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Hydrobiologia 383: 155160, 1998.

E. Schockaert, N. Watson & J.-L. Justine (eds), Biology of the Turbellaria.


1998 Kluwer Academic Publishers. Printed in the Netherlands.

155

A phylogeny of the Platyhelminthes: towards a total-evidence solution


D. T. J. Littlewood1,2,, R. A. Bray1 & K. A. Clough1
1

Department of Zoology, The Natural History Museum, Cromwell Rd, London SW7 5BD, U.K.
Division of Life Sciences, Kings College, University of London, London W8 7AH, U.K. ( author for
correspondence)
2

Key words: Platyhelminthes, total-evidence, phylogeny, ultrastructure, rRNA, cladistics


Abstract
We advocate a total-evidence approach for the reconstruction of working phylogenies for the Turbellaria and
the phylum Platyhelminthes. Few morphology-based character matrices are available in the systematic literature
concerning flatworms, and molecular-based phylogenies are rapidly providing the only means by which we can
estimate phylogenies cladistically. Character matrices based on gross morphology and ultrastructure are required
and should be internally consistent, i.e. character coding should follow a set of a priori guidelines and character
duplication and contradiction is avoided. In order to test our molecular phylogenies we need complementary data
sets from morphology. To understand morphological homology we need phylogenetic evidence from independent
(e.g. molecular) data. Fully complementary morphological and molecular data sets enable us to validate phylogenetic hypotheses and the combination of these sets in phylogenetic reconstruction utilises all statements of
homology. Working phylogenies which include all phylogenetic information not only shed light on individual
character evolution, but form a strong basis for comparative studies investigating the origin and evolutionary
radiation of the taxonomic group under scrutiny.
Introduction
The interrelationships of the Platyhelminthes continue
to pose problems for phylogeneticists whether we take
a traditional morphological or molecular approach
(Rohde, 1994; Blair et al., 1996). Indeed, the position of the Platyhelminthes amongst the Metazoa and
the monophyly of the group remain contentious, albeit
fundamental, issues (Smith et al., 1986). For example, a recent cladistic analysis of morphological and
developmental features of the animal kingdom, defined by Nielsen (1995) places the Platyhelminthes
as sister group to the Nemertini and yet the authors
(Nielsen et al., 1996) urge caution in the acceptance
of a PlatyhelminthesNemertini clade because of the
lack of supporting characters. Even the very foundation of kingdom-wide phylogenetic hypotheses based
on morphology, the trochaea-theory in the case of
Nielsens work, have yet to be widely accepted (e.g.
see Willmer, 1990; Haszprunar, 1995; Haszprunar et
al., 1995).
As new phylogenetic and comparative techniques
are developed, old problems resurface for reassess-

ment. Consequently, established data sets may be


revised, new characters added, and new independent
data sets generated. Two techniques are presently in
vogue as a means to increase our knowledge base
for the flatworms, namely electron microscopy and
molecular systematics. Both approaches are in need
of constant reappraisal with respect to phylogeny
reconstruction, particularly as our understanding of
character homology often changes as new data are
amassed. Some workers, arguably too few, explicitly
test the homology of characters prior to their incorporation in phylogenetic schemes. Ultrastructural studies
generally aim to revise and add to existing morphological schemes, although new homologous features are
always being sought, whereas molecular sequences
are generally collected in order to establish independent data sets for comparison with morphology-based
schemes. For the Platyhelminthes molecular data sets
have often been constructed, analysed and presented
in isolation where little or no morphological scheme
exists or, more rarely, as a basis for comparison with
morphologically derived phylogenies (e.g. Litvaitis et
al., 1996). This may not be so surprising consider-

156
ing the confusion presented by existing morphological
data (e.g. see Rohde, 1994; Rieger & Tyler, 1995),
and yet, comparing phylogenies derived from independent data sets is by far the most valuable approach
since all available evidence is taken into consideration.
Although, sensu stricto this is not the total-evidence
approach of Kluge (1989), it is certainly one which
involves all phylogenetic data.
Some systematists may be alienated by a molecular phylogeny presented without consideration of its
biological significance, and it is now generally recognised that a morphological versus molecular debate
is redundant and counter-productive (Hillis, 1987;
Miyamoto & Fitch, 1995). In a strict sense, data sets
and their individual characters are of value because
they represent statements about homology, i.e. features supporting similarity by common ancestry or genetic relatedness. Recognising homology is the foundation underlying phylogenetic reconstruction; for an
expansive treatment on homology in morphological
and molecular studies see papers in Hall (1994). Homoplasy, the counterpart of homology, where characters have undergone convergent or parallel evolution,
is the noise which dampens phylogenetic signal. Unfortunately, homoplasious characters are unavoidable
and where the noise they generate is large, we aim
to reduce it by adding more data or by recognising
homoplasious characters and eliminating them from
the analysis. The recognition of homoplasy may be
easier with morphological data (e.g. see Tyler, 1988).
Often it is easier to add more molecular data than
to resolve contention over homologous morphological
characters, although this approach is not necessarily
more productive. Adding new nucleotide data must be
done with care as nucleotide positions can quickly become saturated with change if the nucleotide sequence
is evolving too rapidly and prohibitively expensive
if it is evolving too slowly to generate additional
phylogenetically informative data.
Molecular systematics may hold a key to resolving turbellarian phylogeny but, as Margulis (1996, p.
1074) recently stated, natural selection acts throughout the life-history of all organisms in specific habitats
at given times . . . therefore, whole-organism biology
(including all genetics and metabolism that determines
life cycle) not just molecular sequence must undergird
phylogenetic classification. Both morphological and
molecular data play important roles in phylogenetic
reconstruction but we do not recognise any one technique as a substitute for another. Here we advocate
a total-evidence approach utilising all available data,

and highlight problems associated with morphology,


molecular data and a way forward in resolving a robust
turbellarian, and wider platyhelminth, phylogeny.
This review does not discuss methods of phylogenetic reconstruction other than advocating the
maximum-parsimony method as one more readily
amenable in allowing the construction of combined
morphological and molecular data sets. Instead, we assess the problems associated with existing morphological and molecular data sets and suggest ways in which
they may be improved so that they are complementary
and may be used in a total-evidence approach.
Morphology
Problems with morphology
The morphological data set of the platyhelminths is
vast but poorly structured for phylogenetic use. Few
authors, in describing worms, give more than implied
information on the homology of characters, or indeed
are required to demonstrate a formal analysis of homology. Often there appears to be confusion between
homology and character-state identity. Characters and
character states routinely used for identification in the
platyhelminths are few and many of them are of little value in phylogeny as, for the platyhelminths at
least, there are few satisfactory criteria for assessing character-state identity (but see Rieger & Tyler,
1979). Problematic characters include those based on
size or ratios and on relative position of organs. More
presence/absence characters, and those discrete characters that lend themselves to placement in transformation series are needed. Perhaps the relative scarcity
of published matrices of platyhelminth characters results from these difficulties although some studies
have included full matrices (e.g. Bandoni & Brooks,
1987a,b). Nevertheless, several major cladistic studies
in the platyhelminthes (e.g. Ehlers, 1985; Brooks et
al., 1985a,b; Brooks & McLennan, 1993) have not included matrices, and data has to be reclaimed from the
cladograms and the text, rather than an explicit matrix. In the early execution of cladistic methodology
few potential homoplasious characters were included
on cladograms (e.g. Ehlers, 1985) and so we are left
with few synapomorphies and often many autapomorphies. Furthermore there remain contentious issues
even amongst the few cases where characters have
been detailed for rigorous, algorithm-driven cladistic
analyses. For example in one case, Pearson (1992) attempted to reclaim character information from Brooks

157
et al.s (1985b) analysis of the Digenea, and found a
high level of error. Few morphologically based character matrices for flatworm groups have found widespread acceptance and yet authors who publish them
should be praised for presenting data for scrutiny.
For higher-level phylogenies, ultrastructure appears to add much useful data (e.g. sperm morphology,
Watson & Rohde, 1995; protonephridial structure,
Rohde, 1993), although no formalised character matrix has yet been constructed for these data. Watson
& Rohde (1995) warn of various problems with the
current status of our knowledge of sperm ultrastructure. Indeed, our own preliminary analyses with these
characters yield a highly polytomous tree [data from
Table 1 of Watson & Rohde, 1995 analysed with
MacClade (Maddison & Maddison, 1992) and PAUP
(Swofford, 1993); results not shown]. It may well be
that at the ultrastructural level, morphological homology is easier to recognize and score although denser
sampling is still required. In contrast, Tyler (1979)
suggests that homology may be more difficult to establish at the ultrastructural level. As with molecular
data in phylogenetics, morphological data (from the
gross anatomic to the ultrastructural) lend themselves
to use at different taxonomic levels.
What is neededin the future is more phylogenetically centred descriptive work. If it became standard for systematists to include matrices in their
descriptive papers, or at least to deposit them
in a suitable electronic database (e.g. TreeBase;
http://herbaria.harvard.edu/treebase/), then phylogenetic considerations would enter at an early stage,
and the assessment of homologies and character-state
identity be made with specimens at hand. In the meantime it seems incumbent upon the morphologist to
present annotated morphological character matrices
which can be used as a basis for debate and more thorough cladistic analyses. We hope to utilize existing literature to present formal character matrices for analysis and discussion although we realise that turbellarian systematics and the distribution of morphological
features about the phylum are still poorly known.

nucleotide and protein sequences, respectively, largely


due to the efforts of the Schistosome Genome Project
(Rollinson & Johnston, The Natural History Museum,
London), and research inspired by the medical importance of schistosomiasis. Of the remaining sequences,
fewer than 30% were from turbellarians. Protein sequences of turbellarians were more common (43%
of accessions excluding all schistosomatids), probably as a result of turbellarians being favoured model
organisms for developmental genetics.
In spite of this wealth of biochemical data few
sequences are of immediate use in determining a molecular phylogeny of the turbellarians, and those that are
tend to have been born from a few systematic studies
involving small subunit 18S-like rRNA (or the gene
that codes for it, rDNA), which in turn were used
for addressing phylogenetic problems at lower or even
higher taxonomic levels than the interrelationships of
the turbellaria or indeed, the Platyhelminthes. Those
few molecular systematic studies which have centred
on the flatworms have attracted, and continue to attract criticism. Here, we briefly summarise the main
problems we perceive in establishing robust molecular
phylogenies over a range of taxonomic levels.
A significant problem with nucleotide sequences in
general is the possibility of only four character states
(G. A. T. and C), or five if insertion/deletion events are
included. Although rate-dependent, homologous positions in a sequence alignment will eventually become
saturated with changes as lineages diverge through
time, including multiple changes at single sites (overprinting or base saturation), high levels of homoplasy,
and leading to less robust or spurious tree topologies.
Other problems, such as different rates of evolution
between lineages leading to long branches and the
phenomenon of long-branch attraction (Felsenstein,
1978), affect not only choice of taxa but choice of
gene, i.e. sampling strategy. As Baverstock & Moritz
(1996) point out, sampling strategy rests on a balance
between having a manageable data set and having confidence in the phylogenetic reconstruction that results
from a larger data set.

Molecular data

Choice of taxa

At the moment this manuscript was being prepared (July 1996) there were 2204 nucleotide and
624 protein sequences for Platyhelminthes registered
and available from GenBank (NCBI). Schistosoma
mansoni (Digenea: Strigeidida: Schistosomatida) sequences accounted for over 79% and 44% of the

Given any particular phylogenetic problem choice of


taxa is critical. It is generally assumed that a species
provides a sequence representative of the sequence
of the supposed monophyletic group one chooses to
sample (Lecointre et al., 1993). This assumption is
often wrong. It has been shown empirically that not

158
only choice of taxa affects the robustness and topology of trees, but so too does the density of sampled
taxa per presumed monophyletic group and the choice
and sampling of outgroups (Patterson, 1989; Lecointre et al., 1993). Parsimony analysis, for example,
works on the principle of establishing common ancestry through the least number of character changes. To
gain confidence in the tree we should aim to reconstruct common ancestors of the groups in question by
sequencing the clade densely and not relying on single
representatives. In other words, we should be sampling
at a taxonomic category lower than the one that will
make up the tree; e.g., sequence various and distinct
genera for family level resolution, various and distinct
families for order level-resolution, and so on. Ideally,
subsampling any combination of taxa from the clades
under scrutiny will generate the same tree topology,
and as clades are more densely sampled the tree will
become more robust.
A review of molecular phylogenetic studies at
higher taxonomic levels of platyhelminths highlights
the problem of poor species sampling e.g., poor
sampling in Baverstock et al. (1991) and Rohde et al.
(1993) lead to contentious conclusions regarding the
interrelationships of the phylum. Many studies have
involved the sequencing of single species, adding to
small existing data sets and subsequently drawing farreaching conclusions about the orders to which they
belong e.g., Rohde et al. (1994) placing the enigmatic Kronborgia isopodicola, and subsequently the
fecampiid rhabdocoels in a wider phylogenetic context, or a similar attempt by Blair (1993) to place
the aspidobothreans on the basis of a single sequence.
Although these data are unquestionably useful, the
groupings and phylogenetic solutions they support still
need to be tested further with the denser sampling of
key taxa, particularly so that long branches can be split
up.
Choice of gene
There are no hard-and-fast rules for determining the
phylogenetic informativeness of any particular gene
for any particular taxonomic problem. However, the
history of molecular systematics has tended to set
precedents for tackling divergences over different time
scales (e.g. Hillis & Dixon, 1991). Also, more ribosomal RNA gene sequences are available for analysis
than any other gene and it has been more convenient
to add to these data sets. There seem to be no studies comparing or contrasting the phylogenetic utility

of various genes in platyhelminth phylogenetics, and,


perhaps more importantly, there are few studies involving the data from more than one gene. Many
studies involving 18S-like small subunit rRNA genes
have only utilised partial data and this has limited the
use of all available sequences in a phylum wide study.
Our study is accumulating complete 18S rDNA
sequences for a range of taxa and we are also sequencing partial sequences of 28S rDNA and mitochondrial
cytochrome oxidase I when greater resolution is required. Not only will these data complement existing
partial data sets but, we believe, will supercede them
in terms of phylogenetic resolution and robustness.
This prediction is based on increased resolution of
complete over partial 18S rRNA sequences in understanding higher level relationships in other groups, e.g.
echinoderms (Littlewood, 1995) and the Metazoa in
general (Philippe et al. 1994), as well as flatworms
(our preliminary results).
Reduced data sets and consensus sequences
Large, densely sampled data sets give us more robust
phylogenetic trees and, therefore, greater confidence
in the hypotheses of phylogenies we derive from them.
However, large data sets are also cumbersome and
difficult to handle with most of the algorithms currently available. There are two solutions for dealing
with large molecular data sets. The first is simply to
analyse the data at lower taxonomic levels than the
one in question. If we have a priori knowledge as to
the monophyly of any particular clade (e.g., from morphology), then we can analyse the molecular data for
the smaller reduced data sets. In turn we can select
early divergent members of the individual lower level
clades and use these to run the fuller analyses. Similarly, we can select a few taxa randomly from these
lower level clades and test for the phylogeny of the
larger group repeating the procedure with a different
selection of a few representative taxa.
Another method is to reduce the molecular data
sets into consensus sequences. Again, if we have a
priori knowledge as to the monophyly of particular
clades, whether this is from an independent data set
or indeed a full analysis of the molecular data, we can
generate a consensus sequence that will reflect all the
sequences in the clade. For any single unambiguously
aligned base position a consensus will reflect base
commonality (e.g., g, A, T, C or insertion/deletion).
Where there are within-clade differences obvious autapomorphic changes can be ignored; at the very least,

159
bases can be scored as purines (R) or pyrimidines (Y).
As with a full alignment, ambiguous positions should
be removed from the analysis.
Consensus sequences reduce the number of taxa
markedly and allow branch-and-bound or even exhaustive searches to be performed. In this way we
can detect phylogenetic signal (Hillis, 1991; Hillis &
Huelsenbeck, 1992), compare the phylogenies of solutions close to the most parsimonious, and bootstrap
all the sequence data more quickly without losing any
signal in the individual sequences that make up the
consensus.

Total-evidence: combining data in phylogenetic


analysis
Ultimately, all available phylogenetic information
must be brought to bear on any phylogenetic problem.
We are aiming for a total-evidence approach, wherein
individual base positions in a nucleotide alignment
and columns in a morphological character matrix are
treated in the same way, namely as individual statements about homology. Although this may suggest
that the volume of molecular data can easily swamp
the morphology-based data, examples so far suggest
that the higher levels of homoplasy, intrinsic in molecular data sets, are balanced by fewer, more informative
morphologically-derived characters (e.g. in echinoderms; Littlewood & Smith, 1995; Littlewood et al.,
1997). The philosophy, advantages and disadvantages
of combining independent data sets have been reviewed elsewhere (Bull et al. 1993; Miyamoto &
Fitch, 1995) and most recently by Huelsenbeck et al.
(1996). By establishing fully complementary independent data sets we can test for congruence between the
data sets, estimate phylogeny independently and in
combination, and with reference to whole organisms
and their biology, determine the viability of any working phylogenetic hypothesis. Initially we advocate a
conditional combination approach whereby independent data sets are added only if they pass homogeneity tests (e.g. the KishinoHasegawa test; Kishino
& Hasegawa, 1989; or Templetons variation on the
non-parametric Wilcoxons signed rank test, Larson,
1994). Selecting key taxa and providing internally
consistent morphologically based character matrices,
complemented by molecular data for the same taxa,
should provide the best opportunity for establishing
working phylogenies. In turn, working phylogenies
will become the basis for a fully comparative approach

in understanding the origin and evolutionary radiation


of the flatworms.

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