Inlernalionol Journal/or Parasilo/og.y, Vol. 26, No. 6, pp. 589417, 1996 Copyright ~0 1996 Australian Society for Parasitology. Pubhshed by Elsevia Science Ltd Pergamon Printed in Great Britain PII: SOO20-7519(96)00044-6 002&7519/96 $15.00+0.00 INVITED REVIEW Phylogenetic Tree-building DAVID A. MORRISON Molecular Parasitology Unit, University of Technology Sydney, Westbourne Street, Gore Hill, NS W 2065, Australia (Received 13 October 1995; accepted 3 March 1996) Abstract-Morrison D. A. 1996. Phylogenetic tree-building. Iniernationul Journal fir Parasitology 26: 589-617. Cladistic analysis is an approach to phylogeny reconstruction that groups taxa in such a way that those with historically more-recent ancestors form groups nested within groups of taxa with moredistant ancestors. This nested set of taxa can be represented as a branching diagram or tree (a cladogram), which is an hypothesis of the evolutionary history of the taxa. The analysis is performed by searching for nested groups of shared derived character states. These shared derived character states dehne monophyletic groups of taxa (clades), which include all of the descendants of the most recent common ancestor. If all of the characters for a set of taxa are congruent, then reconstructing the phylogenetic tree is unproblematic. However, most real data sets contain incongruent characters, and consequently a wide range of tree-building methods has been developed. These methods differ in a variety of characteristics, and they may produce topologically distinct trees for a single data set. None of the currently-available methods are simultaneously efficient, powerful, consistent and robust, and thus there is no single ideal method. However, many of them appear to perform well under a wide range of conditions, with the exception of the UPGMA method and the fnvariants method. Copyright 0 1996 Australian Society for Parasitology. Published by Elsevier Science Ltd. Key words: Phylogeny; evolution; cladistics; cladograms. INTRODUCTION English of Hennig (1966). These methods are now usually referred to as “cladistics”, and the evolution- If we accept the proposition that evolution exists, ary diagrams they produce “cladograms”, to distin- then meaningful comparisons among organisms must guish them from all prior phylogenetic studies, many ultimately include a phylogenetic context (Maddison of which were neither explicit nor repeatable (note & Maddison, 1992). This is because the evolutionary that I am using the word cladistics to include a wide relationships among a group of taxa constrain any class of explicit and repeatable phylogenetic analyses, other possible relationships that might exist. It is thus which may be a broader definition than would not surprising that in biology there has been a long be accepted by many phylogeneticists, who would history of attempts to deal with the reconstruction of restrict the term to the more strictly Hennigian genealogical history (Nelson & Platnick, 1981; Mayr, methods). The current interest in cladistic analyses 1982; Stevens, 1994), notwithstanding the difficulties has inevitably led to a proliferation of data analysis associated with producing testable hypotheses about techniques; and the apparent plethora of methods for historically unique events. phylogenetic analysis is typical of a young science It is, however, only in the last 30 years that still coming to terms with both its aspirations and its widespread attempts have been made by systematists constraints. to produce explicit and repeatable methods for It is therefore important for practitioners to under- the construction of phylogenetic trees (Felsenstein, stand the limitations of the available techniques as 1982), notably with the translation from German into well as to appreciate their capabilities (Felsenstein, Tel: +61-2-3304159; Fax: +61-2-3304003; 1982). Unfortunately, the current wide choice among E-mail: [email protected]. possible phylogenetic methods seems to be daunting 589 590 D. A. Morrison for many people, and they thus acquire little knowl- PHYLOGENETIC ANALYSIS edge of the relative advantages and disadvantages of the various methods. This is unfortunate, because the Cladistics choice of data-analysis methods should be based on The study of evolutionary processes has often been their apparent appropriateness for the data at hand, considered to be unscientific because it deals with rather than on the local availability of computer historically unique events (Popper, 1957). Hypoth- programs or on historical inertia (Hillis, Allard & eses concerning these events are thus not universal (in Miyamoto, 1993). It is my purpose here to review the either space or time) and, therefore, they are consid- phylogenetic inference methods that are currently ered to be untestable in the contemporary world. The available, and to indicate what is currently known sociological development of phylogenetic analysis about their strengths and weaknesses. This will allow has consequently been based largely on the erection a more informed decision to be made when assessing of what have been called “evolutionary scenarios” which of the methods might be appropriate for a describing the presumed genealogical history of particular data set. the organisms under study. The number of such Along the way, I will attempt to make clear some scenarios that may be created is, of course, limited of the aspects of phylogenetic analysis that are obvi- solely by the imagination of the researcher, and none ously misunderstood by non-specialists, and to dispel of the scenarios are likely to be open to falsification. a few widely-held misconceptions. My discussion will Cladistic analysis can thus be seen as an attempt to focus on molecular sequence data (particularly DNA base phylogenetic analysis on a more objective foot- and RNA), since trees derived from this source are ing, where the phylogenetic hypotheses are explicitly increasingly those with which parasitologists are stated, along with the evidence supporting (and con- working (e.g., Nadler, 1990), there being a limit to tradicting) them, and are then subjected to quantita- the usefulness of phenotypic characteristics for tive testing. Its practitioners therefore claim that constructing phylogenetic trees for most parasites. cladistics is designed to make phylogenetic analysis Indeed, it is the proliferation of molecular data sets into an hypothetico-deductive science, where explicit that is introducing many people from outside of hypotheses are subjected to repeatable attempts at systematics to the science of phylogeny (Miyamoto & falsification. Cracraft, 1991; Hillis, Huelsenbeck & Cunningham, Note that the claimed advantages of cladistic 1994a); and it is for this reason that phylogenetic analysis are not intended to denigrate pre-cladistic principles need to be clearly introduced to non- biologists, nor is there any suggestion that these experts. Furthermore, many of the recent advances in biologists did not apply their minds to phylogenetic cladistics have been motivated by attempts to deal questions. However, it is clear that pre-cladistic phy- with problems that are specific to molecular data logenetic analyses were not necessarily based on (Penny et al., 1990), and the similarities and differ- repeatable methods that produced explicit hypoth- ences between traditional and molecular phylogeny eses of evolutionary relationship which could be thus need to be emphasized. subjected to falsification (Nelson & Platnick, 1981). I do not intend to describe the tree-building Furthermore, the taxonomic groups produced by techniques in any great detail, partly because most pre-cladistic biologists were not necessarily mono- of them are covered in the excellent review by phyletic (see below), and therefore did not always Swofford & Olsen (1990) and in the books by Nei reflect evolutionary history. Post-Darwinian biolo- (1987) and Li & Graur (1991), and partly because gists have had the unenviable task of producing nothing is more intimidating to most biologists than taxonomic schemes that should, in theory, reflect mathematics. I concentrate much more on those evolutionary history, without any theoretical frame- aspects of phylogenetic analysis that are likely to be work for how they should go about discovering what of most practical and theoretical interest to non- the evolutionary history actually was (Stevens, 1994). experts. I start by summarizing the principles of Cladistics is an attempt to provide this theoretical cladistic analysis, before proceeding to a review of framework. the alternative methods for constructing clado- Cladistic analysis as an approach to phylogeny grams. A number of introductory reviews covering attempts to group taxa on the basis of their ancestry. similar topics, but from different perspectives, in- In the analysis, taxa are grouped in such a way that clude those of Felsenstein (1988), Olsen (1988) those with historically more-recent ancestors form Sneath (1989), Beanland & Howe (1992), Hillis groups nested within groups of taxa with more- et al. (1993) and Stewart (1993); and there is also distant ancestors. The analytical technique is the worthwhile introductory book by Forey et al. based on a widely-held view of the mode of the (1992). evolutionary process: species are lineages undergoing Invited Review 591 divergent evolution with modification of their for Character 16 in Table 1 possession of denticles, intrinsic attributes, the attributes being transformed dermal scales, epidermal scales, feathers and