On the TTSC–FTSC Formulation of Standard Parsimony

Standard parsimony analysis has recently been described in a “three-taxon-like” way (the three-taxa statements for contiguous series–four-taxa statements for contiguous series, or TTSC–FTSC procedure) in order to clarify the differences between the standard approach and three-taxon analysis. It is shown that the alleged equivalence of standard parsimony analysis and the TTSC–FTSC procedure does not hold. Some minor defects of the procedure can be fixed within the TTSC–FTSC logic, but no solution is available for two basic problems: (1) the elementary three-taxon-like statements of the TTSC–FTSC procedure are highly artificial; and (2) the equivalence with standard parsimony depends on an incomplete correction for nonindependence between these statements. However, these findings do not invalidate the reported superiority of standard parsimony as a method for biological systematics.     

Taxic Homology = Overall Similarity

Modified three-taxon analysis (m3ta), a method in which three-taxon statements are produced from a nonadditive binary coding of the original data, has been proposed as a model-free way of assessing monophyly of groups, utilizing the taxic concept of homology. In fact the taxic concept amounts to a model, and, further, one that seems to conflict directly with evolution. M3ta is a type of grouping by all similarities and, like all such methods, would require a clock assumption if the tree were to be interpreted phylogenetically. Groupings based on this method, consequently, are phenetic, and they have little to do with monophyly. It has been proposed to define phylogenetic systematics in terms of grouping only by presences. While popular among advocates of 3ta, such definitions are completely inadequate, both because absences may be apomorphic and because phenetic methods can disagree with phylogenetic ones even when no absences are involved.     

Taxic and Transformational Homology: Different Ways of Seeing

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.     

THREE-TAXON STATEMENTS: A MORE PRECISE USE OF PARSIMONY?

Abstract— Binary characters can be represented in data matrices by the three-taxon statements they imply. Transforming characters into three-taxon statements may increase the sensitivity of parsimony to differences in the fit of data to alternative cladograms. Extrapolation of the technique to multistate features allows semi-additive characters to be coded accurately. In many cases, analysis of the transformed data produces fewer equally parsimonious solutions than does analysis of the raw data. In other cases, additional equally parsimonious solutions, or even different solutions, may be produced; in those cases, the results appear to accommodate information from a larger number of characters than do the results from raw data.     

Cladistic analysis of molecular and morphological data

Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i. e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i. e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i. e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter λ (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e. g., the exemplar method vs. “compartmentalization” (a new approach involving substituting an inferred “archetype” for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, “total evidence” analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis. © 1994 Wiley-Liss, Inc.     

A COMPARISON OF TWO METHODS TO STUDY CORRELATED DISCRETE CHARACTERS ON PHYLOGENETIC TREES

Abstract — We use a simulation approach to study two methods proposed for the analysis of correlated discrete characters on cladograms, the concentrated changes test (CCT) and the contingent states test (CST). Both of these consider the case where there is an independent and a dependent character and assign probabilities to various events in the dependent character given one or the other state of the independent character. The CCT gives different results for symmetric and asymmetric cladograms. In the latter case, the proportion of branches reconstructed as having the derived state has less influence on the resulting probabilities. The CST is only sensitive to the proportion of derived branches, regardless of whether the tree is symmetric or asymmetric. The CCT calculates probabilities by considering character state reconstructions which are not allowed by parsimony algorithms, thereby increasing the probability of rejecting a true null hypothesis (type I error rate). We discuss some alternative questions that could be studied using these tests and also derive equations for calculating the number of possible events in the dependent character for unresolved parts of the phylogeny.     

Cycles

Intended to support three-taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methods should not account for plesiomorphies. Parsimony does not correspond to interpretation 1 for incompletely resolved cladograms. The main argument common to Nelson's (1996) and Nelson and Platnick's (1991) advocacy of three-taxon analysis rests on presupposing its conclusion. While suggesting that parsimony rests on an inferior evolutionary model, Nelson (1996) neither offered nor provided evidence for any alternative. 3ta sometimes favors reversal over parallelism, but in other cases may disregard reversed characters, so that the method seems to lack any coherent theoretical basis.     

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three‐item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three‐item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter‐tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Our empirical examples provide equivocal results. Parsimony unordered states yield less resolving power and more artefactual resolutions than parsimony ordered states, both with our simulated and empirical data. Relationships between three operational taxonomic units (OTUs), irrespective of their relationships with other OTUs, are called three‐item statements (3is). We compare the intersection tree (which reconstructs a single tree from all of the common 3is of source trees) with the traditional strict consensus and show that the intersection tree retains more of the information contained in the source trees. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 914–930.     

THREE-TAXON STATEMENTS AND PHYLOGENY CONSTRUCTION

Abstract — The differences between the three-taxon statement analysis and the standard approach are in the way they explicitly or implicitly consider character homology and modes of character evolution. The differences in the two methods have implications relative to the general model of evolution viewed as descent with modification of characters.     

BIOGEOGRAPHY OF NEW WORLD TAIGA-DWELLING MICROTUS (MAMMALIA: ARVICOLIDAE): A HYPOTHESIS TEST THAT ACCOUNTS FOR PHYLOGENETIC UNCERTAINTY

If we adopt a statistical approach to systematics and recognize that phylogenies are estimated with error, then we can begin to explore statistically justified methods for testing a variety of comparative hypotheses, including those concerning the evolution of life-history characters and biogeography. In this paper I examine two biogeographic hypotheses concerning the rodent genus Microtus. Like many comparative hypotheses, these can be phrased so that each predicts the existence of a particular monophyletic group. Neither of the predicted groups appear on the single best phylogeny as determined by both Dollo parsimony and maximum likelihood analysis of restriction site maps of mitochondrial DNA. Simulation studies, however, suggest that often the best phylogeny from a single data set has only a low probability of being exactly correct. We must also examine those trees that, while not the single best-supported tree, are not rejected by the data. If we find the best phylogeny for which a hypothesis is satisfied, then likelihood methods can be used to test whether that phylogeny is significantly worse then the best tree overall. If that tree can be rejected, then so can the hypothesis. Computational constraints limit the use of likelihood methods for searching among topologies, so parsimony is used as a data exploratory tool. One of the predicted groups cannot be rejected, even though the most parsimonious tree which includes that group requires 11 more steps than does the most parsimonious tree.     

The language of systematics,and the philosophy of ‘total evidence’

This contribution analyses the primacy of classification over generalization, and the philosophy of total evidence that emerges from the relation of homology to character statements. Primary conjectures of homology are basic character statements, i.e. statements that predicate properties of organisms, properties that are instantiated by those organisms and/or their parts. Secondary conjectures of homology are embedded in a second‐level (metalinguistic) discourse that turns on the coherence or incoherence of those basic character statements relative to a hierarchy. The coherence or incoherence of character statements is a logical relation between statements, not a causal (historical) relation between organisms. The choice of the hypothesis of relationships that is supported by the largest set of coherent basic character statements is based on the empirical presupposition that the properties referred to by the set of coherent character statements are grounded in causally efficacious relations of inheritance and ontogeny, and co‐instantiated because they are inherited through common ancestry (Hennig's auxiliary principle). Unless that empirical presupposition is causally grounded, phylogeny reconstruction is of an inherently probabilistic nature, whether under parsimony or other models of analysis. The causal grounding of a coherent set of character statements typically seeks a link between character statements and causally efficacious generative mechanisms for morphological characters (as is defeasibly indicated by topology and connectivity), or secondary structure information for molecular characters.     

Phylogenetic systematics and biomecha cs in ecomorphology

Synopsis Research in all fields of biology increasingly uses phylogenetic systematics to interpret biological data in an evolutionary context. It is becoming widely accepted that comparative studies of the correlation of biological features, such as ecomorphological studies, must frame their analyses within the context of a phylogenetic hierarchy rather than treating each taxonomic unit as an independent replicate. Recent methods for the interpretation of ecological and functional data in the framework of a phylogeny can reveal the degree to which ecomorphological characters are correlated with one another, and are congruent with hierarchical cladistic groups. An example of the ecomorphology of labrid fishes is used here to illustrate the application of several of these methods. The structural design and mechanics of the jaws of labrids are tested for ecomorphological associations with the natural diets of these fishes. Methods for analysis of the correlated evolution of both discrete and continuous quantitative characters within a phylogeny are practiced on a single ecomorphological data set. Techniques used include character coding, character mapping, phylogenetic autocorrelation, independent contrasts, and squared change parsimony. These approaches to diverse biological data allow the study of ecomorphology to account for patterns of phylogenetic ancestry. Biomechanics or functional morphology also plays a vital role in the determination of ecomorphological relationships by clarifying the mechanisms by which morphologies can perform behaviors important to the organism's ecology. The synthesis of systematics with biomechanics is an example of interdisciplinary study in which information exchange can elucidate patterns of evolution in ecomorphology.     

Is there a direct ontogenetic criterion in systematics?

Much recent literature focuses on whether ontogenetic information can be used as a direct criterion for determining the polarity of character trasformations in systematic analysis. This paper reviews the relevant literature and concludes that the ontogenetic criterion is dependent on parsimony rather than the sequence observed during ontogeny. It is not, therefore, based on the discredited arguments of recapitulation. From the perspective of phyologenetic systematics the ontogenetic criterion is a valid means of polarizing character transformations that represents a special case of a broader methodology involving parsimony. The alternative perspective perspective of patttern cladistics holds that polarity should be contained within the data and not imposed upon it. Thus, ontogeny is not required to polarize characters, but ontogenetic information can generate unequivocal character interpretations in terms of the relative generality of related attributes, and in the sense that absence precedes presence. Furthermore, ontogeny is central to systematics, providing empirical evidence of character transformation, information on the whole life cycle and an escape from systematics being teleologically related to phylogenetic inference and the theory of evolution.     

Computer-Intensive Randomization in Systematics

There has been a sort of cottage industry in the development of randomization routines in systematics beginning with the bootstrap and the jackknife and, in a sense, culminating with various Monte Carlo routines that have been used to assess the performance of phylogenetic methods in limiting circumstances. These methods can be segregated into three basic areas of interest: measures of support such as bootstrap, jackknife, Permutation Tail Probability, T‐PTP, and MoJo; measures of how well independent data are correlated in a phylogenetic framework like PCP for coevolution and Manhattan Stratigraphic Measure (MSM) for stratigraphy; and simulation‐based Monte‐Carlo methods for ascertaining relative performance of optimality criteria or coding methods. Although one approach to assessing cospeciation questions has been the randomization of, for example, hosts and parasite trees, it is well established that in questions that are of a correlative type, the association themselves are what should be permuted. This has been applied to Brooks' parsimony analysis previously and here to the recent reconciled tree approach to these questions. Although it is debatable whether the extrinsic temporal position of a fossil can stand as refutation of intrinsic morphological character‐based cladograms, one can, nonetheless, determine the strength and significance of fit of stratigraphic data to a cladogram. The only method available in this regard that has been shown to not be biased by tree shape is the MSM and modifications of that. Another similar approach that is new is applied to evaluating the historical informativeness of base composition biases. Incongruence length difference tests too are essentially correlative in nature and comparing the behavior of “perceived” partitions to randomly determined partitions of the same size has become the standard for interpreting the relative conflict between differently acquired data. Unlike the foregoing, which make full use of the observed structure of the data, Monte Carlo methods require the input of parameters or of models and in that sense the results tend to be lacking in verisimilitude. Nonetheless, these kinds of questions seem to have been those most widely promulgated in our field. The well‐established theoretical proposition that parsimony has problems with adjacent long‐branches was of course illustrated through such methods, much to the concern and angst of systematists. That likelihood later was shown to perform worse than parsimony when those long branches might repel each other has generated less concern and angst. But then many such circumstances can be divined, like the “short‐branch‐mess” problem wherein likelihood has difficulty placing just a single long branch. Overall, then, in the interpretation of these or any other Monte Carlo issues it will be important to critically examine the structure of the modeled process and the scope of inferences that can be drawn therefrom. Modeling situations that are bound to yield results favorable to only one approach (such as unrealistic even splitting of ancestral populations at unrealistically predictable times in examination of the coding of polymorphic data) should be viewed with great caution. More to the point, since history is singular and not repeatable, the utility of statistical approaches may itself be dubious except in very special circumstances—most of the requirements for stochasticity and independence can never be met.     

A Bayesian perspective on a non-parsimonious parsimony model

Several stochastic models of character change, when implemented in a maximum likelihood framework, are known to give a correspondence between the maximum parsimony method and the method of maximum likelihood. One such model has an independently estimated branch-length parameter for each site and each branch of the phylogenetic tree. This model--the no-common-mechanism model--has many parameters, and, in fact, the number of parameters increases as fast as the alignment is extended. We take a Bayesian approach to the no-common-mechanism model and place independent gamma prior probability distributions on the branch-length parameters. We are able to analytically integrate over the branch lengths, and this allowed us to implement an efficient Markov chain Monte Carlo method for exploring the space of phylogenetic trees. We were able to reliably estimate the posterior probabilities of clades for phylogenetic trees of up to 500 sequences. However, the Bayesian approach to the problem, at least as implemented here with an independent prior on the length of each branch, does not tame the behavior of the branch-length parameters. The integrated likelihood appears to be a simple rescaling of the parsimony score for a tree, and the marginal posterior probability distribution of the length of a branch is dependent upon how the maximum parsimony method reconstructs the characters at the interior nodes of the tree. The method we describe, however, is of potential importance in the analysis of morphological character data and also for improving the behavior of Markov chain Monte Carlo methods implemented for models in which sites share a common branch-length parameter.     

IS FARRIS OPTIMIZATION PERFECT?: THREE-TAXON STATEMENTS AND MULTIPLE BRANCHING

Abstract — The three-taxon approach to phylogenetic analysis separates the universe of cladograms into a larger number of classes of solutions showing decreasing degrees of fit to data than does conventional Farris optimization. The three-taxon approach applies to character analysis Nelson and Platnick's interpretation 2 of multiple branching in cladograms.     

A method for measuring support for synapomorphy using character state distributions on phylogenetic trees

Synapomorphies are fundamental to phylogenetic systematics as they offer empirical evidence of monophyletic groups. However, no method exists to directly measure synapomorphy. Here, we propose a method that quantifies synapomorphy using the pattern of character state distribution over a cladogram separately for each character and for each clade. We define a fully synapomorphic character state as one shared by all of a clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade. The extent to which this condition is met corresponds to the support for the character state being synapomorphic or, in short, support for synapomorphy. It is calculated as the probability of randomly selecting, by multi‐stage sampling following the topology of the tree, two terminals from inside a clade sharing the same character state and one terminal from outside the clade bearing a different character state. The method is independent of tree inference and free of transformational assumptions, and so can be applied to any tree and used for any type of discrete character. By measuring synapomorphy, the method offers a potential tool for determining diagnostic character states for taxa on different hierarchical levels, for evaluating alternative systems of character coding, and for evaluating clade support. We show how the method differs from ancestral character state reconstruction methods and goodness‐of‐fit indices. We demonstrate the behaviour of our method with several hypothetical scenarios and its potential use with two real‐life examples.     

Testing phylogenetic hypothess using an Hennigian approach and DNA sequnence data

The assumption that maximum parsimony in a phylogenetic tree is achieved by the reduction of the number of overall homoplasies to a minimum is questioned and an alternative approach of using the most parsimonius distribution of taxa at each dichotomy suggested. This approach can be put into practice using Hennigian logic to determine relationships, DNA sequences data as the character set and standard statistical techniques to determine the significance to be placed on the resultipng phylogenetic tree. The logic and robustness of such an approach is described. A software package, SYNAPO, is availabe to assist such analyses.     

Chloroplast DNA systematics: a review of methods and data analysis

The field of plant molecular systematics is expanding rapidly, and with it new and refined methods are coming into use. This paper reviews recent advances in experimental methods and data analysis, as applied to the chloroplast genome. Restriction site mapping of the chloroplast genome has been used widely, but is limited in the range of taxonomic levels to which it can be applied. The upper limits (i.e., greatest divergence) of its application are being explored by mapping of the chloroplast inverted repeat region, where rates of nucleotide substitution are low. The lower limits of divergence amenable to restriction site study are being examined using restriction enzymes with 4-base recognition sites to analyze polymerase chain reaction (PCR)-amplified portions of the chloroplast genome that evolve rapidly. The comparison of DNA sequences is the area of molecular systematics in which the greatest advances are being made. PCR and methods for direct sequencing of PCR products have resulted in a mushrooming of sequence data. In theory, any degree of divergence is amenable to comparative sequencing studies. In practice, plant systematists have focused on two slowly evolving sequences (rbcL and rRNA genes). More rapidly evolving DNA sequences, including rapidly changing chloroplast genes, chloroplast introns, and intergenic spacers, and the noncoding portions of the nuclear ribosomal RNA repeat, also are being investigated for comparative purposes. The relative advantages and disadvantages of comparative restriction site mapping and DNA sequencing are reviewed. For both methods, the analysis of resulting data requires sufficient taxon and character sampling to achieve the best possible estimate of phylogenetic relationships. Parsimony analysis is particularly sensitive to the issue of taxon sampling due to the problem of long branches attracting on a tree. However, data sets with many taxa present serious computational difficulties that may result in the inability to achieve maximum parsimony or to find all shortest trees.