrally produces
a much more evenly tapered trailing edge
and reduces drag production. I know of
no counterbalancing advantage of a vertical occipital band. Therefore, scenarios
and trees suggesting its derivation from
either the dorsally oriented or the ventrally oriented condition seem unlikely. The
dorsally and ventrally oriented bands are
thus best interpreted as independently derived conditions representing alternative,
functionally equivalent modifications of
the primitive vertical condition. Their appearance as modifications of the primitive
condition is not surprising, but I would not
expect either one of them to be derived
from the other (since this would require
either an initial increase in drag production or a complete reduction and redevelopment of the occipital band). Functional
analysis thus favors the first interpretation
of polarity mentioned above, by falsifying,
if you will, the second and third possibilities. Therefore, unless we want to interpret the occipital band of each of these
species as independently derived from the
primitive condition, A. brevis cannot be a
sister to E. danae. The most parsimonious
interpretation is the solid cladogram of
Figure 4B.
Limulitella bronni Schimper^Lmm/«j polifa
phemus Linne-P. avitus. As a final example,
consider these taxa. There are no characters that appear to be derived and shared
by Limulitella bronni and P. avitus, but not
by Limulus polyphemus. T h e solid clado-
gram of Figure 4C is consistent with the
conventional genealogical tree, reconstructing P. avitus as ancestral to Limulitella
bronni, and it in turn as ancestral to Limulus
polyphemus (St0rmer, 1952, 1955), but this
interpretation is based on little more than
the occurence of P. avitus in the Permian,
Limulitella bronni in the Triassic, and Limulus polyphemus in the Recent. More careful
character analysis turns up apparent synapomorphies arguing for both cladograms
in Figure 4C. P. avitus and Limulus poly-
phemus both exhibit the derived conditions
of having an enlarged and elevated pleurite on the opercular (O2) segment and of
having lost the moveable marginal spine
located just posterior to this. Though it has
not been recognized previously, Limulitella
bronni shows the complementary primitive
conditions, with an opercular pleurite similar to more posteriorly located pleurites
and with the associated spine present. Limulitella bronni and Limulus polyphemus, on
the other hand, both exhibit the derived
condition of having relatively widely
spaced ophthalmic ridges and more complete effacement of topography on the
opisthosomal axial and opisthophthalmic
ridges.
Morphologic analysis of this case offers
no clear answer. A somewhat dubious argument can be made that the effacement
of topography is the least dependable
character. It has certainly proceeded to a
different extent in Limulitella bronni and
Limulus polyphemus, and if we were to bring
in morphological evidence on other taxa,
we would find clear examples of convergence in effacement. However, without
additional synapomorphies, a choice between the cladograms of Figure 4C would
be difficult.
HORSESHOE CRAB PHYLOGENY
Functional analysis, on the other hand,
opens another dimension for comparison.
The widely spaced ophthalmic ridges of
Limulitella bronni and Limulus polyphemus
are related to an increase in the relative
£ize of the basal masticatory podomeres
(gnathobases) of the prosomal appendages, and probably have to do with a
trophic adaptation (coarser and/or larger
food items). The loss of spines on the opisthosomal ridges has to do with drag reduction during swimming. The first of
these explanations offers no strong independent evidence on either homology or
polarity. The second strongly confirms the
morphological analysis of polarity, but is
indeterminate on homology. It is clear,
however, that the two derived characters
shared by Limulitella bronni and Limulus
polyphemus represent functionally independent modifications.
In contrast to this, the characters shared
by P. avitus and Limulus polyphemus show
a clear, though not mutual, dependence.
The enlarged and elevated opercular pleurite is oriented in such a way that it roofs
over a narrow channel, developed between
the posteromedial margin of the genal angle and the anterolateral margin of the
opisthosoma, which serves as the incurrent
site for respiratory currents that are maintained during shallow burial (Eldredge,
1970). Some such "roof is required to
keep this channel from being continually
clogged by sediment (even with it, the
channel must be occasionally cleared by
protrusion of the distal end of the sixth
prosomal appendage), and I would expect
it to develop along with an increase in the
importance or frequency of burial in a
horseshoe crab behavioral repertoire. The
moveable marginal spines are part of a
very different system. They are mechanoreceptors which play a role in righting behavior, but whose distal tips also just touch
the substrate during scuttling. Integration
of information from them allows the opisthosoma to maintain very precisely a posture, relative to the substrate, which maximizes the thrust produced by the retraction
of the flap-like opisthosomal appendages.
The modification of the opercular pleurites associated with burrowing behavior
57
displaces the site of the anteriormost
moveable marginal spine far dorsally,
making it difficult or impossible for it to
maintain the same relationship to the substrate. In fact, its presence in any form
would interfere with the flow of water
through the incurrent aperture and with
the channel maintenance movements of
the sixth prosomal appendage. The reduction and loss of this spine is thus a predictable consequence of the differentiation
of the opercular pleurite. Since these two
characters are therefore not independent,
the plausibility of them occurring together, through convergence, is greatly increased. Because of this functional dependence, they do not really represent two
separate steps. Therefore, the characters
shared by Limulitella bronni and Limulus
polyphemus are more readily accepted as
synapomorphous, and I am led to prefer
the solid cladogram of Figure 4C.
Phylogenetic trees involving xiphosurans
It should be obvious by now that if
cladograms are constructed by determining the set of most parsimonious trees,
there is nothing left to do at tree level after
the cladogram is finished—unless, of
course, we bring additional data to bear on
the problem. If, and only if, each OTU has
been attributed with one or more autapomorphies during the analysis, the parsimony criterion will have narrowed down
the choice of phylogenetic trees to certain
ones that are consistent with the one genealogical tree that is isomorphic to the
chosen cladogram (otherwise, certain phylogenetic trees consistent with one or more
other genealogical trees will be equally
parsimonious). Even when autapomorphies are recognized in all OTUs and only
one hypothesis of synapomorphy has been
rejected by the parsimony criterion, two
equally parsimonious trees will remain.
In the case of the first horseshoe crab
example considered above (where autapomorphies were not discussed), these two
phylogenetic trees are representative respectively of two residual classes of equally
parsimonious trees, which can be differentiated as follows: (1) ones in which opisthosomal fusion is considered convergent
58
DANIEL C. FISHER
in P. avitus and E. danae; and (2) ones in
which the mobile opisthosomal segments
of B. koenigianus are considered a reversal
to the primitive condition. There are, of
course, other phylogenetic trees that might
be picked out by one of these criteria, but
that are less parsimonious. In this case, although comparative morphological analysis cannot make any further headway in
tree selection, the functional arguments
available for homology and polarity clearly
favor trees in the first group mentioned
above. They allow this greater resolution
by bringing in a different kind of evidence.
Under the "best" circumstances, they
would be able to select a single most parsimonious phylogenetic tree.
On the vexed question of whether or not
ancestors can be recognized, the present
approach to phylogenetic trees does not
provide the necessary resolution. That is,
under no circumstances, with the parsimony
criteria used thus far in this discussion, will
a phylogenetic tree hypothesizing an OTU
as an actual ancestor be more parsimonious
than one (or more) of the phylogenetic
trees isomorphic to the cladogram. However, the entry of other factors into the
parsimony evaluation could significantly
alter this (see below).
Scenarios involving xiphosurans
Since I have argued that scenarios are
involved, implicitly if not explicitly, even
in the construction of cladograms, it is not
surprising to find that they, like trees, need
not now be elaborated upon in any great
detail. Functional analysis is, almost by definition, involved in the complex hypotheses which comprise scenarios, but the really important issue is whether it can be used
rigorously to test and reject scenarios {i.e.,
render them less parsimonious). I have
certainly argued as if it can be, but this is
considered in greater detail below.
DISCUSSION
As noted by Cracraft (in this symposium) the distinction between adaptation
as a result of evolution and adaptation as
a process of evolution is both familiar and
useful. It may also be an artifact of looking
at systems in an insufficiently dynamic
way, but it can still play a part in discussions such as this. Adaptation-as-result involves relationships between various features of an organism, and between the
organism and the context in which it occurs (Bock and von Wahlert, 1965). TheS#
relationships are just as much attributes of
an organism as are spines and legs, though
they do have a higher, or at least a different, dimensionality. For Recent organisms,
they can be investigated by direct experimentation or observation. We can test our
understanding of these relationships by
using laws of geometry and physics to develop, from observations on one set of features (morphological, behavioral, etc.),
predictions concerning the state of expression of other features. Although testing is
usually more difficult in the context of fossil organisms (simply because fewer attributes can be observed directly); I have argued (Fisher, 19756, 19776, 1979) that the
same type of hypothetico-deductive approach can be applied in studying their
adaptations. All of this is quite independent of studying adaptation-as-process. It
makes no assumption that adaptation-asprocess is the only important mechanism
of evolution, or even that it is the dominant one.
It is part of the nature, or structure, of
relationships, including the relationships
we call adaptation, to have consequences
in a temporal as well as a spatial dimension. In any given case, often depending
on its complexity, we may or may not be
able to deduce what those consequences
would be. However, through studies of
both natural and artificial selection, using
Recent organisms, any such predictions
that can be made, can also be tested, at
least "in the small." I do not at present see
the necessity or the possibility of arguing
that such observations give us direct insight
into the longer term effects of selection, or
into the importance (relative to other factors) of adaptation as a mechanism of evolution. Nevertheless, they do seem sufficient to test our understanding of the
potential effects of adaptation-as-result,
ceteris paribus. They give us a more or
less informed basis on which to construct
scenario level hypotheses concerning
HORSESHOE CRAB PHYLOGENY
the direction (not the magnitude) of the
influence of adaptation-as-result on evolutionary history. In order to operate in
the phylogenetic context I have proposed,
these scenario level hypotheses take one
w two forms. Hypotheses involving questions of polarity must be able to argue
that relationships between features of an
organism tend to constrain the direction of
character transformation, allowing us to
reject as less parsimonious those scenarios
involving transformations inconsistent with
those constraints. There are surely many
cases in which this relatively stringent demand cannot be met and in which transformation in either direction thus appears
equally plausible. Any hypothesis of polarity may be falsified at the scenario level
(just as one hypothesis of synapomorphy
may be said to falsify another), by an alternative hypothesis with contrary predictions (based, for instance, on physical principles not taken into account in the first).
As discussed below, it may also be falsified
at tree level, by a character distribution
with conflicting implications. It may not,
however, be falsified by finding that the
condition hypothesized as primitive persists in some taxa. The polarity hypothesis
is conditioned upon the occurrence of
change. It suggests that the direction of
change is constrained, without necessarily
predicting that change will occur. Hypotheses involving questions of homology, on
the other hand, must be able to argue that
the interactions between particular features of an organism are such that the
presence or absence of those features can
or cannot be treated as independent
events. Effective independence between
two features can arise either through minimal interaction between them, or through
a dependent relationship with the structure of a one-to-many mapping (i.e., the
phenomenon of multiple solutions; the
distinction between these two forms of "independence" disappears if several levels of
organization are considered). Again, these
hypotheses can be falsified at either scenario or tree level. Their interpretation,
however, is somewhat more complex than
for hypotheses of polarity. If it can be argued that features are independent, then
59
this corroborates the parsimonious tree argument (which counts features as independent) by which their homology was hypothesized. If it is argued that features are
not independent, this does not necessarily
imply that their cooccurrence in two taxa
is not homologous. It only means that trees
which postulate an independent origin of
the features do not thereby incur a "parsimony debt" as great as the number of
features being considered.
Hypotheses of homology and polarity
based on functional analysis could be applied to the analysis of any character for
which they have been developed. However, in the examples I have drawn upon
here, I have allowed these hypotheses to
be decisive only in situations where comparative morphological evidence was indeterminate. While this may raise the
problem of phylogenetic reconstruction to
a higher level of universality, it does not
require an assumption that natural selection dominates as a mechanism of evolution. Even if the constraints imposed by
adaptation on tree construction were treated as being much less important than those
imposed by observed morphology itself,
consideration of functional relationships
could "tip the balance" if it were otherwise
even. The ceteris paribus clause would still
be necessary to cover yet other factors, and
the strategy of inference would not have
changed.
Even if functional analysis can be used
appropriately in phylogenetic reconstruction, it can also be misused. The most obvious place for it to go astray is at the beginning. The functional analysis itself may
suffer in credibility as a result of: inadequate testing; failure to consider relevant
geometrical, physical, or physiological
principles; or failure to consider the whole
animal and its whole behavioral repertoire.
Even a credible functional analysis may be
unsuccessfully applied, if it does not have
the components or the structure necessary
to exclude at least one group of competing
scenarios. Manton (1977), for instance, has
been outspoken in her claims for the relevance of functional analysis for phylogenetic reconstruction, but has produced arguments which have the form: feature x
60
DANIEL C. FISHER
in A functions differently from the rather
similar feature x' in B; x cannot be derived
by a plausible modification of x', nor can
x' be derived from x; therefore x and x'
cannot be homologous. Even if we accept
the two initial premises (which is not always possible), the conclusion does not follow, because the argument does not exclude the possibility that x and x' are
homologous, but that their functional relationships (like details of their morphology) have been modified independently
from the homologous condition x° in their
most recent common ancestor (see Platnick, 1978, for other criticisms). The case
of the occipital band, discussed above, provides an example of such a transformation.
Even when an argument of appropriate
design is available, it may be misused. Eldredge has quite correctly pointed out that
having a ready explanation of the functional significance of one character may
result in our accepting a convergent or
parallel origin for it more readily than for
a character whose "functional significance
remains obscure to us" (1979, p. 179).
However, the functional arguments I have
used are fundamentally comparative.
They do not operate by virtue of one character "having function" and another incongruously distributed character "not
having it." Rather, they rely on the perception of differences between the structure of functional relationships associated
with each of the characters. Just as in comparative morphology, if one of the elements to be compared is "obscure," then
no comparison can be made. I do not
mean by this that perfect clarity is any
more realizable a goal in functional analysis than in other pursuits—only that testable hypotheses must be available on each
side in order to make a meaningful comparison. Problems related to this appear to
be associated with the a priori weighting
scheme advocated by Hecht (1976) and
Hecht and Edwards (1977). Their categories of characters seem to be far from
mutually exclusive and to require comparison of very heterogeneous entities. For instance, I am not sure that 1 could argue
that a given suite of characters was either
developmentally integrated, or function-
ally integrated, or innovative and unique;
and even if I could, I am not sure that
their order of weighting would always be
most appropriate.
Finally, even well designed scenarios
based on thorough comparative function^
analysis can be inappropriately construed
if they are represented as privileged insight, unfalsifiable by comparative morphological data. Exactly when to consider
them falsified is a more complex issue, but
they must be potentially falsifiable on these
grounds.
The desirability of phylogenetic reconstructions that are minimally dependent
on assumptions concerning particular
mechanisms of evolution can hardly be
doubted (Eldredge and Cracraft, 1979),
since such reconstructions would provide
some of the most powerful tests of hypotheses concerning those mechanisms of evolution. Although phylogenetic inference
using only comparative morphology has
frequently been represented as being independent of these "inappropriate" assumptions, I have argued that it actually
proceeds by assuming that the effects of
adaptation (or of any other constraints on
the structure of trees) are negligible on the
scale at which the reconstruction takes
place. Given this, let us imagine the design
of a test of natural selection. To begin
with, let us assume that we reconstruct a
reasonably well corroborated phylogeny,
without recourse to data other than morphology (or analogous attributes). We then
consider a character for which we are able
to develop a strong hypothesis of polarity,
based on functional analysis, and which
also successfully passes tests for its homology in two or more OTUs. What happens
if the distribution of this apparent synapomorphy turns out to be incongruent with
the previously constructed hypothesis of
relationships? If we consider ourselves limited to the cautious application of functional analysis exemplified above, there
would be little choice but to consider the
synapomorphy based on functional analysis to have been falsified. Ordinarily, we
might consider only the specific hypothesis
of polarity or homology to be mistaken,
but if we are explicitly testing natural se-
HORSESHOE CRAB PHYLOGENY
61
lection, we will presumably have chosen for functional analysis even when comparthe (compound) hypothesis of synapomor- ative morphological evidence is not indephy to be as strong as possible. Do we then cisive: Through this strategy, comparative
accept natural selection as having been fal- functional analysis can be seen to have a
sified? Should we scrap it and start again? foundation analogous to that of compara^ r is it possible that the ceteris paribus were tive morphology and a degree of evolunot paribus (if I may be excused a perver- tionary significance that has often, of late,
sion of the ablative absolute)? This possi- been thought beyond its reach.
bility obviously should not be invoked caACKNOWLEDGMENTS
priciously, but if we do not examine it
rigorously to begin with, we will have to
I have appreciated comments from a
sooner or later. We could, of course, seek number of persons on the material preother ways of corroborating the original sented here: J. Cracraft, N. Eldredge, J. S.
reconstruction of relationships. Strati- Farris, S. J. Gould, G. Nelson, R. T. Schuh,
graphic and geographic data may also rep- and J. A. Slater. This work was completed
resent constraints on our reconstruction of during tenure of a grant (DEB-7823288)
trees and are certainly independent of ad- from the National Science Foundation. I
aptation. If they were incorporated into a also thank C. S. Darling for technical asmodel analogous to what I have discussed sistance, D. Robins for typing the manuhere, and if they were accompanied by an script, and K. Steelquist for photographic
appropriately modified parsimony crite- assistance.
rion (to be discussed elsewhere), these data
could resume a role not totally unlike that
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