Abstract A Critique Of Pure Folly

Cladistics 18, 218–236 (2002)
doi:10.1006/clad.2001.0192, available online at http://www.idealibrary
.com on
ABSTRACTS
Abstracts of the 20th Annual Meeting
of the Willi Hennig Society
Darlene Judd and Andy Brower (Local Organizers of the Meeting)
Oregon S
tate Arthropod Collection, 4086 Cordley Hall, Oregon S
tate University, Corvallis, Oregon 97331
Meetings of the Willi Hennig Society are renowned studies of a great variety of taxa to theoretical papers
on philosophy of systematics. There were topical sym-
for their candid and sometimes contentious discussion
of systematic ideas. This is made possible by the ple- posia addressing congruence, philosophy of cladistics,
statistical approaches to phylogenetic inference, and
nary format of the meeting (there is a single session,
so every participant has the opportunity to hear each Linnaean taxonomy vs the PhyloCode, as well as con-
tributed paper sessions and a session devoted to new
speaker) and by the Society rule that prohibits the cut-
ting off of discussion after a talk that raises interesting software and publications. A special feature was a 20th
anniversary lecture by Society founder Steve Farris,
or controversial issues. Anyone who has attended
meetings with concurrent sessions is familiar with the which described the origin and early history of the
Society.
frustration of not being able to challenge a speaker’s
argument because of Procrustean adherence to the Another exceptional feature of the Hennig Society
Meetings are the student presentations, which are inte-
schedule. The Hennig Society’s flexibility in this regard
means that meetings offer not only opportunities to grated by subject matter into the regular sessions,
rather than segregated into poorly attended student
hear polished presentations of completed research
products, but also to debate issues as they arise. Fur- sessions. Particularly noteworthy at these meetings
were the large number of high-quality student papers.
ther, because speakers are aware that their ideas will
be subject to immediate public scrutiny, talks at the The Student Awards Committee consisted of Maureen
Kearney, Jan De Laet, and Cyrille A. D’Haese, and
Hennig meeting are usually better than those at meet-
ings of comparable societies. the Awardees were Marc Branham, the Hennig Prize
($1000), for “The Evolution of Bioluminescent Commu-
The 20th annual meeting of the Hennig Society was
held in Corvallis, Oregon, on the campus of Oregon nication in Fireflies (Coleoptera: Lampyridae)”; Diego
Pol, the Brundin Prize ($500), for “Biases in Maximum
State University, August 26–30, 2001. Participants were
present from universities and museums of 13 countries Likelihood and Parsimony: A Simulation Approach to
a 10-Taxon Case”; and Kurt M. Pickett, Rosen Prize
on five continents. As may be seen from the following
abstracts, the subject matter ranged from empirical ($250), for “Exorcising the Demon: Parsimony Escapes
0748-3007/02 $35.00
218 q 2002 by The Willi Hennig Society
All rights reserved.

Abstracts of the 20th Annual Meeting of the Willi Hennig Society 219
the Felsenstein Zone with More Data from the Same first gained by larvae and appears to function as an
aposematic warning display, while subsequently being
Distribution.” Julián Faivovich, for “On RASA,” Taran
Grant, for “Testing Methods: The Evaluation of Discov- gained in adults and used as sexual signals. Our analy-
sis also suggests that while pheromonal sexual signals
ery Operations in Systematics,” and Roberto A. Keller,
for “The Illogical Basis of Phylogenetic Nomenclature,” are used basally in the family, these are used in conjunc-
tion with and then subsequently replaced by photic
were awarded honorable mentions and a 2-year sub-
scription to Cladistics. signals in the same lampyrid lineages. Both photic sig-
nals and the photic organs used to produce them have
The abstracts presented here offer some insight into
the quality and character of this year’s meeting, but become greatly elaborated in the fireflies that no longer
employ chemical sexual signals. In addition, the ability
to obtain the full Hennig meeting experience, you
really need to be there. to produce a flashed sexual signal appears to have
arisen at least three times in the family Lampyridae.
Convergent evolution is also evident in a number of
adult male photic organ morphologies.
MEETING ABSTRACTS
Cladistics with and without Metaphysical Bom-
bast. A. V. Z. Brower. Department of Entomology,
Testing Congruence among Linked Genes and Oregon State University, 2046 Cordley Hall, Corvallis,
Multigene Families. M. W. Allard, Department of Bio- Oregon 97331-2907.
logical Sciences, George Washington University, Wash- Is Popper a useful weapon, and if so, to whom? “h,
ington, DC 20037. e, b” and other formal schemata will be discussed (with
The incongruence length difference test (ILD) has disdain). It will be suggested that cladistic hypotheses
become an important tool for exploring the patterns do not test “descent, with modification,” do not need
of congruence both between data matrices, as well as to be justified by asserting such claims, and may not
within them. This presentation explores general strate- even fit inside Popper’s demarcation of science if bur-
gies for uncovering congruence among and within ma- dened by evolutionary background knowledge.
trices. Examples discussed include a large multigene
A Critique of Pure Folly. J. M. Carpenter. Depart-
data matrix investigating the origins of incongruence
ment of Entomology, American Museum of Natural
among mammalian mitochondrial protein coding
History, Central Park West at 79th Street, New York,
genes, where we compiled a matrix that included the 13
New York 10024-5192.
protein coding genes for 41 mammals from 14 different
A critique of the draft PhyloCode is presented. Its
orders (Shevchuk and Allard, 2001). A second, study
stated goals cannot be met by the proposals in the
examines the molecular evolution of the GABA gene
current draft, which also fails to uphold its stated prin-
complex, where horizontal gene transfer or a related
ciples. Its internal contradictions include reinvention
reorganization mechanism has occurred within this
of the very aspect of the current Linnaean system that
gene family (Turano et al., 2001). In addition to discus-
the advocates of the PhyloCode most often decry.
sions of strategies for uncovering incongruence within
and between matrices, we also explore the issue of
Congruence between a Range of Molecular and
multiple testing and the use of a Bonferroni correction.
Organismal Character Data Partitions for Gamebirds
(Galliformes). T. M. Crowe, P. Bloomer, E. Randi, J.
The Evolution of Bioluminescent Communication in
Fireflies (Coleoptera: Lampyridae). M. Branham and J. Groth, and R. Kimball. Percy FitzPatrick Institute, Uni-
versity of Cape Town, Rondebosch 7701, South Africa.
Wenzel. Department of Entomology, Ohio State Uni-
versity, 1315 Kinnear Road, Columbus, Ohio 43212. Congruence within and between, and complemen-
tarity between, molecular and morpho-behavioral data
Through a phylogenetic analysis using adult mor-
phological characters, we are able to show that the partitions. Four major data partitions (morpho-behav-
ioral, ovomucoid amino acid, mtDNA cytochrome b
origin of bioluminescence in cantharoid beetles ap-
pears to predate the origin of the family Lampyridae. and mtDNA control region) and sub-partitions for the
Galliformes (chicken-like birds) are compared using
The ability to produce and emit photic signals was
q 2002 by The Willi Hennig Society

220 Abstracts of the 20th Annual Meeting of the Willi Hennig Society
incongruence length difference tests and topological group to Pterygota 1 Zygentoma, the latter being
analysis to determine phylogenetic congruence and paraphyletic due to the position of Lepidotrichidae.
complementarity between/among them. The results Entognatha is also monophyletic. In that clade, Diplura
are discussed in the light of the debate between advo- is monophyletic (Campodeids and Japygids clustering
cates of separate vs combined character analysis. together) and sister group to Protura. Collembola is
monophyletic and sister group to Protura 1 Diplura.
When Does the ILD Test Fail? P. Darlu and G.
Lecointre. INSERM U535, Bat. Gregory Pincus, 80 Rue
Three New Methods for Evaluating the Importance
du General Leclerc, Le Kremlin-Bicêtre, France 94276.
of Characters and Character Linkages in Cladistic
The efficiency of the incongruence length difference
Analyses. D. DeGusta. Museum of Vertebrate Zoology,
test (ILD), used for assessing the character incongru-
University of California, Berkeley, California 94720-
ence between multiple molecular data sets, was exam-
3160.
ined by simulating DNA data sets stemming from con-
A fundamental requirement of the cladistic method
trasted tree topologies and under various evolutionary
is that the characters used be independent, and not
conditions of mutation rates, branch lengths, sequence
genetically, developmentally, or functionally corre-
lengths, and heterogeneity of the substitution rates
lated. However, the general view emerging from geno-
along the sequence. The results show that the probabil-
mic and developmental investigations is that of pleiot-
ity of rejecting the hypothesis of congruence, even
ropy, with relatively few genes determining a variety
when the topologies of the true trees are identical,
of anatomical features that are developmentally corre-
decreases when the number of sites is low, and when
lated in a complex fashion. These results, along with
the substitution rate is large and different from one
those of biomechanical studies, indicate that the sets
branch to another. Moreover, when the number of sites
of morphological characters typically used in cladistics
is low and the heterogeneity of substitution rate be-
almost certainly contain dependent characters. Thus,
tween sites is high, the power to detect true incongru-
“systematics would be well served if researchers more
ence between tree structures can be very weak. We
fully explored the causes and consequences of charac-
conclude that the ILD test has only limited power to
ter correlations that may exist in morphological data
detect incongruence caused by differences in the evolu-
tionary conditions or in the tree topology, except when sets” (Emerson and Hastings, 1998). Three new meth-
numerous characters are present and the substitution ods for evaluating the importance of characters and
rate is homogeneous from site to site in all sets of data. character linkages are presented here.
Character importance ranking (CIR) quantifies the
Phylogeny of the Apterygote Hexapods. C. A.
relative importance of characters in cladistic analyses.
D’Haese. Department of Entomology, American Mu-
CIR identifies the characters with the strongest phylo-
seum of Natural History, Central Park West at 79th
genetic signal in a cladistic analysis. This permits the
Street, New York, New York 10024-5192.
informed prioritization of characters for further inves-
A phylogeny of the basal hexapods, the so-called
tigation via genetic, developmental, and functional ap-
apterygotes, is proposed. Broad taxonomic and charac-
proaches; and highlights characters whose definition,
ter sampling is used to address the placement of Pro-
scoring, independence, and variation should be re-
tura, Diplura, Collembola, Archaeognatha, and Zygen-
viewed with particular care. The results obtained with
toma with respect to Pterygota. A data matrix
CIR indicate that a number of cladograms based on
consisting of nucleotide sequence data for 16s rDNA,
morphological data are dependent upon problematic
histone h3, d1, d2, and d3 regions of the 28S rDNA,
characters.
18S rDNA, and 302 morphological characters was gen-
Sensitivity to character linkage indexing (SCLI)
erated for 118 exemplars representing the major fami-
quantifies the relative sensitivity of different clado-
lies and subfamilies. Analyses were performed
grams to potential character linkages. Different cladis-
through Direct Optimization under a variety of param-
tic analyses are affected differently by linkages among
eter sets.
their characters, with some cladograms changing more
Not surprisingly, apterygotes are paraphyletic. Ec-
tognatha is monophyletic with Archaeognatha sister than others. SCLI quantifies this differential sensitivity

by measuring the average change in a cladogram at Congruence and Reliability: Discovering New
various levels of character linkage (from very few to Clades within the Acanthomorph Bush. A. Dettaı̈,
many linkages). SCLI does not attempt to identify W. J. Chen, C. Bonillo, and G. Lecointre. Institut de
which characters might actually be linked. Instead, Systématique, Muséum National d’Histoire Naturelle,
SCLI quantifies the scope of the problem posed by 43 Rue Cuvier, 75231 Paris Cedex 05, Paris, France.
character linkages, and identifies which cladograms During the past 10 years, only a few studies increased
are the most stable in the face of character linkage (and our understanding of large-scale acanthomorph inter-
can thus be considered the most reliable in this regard). relationships. The huge acanthomorph plasticity and
The results obtained with SCLI demonstrate that even the homoplasy found in morphological characters ren-
very low levels of character linkage will alter the clado- dered morphological synapomorphies very rare. Dur-
gram for most fossil taxa, whereas cladograms of extant ing these 10 years, molecular phylogenetics has been
taxa are generally unaltered even when very high lev- dominated by the “total evidence” paradigm, a situa-
els of character linkage are assumed. tion that did not favor the discovery of new acantho-
The linkage distance between cladograms (LDC) morph clades. Hopefully, 10 years of tremendous in-
method is a technique for estimating how different crease of gene sequence data improved our knowledge
two cladograms (with the same OTUs) are in terms of of tree reconstruction artifacts. These artifacts are so
character linkage. LDC provides an estimate of how widespread in molecular phylogenetics that it is often
much character linkage it would take to transform one impossible to know from a single tree whether the posi-
cladogram into another. This indicates the extent to tion of a taxon is reliable, i.e., due to common ancestry
which the observed differences between cladograms or to artifacts. If non-random molecular homoplasy is
are due to assumptions of character independence. The
particular to each gene taken as a phylogenetic marker,
results obtained with LDC demonstrate that several
genes can be considered as natural partitions. The only
recent tests of the cladistic method are robust, even if
way to detect tree reconstruction artifacts is therefore
the character sets used contain many linked traits.
to analyze sequence data partitions separately without
consensus. Consequently, the reliability of a clade is its
Questioning Quartets: Breaking up Is Not Just
repeatability through separate analysis of independent
Hard to Do. J. E. De Laet. American Museum of
sequence data sets. The tree based on all the available
Natural History, Division of Invertebrate Zoology,
data tells nothing about reliability, nevertheless it is
Central Park West at 79th Street, New York, New York
required for character evolution and support analyses.
10024-5192.
To investigate acanthomorph interrelationships, we are
In recent years, many different methods for phyloge-
working on the separate analyses of eight independent
netic reconstruction have been proposed that are based
molecular data sets, among which: mitochondrial ribo-
on analyses of only four taxa at a time. One of the
somal genes 12s 1 16S (814 bp); the 28s nuclear ribo-
stated advantages of this quartet approach is that it
somal gene (847 bp) and the nuclear gene encoding
allows using optimality criteria, such as ML, that are
rhodopsin (759 bp) for 91 taxa. Following the above
so computationally intensive that they cannot be used
principles, separate analyses are used for reliability,
with data sets of even only moderate size. This prag-
simultaneous analysis for summarizing results, in
matic observation is obviously true, but it leaves open
which some new clades can already be proposed for
the fundamental question if breaking up a data set into
future research in morphology and/or molecular
its quartet sub-data sets is in itself a good thing to
phylogenetics of acanthomophs: Gadiformes plus
do. It is shown that in general, whatever optimality
Zeiformes (less caproids); Beloniformes plus Atherini-
criterion is used, it is impossible to reduce an n-taxon
formes; Channoidei plus Anabantoidei plus Synbran-
problem to a set of quartet problems without losing
chiformes; Syngnathoidei (aulostomids, macroram-
information that is present in the original data. Focus-
phosids) plus Dactylopteridae; Scombroidei (less
ing on the method of likelihood mapping, examples
sphyraenids) plus Stromatoidei plus Chiasmodonti-
(both with hypothetical and empirical data) are pro-
dae; Ammodytidae plus Cheimarrhichthyidae; Zoar-
vided in which this loss of information leads to mis-
leading answers. coidei plus Cottidae; Percidae plus Notothenioidei; and

a clade grouping Carangidae, Echeneidae, Sphyraeni- with the simultaneous analysis of the data free of trans-
fers (except for two strains that were not in their puta-
dae, Menidae, Polynemidae, and Pleuronectiformes.
tive group of origin). Our results suggest that the rough
simultaneous analysis may in fact diminish the effects
Taxonomic and Character Congruence in Molecular
of horizontal gene transfer in phylogenetic reconstruc-
Phylogenies of Escherichia coli. P. Escobar-Páramo,*
tion of bacteria with low level of sex; however, it does
A. Sabbagh,† P. Darlu,† G. Lecointre,‡ and E. Dena-
not eliminate all the misplacements due to transfers.
mur.* *INSERM U458, Hôpital Robert Debré; Paris,
France; †INSERM U535, Hôpital Kremlin Bicêtre; Paris,
Corroboration, Goodness-of-Fit, and Competing
France; and ‡Muséum National d’Histoire Naturelle,
Methods of Phylogenetic Inference. D. P. Faith and
Paris, France.
J. W. H. Trueman. Australian Museum, 6 College Street,
Horizontal gene transfer (sex) is a well-known phe-
Sydney 2000, Australia.
nomenon in bacterial evolution. This movement of
[Abstract as published by Faith and Trueman (2001)
genes among strains with different evolutionary histor-
Syst. Biol. 50, 331.]
ies produces taxonomic incongruence between phylog-
enies reconstructed from different genes. One possible
On RASA. J. Faivovich. Department of Herpetology,
way to overcome this problem is to identify and re- Division of Vertebrate Zoology, American Museum of
move genes acquired through horizontal transfer. Natural History, Central Park West at 79th Street, New
Transfers are identified by evaluating the discord be- York, New York 10024-5192.
tween individual gene phylogenies and the bacterial Relative apparent synapomorphy analysis (RASA)
phylogeny obtained from a reference data set free of has been heralded as an innovative and highly effective
horizontal transfer (e.g., multilocus enzyme electro- tool to measure “phylogenetic signal,” choose optimal
phoresis or ribotyping data). Character incongruence outgroups, and find and eliminate long-branch at-
is then assessed with incongruence length difference traction. In this presentation it is shown with simple
(ILD) tests between each gene and the reference data examples that the criterion of “phylogenetic signal”
set, with taxon removals in order to identify genes employed by RASA has no straightforward relation-
ship with phylogenetic information and that “Optimal
responsible for significant character incongruence. Al-
outgroup analysis” does not provide a logical means
though this method is a valid solution to the problems
to choose among alternative outgroups.
of horizontal transfer, obtaining the reference data set
is troublesome and consequently, alternative methods
RASAandRandomization.J.S.Farris.Molekylärsys-
are needed. In this study we present a method that
tematiska laboratoriet, Naturhistoriska riksmuseet,
easily accounts for the problems of horizontal transfer
Box 50007, SE-104 05 Stockholm, Sweden.
without using a reference data set.
Supposedly based on a relationship between phe-
For bacteria with a low level of sex, such as Esche-
netic and cladistic similarities, “relative apparent syna-
richia coli, it can be assumed that a rough simultaneous
pomorphy analysis” (RASA) actually involves two dif-
analysis may eliminate the effects of horizontal gene
ferent phenetic measures. The significance test tRASA
transfer, allowing the recovery of the global phylogeny
used in RASA does not provide a reliable assessment
of the species. To test this assumption, we sequenced
of phylogenetic structure in data. It can fail to recognize
11 housekeeping genes form 30 E. coli strains from the
the structure of strongly structured matrices, while it
ECOR collection. We compared the results obtained by
often attributes highly significant structure to random-
the rough simultaneous analysis of the 11 genes with ized matrices.
those of the simultaneous analysis with replacement
of identified transfers (by ILD test) with question Corroboration versus PTP. J. S. Farris. Molekylärsys-
marks. We also compared these results with those ob- tematiska laboratoriet. Naturhistoriska riksmuseet,
tained using the supertree method. Rough simultane- Box 50007, SE-104 05 Stockholm, Sweden.
ous analysis and supertree methods gave similar trees In a series of papers D. P. Faith has contended that
PTP (his name for Archie’s permutation test) measures
and both were able to recover the phylogeny obtained

the Popperian corroboration of phylogenetic hypothe- success of parsimony is related to empirical, a posteri-
ori knowledge of character evolution.
ses. His claims are inconsistent with Popper’s discus-
The point here is that, if the realist and dialectical
sion, as has been explained by A. G. Kluge, J. M. Car-
conception of scientific methodology is right, then con-
penter, and the present author. In a recent article (Faith
siderations of the theoretical plausibility of a proposed
and Trueman, 2001), Faith tries to maintain his position,
theory in the light of the actual (and approximately
but his comments do not address the difficulties that
true) theoretical tradition are evidential considerations;
have already been pointed out.
results of such assessments of plausibility constitute
evidence for or against proposed theories” (Boyd,
Empiricism, Realism, and Descent with Modifica-
1983). “Failure to see the importance of practice leads
tion. N. M. Franz. Department of Entomology, Com-
directly to failure to see the importance of success”
stock Hall, Cornell University, Ithaca, New York 14853.
(Putnam, 1974).
“The basic sequence of operations in a cladistic inves-
tigation is to observe similarities and differences
Fossils and the Linnaean System of Nomenclature.
among organisms, formalize these observations as en-
M. Gandolfo and D. Stevenson. L. H. Bailey Hortorium,
tries in a data matrix, and evaluate the data with an
Cornell University, Ithaca, New York 14853.
algorithm that infers hierarchically nested sets among
For the past 90 years, since the publication of the
the organisms from which the observations were
first International Code of Botanical Nomenclature in
drawn. [. . .] Nowhere in the procedures described
1906, the taxonomy of fossils has been treated with
above, which are those used by cladists of every stripe
special care. Although the Botanical Code applies six
today, is an evolutionary assumption required in gen-
principles, which form the basis of the system of Botan-
eral or particular” (Brower, 2000).
ical Nomenclature, to fossils in the same way as for
The arguments in Brower (2000) correspond, roughly,
any other taxonomic group of plants, there are several
to those of the traditional school of logical empiricism
recommendations specifically for fossil plants, among
during the first half of the former century. The denial
them the definition of what constitutes a taxon. Because
of knowledge of “unobservables,” formulated in the
it is both consistent and flexible, the Linnaean System
evidential indistinguishability thesis (EIT), is charac-
of Nomenclature, which is based on agreed-upon rules
teristic of this school. So is its inability to account for
and recommendations and modifications over the
the instrumental reliability of actual scientific practice.
years, has offered a relatively stable system to name
As a response to this, scientific realism (Boyd, 1983), fossils. During the past 10 years a new nomenclature
has deployed the notion of projectibility—plausibility system has been proposed, now dubbed the Phylo-
in the light of the best currently accepted back- Code. The PhyloCode as posted on the web does not
ground theories. address numerous of the major issues regarding fossils
Here I explore the philosophical implications of sci- that have been treated in the current code. The propo-
entific realism for cladistic practice, with emphasis on nents of this new system also claim that the Linnaean
how it might be that the instrumental reliability of system is archaic and insufficient for modern classifi-
homology assessments is contingent upon their pro- cation. One of their primary arguments is that this new
jectibility in light of the theory of descent with modifi- system is more stable than the Linnaean one. However,
cation. Concepts of homology as topographical similar- because their proposed system of designating groups
ity and as evolutionary, natural kind similarity sensu requires phylogenetic topologies and the inclusion of
(Quine, 1969), are contrasted. This will be controversial, fossil taxa in phylogenetic analyses is often difficult,
but it should become apparent that the contemporary fossil taxonomy will be inherently unstable under the
philosophical consensus among empiricists and real- new system. Other problems with the PhyloCode in-
ists is complex and does not support some of the stand- clude the method of designating and naming clades,
ard cladistic arguments for the independence of pattern since the fossil record is imperfect and as new fossils
and process. Finally, it is argued that part of Farris’ are discovered, the inclusion of these new fossils may
(1983) classic defense of parsimony over likelihood is change the composition of clades and therefore add
more instability to the system. For example, a fossil
based primarily on realist arguments, in so far as the

clade known as the Bennettitales is of uncertain posi- designed theoretical and philosophical tests of ideo-
graphic discovery operations may be scientifically
tion in the seed plants because of competing hypothe-
ses based upon morphological analyses. Because of valid. Empirical tests, however, are incapable of evalu-
ating the scientific merits of competing ideographic
this and the fact that the ending “ales” indicates rank
and taxonomic equivalency with sister group of equal discovery operations. Nonetheless, empirical compari-
sons (not tests) of competing discovery operations may
rank, it would seem that the “Bennettitales” should be
abandoned and “Bennies” substituted for purpose of provide insight into the ways they are misleading, and
therefore may play an important role in stimulating
rank neutrality. Furthermore, most fossil “Bennies” are
very poorly known and may not even be Bennies. Be- critical debate and establishing a scientifically optimal
operation. In practice, theoretical and philosophical
cause we do not even know if all Bennies are really
Bennies or what the infra-Bennie phylogeny is, they tests are often combined to test competing discovery
operations as rigorously as possible.
remain enigmatic. Thus, in keeping with the Phylo-
Code desire for simplicity and uninomials, the individ-
On the Relationships among Ranoid Frogs: A Real
ual Bennies should simply be designated with uni-
Review of the Molecular Evidence. T. Grant and
nomials. We suggest starting with ufo1 and continuing
J. Faivovich. Department of Herpetology, American
through a series of ufo2, ufo3, ufo4, etc. This would
Museum of Natural History, Central Park West at 79th
be a much more accurate way of communicating infor-
Street, New York, New York 10024-5192.
mation on Bennies and allows us to emphasize what
Modern quantitative phyletics was born in a paper
we do not know over what we do know and, most
on frogs (Kluge and Farris, 1969), but despite this
importantly, avoids wasting time recognizing ranks
strong beginning there has been little progress in our
since not having been there, we can never know the
understanding of frog relationships. Conventional wis-
true tree.
dom asserts the monophyly of Neobatrachia, which
branches into two putative clades, Hyloidea and Ra-
Testing Methods: The Evaluation of Discovery
Operations in Systematics. T. Grant. Department of noidea, but the relationships within these groups re-
main unclear. A recent paper by Emerson et al. (2000)
Herpetology, American Museum of Natural History,
Central Park West at 79th Street, New York, New York claims to provide a “review of the evidence” on rela-
10024-5192. tionships within Ranoidea. However, a number of
Scientific discovery requires both abstract, theoreti- methodological shortcomings render their conclusions
cally defined concepts and discovery operations doubtful. Here, we re-examine the relationships of
formed by sets of rules that permit the empirical detec- these frogs based on a much more thorough review of
tion of instances of those concepts. This presentation available molecular evidence analyzed by direct opti-
will examine the ontological status of discovery opera- mization (Wheeler, 1996), as implemented in POY
tions and the tests employed to evaluate them in sys- (Gladstein and Wheeler, 1996–2001).
tematics. The distinction will be made between the
Phylogenetics and Multiple Loci. D. Janies. Depart-
nomothetic (universal, predictive) discovery opera-
ment of Invertebrates, American Museum of Natural
tions used in many sciences and the ideographic (his-
torical, retrodictive) ones employed in systematics, and History, Central Park West at 79th Street, New York,
New York 10024-5192.
between complementary and exclusive discovery oper-
ations. Three types of tests of discovery operations are Congruence is a central concept when using multiple
loci in phylogenetics. The recent availability of data
commonly employed in systematics. Theoretical tests
aim to show that an operation is inconsistent with sets of multiple loci requires the examination of several
assumptions. The ubiquity of nucleic acids as the basis
accepted, well-corroborated, empirical theories. Em-
pirical tests evaluate the performance of competing for life suggests a common ancestry of organisms on
earth. Shared features in DNA may result from this
discovery operations in terms of their results when
applied to the same empirical data sets. Philosophical single history or parallel mutation. Despite variations
in rates of evolution among loci parallel mutation
tests aim to show that an operation is inconsistent with
logical and epistemological principles. Appropriately should be random with respect to the phylogenetic

topology best supported by synapomorphies of multi- prudent to assess the effects of incomplete taxa empiri-
ple loci. Various data sets comprised of ribosomal and cally on a case-by-case basis rather than assuming a
protein-coding loci from several animal lineages will general problem prior to analysis.
be used to test these assumptions. Of particular interest
The Illogical Basis of Phylogenetic Nomenclature.
will be whether topologies based on large data sets
become stable despite the addition of loci. R. A. Keller,*,
† R. N. Boyd,‡ and Q. D. Wheeler,* *De-
partment of Entomology, Cornell University, Ithaca,
Fragmentary Taxa, Missing Data, and Ambiguity: New York 14853; ‡Department of Philosophy, Cornell
Mistaken Assumptions and Conclusions. M. Kearney. University, Ithaca, New York 14853; and †Division of
Department of Zoology, Field Museum of Natural His- Invertebrate Zoology, American Museum of Natural
tory, 1400 S. Lake Shore Drive, Chicago, IL 60605. History, Central Park West at 79th Street, New York,
The frequent conclusion that large numbers of equiv- New York 10024-5192.
alent trees and unresolved consensus trees are due to The current advocacy for the so-called “PhyloCode”
missing data for incomplete taxa (especially fossil taxa) has a history rooted in twentieth century arguments
is often an unsubstantiated assumption. Researchers among biologists and philosophers regarding a puta-
have grappled with the “missing data problem” by tive distinction between classes and individuals. From
excluding fragmentary taxa or fragmentary characters this seemingly simple and innocuous discussion have
for analyses and/or by using less-than-strict consensus come supposed distinctions between definitions and
methods. These strategies are attempting to preserve
diagnosis, classification and systematization, and now
resolution, however, they neglect an important consid-
Linnaean and “phylogenetic” nomenclature. Never-
eration, that is, that instability of taxa may be due
theless the metaphysical dichotomy of class vs individ-
alternatively to missing data, conflicting data, or both.
ual, in so far as its standard applications to the issue
I argue that the core of the problem is in operationally
of biological taxonomy are concerned, is an outdated
treating all ambiguity equally in consensus trees, a
remnant of early logical positivist thinking. Current
practice which can misrepresent the original observa-
views on natural kinds and their definitions under a
tions. Also, it is not necessary to exclude data or parti-
scientific realist perspective provide grounds to reject
tion data sets in order to solve the “missing data prob-
the class vs individual dichotomy altogether in so far
lem.” Instead, all relevant characters and taxa
as biological entities are concerned. We review the role
(including their associated question marks) can be
of natural kinds in scientific practice and the nature
combined at the outset and, if results are ambiguous,
of definitions and scientific classifications. Although
this can be addressed after analysis with a variety of
inherent instabilities of the PhyloCode are clearly suf-
appropriate methods. I recommend strategies that may
ficient to argue against the general application of this
be useful under certain conditions and suggest that,
nominally phylogenetic system, our goal here is to
rather than exclude fragmentary taxa, character sup-
address serious and fundamental flaws in its very foun-
port should be assessed for consensus trees derived
dation by exposing the unsubstantiated philosophical
from studies combining fossil and living taxa. I also
assumptions preceding and subtending it.
re-examine several recent analyses that combine living
and fossil taxa and that have broached the “missing
Typology Revisited: The Nature of Definitions in
data problem” in some manner. Despite extensive dis-
Biological Classification. R. A. Keller*,
† and Q. D.
cussion about missing data problems in the literature
Wheeler.* *Department of Entomology, Cornell Uni-
and the widespread assumption of a connection be-
versity, Ithaca, New York 14853; and †Division of Inver-
tween fragmentary taxa, missing data, and ambiguity,
tebrate Zoology, American Museum of Natural His-
it appears that many recent combined analyses (1)
tory, Central Park West at 79th Street, New York, New
achieve increased resolution by including fragmentary
York 10024-5192.
taxa, (2) encounter problems where most of the appar-
In biology, essentialism is associated with anti-evolu-
ent ambiguity is a result of redundancy in incomplete
tionism. Essentialism has been blamed for causing a
taxa and can be easily resolved, or (3) encounter ambi-
guity that has nothing to do with missing data. It is failure to incorporate the “evolutionary paradigm”

into taxonomical practices. It is maintained that defini- Hong Kong during the rainy season and its compara-
tive lower abundance in Malaysia in January.
tions, being a priori statements, imply that the taxo-
nomic groups under consideration are artificial. Be-
Phylogenetic Placement of the Primitive Crane
cause Aristotelian definitions are tied to the concepts of
Flies (Diptera: Ptychopteromorpha: Tanyderidae)
“class” or “natural kinds,” the concept of “individual”
Based on 18S Ribosomal RNA. J. W. Leathers and D.
was introduced as an alternative to “classes” in evolu-
Judd. Department of Entomology, Oregon State Uni-
tionary biology and the term “definition” was replaced
versity, 2046 Cordley Hall, Corvallis, Oregon 97331-
with “diagnosis.” Nevertheless the metaphysical di-
2907.
chotomy thesis of class/individual is an outdated rem-
The “Nematocera” are a paraphyletic assemblage of
nant of early logical positivism thinking. It is argued
superfamilial clades considered to be primitive within
here for a theory of natural kinds, in which definitions
the order Diptera. Within this eclectic group of taxa,
are a posteriori statements and classes are real and
tanyderids have long been considered the basal lineage
discoverable entities. The nature of scientific defini-
of the order. However, morphological studies to date
tions is discussed and it is argued that pre-Darwinian
have suffered from problems in character homology,
taxonomists since Linnaeus were right in their use of
employment of ground plan coding, and specimen
“definitions” when erecting taxa and in their thinking
availability. Similarly, molecular studies have focused
about taxa in terms of essences in order to achieve
only on those lineages of economic importance and
scientifically useful classifications.
none have included the rare, archaic taxon Tanyderi-
dae. Ribosomal 18S sequence data were collected from
Comparative Diversity of Tropical and Subtropical
13 specimens representing 11 families of “primitive”
Entomopathogenic Fungi. T. F. N. Kwong, R. Y. C.
flies. Taxon sampling was increased by adding se-
Kong, L. L. P. Vrijmoed, and E. B. G. Jones. Department
quences from GenBank. Results suggest that the cur-
of Biology/Chemistry, City University of Hong Kong,
rent classification requires revision. Tanyderids are
83 Tat Chee Avenue, Kowloon, Hong Kong S.A.R.
firmly embedded within the paraphyletic “Nematoc-
The occurrence and distribution of entomopatho-
era,” and the families Tanyderidae and Psychodidae
genic fungi in subtropical Hong Kong and tropical
are strongly supported as a monophyletic group. These
Malaysia are little known. To obtain specimens for a
results conflict with current classifications that place
molecular phylogeny study of fungi pathogenic to in-
the Tanyderidae as the sister group to Ptychopteridae
vertebrates, collections were made in these two re-
(Infraorder: Ptychopteromorpha). Further, Ptychopter-
gions. A higher number of entomopathogenic fungi
idae is supported as the sister group to the clade of
were recorded in Malaysia; more than 100 samples, (Tipulomorpha 1 ((Tanyderidae 1 Psychodidae) 1
were found during a 3-day collecting trip in January (Bibionomorpha 1 Brachycera))).
2001 in Malaysia whereas only about 90 samples were
recorded in 15 field trips between July 2000 and June Incongruence and Homoplasy in the Mammalian
2001. The Hong Kong samples comprise six genera, Skeleton. R. C. McCarthy. Doctoral Program in Homi-
with Cordyceps being the dominant in the rainy season nid Paleobiology, George Washington University,
(May–September), while Hypocrella and its anamorph Washington, DC 20052.
Aschersonia were more abundant in the dry period A priori judgments about phylogenetic utility often
(October–April). Aschersonia and Hypocrella were also lead systematists to disregard certain classes of data.
the dominant genera amongst the Malaysian samples, This viewpoint is especially pernicious in mammalian
which were collected in January, the dry season in systematic studies that employ skeletal characters. In
Malaysia. It is proposed that for Hypocrella and Ascher- many of these studies, characters from the postcranium
sonia, a relatively low air humidity and/or drier envi- are underrepresented largely due to the perception that
ronment are more important than the temperature for the postcranial skeleton is too functionally labile to be
their occurrence. Cordyceps on the other hand probably of use for phylogeny reconstruction. However, it is
requires higher water availability in soil to flourish; unknown how exclusion of postcranial data influences
hypotheses of mammalian phylogeny.
again this is supported by their high abundance in

This study analyzes data from forty previously pub- parsimony, and the distortion index can be used to
compare single-character reconstructions. However, no
lished mammalian phylogenetic studies to test the hy-
pothesis that postcranial and craniodental data recon- index has been proposed which can represent the joint
difference of multiple-character reconstructions. The
struct phylogeny differently. Two sets of analyses were
carried out. First, the incongruence length difference latter type of index will be informative when assessing
whether or not a set of characters shows concentrated
(ILD) and local incongruence length difference (LILD)
tests were used to assess character conflict between transformations in a particular subtree of cladogram.
The null hypothesis of the uniformity of character state
craniodental and postcranial data partitions, both glo-
bally and at specific nodes. Second, partitioned Bremer changes over a full cladogram can be tested against
the alternative hypothesis of concentrated changes in
support was used to assess the relative contribution of
craniodental and postcranial data to the total evidence subtrees. A candidate for multiple distortion index of
character state reconstructions can be constructed with
tree. Data were treated as unweighted and unordered
in all analyses. reference to geometric morphometrics. Terminal nodes
with known character states of a cladogram are fixed
Incongruence between craniodental and postcranial
data partitions was present in ten of the forty data sets, in character space whereas internal nodes are not. Hy-
pothetical deformation can be made such that coordi-
but was generally localized to a few taxa rather than
globally distributed on any given tree. In general, phy- nates (one or more characters) of corresponding
internal nodes coincide in character space. The defor-
logenies reconstructed from postcranial data were re-
markably consistent with those reconstructed from mation of character state reconstructions are modeled
by thin-plate spline function. “Bending energy” associ-
craniodental data. Finally, partitioned Bremer support
results indicate that postcranial data add resolution to ated with the deformation represents the joint differ-
ence of multiple-character reconstructions. Moreover,
the total evidence tree. Taken together, these results
suggest that the postcranium is not simply “overwrit- orthogonal decomposition of deformation in character
space is used to distinguish between “affine”-type and
ten” by a functional signal and that characters from
the postcranium should not be excluded from phyloge- “nonaffine”-type character state changes. The former
is some kind of global trend in character transforma-
netic analyses a priori. Instead, postcranial characters
have the potential to significantly contribute to hypoth- tion, the latter is more or less localized concentrations
of changes.
eses of mammalian phylogenetic history.
Quantitative Comparison of Parsimoniously Re- Dies, Areas, and Species. J. Muona. Entomology Di-
vision, Finnish Museum of Natural History, JP-17,
constructed Ancestral Character States in a Clado-
gram. N. Minaka. National Institute for Agro-Environ- 00014-University of Helsinki, Finland.
The idea that cladistic phylogenetic analysis does
mental Sciences, Tsukuba, Ibaraki 305-8604, Japan.
Character state sets of hypothetical ancestors that not require the assumption of evolution has emerged
again recently. According to this view, sometimes iden-
are parsimoniously reconstructed in a cladogram can
be compared quantitatively from a graph-theoretical tified as “pattern cladism,” the character distributions
and the hierarchial structure of the relationships are
viewpoint. MPRs (most parsimonious reconstructions)
of hypothetical character states in internal nodes of a all that is needed. In fact, proponents of this view have
gone as far as saying that evolutionary assumptions
cladogram forms a lattice for which whose ACCTRAN
is the minimal element whereas DELTRAN is the maxi- are detrimental at this stage of analysis. Others see the
situation in an entirely different light. According to
mal one. Differences between a pair of character states
can be quantified as the sum of differences in lengths them, cladistic analysis is based on the idea that evolu-
tion has taken place, not as pattern explanation as in the
of all corresponding subtrees for those cladograms. In
particular, the sum of subtree length differences from maximum likelihood approaches, but as background
knowledge sensu Popper.
ACCTRAN is called the “distortion index.” Several
properties of the distortion index and their phyloge- Cladistic methods can be applied to many kinds of
data—they need not be biological. Human history is
netic implications are discussed. Ancestral character
states are reconstructed character by character under in many ways analogous to phylogenetic history and

it appeared tempting to apply the methodology in his- characters of a living organism were—was suspect.
This would be especially dangerous in biogeography,
torical research. I have done this in a numismatic con-
text. The problem was the minting sequence of the where entire biotas have been and will be destroyed
and replaced with others. The analysis of coin data
Rome mint coins of the emperor Marcus Salvius Otho,
who ruled for three months in AD 69. suggested that phylogenetic analysis requires a mecha-
nism that explained the inseparable connection be-
Coins exhibit all the characteristics pattern cladists
require for data. They are easily defined, have numer- tween specimens, their characteristics and change in
time. To me it appeared obvious that this was a reflec-
ous unambiguous characters and form hierarchial pat-
terns. In addition, they show geographical variation tion of the requirement “modification by decent” and
thus the proponents of pattern cladism were in error—
and “evolutionary” change in time. Roman coins were
minted with a pair of dies that produced on average evolutionary background knowledge is required.
(Abstract submitted after meeting).
30,000 coins. The reverse (“tails”) die usually wore
down sooner than the obverse (“heads”) die and thus
The PhyloCode Is Poorly Reasoned and Fatally
one can discover sequences of die-links as well. These
Flawed, and the Current Codes of Nomenclature Are
will reveal actual “genealogical” relationships between
Not. K. C. Nixon. L. H. Bailey Hortorium, Cornell Uni-
dies, although these sequences are mostly quite in-
versity, Ithaca, New York 14853.
complete.
Promoters of the so-called “PhyloCode” (PC) have
Contrary to the results obtained with biological data,
mounted an intensive and deceptive publicity cam-
those based on coin data can be shown to be incorrect
paign. At the centerpiece of this campaign have been
with external evidence. My analysis of the Otho coins
slogans such as that the “Linnaean” System will “goof
suggested a minting order in conflict with the known,
you up,” that the PhyloCode is the “greatest thing
written evidence—especially the Acts of the Arval
since sliced bread” and that systematists are “afraid”
Brethren. The results could be incorrect because of ei-
to propose new names because of “downstream conse-
ther bad data or problems in the analysis. Calling data
quences.” Aside from such subscientific spin and slo-
bad when results are not as expected is about as bad
ganeering, proponents of the PC have offered nothing
a scientific approach as there is. In this case there was
real to back up claims of greater stability for their new
no reason to believe this to be the case. The assump-
system. They have also misled many into believing
tions of the analysis could have been violated, however.
that the PC is the only truly phylogenetic system. The
When I considered this, two obvious, related explana-
confusion that has been fostered involves several dis-
tions emerged. The characteristics of coins could reflect
crete arguments, concerning (1) a new “method” of
separate, conflicting “phylogenies.” The actual images
“designating” names; (2) rank-free taxonomy; (3) unin-
of the emperor (on obverse) and the reverse image
omial nomenclature; (4) issues of priority. Claims that
(often a divine figure) as well as the legends on both
the PhyloCode produces a more stable nomenclature
sides served purposes of propaganda and were
are false, as shown with the example of paleoherbs.
changed accordingly. The characteristics of the actual
A rank-free system of naming requires an annotated
coin (metal, weight, flan size, etc.) were adjusted quite
reference tree for even the simplest exchanges of infor-
independently of the obvious features of the coins and
mation, would be confusing at best, and would cripple
for other reasons. In addition to this problem, any set
our ability to teach, learn, and use names in the field
of characteristics of a coin could change overnight
or in publications. We would be confronted by a mass
when an emperor died and his successor so decided.
of polynomial names, tied together only by a tree
Clearly coin data suffered from the possibility of show-
graphic, with no agreed upon name (except a unino-
ing evidence of “multiple real phylogenies” as well
mial, conveying no hierarchy) to use for any particular
as from the possibility that most characters could be
species. The separate issue of stability in reference to
removed and replaced as a block by another, entirely
rules of priority and rank can be easily addressed
new set of characters. The latter problem appeared
within the current codes, by implementing some sim-
especially dangerous. It also suggested that any biolog-
ple changes as will be proposed here. Thus, there is
ical analysis based on characters that are not insepara-
bly combined with the unit of analysis—as inherited no need to “scrap” the current “Linnaean Code” for

a poorly reasoned, logically inconsistent, and fatally this site will be to integrate the various important as-
pects of systematics, without a blind and transparent
flawed new code that will only bring chaos.
emphasis on “tree thinking.” Instead, trees and tree
An Integrated Taxonomic Computer Package for classifications will be used as navigation tools to en-
Desktops, Handhelds, and the World Wide Web for hance the ability of the user to retrieve information—
Management and Analysis of Cladistic, Diagnostic, including descriptions and images to be used in teach-
Image, and Monographic Data. K. C. Nixon. L. H. ing. As such, diagnostic keys will be available for use
Bailey Hortorium, Cornell University, Ithaca, New directly over the web, or as free downloads for use
York 14853. on desktops and, more importantly, on handhelds in
The most pressing problem that faces the modern the field.
taxonomist is management of the massive amount of
Higher Level Phylogeny of Ephemeroptera: Molec-
data that have become available in recent years. While
ular Evidence. T. H. Ogden and M. F. Whiting. Brigham
many novice workers are highly impressed with mo-
Young University, 574 WIDB, Provo, Utah 84602.
lecular data, the more traditional taxonomists who ac-
Phylogenetic relationships among mayflies are
tually work in the field and know and study real taxa
poorly known and current classifications do not appear
have been presented with the opportunity to develop
to closely reflect phylogeny. DNA sequence data were
and present useful information in novel ways. The
collected for a wide range of mayfly taxa representing
internet and web-based information systems are most
every major lineage. These data were used to estimate
prominent and accessible at this time, but are mostly
phylogenetic relationships at the familial level and to
restricted to stationary desktop systems and cannot be
illuminate the phylogenetic position of Ephemeroptera
used in the field.
relative to other insect orders. The monophyly of Pa-
Over the past year, I have developed a diagnostic
leoptera (Odonata 1 Ephemeroptera) and the currently
interface within the program Winclada that allows the
recognized mayfly suborders will be discussed in light
user to interactively key taxa using the same data for-
of these additional data.
mats as supported by Hennig86, NONA, TNT, and
Transposable Elements: Evolution and Phylogeny.
Winclada for cladistic matrices. Support for linking
G. Petersen and O. Seberg. Botanical Institute, Univer-
digital images to taxa, characters, and trees in various
sity of Copenhagen, Copenhagen, Denmark.
formats (e.g., jpeg and gif) have also been added to
Transposable elements may take up very large pro-
Winclada. The diagnostic program within Winclada
portions of the eukaryote genome, in Zea even up to
has also been successfully ported to handheld, clam-
95%. Many studies have tried to explore transposable
shell and pocket PC computers running the Win-
element evolution, but often these studies are flawed
dowsCE operating system. The handheld versions are
by their lack of a solid phylogenetic background. Some
fully useable in the field, including the entry and edit-
transposable elements have also been used for phylo-
ing of both diagnostic and cladistic data; data entered
genetic analyses, but due to the copious nature of most
in the field can then be used directly as either cladistic
elements, problems of homology assignment burden
or diagnostic data in the desktop version. In addition
many of these studies. Absence/presence of certain
to these extensions of Winclada, a Winclada tree viewer
types of elements has even been regarded as characters
written in JAVA is now available for viewing of small
free from homoplasy. Based on empirical studies of
or very large cladistic trees remotely over the web. The
transposable elements belonging to the Stowaway fam-
WebTree interface can quickly and easily display trees
ily of transposable elements the idea of a “homoplasy
with 500 or more taxa—with average time from begin-
free” character must be refuted. Based on phylogenetic
ning of download to full display over phone modems
analyses of sequences flanking the Stowaway elements
of less than 5 seconds (including the applet) for the
evolutionary aspects of these elements can be explored.
567-taxon 3-gene seed plant tree. This interface will
be the basis of a new taxon-oriented Web site, www. Exorcising the Demon: Parsimony Escapes the
diversityoflife.org, that will be a repository for cladistic Felsenstein Zone with More Data from the Same Dis-
matrices, phylogenetic trees, interactive diagnostic tribution. K. M. Pickett. Department of Entomology,
Ohio State University, Columbus, Ohio 43210.
keys, descriptions, and image galleries. The intent of

A fundamental assumption of the maximum likeli- results of the sensitivity analysis suggest the presence
hood school is that parsimony produces wrong trees of possible biases affecting the performance of most of
with data from certain distributions, and adding more these measures. Parameters such as tree shape, tree
of the same data will not rescue the analysis. Using size, and number of possible ages are found to have
590 bases of COI sequenced from the social wasp genus an important impact on the mean values of all available
Apoica and its relatives, one hundred bases were ran- measures. Empirical data sets are also analyzed testing
domly selected, and parsimony tree(s) reconstructed. the presence of the suggested biases.
To these, 100 bases of the remaining 490 were added,
and parsimony tree(s) reconstructed. The stepwise ad- The Phylogeny of the Collembola Based on Mor-
dition of 100 of the unsampled bases continued until phological and Molecular Data. J. A. Robertson and
all bases were added. This procedure was repeated 100 C. A. D’Haese. 574 WIDB, Brigham Young University,
times. A large percentage of the smaller partitions of Provo, Utah 84602.
data demonstrate a condition consistent with long A better understanding of the phylogeny of the Col-
branch attraction, according to the criteria set forth by lembola could provide insight into the ordinal relation-
advocates of maximum likelihood, yet the tree deriving ships and habits of the early Collembola. Morphologi-
from all the data shows no such error. This calls into cal and molecular data sets (18S rDNA, 28S rDNA,
question whether the theoretical foundation of maxi- 16S rDNA, and histone 3) from a broad taxonomic
mum likelihood applies to natural data. sampling were used to assess the phylogenetic relation-
ships within the Collembola. Specifically, the mono-
Biases in Maximum Likelihood and Parsimony: A
phyly of the major lineages within the Collembola and
Simulation Approach to a 10-Taxon Case. D. Pol.
their placement relative to each other was investigated.
Department of Vertebrate Paleontology, American
Analyses were performed using Direct Optimization
Museum of Natural History, Central Park West at
under a variety of parameter settings. A sensitivity
79th Street, New York, New York 10024-5192.
analysis was performed and the resulting tree from the
Biases present in maximum likelihood and parsi-
parameter set that maximized congruence among the
mony are investigated through a simulation study in
data sets was retained as the best phylogenetic esti-
a ten-taxon case in which several long branches coexist
with short branches in the modeled topology. The per- mate. Collembola, Poduromorpha, Neelipleona, and
formance of these methods is explored while increasing Symphypleona were recovered as monophyletic
the length of the long branches with different amounts groups. There is resolution at the familial level. Podura
of data. Also, simulations with different taxonomic aquatica is not basal but is nested within the Poduro-
sampling schemes are examined through this study. morpha.
The presence of a strong bias in parsimony is corrobo-
rated: the largely known long branch attraction. Likeli- The Linnaean System and Its 250-Year Persistence.
hood performance is found to be sensitive to the mere R. T. Schuh. Department of Entomology, American Mu-
presence of extreme branch length disparity, retrieving seum of Natural History, Central Park West at 79th
long branch attraction and long branch repulsion to- Street, New York, New York 10024-5192.
pologies, irrespective of the correctness of the model The Linnaean system of nomenclature has been used
used. and adapted by biologists over a period of almost 250
years. Under the current system of codes it is now
Performance of Several Measures of Stratigraphic
applied to more than 2 million species of organisms.
Fit to Phylogenetic Hypotheses. D. Pol and M. A.
Inherent in the Linnaean system is the indication of
Norell. Department of Vertebrate Paleontology, Ameri-
hierarchic relationships.
can Museum of Natural History, Central Park West at
The Linnaean system has been justified primarily on
79th Street, New York, New York 10024-5192.
the basis of stability. Stability can be assessed on at
Measures designed to evaluate the congruence be-
least two grounds: the absolute stability of names, irre-
tween stratigraphic and phylogenetic temporal infor-
spective of taxonomic concept; and the continuing ap-
mation are evaluated here using sample cases and sen-
sitivity analysis to different parameter values. The plication of the same names to the same concepts. More

recent arguments have invoked conformity to phyloge- is shown that the “risk” of inconsistency is overesti-
mated by Felsenstein’s equation (1978), due to the sim-
netic methods as the primary basis for choice of nomen-
clatural systems, but even here stability of names as ple nature of his model.
they relate to monophyletic groups is claimed as the
Homology Misunderstood! O. Seberg and G. Pet-
ultimate objective. The idea of absolute stability was
ersen. Botanical Institute, University of Copenhagen,
wrong from the start. The reasons are several. First,
Copenhagen, Denmark.
taxa are concepts, no matter the frequency of assertions
The concept of homology is of utmost importance in
to the contrary; as such, they are subject to change at
comparative biology. Recent discussions have mainly
all levels and always will be. Second, even if the true
centered on the meaning of homology in traditional
nature of all taxa could be agreed upon, the goal would
parsimony analysis and three-taxon statement analy-
require that we discover them all and correctly recog-
sis. However, homology is also used to describe the
nize them for what they are. Much of biology is far
behavior of pairing chromosomes during meiosis and
from that goal at the species level and even further for
the level of chromosome pairing in interspecific hy-
generic and higher groups. Botanical nomenclature is
brids has been used as an indicator of relationship of
more stable than zoological in the spelling of species
the parent species. This use of the concept of homology
epithets. This simplifies database creation and mainte-
in cytology is briefly discussed and is shown to be an
nance. Yet, stability at this level is superficial. Nomen-
unnecessary statement of variable categorical signifi-
clature serves as a tool for biology. Absolute stability
cance and a source of confusion.
would hinder scientific progress rather than promote
it. It can been demonstrated that the scientific goals of Congruent and Incongruent Mammalian Mito-
chondrial Genes. N. A. Shevchuk and M. W. Allard.
systematists are far from achieved. Thus, the goal of
nomenclatural stability is illusory and misguided. The Department of Biological Sciences, George Washington
University, Washington, DC 20037.
primary strength of the Linnaean system is its inherent
ability to portray hierarchic relationships; stability is We compiled a matrix that included all mitochon-
drial protein coding genes for 41 mammals from 14
secondary.
different orders in order to isolate the source of incon-
Inconsistency of Maximum Parsimony Revisited: gruence among the genes. This matrix was examined
In Search of the Felsenstein Zone. S. Schulmeister. for congruence using different partitioning, weighting
Institute of Zoology, Berliner Strasse 28, 37073 Göt- and sampling strategies. The incongruence length dif-
tingen, Germany. ference test shows significant incongruence among the
Felsenstein (1978) showed that the method of maxi- 13 gene partitions used simultaneously, regardless of
mum parsimony can be inconsistent, i.e., lead to an the weighting method (equal, third codon or transver-
incorrect result with an infinite amount of data. The sion weighting). Omission of any of the 14 mammalian
situation in which this inconsistency occurs is often orders alone or in combinations from the matrix does
called the “Felsenstein zone,” the phenomenon also not result in a statistically significant improvement of
known as “long-branch attraction.” congruence, suggesting that taxonomic sampling will
First, an introduction to Felsenstein’s approach is not improve congruence among the data sets. How-
given in the talk. He derived an inconsistency condi- ever, in pairwise comparisons, most of the 13 genes
tion from a model for four taxa with only two different are congruent with the rest of the genes combined
parameters for the probability of change on the five except for NADH: ubiquinone oxidoreductase subunit
branches connecting the four taxa. His approach is 6 gene (ND6), cytochrome oxidase subunit II (COII),
used to derive the inconsistency condition of maxi- and cytochrome oxidase subunit III (COIII) gene. These
mum parsimony from the most general model for four genes each show significant incongruence with the rest
taxa, i.e., with five different parameters for the proba- of the matrix. Omission of ND6, COII, and COIII sig-
bilities of change on the five branches and characters nificantly improved congruence among mitochondrial
with k states. This general inconsistency condition is protein coding genes. Nevertheless, phylogenetic trees
examined analytically and compared to a condition resulting from the complete matrix and the truncated
matrix (both with equal weighting of characters) are
from a two-parameter model for k-state characters. It

almost identical, suggesting that incongruence is not were used (resolution, branch support, and congruence
with independent evidence). The nucleotide-based
a valid basis for exclusion of data from phylogenetic
analyses. The three proteins encoded by ND6, COII, jackknife tree was much more resolved than the amino
acid-based tree, for both large and small clades. Nearly
and COIII perform ancillary or disposable roles in their
respective multisubunit enzymes, which can be the twice the percentage of well supported clades resolved
in the 18S rDNA tree were resolved using nucleotide
reason for their divergent properties.
characters (91.7%) relative to amino acid characters
Comparison of Parsimony and Likelihood in Rela-
(50%). The well supported clades resolved by both
tion to Some Simple Data Sets and Some Principles of
character types were much better supported by nucleo-
Corroboration. M. E. Siddall. Division of Invertebrate
tide characters (98.7% vs 83.8% average jackknife sup-
Zoology, American Museum of Natural History, Cen-
port). Nucleotide characters outperformed amino acid
tral Park West at 79th Street, New York, New York
characters even when both matrices were reduced to
10024.
the same number of parsimony-informative characters.
The stark differences of opinion between parsimony
For the reduced nucleotide-based matrix, 73.3% of the
and likelihood modes of inference are illustrated in
well supported clades were resolved, and the well-
the context of several simple data sets that are easily
supported clades resolved by both character types
visualized. Moreover, the performances, of likelihood
were better supported by nucleotide characters (91.5%
and parsimony are compared in relation to varying
vs 86.4%). The faster evolving nucleotide characters
character inclusiveness and taxonomic inclusiveness
with a smaller average character-state space outper-
on these simple data sets. Both likelihood and parsi-
formed the slower evolving amino acid characters with
mony are evaluated in terms of Popperian corrobora-
a larger average character-state space. The increase in
tion on one of these data sets and it is argued that the
character-state space for amino acid characters was
likelihood approach reduces testability to zero, thus
found to be minimal; excluding polymorphisms and
annihilating any possibility for corroboration. The
autapomorphies, amino acid characters had, on aver-
“idea of a law which determines the direction and
age, only a 17% increase in character-state space rela-
character of evolution is a typical 19th century mistake,
tive to nucleotide characters. The nucleotide characters
arising out of the general tendency to ascribe to ‘Natu-
had an average of 21.6% more steps per parsimony-
ral Law’ the junctions traditionally ascribed to God”
informative character. These results indicate that char-
(Popper, 1963: 339).
acters should not be inversely weighted (or excluded
altogether) by their inferred frequency of change. Nu-
Conflict between Nucleotide and Amino Acid
Characters. M. P. Simmons, H. Ochoterena, and J. V. cleotide characters outperformed amino acid charac-
ters even with 90% of the terminals deleted. The lack
Freudenstein. Ohio State University Herbarium, Ohio
State University, 1315 Kinnear Road, Columbus, of resolution on the amino acid jackknife trees appears
to be caused by a lack of congruence among the amino
Ohio 43212.
Slowly evolving characters, such as amino acids and acid characters, not a lack of replacement substitutions.
Of the 123 clades resolved on the amino acid jackknife
replacement substitutions have generally been favored
over faster evolving characters for inferring phyloge- tree, 11% (14) conflicted with clades resolved by the
nucleotide characters. There is independent evidence
netic relationships. But amino acids constitute compos-
ite characters and, because of the degenerate genetic for 12 of these 14 conflicts. Independent evidence sup-
ported the nucleotide-based resolution for 92% (11) of
code, are subject to convergence. The Soltis et al. (2000)
567-terminal simultaneous analysis of atpB, rbcL, and these conflicts and the amino-acid-based resolution for
only one of these conflicts. Of the 13 conflicts in the
18S rDNA was used as an empirical example to test the
use of amino acid vs nucleotide characters for protein- amino acid tree that were not supported by indepen-
dent evidence, eight were supported by composite
coding genes at deeper taxonomic levels. Nucleotide
characters for atpB and rbcL had 6.5 times the amount and/or convergent character states. These findings
suggest that coding nucleotide sequences only as
of possible synapomorphy as amino acid characters.
Nucleotide characters outperformed amino acid char- amino acid characters for phylogenetic analysis pro-
vides little benefit and may yield misleading results.
acters for all three measures of phylogenetic signal that

Artifacts of Coding Amino Acids and Other Com- to as synapomorphies, character polarity, and the gen-
eration of relationships from character state distribu-
posite Characters for Phylogenetic Analysis. M. P.
Simmons and J. V. Freudenstein. Ohio State University tions. Bolin argued that systematists need to focus more
attention to the reconstruction of evolutionary histor-
Herbarium, Ohio State University, 1315 Kinnear Road,
Columbus, Ohio 43212. ies, and he argued that this was the “pivot around
which modern taxonomy should revolve.” Bolin con-
A phylogenetic analysis can be no better than the
characters on which it is based. Just as it is inappropri- tinued by arguing that “naming and describing are
necessary steps in systematic work, but it is the inter-
ate to code character states of individual characters as
separate presence/absence characters, it is inappropri- pretation of the morphological data into evolutionary
history which elevates this study to the status of a
ate to combine independent characters because not all
information in the data is being utilized. Composite science.” The historical importance of Bolin’s system-
atic views will be outlined, discussed, and compared
characters link otherwise discernible states from differ-
ent characters together to form new character states. to Hennig’s work and its modern incarnation. Finally,
Bolin’s phylogenetic analysis of the marine sculpin Ge-
There are two related problems with this coding. First,
there is a loss of hierarchic information between the nus Icelinus is compared to my recent analysis of this
genus to highlight similarities and differences between
reductive and composite characters when unordered
states are used. Second, the linking of independent these two independently derived sets of systematic
principles.
characters that occurs during the construction of com-
posite character states creates putative synapomor-
Molecular Phylogeny of Costaceae (Zingiberales):
phies that were not present in the independent charac-
Floral Evolution in a Family of Tropical Monocots.
ters. For amino-acid characters, the problem may occur
C. D. Specht. New York Botanical Garden, Bronx, New
whenever more than one position of a codon is variable
York 10458.
among the terminals sampled. Groups that are re-
The phylogenetic relationships of Costaceae, a tropi-
solved as paraphyletic using reductive coding may be
cal monocotyledonous family sister to the gingers (Zin-
resolved as monophyletic using composite coding. The
giberaceae), were investigated with a combination of
artificial character states indicated by the amino-acid
two chloroplast loci (trnL-F locus including the trnL
characters are unlikely to be congruent with the true
intron, 3 trnL exon, and the trnL-F intergenic spacer
gene tree, and therefore, these artificial character states
and the trnK locus including the trnK intron and matK
are likely to be homoplasious. Amino-acid characters
coding region) and one nuclear locus (ITS1 5.8s ITS2).
have been considered to be more conservative than
The resulting parsimony analysis of selected taxa that
nucleotide characters. While the intent may be one of
demonstrate the range of floral morphological varia-
conservatism, the actual effect, with the complications
tion in the family shows that the Caldavena-type floral
caused by the use of composite characters, is not.
morphology is ancestral to the group and that both
Tapeinochilos species and a Monocostus 1 Dimerocostus
Early “Cladistic” Principles in Systematic Ichthyol-
ogy: Rolf Bolin’s 1934 Stanford University Doctoral clade represent recent divergences. The genus Costus
is broadly paraphyletic but Costus subgenus Eucostus
Dissertation. W. L. Smith. Department of Ichthyology,
American Museum of Natural History, Central Park K. Schum represents a large monophyletic radiation
that is poorly resolved. Within this clade, secondary
West at 79th Street, New York, New York 10024.
In a response to his problems with the evolutionary analyses suggest that pollination syndrome, tradition-
ally used for taxonomic and classification purposes
classifications generated by North American ichthyolo-
gists at the turn of the century, Rolf Bolin presented a within the genus Costus, is a relatively plastic trait of
limited phylogenetic utility. This represents the first
systematic study of the sculpins (Teleostei: Cottidae)
of California in which he outlined a set of systematic detailed investigation into intrageneric and interspe-
cific evolutionary relationships within the family Cos-
principles that is similar to the principles outlined in
Hennig’s Phylogenetic Systematics. Bolin’s disserta- taceae and presents some novel evolutionary trends
with respect to floral morphology and biogeography.
tion discussed the use of what would now be referred

A Molecular Phylogeny of the Orthopteroid Insect According to theoretical studies, recently diverged
species may contain nonmonophyletic gene lineages.
Orders. M. D. Terry and M. F. Whiting. Brigham Young
University, Provo, Utah 84604. Different modes of speciation can explain the presence
of poly-, para- and monophyletic lineages within spe-
The Orthopteroid insects, also referred to as Poly-
neoptera, is a putatively monophyletic group that in- cies. We have studied the diversity of mitochondrial
DNA lineages in ten of eleven butterfly species belong-
cludes the basal orders of neopterous insects: Plecop-
tera (stoneflies), Dermaptera (earwigs), Isoptera ing to the genus Phyciodes (Lepidoptera: Nymphali-
dae). We sequenced a 1450-bp segment of the COI gene
(termites), Blattaria (cockroaches), Mantodea (praying
mantids), Embiidina (webspinners), Phasmida (stick for 96 individuals and found 68 unique haplotypes. A
cladistic analysis of the 68 sequences produced 4
insects), Grylloblattoidea (ice bugs), Orthoptera (grass-
hoppers and crickets), and perhaps Zoraptera (zorap- equally parsimonious trees, which revealed numerous
poly- and paraphyletic lineages in 4 of the 10 species
terans). Past and current hypotheses regarding the phy-
logeny of this group are varied and quite incongruent. sampled. The great variation in mtDNA complements
the great variation in morphological features of taxa in
Nucleotide sequence data for 3 genetic markers (18S
rDNA, 28S rDNA, and histone-3) for approximately the genus Phyciodes, suggesting that this is a relatively
young group of species that is perhaps still going
135 taxa representing a broad diversity of polyneop-
teran and outgroup taxa are presented. Preliminary through the process of speciation. The greatest incon-
gruence between mtDNA and morphologically de-
analysis of ribosomal data support a monophyletic
Polyneoptera (excluding Zoraptera), Dictyoptera fined species is found in one of the three informal
species groups. This group of four species shows ex-
(Isoptera 1 Mantodea 1 Blattoidea), and Orthoptera
1 Phasmida. A robust phylogeny of Polyneoptera is treme polyphyly of mtDNA lineages in three species.
The complex pattern is likely to be the result of both
an important step toward an understanding of the evo-
lution and diversification of early neopterous insects. incomplete lineage sorting and introgressive hybrid-
ization, both recent and historical. Our results show
Expressed Sequence Tags for Molecular Syste-
that systematic studies of closely related species based
matics of Beetles. A. Vogler,* K. Theodorides,* J.
on mtDNA must have a carefully planned sampling
Gomez-Zurita,† A. de Riva,† and P. Foster.† *The Natu-
strategy to provide a reliable picture of the relation-
ral History Museum, London, United Kingdom; and
ships of the species. When mtDNA is the only feasible
†Imperial College at Silwood Park, Ascot, United
source of molecular data, we would recommend that
Kingdom.
several individuals per species be sampled, with the
Generating trees from multiple genetic loci is difficult
sample size being increased in cases where much varia-
in taxa where little sequence information from close
tion is noticed within species.
relatives is available. In Coleoptera (beetles) very few
sequences for single copy nuclear genes are known,
A Higher Level Phylogenetic Study of the Skipper
and hence a degenerate PCR approach for determining
Butterflies (Lepidoptera: Hesperiidae). A. D. Warren.
basal relationships in the Order is problematic. We are
Department of Entomology, 2046 Cordley Hall, Oregon
using entire cDNA libraries for phylogeny reconstruc-
State University, Corvallis, Oregon 97331-2907.
tions, altogether circumventing PCR based ap-
The purpose of this study is to propose a phyloge-
proaches. This talk will provide a preliminary analysis
netic classification for the family Hesperiidae at the
of data obtained so far, with emphasis on the magni-
world-level. The classification proposed by Evans
tude of paralogy confounding phylogenetic analysis.
(1937, 1949, 1951, 1952, 1953, 1955) considers the fauna
Congruence of phylogenetic signal is a key criterion
of each world region separately, and made little at-
for detecting paralogy in comparative genomics.
tempt to indicate relationships between closely related
genera in different world regions. In this study, at least
Poly-, Para-, and Monophyletic mtDNA Lineages
100 genera from all of Evans’ groups and world regions
in Phyciodes Butterfly Species (Lepidoptera: Nymph-
will be studied. A detailed morphological study will
alidae). N. Wahlberg, R. Oliveira, and J. A. Scott. De-
complement DNA sequence analyses from regions of
partment of Entomology, Stockholm University, 10691
Stockholm University, Sweden. one mitochondrial (COI and II) and two nuclear genes

(Ef-1a and wingless). Separate and combined analyses Understanding the relationships between members
are made of these data sets. Preliminary results suggest of the Myxozoa and other taxa has advanced signifi-
that the Trapezitinae are monophyletic, and highlight cantly over the past several years. Molecular systemat-
the close relationships between the Hesperiinae and ics, with emphasis on 18S rDNA sequences, has re-
Megathyminae as well as the Pyrrhopyginae and Pyr- solved some relationships within this interesting
ginae. group, but has left others unanswered. To date there are
over 65 18S rDNA sequences available for myxozoans.
Limitations of Relative Apparent Synapomorphy Regarding higher phylogeny, the Myxozoa group
Analysis (RASA) for Measuring Phylogenetic Signal. within the Cnidaria, with support both from molecular
J. W. Wenzel, M. P. Simmons, C. P. Randle, and J. V. and from morphological data. Within the Myxozoa
Freudenstein. Department of Entomology, Ohio State relationships agree in many ways with traditional clas-
University, 1315 Kinnear Road, Columbus, Ohio 43212. sification schemes, however there are some discrepan-
RASA is a method intended to measure phylogenetic cies. Members of the order Multivalvulida are one of
signal in matrices, to assist with rooting a tree, and to the most stable groups. Traditionally, this order is sub-
identify taxa subject to long branch attraction. We show
divided into families based on the number of polar
that RASA may fail to find signal in matrices with
capsules observed in spores and includes the genera
strong signal or may indicate high levels of phyloge-
Kudoa, Hexacapsula, Trilospora, and Unicapsula. Recent
netic information for matrices that are indecisive. An
analysis of a Hexacapsula sp. (family Hexacapsulidae)
empirical example shows how RASA may indicate in-
from Australia showed that it groups within a clade
creasing phylogenetic signal for matrices for which the
comprised of Kudoa spp. (family Kudoidae). Although
strict consensus of most parsimonious trees is progres-
this information is preliminary (i.e., based on only one
sively more poorly resolved. Another empirical exam-
gene), it suggests a need for revision of family level
ple shows that RASA chooses an ingroup terminal as
classification within the Multivalvulida. Another inter-
the ideal outgroup, rather than either of the two actual
esting member of this order is Kudoa thyrsites, a parasite
outgroups. In a hypothetical example, RASA identifies
of economic concern in fisheries with a surprisingly
a terminal with a zero-branch length as being a prob-
broad host and geographic distribution (found world-
lematic long branch terminal, and following RASA
wide and in greater than 30 different fish hosts of sev-
methodology generates a long branch problem that did
eral families). Using rDNA analyses of isolates from
not exist in ordinary parsimony analysis.
various hosts and regions of the world, we found that
they separate into two clades regardless of host: one
Search-Based Character Optimization. W. Wheeler.
clade of Atlantic isolates and the other of Pacific iso-
American Museum of Natural History, Central Park
lates. In addition, two isolates morphologically indis-
West at 79th Street, New York, New York 10024.
tinguishable from typical K. thyrsites (one from Chile
A novel method for optimizing molecular sequence
and one from Australia) cluster completely separately
characters is proposed. This method is based on a
from the two major clades of this species. We are cur-
search for hypothetical ancestral sequences as opposed
rently studying relationships of K. thyrsites within more
to estimation. This procedure can yield more parsimo-
narrow geographic regions utilizing more variable
nious cladograms than Multiple Sequence Alignment
sequences.
or Optimization Alignment. Computational properties
are discussed as well as the extension of this method
A Synopsis of Similarity Classifications. B. Wiesem-
to other forms of genomic level character analysis.
üller and H. Rothe. Institut für Zoologie und Anthropo-
logie, Universität Göttingen, Göttingen, Germany.
Advances in Our Understanding of the Myxozoa
Highlighting distinctions between different kinds of
and Relationships among Parasites of the Order
character correspondences is imperative when dis-
Multivalvulida. C. M. Whipps, M. E. Siddall, and M.
cussing the practice of systematics. However, different
L. Kent. Center for Salmon Disease Research, Depart-
authors tend to use varied terminologies to classify
ment of Microbiology, 220 Nash Hall, Oregon State
University, Corvallis, Oregon 97331-3804. similarities. The aim of this presentation is to surmount

existing communication problems between syste- convergence. When Wagner (1961) presented his phy-
logenetic method, he only distinguished between “gen-
matists, by presenting a comparative survey of these
different terminologies. Overall, three questions arise eralized or primitive” and “specialized or secondary”
conditions, which correspond to plesiomorphic and
in the phylogenetic classification of similarities: Firstly,
whether the shared similarity is derived (apomorphy); apomorphic conditions in Hennig’s terms. Farris and
Kluge applied the names “symplesiomorphy” and
secondly, whether the similar characters are descended
from the same ancestral character (homology); and “synapomorphy” from Hennig to these terms from
Wagner. As a result, they combined Hennig’s concepts
thirdly, whether the similar character states evolved
independently (homoplasy). Considering all these as- of synapomorphy and convergence, calling both “syna-
pomorphy” (see, e.g., Kluge, 1999). This simplified
pects, Mayr (1976) distinguished four types of similar-
ity: symplesiomorphy, synapomorphy, parallelism, approach is sufficient for calculating Wagner trees, but
unsuitable for systematics in Hennig’s sense. Although
and convergence—the difference between parallelism
and convergence being that the former involves homol- our findings agree with Hennig’s terminology for
phylogenetic systematics, it is recommended to adopt
ogous characters, whereas the latter are non-homolo-
gous. Hennig (1966) disagreed with this final distinc- Mayr’s terms, since these allow the most accurate anal-
ysis of character evolution. For example, Hennig’s
tion, regarding it as unnecessary for phylogenetic
systematics, and designated both as convergence. Con- concern with “homoiologies” can be simplified by
making a distinction between parallelism and con-
sequently, Hennig’s terminology has only three types
of similarity: synapomorphy, symplesiomorphy, and vergence.

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