bluuebunny/crossref_metadata_2025 huggingface dataset:
RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) AND PARSIMONY METHODS
Authors: Backeljau Thierry , De Bruyn Luc , De Wolf Hans , Jordaens Kurt , Van Dongen Stefan , Verhagen Ron , Winnepenninckx Birgitta
Published: July 2005

Abstract — Random amplified polymorphic DNA (RAPD) data possess a number of undesirable features for parsimony analysis. These features include their non‐codominant inheritance, their anonymous nature, their different (a)symmetrical transformation probabilities, and their possible GC priming bias. As a consequence, no single parsimony method seems appropriate for RAPD data. Moreover, the presence/absence coding of RAPDs is equivalent to the invalid independent allele model for allozymes. These issues are discussed and the way in which parsimony analysis of RAPDs can be misleading is illustrated.
PHYLOGENETIC RELATIONSHIPS AMONG EXTANT BRACHIOPODS
Authors: Carlson Sandra J.
Published: July 2005

Abstract—The monophyletic status of the Brachiopoda and phylogenetic relationships within the phylum have long been contentious issues for brachiopod systematists. The relationship of brachiopods to other lophophore‐bearing taxa is also uncertain; results from recent morphological and molecular studies are in conflict. To test current hypotheses of relationship, a phylogenetic analysis was completed (using PAUP 3.1.1) with 112 morphological and embryological characters that vary among extant representatives of seven brachiopod superfamilies, using bryozoans, phoronids, pterobranchs and sipunculids as outgroups. In the range of analyses performed, brachiopod monophyly is well supported, particularly by characters of soft anatomy. Arguments concerning single or multiple origins of a bivalved shell are not relevant to recognizing brachiopods as a clade. Articulate monophyly is very strongly supported, but inarticulate monophyly receives relatively weak support. Unlike previous studies, the nature of uncertainties about the clade status of Inarticulata are detailed explicitly here, making them easier to test in the future. Calcareous inarticulates appear to share derived characters with the other inarticulates, while sharing many primitive characters with other calcareous brachiopods (the articulates). Experimental manipulation of the data matrix reveals potential sources of bias in previous hypotheses of brachiopod phylogeny. Although not tested explicitly, lophophorate monophyly is very tentatively supported. Molecular systematic studies of a diverse group of brachiopods and other lophophorates will be particularly welcome in providing a test of the conclusions presented here.
THE PHYLOGENY OF ELATEROIDEA (COLEOPTERA), OR WHICH TREE IS BEST TODAY?
Authors: Muona Jyrki
Published: July 2005

Abstract —The relationships of the clicking Elateroidea beetles were studied with the help of parsimony analysis using Hennig86. The character matrix included 70 characters and 27 taxa. The results demonstrate the monophyly of the group ThroscidaesensuCrowson, contrary to views presented in other papers. Methods for solving this problem were sought. When several minimum length solutions were obtained, successive weighting and a search for a strict consensus tree identical with one of the original trees appeared to be acceptable ways for trying to identify the preferred solution. When conflicting trees from separate data sets were compared, a combined global analysis turned out to be impossible to perform because the data sets used different terminal taxa. In this case, the incongruence and total support tests provided by Farris' programs RNA and KON proved indispensable. The conflict found between the results obtained here and those presented by other workers using a large suite of larval characters were shown to be caused by an incongruent data matrix used in the latter study—the larval data set resulted in a polyphyletic ingroup and suggests relationships quite different from adult data alone. Directed large scale homoplasy due to repeated re‐invasion of two major habitats by separate clades may be the factor causing difficulties in coding the larval characters.
A PRELIMINARY PHYLOGENETIC AND BIOGEOGRAPHIC ANALYSIS OF THE DYAKIIDAE (GASTROPODA: STYLOMMATOPHORA) AND A BIOGEOGRAPHIC ANALYSIS OF OTHER SUNDALAND TAXA
Authors: Hausdorf Bernhard
Published: July 2005

Abstract —The phylogeny of the Dyakiidae, an early diverging lineage of the Limacoideasensu lalo, is reconstructed. In the Dyakiidae a unique transformation series of different genital accessory organs, the so‐called “stimulators”, is preserved which is an important argument for the hypothesis that the different stimulator types of the Stylommatophora are homologous. The biogeographic distribution patterns of the genera of the Dyakiidae are summarized and the ancestral areas of the major clades are analysed. The analysis of the area cladograms of the Dyakiidae and of several butterfly and heteroptera genera occurring in Sundaland revealed neither a general pattern of relationship between the areas of endemism in Sundaland, nor a general pattern of relationship between Sundaland and other areas. The area cladogram of the rather immobile Dyakiidae endemic to Sundaland might reflect older events than the area cladograms of the more mobile and widespread butterfly and plant bug genera. The general incompatibility of the area cladograms involving Sundaland taxa suggests that dispersal across barriers has played a major role in the historical biogeography of the analysed groups and challenges the hypothesis of vicariance biogeography that the distribution patterns of organisms are largely due to the fragmentation of an ancestral biota.
LEFKOVITCH'S ERROR
Authors: Farris James S. , Källersjö Mari
Published: July 2005

Abstract — Lefkovitch's formula for the probability of incompatibility between two binary characters can give incorrect results because it redundantly counts some possible compatibilities. The inaccuracy occurs when the characters have the same number of terminals showing the apomorphic state.
METHODS FOR FASTER PARSIMONY ANALYSIS
Authors: Goloboff Pablo A.
Published: July 2005

Abstract — Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations as suboptimal by checking just one node. Three different algorithms for faster estimation of final state assignments for the divided tree based on calculations for the whole tree are presented. The first of these is approximate; it uses information from the final state sets for the whole tree. The second is exact, but it is slower than the first, and requires more memory; it is based on the union of the state sets of the descendants for each node. The third is also exact; it requires more memory and programming effort than the other two but it is faster, it is based on final and preliminary state sets for the whole tree (“incremental two‐pass optimization”). Efficient ways to derive state assignments for collapsing trees, based on final states for the divided tree, are described. The recently proposed method of “incremental optimization” is discussed. It is likely that searches using that method will be no faster than searches using indirect calculation as originally described, and will be quite slower than the modified indirect calculation described here. Searches using that method will probably be significantly slowed down when zero‐length branches are to be collapsed, since shortcuts for faster collapsing are not directly applicable.
NAMES AND ORIGINS
Authors: Farris James S.
Published: July 2005

Abstract — Contrary to the impression given by Trueman (1996), Bremer (1988) introduced what is now called Bremer support; Faith (1991) did not. Neither did Mishler and Donoghue (1991). Attaching Faith and Cranston's (1991) acronym PTP to Archie's (1989) test does not help make the authorship clear, and the same applies to Källersjö et al.'s (1992) total support test.
THREE‐TAXON STATEMENTS AND PHYLOGENY CONSTRUCTION
Authors: Deleporte P.
Published: July 2005

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.
CLADISTIC AND BIOGEOGRAPHIC ANALYSES OF HAWAIIAN PIPUNCULIDAE (DIPTERA) REVISITED
Authors: De Meyer Marc
Published: July 2005

Abstract — Pipunculidae (Diptera) of the Hawaiian islands belong to the endemichawaiiensissubgroup of the subgenusCephalops(Semicephalops). In total 36 species are known from the Hawaiian islands. Cladistic analysis of 31 species, using 21 morphological characters from the male terminalia, resulted in 480 equally parsimonious trees. Three rounds of successive weighting resulted in 610 equally parsimonious trees. A biogeographic analysis was carried out, using the three‐area statement technique and based on the strict consensus tree produced from the tree set obtained by successive weighting. The analysis puts the sequence of the island groups in congruence with the geological history of the islands. The results of the cladistic and biogeographic analyses were compared with earlier similar analyses.
ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE
Authors: Nixon Kevin C. , Carpenter James M.
Published: July 2005

Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter‐cladogram character conflict for all characters among a set of cladograms.
THE CONTINENTAL ASIAN ELEMENT IN THE FAUNA OF THE PHILIPPINES AS EXEMPLIFIED BY COLADENIA MOORE, 1881 (LEPIDOPTERA: HESPERIIDAE)1
Authors: de Jong Rienk
Published: July 2005

Abstract — The Philippines are an archipelago composed of oceanic islands originating from different island arcs, and a few pieces of continental origin. The continental fragments can be found in N Palawan, the Calamian Islands, W Mindoro and W Panay. This study aims at answering the question whether traces can be found of a terrestrial fauna travelling on these fragments to the east to become part of the Philippine fauna. A phylogenetic analysis of the genusColadenia(Lepidoptera: Hesperiidae) based on morphological characters has been carried out. Three methods for detecting distribution patterns have been applied and compared, viz. Page's Tree Reconciliation, Brooks Parsimony Analysis, and a method similar to character optimization and here called Area Optimization. It is concluded that there is evidence of a continental element in the Philippine fauna. The (expected) generality of this pattern can only be demonstrated when more phylogenetic analyses of relevant groups become available.
WIDESPREAD TAXA, SYMPATRY, DISPERSAL, AND AN ALGORITHM FOR RESOLVED AREA CLADOGRAMS
Authors: Enghoff Henrik
Published: July 2005

Abstract — It is argued that in area biogeographical studies, the information content of widespread taxa is comparable to that of endemic taxa; widespread taxa should therefore be treated under Assumption 0. For areas of sympatry (redundant distributions) on the other hand, Assumption 2 is warranted because dispersal must always be invoked to explain sympatry. It is argued that all occurrences in an area of sympatry should be treated equally, regardless of whether the taxa are widespread or endemic, and regardless of whether the taxa occupy terminal or basal positions on the cladogram. An algorithm for translation of taxon‐area cladograms into resolved area cladograms under these conditions is given. As an example, this algorithm is applied to inocelliid snakeflies and gerrine pondskaters.
OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS?
Authors: Wheeler Ward
Published: July 2005

Abstract—A method is described to assess directly the number of DNA sequence transformations, evolutionary events, required by a phylogenetic topology without the use of multiple sequence alignment. This is accomplished through a generalization of existing character optimization procedures to include insertion and deletion events (indels) in addition to base substitutions. The crux of the model is the treatment of indels as processes as opposed to the patterns implied by multiple sequence alignment. The results of this procedure are directly compatible with parsimony‐based tree lengths. In addition to the simplicity of the method, it appears to generate more efficient (simpler) explanations of sequence variation than does multiple alignment.
THE HIGHER CLASSIFICATION OF THE ORDER EMBIOPTERA: A CLADISTIC ANALYSIS
Authors: Szumik Claudia A.
Published: July 2005

Abstract— A matrix of 41 Embiid taxa (representing the 8 formally recognized families of the Order) and 36 characters were cladistically analysed as a first attempt for understanding the higher classification of the Order Embioptera. The resulting trees were rooted with Clothodidae as the sister group of the other Embioptera. The results suggest that the current classification contains several artificial groups. With the rooting used, only Anisembiidae and Australembiidae are monophyletic. Embiidae is polyphyletic, as Australembiidae+ Notoligotomidae,Enveja(incertae sedis) and Oligotomidae+Teratembiidae appear within Embiidae, and the “embiid”Microembiaappears within Notoligotomidae. Oligotomidae is paraphyletic in terms of Teratembiidae. Four of the genera included in the analysis are paraphyletic:Mesembia, Chelicerca(in terms ofDactylocercaandPelorembia),Aposthonia(in terms ofOligotoma), andMetoligotoma(in terms ofAustralembia).PelorembiaandDactylocercaare synonymized withChelicerca.
PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING
Authors: Farris James S. , Albert Victor A. , Källersjö Mari , Lipscomb Diana , Kluge Arnold G.
Published: July 2005

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.
Efficient Incremental Character Optimization
Authors: Gladstein David S.
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.
A Phylogenetic Analysis of the Evolution of the Stridulatory Apparatus in True Crickets (Orthoptera, Grylloidea)
Authors: Desutter‐Grandcolas Laure
Published: July 2005

The stridulatory apparatus (or stridulum) is currently assumed ancestral in crickets. Models of its subsequent evolution consider only one modality of evolutionary change: the stridulum would have been progressively lost in multiple cricket lineages. A phylogenetic test of this hypothesis is presented here. The morpho‐functional types of stridulum have been optimized on the cladistic phylogenies of two monophyletic cricket clades, and parsimonious evolutionary scenarios of the evolution of the stridulum in these clades have been derived. The phylogenetic patterns thus obtained support the hypothesis that the stridulum has been lost several times convergently in crickets. They indicate, however, that the loss of the stridulum could be reversible, and that several modalities of evolutionary change exist for the stridulum. Phylogenetic analysis thus reveals an unsuspected complexity in the evolution of acoustic communication in crickets.
Phylogeny of the New World Dysdercus (Insecta: Hemiptera: Pyrrhocoridae) and Evolution of their Colour Patterns
Authors: Zrzavý Jan , Nedved Oldrich
Published: July 2005

Evolution of colour patterns is reconstructed in the case of the New World species of Dysdercus (Hemiptera: Pyrrhocoridae). The phylogenetic species concept was applied to this group, elevating five subspecific taxa to specific rank (D. capitatus, D. discolor, D. fervidus, D. luteus, and D. neglectus), and the resulting 41 phylogenetic species were analysed cladistically. Using optimization methods, evolution of colour patterns of the group is hypothesized, and possible developmental mechanisms of colour‐pattern evolutionary changes are inferred.
Circularity and Independence in Phylogenetic Tests of Ecological Hypotheses
Authors: Luckow Melissa , Bruneau Anne
Published: July 2005

It has been asserted that in order to avoid circularity in phylogenetic tests of ecological hypotheses, one must exclude from the cladistic analysis any characters that might be correlated with that hypothesis. The argument assumes that selective correlation leads to lack of independence among characters and may thus bias the analysis. This argument conflates the idea of independence between the ecological hypothesis and the phylogeny with independence among characters used to construct the tree. We argue that adaptation or selection does not necessarily result in the non‐independence of characters, and that characters for a cladistic analysis should be evaluated as homology statements rather than functional ones. As with any partitioning of data, character exclusion may lead to weaker phylogenetic hypotheses, and the practice of mapping characters onto a tree, rather than including them in the analysis, should be avoided. Examples from pollination biology are used to illustrate some of the theoretical and practical problems inherent in character exclusion.
Phylogenetic Relationships of the Creek Chubs and the Spine‐Fins: an Enigmatic Group of North American Cyprinid Fishes (Actinopterygii: Cyprinidae)
Authors: Simons Andrew M. , Mayden Richard
Published: July 2005

Phylogenetic analyses based on the complete nucleotide sequence of the mitochondrial 12S ribosomal RNA gene were performed for representatives of major North American cyprinid clades. These analyses resolved four monophyletic groups: (1) Western Clade, represented byAcrocheilusandGila, (2) Creek Chub Clade, represented byCouesius, Hemitremia, Semotilus, andMargariscus, (3) Open Posterior Myodome Clade, represented byCampostoma, Phenacobius, Cyprinella, Notropis, Platygobio, andRhinichthys, and (4) Plagopterin Clade, represented bySnyderichthys, Lepidomeda, andMeda. The overall results of these analyses refute previous hypotheses of relationships of North American Cyprinidae based on morphological data. Our analyses support recognition ofSnyderichthys, formerly considered a subgenus ofGila,and indicate that the Plagopterin Clade is sister to the Creek Chub Clade. Furthermore, this analysis indicates that hypotheses of relationship between plagopterins and other Western taxa are unsupported and the Open Posterior Myodome Clade is a monophyletic group.
Molecular Phylogeny of Fulgoromorpha (Insecta, Hemiptera, Archaeorrhyncha). The Enigmatic Tettigometridae: Evolutionary Affiliations and Historical Biogeography
Authors: Bourgoin T. , Steffen‐Campbell J.D. , Campbell B.C.
Published: July 2005

Previous morphologically based studies by several taxonomists disagree on whether the Tettigometridae represent a sister group to all other fulgoromorphans or whether they are a relatively derived family within the Fulgoromorpha. In this study, several parsimony‐based analyses using data sets composed of nucleotide sequences of 18S rDNAs (genes encoding 18S rRNAs) support a monophyletic Fulgoromorpha. All analyses depict Tettigometridae as a relatively derived lineage in a monophyletic relationship with Tropiduchidae. Unscored and unweighted data sets position the tettigometrid + tropiduchid clade as sister to Flatidae. The tettigometrid + tropiduchid clade is supported by four synapomorphic sites, two deletions and two transversions. Constraining tettigometrids to a basal fulgoromorphan lineage significantly reduces parsimony, with several hundreds to thousand of trees being more parsimonious. An analysis employing the Barriel method for scoring potential phylogenetic information in regions containing deletions also supports a non‐basal tettigometrid + tropiduchid clade. However, this method results in three equally most parsimonious trees and a sister relationship of the tettigometrid + tropiduchid clade to Flatidae becomes ambiguous.

The molecular‐based results showing a derived Tettigometridae agree with previous morphological interpretations of Bourgoin. The current biogeographical distribution of tettigometrids and morphological features supporting the 18S rDNA‐based phylogeny are discussed.
Self‐Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs
Authors: Goloboff Pablo A.
Published: July 2005

A method to assess the cost of character state transformations based on their congruence is proposed. Measuring the distortion of different transformations with a convex increasing function of the number of transformations, and choosing those reconstructions which minimize the distortion for all transformations, may provide a better optimality criterion than the linear functions implemented in currently used methods for optimization. If trees are optimized using such a measure, transformation costs are dynamically determined during reconstructions; this leads to selecting trees implying that the possible state transformations are as reliable as possible. The present method is not iterative (thus avoiding the concern of different final results for different starting points), and it has an explicit optimality criterion. It has a high computational cost; algorithms to lessen the computations required for optimizations and searches are described.
Cladistics of the New World Genera of Listroderina (Coleoptera: Curculionidae: Rhytirrhinini)
Authors: Morrone Juan J.
Published: July 2005

The weevil subtribe Listroderina belongs in the tribe Rhytirrhinini (subfamily Cyclominae), and has 25 genera and 300 species in the Americas. A cladistic analysis of the American genera was undertaken, using 53 characters from the external morphology, mouthparts, body vestiture, and male and female genitalia, and considering Rhigopsidius Heller (subtribe Rhytirrhinina) as the outgroup. The analysis yielded 20 equally parsimonious cladograms (108 steps, CI=0.42, RI=0.64), which after successive weighting resulted in three minimum‐length cladograms (256 steps, CI=0.67, RI=0.82). In the strict consensus cladogram, which has the same topology as one of the original cladograms, the genera follow the sequence (Philippius, (Trachodema, (Lamiarhinus, (Acrorius, (Acroriellus, ((Rupanius, (Adioristidius, Amathynetoides, (Puranius, (Macrostyphlus, Andesianellus)))), (Hyperoides, (Germainiellus, (Antarctobius, Nacodius)), ((Haversiella, (Listronotus, Neopachytychius)), (Listroderes, Acrostomus), (Falklandiellus, (Falklandiopsis, (Telurus, (Falklandius, Lanteriella)))))))))))). A phylogenetic classification for the genera of American Listroderina is proposed, where the five principal lineages are recognized as generic groups:Macrostyphlus group (Rupanius, Adioristidius, Amathynetoides, Puranius, Macrostyphlus, and Alndesianellus),Antarctobius group (Germainiellus, Antarctobius, and Nacodius),Listronotus group (Haversiella, Listronotus, and Neopachytychius),Listroderes group (Listroderes and Acrostomus), and Falklandius group (Falklandiellus, Falklandiopsis, Telurus, Falklandius, and Lanteriella)
The AIDS Pandemic is New, but is HIVNotNew?
Authors: Siddall Mark E.
Published: July 2005

The determinations made by Mindell, Shultz and Ewald regarding the ancestral host for immunodeficiency retroviruses, and their conclusion that monkeys acquired their infections as a result of a host‐switch from humans, do not withstand rigorous scrutiny. Their hypothesis requires the complete uniformativeness of third position transitions and of gapped regions in the alignment. When all of the data are permitted to corroborate or refute relationships, optimizing hosts on the viral phylogeny renders either equivocal statements or an unequivocal simian ancestry. However, merely optimizing hosts as characters on the viral phylogeny is illogical. Not only does this treat hosts as dependent on the viruses (instead of the reverse) but it ignores 15 years of methodological developments specifically designed to answer questions regarding cospeciation or host‐switching.
Primary Homology Assessment, Characters and Character States
Authors: Hawkins Julie A. , Hughes Colin E. , Scotland Robert W.
Published: July 2005

We discuss contrasting approaches to cladistic character definition and thus to cladistic data matrix compilation. The conventional approach considers character states as alternate forms of the “same thing” (the character). A review of the challenges to this convention is presented, and their implications evaluated. We argue that the recognition of structures which are alternate forms is a vital stage of primary homology assessment and is equivalent to the conceptualization of a transformational homology. Such a view complies with the demand that characters are independent and that character states are hierarchically related. We identify one justifiable solution to the inapplicable data coding problem (coding for organisms which have red tails, blue tails or no tails), and show that alternative approaches to character definition support spurious solutions which deny the relation of structures which are “the same but different”. We propose that the term character can be defined, in a cladistic context, as the descriptive label referring to a transformational homology evidenced by the similarity criterion.
Higher Level Phylogeny of Curculionidae (Coleoptera: Curculionoidea) based mainly on Larval Characters, with Special Reference to Broad‐Nosed Weevils
Authors: Marvaldi Adriana E.
Published: July 2005

A cladistic analysis of Curculionidae was performed using 49 characters (41 from larvae, three from pupae, and five from adults). Illustrations of characters of immatures are provided. The analysis involved 19 terminal units and a hypothetical ancestor determined by the outgroup comparison method used to root the tree. One most parsimonious cladogram was obtained based on the complete data set and the following phylogenetic hypothesis is proposed: Ithycerinae, Microcerinae, and Brachycrinae sensu stricto are broad‐nosed weevils placed sequentially at the base of the cladogram. The remaining weevil subfamilies form two major natural groups: one constituted by the sister taxa Rhynchophorinae—Platypodinae; the other with Erirhininae at the base, as sister taxon of the “Curculionidae sensu stricto” which show an unresolved trichotomy involving Curculioninae, Cossoninae—Scolytinae, and the clade including the Entiminae and allied subfamilies. This latter clade of broad‐nosed weevils has Thecesterninae at the base; the next branch is Amycterinae, the sister taxon of the clade comprising two groups: one constituted by Aterpinae, Rhytirrhininae, and Gonipterinae; the other is Entiminae whose units form two main clades: one constituted by the sister tribes Pachyrhynchini—Ectemnorhinini, and the other by Alophini, Sitonini, and Entimini. When the analysis was done using only immature characters, results congruent with those based on the complete data set were obtained, except for the placement of Erirhininae. According to the results the hypothesis of monophyly of broad‐nosed weevils is not accepted; the Entiminae are justified as monophyletic and their natural classification into tribes is proposed and the phylogenetic position and relationships of higher taxa of Curculionidae are discussed. This paper shows the importance of immature characters in recognition of natural groups and relationships in Curculionidae.
Phylogenetic Relationships within the Excavating Hadromerida (Porifera), with a Systematic Revision
Authors: Rosell D. , Uriz M.J.
Published: July 2005

This study was performed to ascertain the relationships among clionid and spirastrellid species from the Mediterranean Sea, based on phylogenetic criteria. A matrix of 34 taxa and 20 characters was analysed. Cladistic analysis using PAUP produced 12 equally parsimonious trees of 54 steps (CI=0.648, RI=0.865). Resolution was high in all parts of the strict consensus tree except in those which involved relationships among the most characteristic clionid species: those having only tylostyles as megascleres and, if microscleres are present, these being spirasters. Six monophyletic groups, three of them represented by monospecific clades, appear in the totally resolved part of the trees, which supports their separation into different genera. On the basis of the results obtained, the species at present within the genus Cliona have been allocated to five different genera:Scantilletta, Pione, Volzia, Bernatia and Cliona, while Dotona and Cliothosa are maintained as separate genera.Scantilletta and Pione are genera erected by de Laubenfels (1936 Pap. Tortugas Lab. 30, 1–225) and Gray (1867 Proc. Zool. Soc. Lond. XXXII , 492–558) respectively, and whose diagnoses are amended here.Volzia and Bernatia are proposed as new genera to include Cliona albicans and Cliona rovignensis, and Cliona vermifera, respectively. Thus, the genus Cliona clearly appears in our analysis as a polyphyletic group. It is only maintained provisionally to harbour species whose position cannot be clearly ascertained from the information at hand. Skeletal characters such as spicule types and skeletal arrangement have proven to be useful in discriminating some genera and families but they do not completely resolve the phylogeny of this group of species. Biochemical, genetic, cytological or reproductive information, when available, may help in the resolution of the phylogenetic tree.
Forum – Taxonomic Stability is Ignorance
Authors: Dominguez Eduardo , Wheeler Quentin D.
Published: July 2005

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990:Syst. Zool. 39, 307–322; 1992:A. Rev. Ecol. Syst. 23, 449–480; 1994:Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.
A Phylogeny of the Gulls (Aves: Larinae) Inferred from Osteological and Integumentary Characters
Authors: Chu Philip C.
Published: July 2005

Abstract —Gulls (Aves: Larinae) are among the best‐studied of birds, yet prior attempts to reconstruct gull relationships have met with little success. In the present study I use 117 characters from the skeleton and 64 from the integument to test gull monophyly and estimate gull phylogeny. One shortest tree, requiring 9747 unweighted changes and having a CI of 0.267, wasLarusis polyphyletic. Although the tree is fully resolved, support for many of the inferred clades is poor. In a comparison of osteological and integumentary evidence, I found that incongruence between the osteological and integumentary character sets accounts for only a minority of the total incongruence observed, and suggest that low between‐set incongruence may be a consequence of the low signal‐to‐noise ratio in each set of characters. I also found that osteological evidence is particularly important for determining higher‐level structure, whereas integumentary evidence is important for resolving lower‐level relationships within the gull group. Finally, I found that integumentary characters are not dramatically more homoplasious than osteological characters, and argue that casual dismissal of integumentary characters as “too labile” is unwarranted.
Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification
Authors: Kluge Arnold G.
Published: July 2005

Miyamoto and Fitch's (1995,Syst. Biol.44: 64–76) verificationist arguments for taxonomic congruence are evaluated and found to be unconvincing. In particular, there is no logical connection between the truth of phylogenetic hypotheses and the independence of the sets of characters analysed for their consensus. Further, the character set partitions emphasized by Miyamoto and Fitch must be considered arbitrary, because they are based on untestable process assumptions.
Asymmetry and Explanations
Authors: Farris James S. , Källersjö Mari
Published: July 2005

In Colless’ (1995,Syst. Biol. 44, 102–108) results, cladograms for randomly generated matrices were strongly asymmetrical, and he used this to maintain that real cladograms provide little evidence on asymmetry of phylogeny. His position, however, depended on retaining poorly supported groups as if they were well‐supported. If poorly supported groups are removed, as with parsimony jackknifing, well‐structured real data can still give strong asymmetry, while random matrices simply yield unresolved trees, obviating Colless’ argument.
The Phylogeny of the Extant Chelicerate Orders
Authors: Wheeler Ward C , Hayashi Cheryl Y
Published: July 2005

The phylogeny of the extant chelicerate orders is examined in the light of morphological and molecular evidence. Representatives from each of the chelicerate ‘orders’ and mandibulate and onychophoran outgroups are examined. Molecular (small and large ribosomal subunit DNA) and morphological information is combined in a total evidence regime to determine the most consistent picture of extant chelicerate relationships for these data. Multiple phylogenetic analyses are performed with variable analysis parameters yielding largely consistent results. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis with lowest character incongruence yields the scheme of relationships (Pycnogonida+ (Xiphosura+((Opiliones+((Solifugae+Pseudoscorpiones)+Scorpiones))+((Ricinulei+Acari)+(Palpigradi+ ((Thelyphonida+Schizomida=Uropygi)+(Amblypygi+ Araneae))))))). This result is fairly robust to variation in analysis parameters, with the placement of solifugids and the status of the pedipalps responsible for most disagreement.
Forum. Stratigraphic Fit to Phylogenies: A Proposed Solution
Authors: Siddall Mark E.
Published: July 2005

Three measures intended to assess the fit of stratigraphic age to the fossil record have been suggested previously: the Spearman Rank Correlation (SRC), the Stratigraphic Consistency Index (SCI) and the Relative Completeness Index (RCI). The original formulation of SRC is intractable to all but pectinate trees and the corrective pruning procedure that circumvents this precludes whole‐tree estimates of fit. SCI, though it has been claimed otherwise, is strongly biased by tree shape, particularly as one adds more information. RCI is a measure of the amount of gap in the fossil record but has awkward consequences for evolutionary biology when it is maximized. A new approach, the Manhattan Stratigraphic Measure, uses the Manhattan distance between stratigraphic ages to determine fit to a tree. It is not biased by tree shape, it is sensitive to the magnitude of age discrepancy and there is an obvious significance test.
Success of Parsimony in the Four‐Taxon Case: Long‐Branch Repulsion by Likelihood in the Farris Zone
Authors: Siddall Mark E
Published: July 2005

The accuracy of phylogenetic methods is reinvestigated for the four‐taxon case with a two‐edge rate and a three‐edge rate. Unlike previous studies involving computer simulations, the two‐edge rate relates to branches that are sister taxa in the model tree. As with previous studies, certain methods are found to behave inaccurately in a portion of the parameter space where the two‐edge rate is proportionally large. This phenomenon, to which parsimony is immune, is termed “long‐branch repulsion” and the region of poor performance is called the Farris Zone. Maximum likelihood methods are shown to be particularly prone to failure when closely related taxa have long branches. Long‐branch repulsion is demonstrated with an empirical case involving Strepsiptera and Diptera.
The Logical Basis for the use of Continuous Characters in Phylogenetic Systematics
Authors: Rae Todd C
Published: July 2005

It has been argued that continuous characteristics should be excluded from cladistic analysis for two reasons: because the data are considered inappropriate; and because the methods for the conversion of these data into codes are considered arbitrary. Metric data, however, fulfill the sole criterion for inclusion in phylogenetic analysis, the presence of homologous character states, and thus cannot be excluded as a class of data. The second line of reasoning, that coding methods are arbitrary, applies to gap and segment coding, but quantitative data can be coded in a nonarbitrary manner by means of tests of statistical significance. These procedures, which are both objective and repeatable, determine the probability that two taxa possess an homologous character state; that is, if they have inherited a particular central tendency and distribution of individual variates unchanged from a common ancestor. Thus, the application of statistical tests to quantitative data empirically detects the presence of evolu tionary change, the raw material of phylogenetic reconstruction.
Tree Searches Under Sankoff Parsimony
Authors: Goloboff Pablo A.
Published: July 2005

Algorithms to speed up tree searches under Sankoff parsimony are described. For T terminal taxa, an exact algorithm allows calculating length during searches T to 2T times faster than a complete down‐pass optimization. An approximate but accurate method is from 3T to 8T times faster than a down‐pass. Other algorithms that provide additional increases of speed for simple symmetrical transformation costs are described.
Phylogeny of the Metazoa Based on Morphological and 18S Ribosomal DNA Evidence
Authors: Zrzavý Jan , Mihulka Stanislav , Kepka Pavel , Bezděk Aleš , Tietz David
Published: July 2005

Cladistic analysis of traditional (i.e. morphological, developmental, ultrastructural) and molecular (18S rDNA) data sets (276+501 informative characters) provides a hypothesis about relationships of all meta‐zoan higher taxa. Monophyly of Metazoa, Epith‐eliozoa (= ‐03non‐Porifera), Triploblastica, Mesozoa, Eutriploblastica (=Rhabditophora+Catenulida+“higher triploblasts”=Neotriploblastica, including Xeno‐ turbellida and Gnathostomulida), Rhabditophora, Syndermata (=“Rotifera”+Acanthocephala), Neotrichozoa (=Gastrotricha+Gnathostomulida), Nematozoa (=Nematoda+Nematomorpha), Panarthropoda (=Onychophora+Tardigrada+ Arthropoda), Cephalorhyncha, Deuterostomia, Ambulacralia (=Hemichordata+Echinodermata), Chordata, Phoronozoa (=Phoronida+“Brachiopoda”), Bryozoa, Trochozoa (=Eutrochozoa+Entoprocta+ Cycliophora), Eutrochozoa, and Chaetifera (=Annelida+ Pogonophora+Echiura) is strongly supported. Cnidaria (including Myxozoa), Ecdysozoa (=Cepha‐ lorhyncha + Nematozoa + Chaetognatha + Panarthropoda), Eucoelomata (=Bryozoa+Phoronozoa+Deuterostomia+Trochozoa, possibly including also Xenoturbellida), and Deuterostomia+Phoronozoa probably are monophyletic. Most traditional “phyla” are monophyletic, except for Porifera, Cnidaria (excluding Myxozoa), Platyhelminthes, Brachiopoda, and Rotifera. Three “hot” regions of the tree remain quite unresolved: basal Epitheliozoa, basal Triploblastica, and basal Neotriploblastica. A new phylogenetic classification of the Metazoa including 35 formally recognized phyla (Silicispongea, Calcispongea, Placozoa, Cnidaria, Ctenophora, Acoela, Nemertodermatida, Orthonecta, Rhombozoa, Rhabditophora, Catenulida, Syndermata, Gnathostomulida, Gastrotricha, Cephalorhyncha, Chaetognatha, Nematoda, Nematomorpha, Onychophora, Tardigrada, Arthropoda, Echinodermata, Hemichordata, Chordata, Phoronozoa, Bryozoa s. str., Xenoturbellida, Entoprocta, Cycliophora, Nemertea, Mollusca, Sipuncula, Echiura, Pogonophora, and Annelida) and few i ncertae sedis g roups (e.g. Myzostomida and Lobatocerebromorpha) is proposed.
Is the PTP Test Useful?
Authors: Slowinski Joseph B , Crother Brian I
Published: July 2005

We show empirically that the PTP test has very little discriminatory power, with highly significant PTP test probabilities often being associated with parsimony data that produce trees with low confidence (as measured by bootstrapping) and resolution. Because of this, we argue that the PTP test is useful only in the following, very limited way: if a data set fails the PTP test, it should not be used in a phylogenetic analysis. More conservative methods of measuring confidence such as the bootstrap or decay index are preferable.
A/The Brief History of Three‐Taxon Analysis
Authors: Farris James S , Kluge Arnold G
Published: July 2005

Recent claims by its advocates notwithstanding, three‐taxon analysis (3ta) provides no method for recognizing reversals or for applying them as apomorphies. Accordingly, 3ta could be used as a phylogenetic method only under an assumption of irreversibility. Being a method for calculating trees from character data, 3ta is not connected to any particular rule (“interpretation”) for selecting resolutions of consensus trees considered as abstract diagrams. 3ta cannot be justified simply by invoking a general minimization principle such as Occam's Razor, since that would cover almost any method. Some more specific basis is needed, and consideration of proposed bases for 3ta shows that none is even remotely adequate.
On the Three‐Taxon Approach to Parsimony Analysis
Authors: De Laet Jan , Smets Erik
Published: July 2005

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.
Fast Fitch‐Parsimony Algorithms for Large Data Sets
Authors: Ronquist Fredrik
Published: July 2005

The speed of analytical algorithms becomes increasingly important as systematists accumulate larger data sets. In this paper I discuss several time‐saving modifications to published Fitch‐parsimony tree search algorithms, including shortcuts that allow rapid evaluation of tree lengths and fast reoptimization of trees after clipping or joining of subtrees, as well as search strategies that allows one to successively increase the exhaustiveness of branch swapping. I also describe how Fitch‐parsimony algorithms can be restructured to take full advantage of the computing power of modern microprocessors by horizontal or vertical packing of characters, allowing simultaneous processing of many characters, and by avoidance of conditional branches that disturb instruction flow. These new multicharacter algorithms are particularly useful for large data sets of characters with a small number of states, such as nucleotide characters. As an example, the multicharacter algorithms are estimated to be 3.6–10 times faster than single‐character equivalents on a PowerPC 604. The speed gain is even larger on processors using MMX, Altivec or similar technologies allowing single instructions to be performed on multiple data simultaneously.
Transition Confidence and Modified Mean Values: Confidence Measures for Hypotheses of Character State Transition between Nodes and Ancestral State Optimizations
Authors: Sharkey Michael J.
Published: July 2005

A measure is introduced to quantify the reliability of character state transitions and character state stasis (lack of character state change between nodes). The mean value of a character state at an internal node is altered to obtain a measure termed the modified mean. Modified mean values at connecting nodes are employed to determine the support for hypotheses of character state transition/stasis between the nodes. The lowest of the two neighboring modified mean values implied by an hypothesis of character state transition/stasis is used as a direct measure of support for that hypotheses of character state transformation or stasis between the respective nodes.