On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

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.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS

Abstract— A cladistic analysis of the "blue ash" eucalypts ( Eucalyptus , Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series ( Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae , informal subgenus Monocalyptus ) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.     

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.     

IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE-AREA STATEMENTS

Abstract— Three quantitative cladistic biogeographic methods, namely, component analysis, Brooks parsimony analysis (BPA), and three-area statements (TAS) have been proposed for obtaining general area cladograms from taxon-area cladograms. Available programs implementing these methods include COMPONENT versions 1.5 and 2.0 for component analysis, TAS for three-area statements, and Hennig86 for analysing matrices for both three-area statements and BPA. Ten different data sets were analysed with these programs and items of error were used to evaluate the general area cladograms obtained. None of the computer implementations of the methods compared proved to be more effective than the others.
"…all methodologies, even the most obvious ones, have their limits…"
Feyerabend (1993:231)     

PASOS: a method for the phylogenetic analysis of shape ontogenies

We present a novel phylogenetic approach to infer ancestral ontogenies of shape characters described as landmark configurations. The method is rooted in previously published theoretical developments to analyse landmark data in a phylogenetic context with parsimony as the optimality criterion, in this case using the minimization of differences in landmark position to define not only ancestral shapes but also the changes in developmental timing between ancestor–descendant shape ontogenies. Evolutionary changes along the tree represent changes in relative developmental timing between ontogenetic trajectories (possible heterochronic events) and changes in shape within each stage. The method requires the user to determine the shape of the specimens between two standard events, for instance birth and onset of sexual maturity. Once the ontogenetic trajectory is discretized into a series of consecutive stages, the method enables the user to identify changes in developmental timing associated with changes in the offset and/or onset of the shape ontogenetic trajectories. The method is implemented in a C language program called SPASOS. The analysis of two empirical examples (anurans and felids) using this novel method yielded results in agreement with previous hypotheses about shape evolution in these groups based on non-phylogenetic analyses.     

One-pot fluorescent labeling of saccharides with fluorescein-5-thiosemicarbazide for imaging polysaccharides transported in living cells

A simple and efficient procedure for the fluorescent labeling of saccharides is a prerequisite step for imaging the transport of polysaccharides in living cells. We report a one-pot strategy for the fluorescent labeling of saccharides with fluorescein-5-thiosemicarbazide (FTSC), which introduces the thiosemicarbazide group of FTSC to the aldehyde group at the reducing end of saccharides to form stable amino derivatives via reductive amination. The Glc-FTSC derivative was characterized by HPLC–MS, HRESIMS and NMR spectroscopy. Saccharides were quantitatively labeled with FTSC at 75 °C for 1 h under optimum reaction conditions. Fluorescence studies illustrated that the conjugation of FTSC to saccharides did not change its florescence properties (λ_ex = 495 nm, λ_em = 517 nm), presenting desirable compatibility with commonly used fluorescence equipment. Polysaccharide AAG-FTSC derivatives exhibited rather low levels of cytotoxicity against rat thymus cells, and the fluorescent labeling procedure had slight impact on their anti-tumor activity. Results indicate that the assay neither introduces discernible cytotoxicity against living cells nor obviously alters the functional activities of polysaccharides, and provides a convenient, highly efficient fluorescent labeling approach for imaging the transport of polysaccharides in living cells.     

A molecular perspective on the phylogeny of placental mammals based on mitochondrial 12S rDNA sequences,with special reference to the problem of the Paenungulata

Part of the 12S rDNA gene was amplified and sequenced for 11 placental mammals, 3 marsupials, and 2 monotremes. Multiple alignments for these sequences and nine additional placental sequences taken from GenBank were obtained using CLUSTAL. Phylogenetic analyses were performed using standard parsimony, transversion parsimony, and Lake's method of invariants. All of our analyses uniteLoxodontia withDugong. Procavia, in turn, is a sister group to these taxa, thus supporting the monophyly of the Paenungulata. Perissodactyls are a sister group to paenungulates when transitions and transversions are both included but not when transitions are omitted. Likewise, cetaceans are a sister group to artiodactyls on minimum length trees under standard parsimony but not under transversion parsimony. Rodent monophyly and bat monophyly also receive mixed support, as does a putative alliance between primates and lagomorphs. Interestingly, the percentage divergence between the echidna and the platypus is less than for the rat and mouse.     

Follow-up investigations of bladder cancer patients by titration of natural and specific lymphocyte-mediated cytotoxicity

Summary A 44-hour incubation microcytotoxicity assay (MA) was used to titrate the lymphocyte-mediated cytotoxicity in 47 transitional cell carcinoma (TCC) bladder cancer patients and 65 clinical control patients. All titrations included three target cell lines: HU 456 (TCC), HU 609 (normal urothelium), and SAOS 2 (osteosarcoma). Tumor-specific cytotoxicity (TSC) was calculated as the difference between cytotoxicity to HU 456 and HU 609, and tumor type-specific cytotoxicity (TTSC) as the difference between cytotoxicity to HU 456 and SAOS 2. On the basis of TSC and TTSC values obtained before treatment TCC patients were divided into one group with high-grade specific cytotoxicity (HSC) and another with low-grade specific cytotoxicity (LSC). A prospective follow-up study of these patients revealed a significantly lower survival rate for patients with LSC compared with patients with HSC, even when the groups were corrected for differences in distributions according to clinical and histological tumor gradation. This indicates a growth-controlling function of the cellular immune reaction.Repeated cytotoxicity tests in a follow-up study of 26 TCC patients and one patient with a squamous cell carcinoma of the urinary bladder revealed a positive correlation between positive specific cytotoxicity and the presence of tumor tissue Gr 2–4. The reactivity vanished within 1 month after surgical removal of the tumor or at the end of radiotherapy. An increased cytotoxicity against HU 609, representing normal urothelium, was seen immediately following radiotherapy, and in a few cases after surgical treatment. Reapearance of elevated TSC and TTSC was noted during the months following radiotherapy. When the MA was considered as a diagnostic marker of tumor tissue during clinical control of patients with suspected TCC, 22% of positive reactions proved to be false-positive and 44% of negative reactions were false-negative. Thus, a negative result cannot be used to exclude recurrence, but a positive result may indicate the need for additional clinical examinations.Abbreviations NC natural cytotoxicity - TCC transitional cell carcinoma - TSC tumor-specific cytotoxicity - TTSC tumor type-specific cytotoxicity - MA microcytotoxicity assay - HSC high-grade specific cytotoxicity - LSC low-grade specific cytotoxicity - ICI integrated cytotoxicity index     

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.     

A question of conflict: Three‐item and standard parsimony compared

A simple example of conflicting data, relevant to comparison between standard and three‐item parsimony analysis, is two characters (nodes, trees) differently relating four taxa: (AB)CD and A(BCD). This conflict is differently resolved by standard and three‐item analysis, which with fractional weighting yields the unique result (AB)(CD). There is reason to consider this result as the more accurate resolution of these conflicting data.     

Equivalence analyses of dissolution profiles with the Mahalanobis distance

For some postapproval changes, the manufacturer has to demonstrate that the dissolution profile of the drug product before the change is statistically equivalent to the dissolution profile after the change. Guidelines suggest the so‐called similarity factor f₂ as standard approach for the equivalence analysis. f₂ is a statistically questionable transformation of the Euclidean distance between both profile means and does not allow a control of the type I error rate. An alternative multivariate distance measure for quantifying the dissimilarity between both profile groups is the Mahalanobis distance. Current equivalence procedures based on the Mahalanobis distance implicate some practical problems in the dissolution context: either one chooses an exact method but the determination of a product independent equivalence margin will not be practically feasible or one chooses an approximate alternative that suffers from the bias of the Mahalanobis distance point estimate. This paper suggests the T2EQ approach for dissolution profile comparisons. T2EQ is a practically feasible equivalence procedure based on the Mahalanobis distance with an internal equivalence margin for comparing dissolution profiles. The equivalence margin is compliant with current dissolution guidelines. The operating characteristics (size, robustness, and power) are investigated via simulation: T2EQ meets the needs of both authorities and industry: not affected by the bias of the point estimate the type I error rate can be reliably controlled for various distribution assumptions and the power of T2EQ exceeds the power of methods recently discussed in the literature. These results were presented for the first time at CEN‐ISBS 2017.     

Phylogenetic classification of the frog pathogen Amphibiothecum (Dermosporidium) penneri based on small ribosomal subunit sequencing

We determined 1,600 base pairs of DNA sequence in the 18S small ribosomal subunit from two geographically distinct isolates of Dermosporidium penneri. Maximum likelihood and parsimony analysis of these sequences place D. penneri in the order Dermocystida of the class Mesomycetozoea. The 18S rRNA sequences from these two isolates only differ within a single region of 16 contiguous nucleotides. Based on the distant phylogenetic relationship of these organisms to Amphibiocystidium ranae and similarity to Sphaerothecum destruens we propose the organism be renamed Amphibiothecum penneri.     

The tribal radiation of the family Bovidae (Artiodactyla) and the evolution of the mitochondrial cytochrome b gene

The nucleotide sequence of the complete mitochondrial cytochrome b gene has been determined and compared for 51 species of the family Bovidae and 10 potential pecoran and tragulid outgroups. A detailed saturation analysis at each codon position relative to the maximum parsimony procedure indicates that all transitions on third codon positions do not accumulate in a similar fashion: C-T are more saturated than A-G substitutions. The same trend is observed for second positions but not for first positions where A-G and C-T transitions exhibit roughly the same levels of saturation. Maximum parsimony reconstructions were weighted according to these observations. Maximum parsimony, maximum likelihood, and distance phylogenetic reconstructions all depict a major split within Bovidae. The subfamily Bovinae includes four multifurcating tribes and subtribes: Boselaphini, Tragelaphini, cattle-Bovini (Bos and Bison), and buffalo-Bovini (Bubalus and Syncerus). Its sister group is the subfamily Antilopinae, i.e., all non-Bovinae taxa, represented by seven lineages: Antilopini (including Saiga), Caprini sensu lato (i. e., Caprinae including Pantholops), Hippotragini, Alcelaphini, Reduncini (including Pelea), Aepyceros possibly linked to Neotragus, and Cephalophini possibly linked to Oreotragus (the suni and the klipspringer being members of a polyphyletic Neotragini). These various tribes and major lineages were produced by two noteworthy explosive radiations, which occurred simultaneously between 12.0 and 15.3 MY (Middle Miocene) in the subfamilies Bovinae and Antilopinae.     

Choice of delta: requirements and reality--results of a systematic review

An essential problem in planning clinical non-inferiority or equivalence studies is the specification of the 'irrelevant difference' (irrelevance margin; delta). This quantifies the amount of non-inferiority or difference, respectively, between a new test therapy and an established standard treatment which is to be considered as tolerable. In the past, most recommendations and guidelines for clinical non-inferiority and equivalence studies contained only general statements and formulations concerning the specification of delta. The current unsatisfactory situation was the reason for performing a systematic review of published clinical non-inferiority and equivalence studies. It was the aim to gain an overview on the irrelevance margins used in such studies, and on reasons for choosing the particular margins. For the sake of comparability, the irrelevance margins were converted into standardized differences and odds ratios. Overall, there were 332 non-inferiority or equivalence trials obtained by means of an extensive literature search. The results of the systematic review show that current requirements on the choice of delta and the reality of recent clinical non-inferiority and equivalence trials differ substantially. In about one half of the trials a difference of 0.5 standard deviations or more was regarded as 'irrelevant' explicitly or implicitly. Estimates of standard-placebo differences formed the basis of the irrelevance margin in less than every tenth trial. Reasons for this very low proportion might be (1) the possibly resulting very small irrelevance margins, and (2) unsolved problems of the requirements themselves. Overall, it seems that a more global definition of 'irrelevance' might be warranted.     

Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods

The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.     

Likelihood, parsimony, and heterogeneous evolution

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.     

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING

Abstract— Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor-joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch-swapping, yet is better able to screen out poorly-supported groups.     

Multiple testing to establish superiority/equivalence of a new treatment compared with k standard treatments for unbalanced designs

In clinical studies, multiple superiority/equivalence testing procedures can be applied to classify a new treatment as superior, equivalent (same therapeutic effect), or inferior to each set of standard treatments. Previous stepwise approaches (Dunnett and Tamhane, 1997, Statistics in Medicine16, 2489-2506; Kwong, 2001, Journal of Statistical Planning and Inference 97, 359-366) are only appropriate for balanced designs. Unfortunately, the construction of similar tests for unbalanced designs is far more complex, with two major difficulties: (i) the ordering of test statistics for superiority may not be the same as the ordering of test statistics for equivalence; and (ii) the correlation structure of the test statistics is not equi-correlated but product-correlated. In this article, we seek to develop a two-stage testing procedure for unbalanced designs, which are very popular in clinical experiments. This procedure is a combination of step-up and single-step testing procedures, while the familywise error rate is proved to be controlled at a designated level. Furthermore, a simulation study is conducted to compare the average powers of the proposed procedure to those of the single-step procedure. In addition, a clinical example is provided to illustrate the application of the new procedure.