bluuebunny/crossref_metadata_2025 huggingface dataset:
PHYLOGENY OF THE SUBFAMILIES OF THE FAMILY BRACONIDAE: A REASSESSMENT ASSESSED
Authors: van Achterberg Kees , Quicke Donald L.J.
Published: July 2005

Abstract— Wharton et al. (1992) provided an extensive reappraisal of the phylogenetic analysis of the subfamilies of Braconidae by Quicke and van Achterberg (1990). In this critique they drew attention to a number of errors in our data matrix and made a number of useful suggestions regarding character coding and polarization. However, they also make a number of erroneous statements that, if anything, present our work in a worse light. We therefore provide here some discussion of the comments by Wharton et al. indicating where we are in agreement and where we believe our initial interpretations were correct. We also take this opportunity to correct some additional mistakes that have subsequently been unearthed in our original data matrix.
SKEWNESS AND PERMUTATION
Authors: Källersjö Mari , Farris James S. , Kluge Arnold G. , Bult Carol
Published: July 2005

Abstract— The skewness criterion of phylogenetic structure in data is too sensitive to character state frequencies, is not sensitive enough to number of characters (degree of corroboration) and relies on counts of arbitrarily‐resolved bifurcating trees. For these reasons it can give misleading results. Permutation tests lack those drawbacks and can be performed quickly by using approximate parsimony calculations, but the test based on minimal tree length can imply strong structure in ambiguous data. A more satisfactory test is obtained by using a support measure which takes multiple trees into account.
EVOLUTIONARY ORIGIN OF THE CYCLORRHAPHA (DIPTERA): TEST OF ALTERNATIVE MORPHOLOGICAL HYPOTHESES
Authors: Wiegmann Brian M. , Mitter Charles , Thompson F. Christian
Published: July 2005

Abstract— The higher flies, infraorder Cyclorrhapha [=Muscomorpha (McAlpine, 1989)], have undergone enormous radiation since the Cretaceous (∼100 Myr). Rapid morphological evolution in cyclorrhaphans has made their phylogenetic placement with respect to more primitive clades a long‐standing problem in dipteran systematics. Of the two most plausible hypotheses, one treats the Cyclorrhapha as sister group to the orthorrhaphous superfamily Empidoidea [=Empidiformia (Hennig, 1948), Orthogenya (Brauer, 1883)], while the other places them within the empidoids. The debate over cyclorrhaphan origin has heretofore focused on homology interpretations for a few character systems, particularly the male genitalia. We provide the first attempt to assemble and quantify all of the available morphological evidence. By cladistic analysis of these data under alternative codings of genitalic features reflecting opposing homology theories, and then excluding these features altogether, we sought to judge which genitalic theory is better supported by the evidence as a whole, and how much the debate matters to resolving cyclorrhaphan origins. Using the analog of a factorial design, we also measured the effect of alternative transformation series in several other controversial characters, of outgroup choice and of successive weighting. Under all manipulations, including both genitalic codings, the Cyclorrhapha originate within the Empidoidea, near the family Atelestidae. However, trees in which the Empidoidea are constrained to be monophyletic are only 1‐6 steps longer (out of ∼150), a fit not significantly worse under a permutation test for monophyly. Adult morphological data may not suffice to settle either the placement of Cyclorrhapha or the debate over genitalic homology. Moreover, the issue of genitalic homology does not appear critical to that of cyclorrhaphan origin.
CLADISTIC ANALYSIS OF METAZOAN RELATIONSHIPS: A REAPPRAISAL
Authors: Backeljau Thierry , Winnepenninckx Birgitta , Bruyn Luc De
Published: July 2005

Abstract— A recently published cladistic analysis of metazoan relationships based on 77 embryological and morphological characters is shown to be defective with respect to both methodological issues and the interpretation of certain characters. Consequently, many conclusions of this analysis are not supported by the data. Alternative phylogenetic hypotheses are therefore proposed, based on a re‐evaluation of an adapted data set.
EXACT INDICES, CRITERIA TO SELECT FROM MINIMUM LENGTH TREES
Authors: Sharkey Michael J.
Published: July 2005

Abstract— Modifications of the consistency, retention and rescaled consistency indices are introduced. These apply to particular transformations of a character state rather than all of the transformations of a character. For example, if one observes relatively many losses in a character state over a suite of minimum length trees, a low weight is applied to the transformation to a loss; however, these observations infer nothing on the probability of the character state being gained independently. If the same character state shows few or no convergent gains on the suite of minimum length cladograms, then gains receive a relatively high weight. Conversely, if for a particular character state, convergent gains are common and losses rare, the transformation to a loss is given a higher weight than the transformation to a gain. For multistate characters, each possible transformation is weighted independently. Three indices are proposed, i.e. the exact consistently index, the exact retention index and the exact rescaled consistency index. The consistency index is modified to deal with characters with unknown entries.

The methods outlined not only select (or generate) preferred tree topologies but they also choose character optimizations, even for trees of identical topology.
THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA
Authors: Thiele Kevin
Published: July 2005

Abstract— Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non‐overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non‐overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as “not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non‐sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.
PHYLOGENETIC INTERRELATIONSHIPS AND REDUCTIVE EVOLUTION IN NEOTROPICAL CHARACIDIIN FISHES (CHARACIFORMES, OSTARIOPHYSI)
Authors: Buckup Paulo Andreas
Published: July 2005

Abstract—Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae.

Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships amongElachocharax, Klausewitzia, OdontocharacidiumandMicrocharacidium. An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non‐simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the “presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.
HAEMATOTHERMIA: WARM‐BLOODED AMNIOTES
Authors: Gardiner Brian G.
Published: July 2005

Abstract— An exhaustive parsimony analysis of amniote phylogeny using 97 characters has substantiated the hypothesis that mammals and birds are sister groups. This deduction is further supported by parasitological and molecular evidence.

The presumed importance of “synapsid” fossils in amniote phylogeny is questioned and it is concluded that they represent a transformation series which when broken down into constit uent, monophyletic groups does not support the separation of the Mammalia from the remainder of the amniotes.

Fossil members of the Haematothermia include pterosaurs and “dinosaurs” (both stem‐group birds) and Dinocephalia, Dicynodontia, Gorgonopsida and Therocephalia (all stem‐group mammals). The Dromaeosauridae are the most crownward stem‐group birds and the Morganucodontidae the most crownward stem‐group mammals.

"Criticism of our conjectures is of decisive importance: by bringing out our mistakes it makes us understand the difficulties of the problem which we are trying to solve.” (K. R. Popper, 1972)
CLADISTIC AND BIOGEOGRAPHIC ANALYSES OF THE WEEVIL GENUS LISTRODERES SCHOENHERR (COLEOPTERA: CURCULIONIDAE)
Authors: Morrone Juan J.
Published: July 2005

Abstract— The weevil genus Listroderes Schoenherr is a monophyletic group defined by the body vestiture consisting of subcircular to suboval scales, and comprises 35 species endemic to southern South America. A cladistic analysis of the genus was carried out using 44 characters from external morphology, body vestiture, and male and female genitalia. The curvipes (three species), nodifer (five species) and robustus (four species) species groups and the 23 species of the costirostris species group were considered terminal taxa. Apomorphic states were identified using the genus Hyperoides Marshall as outgroup. The analysis yielded 122 equally parsimonious cladograms, each with 89 steps and a consistency index of 0.42; a successive weighting procedure resulted in nine cladograms (consistency index of 0.69 and retention index of 0.85). In the general consensus cladogram, nodifer‐robustus and curvipes‐costirostris are two pairs of sister species groups. The costirostris group comprises the subgroups foveatus, angusticeps, costirostris, delaiguei, bimaculatus and elegans, in phylogenetic order. A distributional analysis of the species of Listroderes led to identification of four areas of endemism, namely central Chile, sub‐Antarctic, central Argentina and Chaco. A vicariance biogeographic analysis of these areas, based on area cladograms of Listroderes, Hyperoides, Naupactus taeniatulus species group (Coleoptera: Curculionidae), and Lucilia generic group (Asteraceae) was carried out applying the three‐area statements technique. According to the general area cladogram the sequence of area‐fragmentation is as follows: (central Chile (sub‐Antarctic (central Argentina, Chaco))). This sequence is congruent with the history hypothesized for the region, where the uplift of the Andes (Oligocene‐Pliocene) led to a progressive aridification, replacing the ancient subtropical forest by open‐country environments.
IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE‐AREA STATEMENTS
Authors: Morrone Juan J. , Carpenter James M.
Published: July 2005

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)
PARALLEL PHYLOGENIES: RECONSTRUCTING THE HISTORY OF HOST‐PARASITE ASSEMBLAGES
Authors: Page Roderic D.M.
Published: July 2005

Abstract— A method for reconstructing the history of a host‐parasite assemblage is described. This method has the advantage of making explicit the relationship between the host and parasite trees, and it allows a visually intuitive representation of that history. It also enables host switches to be incorporated as an explanation of the observed pattern of host‐parasite associations, without the spurious overestimates of the number of host switches that can be obtained using Brooks parsimony analysis (BPA). Reconstructions that maximize the number of cospeciation events have the greatest explanatory power and are hence preferred over reconstructions with fewer cospeciation events. A heuristic algorithm to find a single maximal reconstruction, and an exact algorithm to find all such reconstructions are presented. Two empirical applications of the method are given.
“TOTAL EVIDENCE” AND THE EVOLUTION OF HIGHLY SOCIAL BEES
Authors: Chavarria Gabriela , Carpenter James M.
Published: July 2005

Abstract— Recent cladistic analyses of the relationships of the tribes of apine bees have produced conflicting results. The question of single or multiple origins of advanced eusociality in the group is thus unresolved. However, the previous studies have each treated only a limited part of the character data available. A “total evidence” analysis is essayed here, combining the published morphological characters with sequence data from rRNA and mtDNA. The resulting cladogram is: Euglossini + (Bombini + (Meliponini + Apini). This supports a single origin of advanced eusociality, from a stage of primitive eusociality.
BRANCH SUPPORT AND TREE STABILITY
Authors: Bremer Ka˚re
Published: July 2005

Abstract— Branch support is quantified as the extra length needed to lose a branch in the consensus of near‐most‐parsimonious trees. This approach is based solely on the original data, as opposed to the data perturbation used in the bootstrap procedure. If trees have been generated by Farris's successive approximations approach to character weighting, branch support should be examined in terms of weighted extra length needed to lose a branch. The sum of all branch support values over the tree divided by the length of the most parsimonious tree[s] provides a new index, the total support index. This index is a measure of tree stability in terms of supported resolutions, which is of prime importance in cladistic analysis.
PHYLOGENETIC RETICULATIONS AND CLADISTICS: DISCUSSION OF METHODOLOGICAL CONCEPTS
Authors: Skála Zdeněk , Zrzavý Jan
Published: July 2005

Abstract— Some problems associated with a cladistic treatment of complex taxa (hybrids and holobionts) are reviewed and discussed. The authors recommend aplication of standard cladistic analysis to all taxa, regardless of their supposed mode of origin. The position of a complex taxon depends entirely on the set of characters it shares with other taxa. This approach is preferable, because there are no means to distinguish deductively between various kinds of character conflicts (the recognition of one character as incongruous with others says nothing about its evolutionary origin). All other approaches have been proposed so as to reflect the topology of reticulate phylogenetic trees, but, at the same time, they require prior knowledge of the complex nature of a taxon.
MONOPHYLY AND COMPARISONS BETWEEN TREES
Authors: Wood Stephen W.
Published: July 2005

Abstract—The Farris method for assessing the empirical status of groups, as either monophyletic, paraphyletic or polyphyletic, is discussed. The reasons for presenting the method in terms of the behaviour of abstract, rather than real, characters are upheld. The method (i) reflects the insight that monophyly and related terms are used in comparisons between trees, (ii) avoids the problems associated with definitions based on the exclusion of subgroups, (iii) avoids the contentious issue of inclusion vs. exclusion of a group's most recent common ancestor. The Farris method is shown to be equivalent to the cluster distortion method for comparing the shapes of a pair of trees. Descriptor variables for each cluster in a reference tree are mapped on to a comparison tree. If a cluster's descriptor requires homoplasy then the cluster is a nonmonophyletic group. If the cluster descriptors behave according to Wagner parsimony, the kind of nonmonophyletic group is determined by the kind of homoplasy exhibited by the descriptor variable. The single cluster distortion coefficient is shown to be equal to (1‐ri), where ri is the retention index of the descriptor variable on the comparison tree. The overall distortion coefficient acts as a tree comparison metric and is defined as (1‐RI) where RI is the ensemble retention index.
THE BEHAVIOUR OF GOLOBOFF'S TREE FITNESS MEASURE F
Authors: Turner Hubert , Zandee Rino
Published: July 2005

Abstract — Goloboff recently introduced a method of character weighting that can be performed concomitantly with tree reconstruction. The basis for this method is his tree fitness measure F. The behaviour of F is examined for a number of hypothetical and real data sets. It depends strongly on the value of the concavity constant k, and does not seem to be predictable. This makes it difficult to make general recommendations about the appropriate value of k in specific cases. The basis for F, the number of extra steps taken by a character on a tree, does remain valuable as a basis for quality measures of trees, because it is independent of the number of states in the character, unlike the total number of steps and measures based on it such as CI and RC. Although no new measure is developed here, a number of requirements are formulated for an ideal tree quality measure.
GROUNDPLANS AND EXEMPLARS: PATHS TO THE TREE OF LIFE
Authors: Yeates D.K.
Published: July 2005

Abstract — During cladistic analysis of a diverse higher taxon it is impractical to code every species as a separate terminal. In such cases, workers proceed in one of two distinct ways: (1) examine a number of member species in order to deduce groundplan character states of the higher group before the analysis is begun, here called the intuitive method, or (2), code a number of real species belonging to the group as terminals in the analysis, called the exemplar method. Both methods have the same aim, to estimate the groundplan of the higher taxon concerned.

Both groundplan estimation methods will lead to identical results when the character in question has the same state in all members of the terminal group, however when the character has two or more states, the two methods may give different results. The precise methods employed in the intuitive approach have not been articulated in the literature, but possible techniques may result in non‐parsimonious ancestral state assignments, even in simple cases.

Groundplan estimation in the exemplar method is an extension of parsimony. The exemplar method allows groundplan state/s at internal nodes to be calculated during tree search. In many cases the exemplar method assigns a number of possible states to the groundplan, and the state assignment is therefore equivocal. This is not a deficiency of the method but reflects the notion that the parsimony criterion alone cannot always distinguish a single state present in a hypothetical ancestor. The optimal choice of exemplars required to estimate the groundplan most efficiently is discussed under a simple and common hypothesis of character transformation. For complex character distributions up to three exemplars may be required, each from a separate lineage of the group close to its hypothetical common ancestral node.
ON SIMULTANEOUS ANALYSIS
Authors: Nixon Kevin C. , Carpenter James M.
Published: July 2005

Abstract — Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow “secondary signals” to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are discussed.
IS FARRIS OPTIMIZATION PERFECT?: THREE‐TAXON STATEMENTS AND MULTIPLE BRANCHING
Authors: Platnick Norman I. , Humphries Christopher J. , Nelson Gareth , Williams David M.
Published: July 2005

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.
PERMUTATION TESTS AND OUTGROUPS
Authors: Trueman John W.H.
Published: July 2005

Abstract — Commonly used permutation tail probability (PTP) and topology dependent permutation tail probability (T‐PTP) tests incorporate an inappropriate treatment of designated outgroup taxa, and for that reason are biased either for (PTP) or for or against (T‐PTP) rejection of the null hypothesis. A modified test is proposed, in which this source of bias is eliminated.
THREE STEPS OF HOMOLOGY ASSESSMENT
Authors: Brower Andrew V.Z. , Schawaroch Valerie
Published: July 2005

Abstract —In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna's term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus taxic homology and explain the application of our terms to DNA sequence data.
COMBINED AND SEPARATE ANALYSES OF MORPHOLOGICAL AND MOLECULAR DATA IN THE PLANT FAMILY RUBIACEAE
Authors: Bremer Birgitta
Published: July 2005

Abstract—The Rubiaceae are one of the largest of the families of angiosperms, with over 10000 species. The tribal and subfamilial classification is provisional due to the lack of phylogenetic hypotheses. The present study of the Rubiaceae is based on 33 genera and three data sets, one morphological and two molecular from chloroplast DNA, restriction sites andrbcL sequences. There is much congruence between the morphological and the molecular data sets, but also conflict. For parsimony reasons, the best phylogenetic hypothesis is a tree based on an analysis of the combined data sets. The so‐called “total evidence” criterion for the combined analysis is simply a reiteration of the principle of parsimony. In this particular study, the classification would be almost the same even if based on the separate analyses instead of the combined. Despite the inapplicability of consensus trees or trees from separate analyses for phylogenetic hypotheses and classification, separate analyses may provide important information. It is the best way to reveal conflicts between different data sets. Knowledge of the conflicts can promote further detailed investigation in order to improve understanding of characters and phylogenetic hypotheses. In this study, the tribe Vanguerieae provides such an example; morphological data support a position in the subfamily Cinchonoideae, but DNA and a tree based on the combined data support a position in subfamily Ixoroideae. The tribe's position in the morphological tree is probably due to missing information concerning the correct pollen presentation system. Bootstrap fractions and K. Bremer's branch support values are used to evaluate the stability of particular nodes in the trees. Interestingly these values are not always correlated, e.g. in the morphological tree, the node with the highest branch support value has very low bootstrap fraction. The reasons for these differences are unclear, but large differences are presumably more likely to occur on short branches.
ON COMBINING PROTEIN SEQUENCES AND NUCLEIC ACID SEQUENCES IN PHYLOGENETIC ANALYSIS: THE HOMEOBOX PROTEIN CASE
Authors: Agosti Donat , Jacobs David , DeSalle Rob
Published: July 2005

Abstract—Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non‐silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non‐silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non‐silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non‐independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impart information to a hypothesis. These two possibilities are cases of non‐independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes fromDrosophila melanogasterto develop a hypothesis of genealogical relationship of these genes in this large multigene family.
THE ORIGIN OF PROTISTAN SYMBIONTS IN TERMITES AND COCKROACHES: A PHYLOGENETIC PERSPECTIVE
Authors: Grandcolas Philippe , Deleporte Pierre
Published: July 2005

Abstract— The controversy over whether protist symbionts ofCryptocercusand termites were inherited from a common ancestor or transferred secondarily has been long standing. We present here the first phylogenetic test of these hypotheses and show that the transfer hypothesis is better supported.
PHYLOGENETIC RELATIONSHIPS OF SCOTUSSA AND LEIOTETTIX (ORTHOPTERA: ACRIDIDAE)
Authors: Cigliano María Marta , Ronderos Ricardo A. , Kemp William P.
Published: July 2005

Abstract— A cladistic analysis of the South American grasshopper generaScotussaandLeiotettixwas performed in order to test the monophyly of these genera.Eurotettix, Chlorusand theDichroplus bergispecies group were included as terminal taxa. The genusAtrachelacriswas used to root the tree. Twenty‐nine characters from external morphology, male genitalia and female ovipositor were used in the analysis. In order to test for association between the structural change that occurred in the ovipositor valves ofScotussaand the functional change of the oviposition habits, the data matrix was partitioned and two analyses were performed. Characters from the female ovipositor were excluded from the data set used in the first analysis and another analysis was performed where all the characters were included in the analysis. Information on oviposition habits was then mapped on the cladogram, to determine the transformation for performance. Both analyses yielded only one most parsimonious tree and produced congruent results, confirming the monophyly ofLeiotettixandScotussaand corroborating their close relationship. Characters from the female ovipositor valves were informative not only at the species level but also at higher levels in the cladogram. The results also support the hypothesis of association between the structural change that occurred in the ovipositor valves ofScotussawith the functional change in the oviposition habits. However, this association did not seem to be correlated with the adaptive radiation in the genus.
PROBLEMS WITH “SOFT” POLYTOMIES
Authors: Coddington Jonathan A. , Scharff Nikolaj
Published: July 2005

Abstract— The “soft” assumption attributes polytomies to lack of data, not simultaneous cladogenesis (the “hard” assumption). Most systematists prefer the first interpretation, but most parsimony programs implicitly use the second. Results can thus be inconsistent with initial assumptions. Under certain circumstances that seem especially typical for large data sets treating higher taxa, it may be valid to eliminate both compatible and incompatible polytomous trees from consideration. Consistent treatment of soft polytomies can reduce the ambiguity of cladistic solutions and improve the resolution, and testability, of phylogenetic hypotheses.
UNINFORMATIVE BOOTSTRAPPING
Authors: Carpenter James M.
Published: July 2005

The effect of uninformative characters on the “significance levels” obtained by bootstrapping in cladistic analysis is investigated empirically. Twenty‐eight data sets from Platnick's benchmarks are analysed with Siddall's Random Cladistics bootstrapping module and Farris’Hennig86 program, using 1000 replicates and exact calculations. Contrary to the assurances of Harshman, inclusion of autapomorphies in a matrix commonly leads to a loss of “significance”.
Marine Area Relationships from Twenty Sponge Phylogenies. A Comparison of Methods and Coding Strategies
Authors: van Soest Rob W.M. , Hajdu Eduardo
Published: July 2005

Published phylogenies of 20 marine sponge groups are used to build general area cladograms of marine areas of endemism under three different methods for which algorithms adapted for personal computers are available, viz. COMPONENT, BPA and TAS, and two different coding strategies, Assumption 0 (A0) and “no assumption” (NA). The latter is a recently proposed procedure for handling the distributions of widespread taxa by treating these as separate areas of endemism, rather than as suites of smaller constituent areas. The 20 phylogenies contained large numbers of problem data which prevented an exhaustive search for all possible equally “best” general area cladograms. The Nelson consensus trees and their equivalents in parsimony analysis for all six attempts (viz. three different methodologies under two different coding strategies) were compared using their fit with the 20 sponge phylogenies as a measure of quality. Fit was determined using the number of “cospeciations” between a general area cladogram and a taxon area cladogram computed with TreeMap 1.0. No single method or coding strategy yielded a clearly better fit, each cladogram fitting variously better or worse with various phylogenies. In general, fit with NA coding was higher than with A0 coding, but random tree tests failed to generate statistically significant support for the conclusion that NA coding improves fit. Assuming that available sponge phylogenies are representative of marine benthic groups, software and hardware limitations are serious obstacles to a successful development of marine general area cladograms under any method or coding strategy.
The Calliphoridae (Blowflies) (Diptera: Oestroidea) are Not a Monophyletic Group1
Authors: Rognes Knut
Published: July 2005

To investigate the monophyly and phylogenetic relationships of the Calliphoridae (blowflies), 23 terminal monophyletic taxa within the Oestroidea and two outgroup taxa (Muscidae and Anthomyiidae) were scored for 45 adult and larval characters and subjected to analyses using parsimony. Search for trees of maximum total fit (using Pee‐Wee) gave nine different trees for the possible values of the concavity constant, whereas search for minimum length trees under equal weights (using NONA and PAUP) gave two, different, trees. The preferred trees are those obtained from the maximum‐fit searches since they are derived from a method that lowers the weight of characters showing within‐terminal as well as within‐tree homoplasy. The family Calliphoridae in various commonly used senses (excluding Oestridae s.lat.; including the Rhiniinae; excluding or including the Rhinoporidae; excluding or includingMystacinobia) does not appear to be a monophyletic group. It appears as such only in trees having a much lower total fit than the optimal trees (maximum fit approach) or only in a very small fraction of the numerous trees five or nine steps longer than the minimum length trees. The assemblage (Rhiniinae+Toxotarsinae+Chrysomyinae), sometimes assumed to be a natural taxon on account of common possession of a row of setae on the upper surface of the stem‐vein, should likewise be rejected. A clade (Ameniini+Euphumosia+Phumosiinae+Mesembrinellinae+Parameniini+Catapicephala) is possibly Gondwanian. A clade (Toxotarsinae+Chrysomyinae+Calliphorinae+Luciliinae+Melanomyinae) contains all the sarcosaprophagous “blowflies”. The group (Tachinidae+Sarcophagidae) is possibly the monophyletic sister group of the Rhiniinae.Mystacinobiaemerges from the analyses as the sister group of all other Oestroidea, and the family Axiniidae as the sister group of all the other non‐mystacinobiine oestroids. AlthoughMystacinobiais a guano‐feeder in all stages, the biology of the other basal oestroid taxa indicates that a reproductive association with living or dead invertebrates is the primitive oestroid pattern. Fossils having a bearing upon the estimation of the age of various oestroid clades are discussed.
Vicariance Events, not Areas, Should be Used in Biogeographical Analysis
Authors: Hovenkamp P.
Published: July 2005

Phylogenetic computer programs work by examining sequences of tree topologies, searching for those trees which yield minimal length. Rather than optimizing each tree from scratch, programs can use computational shortcuts to reduce the work required to compute each new tree's length; however, at least some of the techniques currently in use are approximate, and can miscalculate tree lengths. I describe a new incremental character optimization algorithm which is exact, correct, and comparable in speed to current methods.
Testability and the Refutation and Corroboration of Cladistic Hypotheses
Authors: Kluge Arnold G.
Published: July 2005

Both refutationist and verificationist philosophies and practices are becoming increasingly evident in phylogenetic inference. Refutation and verification are fundamentally different epistemologies, and it seems unlikely that they can continue to coexist as the basis for inferring species history. The refutationist nature of cladistics is explored in terms of Popperian testability, in order to understand better the alternatives and to predict the outcome of the expected revolution. Testability concerns the logical relationship between a hypothesis (h, such as a cladogram), evidence (e, such as synapomorphy), and background knowledge (b). Of particular importance is the direct relationship between the logical improbability ofhand its potential to be tested, because foreto corroborateh,eshould be improbable givenbalone. Simplicity and boldness, amount of empirical content, and logical improbability all refer to the potential to be tested. Thathmust be testable by severe tests is the same as saying that those tests have greater probability of failing, given onlyb. Descent with modification is sufficient as background knowledge (b) in phylogenetic inference, and such a minimal assumption explains the generality of cladistics. Also of interest to the refutationist position is total evidence. In terms of testability, a statement describing the results of multiple tests is less probable than a statement describing only some of the tests, the multiple test result being more improbable, and accordingly more severe, than its component tests. All other cladistic principles and practices considered in this review are also understandable in terms of Popperian testability, refutation and corroboration. These include minimizing ad hoc hypotheses of homoplasy and minimizing explanatory power, and choosing tentatively among cladograms according to their degree of corroboration (support). Differential character weighting is determined to be unacceptable in terms of testability. Also, testability does not provide a basis for assessing the accuracy of hypotheses, but then that is of no consequence to cladists, because they are not preoccupied with knowing the absolute truth, unlike verificationists.
Proportional Change and Patterns of Homoplasy: Sanderson and Donoghue Revisited
Authors: Hauser David L. , Boyajian George
Published: July 2005

The effects of two parameters, (1) the number of taxa and (2) the percentage of characters that change per node (referred to as the amount of proportional change or APC) on the retention index (RI) and the consistency index (CI) were examined. Random data sets were generated with a variety of different combinations of the number of taxa and the APC; five replicates for each unique combination were generated producing a total of 660 data sets. Results suggest that both the number of taxa and the APC are significantly correlated with the CI. In data sets with more than seven taxa, the APC explains more variation in homoplasy than does the number of taxa. The RI was found to be very strongly correlated with the APC and only weakly correlated with the number of taxa.
Cycles
Authors: Farris James S.
Published: July 2005

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.
Uneconomical Diagnosis of Cladograms: Comments on Wheeler and Nixon's Method for Sankoff Optimization
Authors: Swofford David L. , Siddall Mark E.
Published: July 2005

We provide three simple examples demonstrating that Wheeler and Nixon's method of recoding “stepmatrix’ characters can fail to yield most parsimonious reconstructions of character evolution under specified cost (transformation‐weight) schemes. These examples variously indicate undercounting or overcounting of tree lengths due to an inappropriate assumption of independence among the recoded characters. Their method is therefore not equivalent to Sankoff's dynamic programming algorithm, contrary to their claim.
Probabilism and Phylogenetic Inference
Authors: Siddall Mark E , Kluge Arnold G
Published: July 2005

The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration‐based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the task of the historical sciences being one of explanation, not prediction. Thus, frequency probability methods of estimation are inappropriate for making historical inferences. Maximum likelihood estimation procedures are deconstructed from numerous perspectives in spite of their supposed impressive technicalities. Charges of parsimony's inconsistency are rendered mute, because its justification lies elsewhere, yet maximum likelihood is still subject to Wald's dilemma if realism is of any interest. Although all epistemologies make assumptions, the models employed by maximum likelihood are problematic and deterministic, as opposed to the unproblematic background knowledge characteristic of cladistics. Apart from issues of logical and sampling dependencies, the requirements of frequency probability theory are non‐trivial and the maximum likelihood estimation of phylogeny can neither escape, nor satisfy the tenets of calculus independence (e.g. i.i.d.) inherent in the multiplicative relations of the method. If phylogeneticists are to maintain a rational foundation for their epistemology, neo‐justificationist appeals to some metaphysical truth must be abandoned in favour of the realism of sophisticated falsification.
Hypothetical Ancestors and Rooting in Cladistic Analysis
Authors: Bryant Harold N.
Published: July 2005

Most hypothetical ancestors that are used to root trees in cladistic analyses summarize character‐state information in one or more outgroup taxa. Nonetheless, hypothetical ancestors also provide a means of rooting trees using the ontogenetic and paleontological methods of polarizing character transformations, and for incorporating the inferences of more than one of these methods into a single analysis. However, the use of one hypothetical ancestor that combines inferences based on outgroup comparison with those based on other methods of polarizing character transformations to root a cladogram is invalid. Inferences regarding plesiomorphic character states based on outgroup comparison apply to the outgroup node, whereas inferences based on either the ontogenetic or paleontological method apply to the ingroup node. These inferences cannot be combined into a single hypothetical construct. A hypothetical ancestor based on outgroup information is included in the data matrix and used to root the resulting network; however, because this ancestor places potentially problematic constraints on the analysis, the use of actual outgroup taxa is preferable in most instances. Correct use of a hypothetical ancestor inferred with the ontogenetic and paleontological methods involves the Lundberg method in which the shortest ingroup network is rooted at the internode to which the hypothetical ancestor attaches most parsimoniously. Because inferences of polarity based on outgroup comparison cannot be combined directly with those based on other polarization methods, the synthesis of information from all three methods in a single tree must involve taxonomic congruence.
Phylogenetic Characterization lcrD Gene Family: Molecular Evolutionary Aspects of Pathogen‐Induced Hypersensitivity in plants
Authors: Brown Eric W. , Allard Marc W. , van der Zwet Tom
Published: July 2005

Abstract
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Hrp(hypersensitivity response and pathogenicity) genes encode signal‐peptide independent transporter molecules that function in the Type III secretion pathway and are present in a number of plant pathogenic bacterial species. These Hrp transporter molecules largely export harpin and other virulence factors across the bacterial membrane and onto theHrploci are part of a largerlcrD family which encode the low calcium response proteins. Members of this family serve to transport a number of diverse virulence factors in a variety of enteric and other purple bacteria species both pathogenichrp‐induced pathogenicity by different plant pathogenic bacterial species is the result of a single evolutionary event or evolved independently, cladistic analyses were performedlcrD gene family. The results of these studieslcrD orhrpgeneslcrD homologues which comprised the other twohrptransporter genes do not capture the phylogenetic history of their host bacteriallcrD gene was horizontally introduced into each of four different plant pathogenic species which may have resulted from four independent transfer events. This monophyletic partitioning ofhrpgenes precludes their use as reliable taxonomic markers while further supporting the current notion thathrptransport
PTP is Meaningless, T‐PTP is Contradictory: A Reply to Trueman
Authors: Carpenter James M. , Goloboff Pablo A. , Farris James S.
Published: July 2005

Abstract
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The T‐PTP test for monophyly can attribute significance to entirely unsupported groups and even to both of two contradictory alternatives. The method of evaluating “support” after replacing selected groups of terminals with reconstructed ancestors has similar drawbacks. The proposed placement of Onychophora among Arthropoda is unsupported by 12S data, and strongly refuted by other evidence. Attempts to justify T‐PTP on Popperian grounds rest entirely on misunderstanding Popper's ideas. The PTP test assesses neither Popperian corroboration nor statistical confidence of phylogenetic conclusions. It can attribute high significance to data that support no resolved grouping. Efforts to salvage PTP by proposing new interpretations share the weakness that none of the proposed interpretations generally holds. None of these methods seems useful in phylogenetic