bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm formation and modulation of luxS and rpoD expression by Helicobacter pylori
Authors: Cellini L. , Grande R. , Traini T. , Di Campli E. , Di Bartolomeo S. , Di Iorio D. , Caputi S. 
Published: July 2005

Bacteria often choose a sessile biofilm lifestyle as a strategy to overcome environmental stress. In this study, we describe biofilm formation by Helicobacter pylori on a polystyrene surface, evaluating the viability and the morphological dynamics of bacterial cells during multicellular aggregate development. Moreover, we investigate expression of the luxS and rpoD genes, which are involved in biofilm formation.Two clinically susceptible and resistant strains of H. pylori were analyzed, as well as H. pylori ATCC 43629 for reference. The dominant form of expression, clustered bacterial cells arranged in an abundant matrix, was recorded after 2 days of incubation without shaking. Coccoid (spherical) cells with a “wrinkled” aspect presented the prevalent morphology (59.26%) among cells in the biofilm structure as observed by scanning electron microscopy. In aged H. pylori cultures, death occurred in single cells or cells grouped into microcolonies in which degenerated bacteria were localized inside the aggregates. The expression of luxS and rpoD genes among the sessile bacterial population reached a maximum after 2 days, with a significant reduction at subsequent time-points. No differences in gene expression and biofilm formation were recorded in the three evaluated strains.The morphological fickleness expressed in the life cycle by H. pylori strains emphasizes the bacterium's ability to overcome environmental stress, balancing its spread both outside and inside the host.
Transcription in response to physical stress—clues to the molecular mechanisms of exercise‐induced asthma
Authors: Hilberg Thomas , Deigner Hans‐Peter , Möller Eva , Claus Ralf A. , Ruryk Andriy , Gläser Doreen , Landre Julien B. P. , Brunkhorst Frank M. , Reinhart Konrad , Gabriel Holger H. W. , Russwurm Stefan 
Published: July 2005

ABSTRACTTo clarify stress‐induced immunological reactions and molecular events during exercise and the potential relevance to exercise‐induced bronchoconstriction, transcriptional responses to standardized physical stress were determined. Six healthy, young volunteers underwent an endurance exercise of 90% of their individual anaerobic threshold for 90 min. Time‐dependent alterations in the expression pattern of leukocytes from healthy, trained subjects were analyzed by DNA microarrays before and 2 h and 6 h after exercise. Starting out from a large collection of cDNA library clones comprising more than 70,000 human expressed sequence tags, we selected, designed, and immobilized oligonucleotide probes (60–70mers) for transcripts of 5000 stress‐and inflammation‐relevant genes. Exercise‐induced stress provoked changes in the expression of 433 gene activities 2 h and/or 6 h after exercise, which could be grouped into six clusters. The most prominent feature was an enhanced transcription of two genes, coding for 5‐lipoxygenase (ALOX5) and ALOX5‐activating protein. Moreover, enhanced levels of leukotriene B4 (LTB4) and LTC4 (P<0.05) were detected in plasma after exercise. Our data demonstrate that exercise alters the activities of a distinct number of genes. In particular, they possibly provide novel insights into the molecular mechanisms of exercise‐induced bronchoconstriction and suggest that enhanced transcription of ALOX5 and its activating protein together with a present predisposition of the subject critically contribute to exercise‐induced asthma.
EXCESS HOMOPLASY RATIOS
Authors: Farris James S. 
Published: July 2005

Abstract Archie (1990) prefers his “homoplasy excess ratio” HER to Farris' (1989)1 ensemble retention index R. HER, he writes, lacks R's defects: R's minimum is not zero, and varies with number of terminals or characters.HER has those defects. Archie has misunderstood the permutation method on which HER rests, and mistaken the properties of R as well. After explaining those points, I describe other permutation‐based indices and briefly consider their utility. These provide relative measures of congruence among the characters of the data; one corresponds to a significance test.
THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION
Authors: Hauser David L. , Presch William 
Published: July 2005

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non‐additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister‐taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.
THE PHYLOGENETIC RELATIONSHIPS AMONG REQUIEM AND HAMMERHEAD SHARKS: INFERRING PHYLOGENY WHEN THOUSANDS OF EQUALLY MOST PARSIMONIOUS TREES RESULT
Authors: Naylor Gavin J.P. 
Published: July 2005

Abstract— Protein variation among 37 species of carcharhiniform sharks was examined at 17 presumed loci. Evolutionary trees were inferred from these data using both cladistic character and a distance Wagner analysis. Initial cladistic character analysis resulted in more than 30 000 equally parsimonious tree arrangements. Randomization tests designed to evaluate the phylogenetic information content of the data suggest the data are highly significantly different from random in spite of the large number of parsimonious trees produced. Different starting seed trees were found to influence the kind of tree topologies discovered by the heuristic branch swapping algorithm used. The trees generated during the early phases of branch swapping on a single seed tree were found to be topologically similar to those generated throughout the course of branch swapping. Successive weighting increased the frequency and the consistency with which certain clades were found during the course of branch swapping, causing the semi‐strict consensus to be more resolved. Successive weighting also appeared resilient to the bias associated with the choice of initial seed tree causing analyses seeded with different trees to converge on identical final character weights and the same semi‐strict consensus tree.The summary cladistic character analysis and the distance Wagner analysis both support the monophyly of two major clades, the genus Rhizoprionodon and the genus Sphyrna.. The distance Wagner analysis also supports the monophyly of the genus Carcharhinus. However, the cladistic analysis suggests that Carcharhinus is a paraphyletic group that includes the blue shark Prionace glauca.
ON OUTGROUPS
Authors: Nixon Kevin C. , Carpenter James M. 
Published: July 2005

Abstract— The relations among polarity, outgroups and rooting are clarified. The “outgroup algorithm” and “outgroup substitution method” are irrelevant forms of relaxed parsimony. They should be discarded in favor of unconstrained, simultaneous analysis of all terminals. A revised outgroup method is described both in text and with a computer‐generated flowchart. Lundberg rooting is consistent with cladistic parsimony only under specific circumstances involving hypothetical ancestors."Both sides seemed convinced that the ‘real enemy’is a vicious conspiracy of some kind."Hunter S. Thompson (1979: 145).
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.
Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
Authors: Schulmeister Susanne , Wheeler Ward C. , Carpenter James M. 
Published: July 2005

AbstractThe first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000–2700 bp for each taxon) from the nuclear genes 18S and 28S and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae +Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))).
Semi‐strict supertrees
Authors: Goloboff Pablo A , Pol Diego 
Published: July 2005

AbstractA method to calculate semi‐strict supertrees is proposed. The semi‐strict supertrees are calculated by creating the matrix that represents all the groups in the source trees (as done in already existing techniques), and then finding the trees determined by the ultra‐clique. The ultra‐clique is defined as the set of characters where each possible subset is compatible with each possible subset from the entire matrix. Finding the ultra‐clique is computationally complex (since in most cases many of the characters have missing entries), but a heuristic method yields reliable results. When the trees have no conflict, or when there are only two trees, the method produces the exact result for any ordering of the input trees and any ordering of the groups within them; when there are more than two trees and they have conflict, a single ordering or sequence can create some spurious groups, but doing multiple sequences eliminates the spurious groups. The method uses only state set operations, and is thus easily implemented in computer programs. Unlike any existing type of supertree, semi‐strict supertrees display all the groups, and only those groups, that are implied by at least some combination of the input trees and contradicted by none. The idea that supertrees should take into account the number of occurences of a given group, so as to retain some groups even in the case of conflict, is discussed; it is argued that a conceptual equivalent of the majority rule consensus is not possible when the sets of taxa differ among trees. Also, when pruning taxa from a set of trees, the supertree can display groups that contradict the consensus for the entire trees, suggesting that supertrees for matrices with very dissimilar sets of taxa should be interpreted with caution. If (for any valid reason) the data cannot be combined in a single matrix, it is advisable that the taxon sets in the matrices be as similar as possible.
Cladistic coding of genomic maps
Authors: Gallut Cyril , Barriel Véronique 
Published: July 2005

AbstractA new method of genomic maps analysis is described. The purpose of the method is to reconstruct phylogenetic relationships from the genomic organization of taxa. Our approach is based on gene order coding. This coding allows the description of genome topology without a prior hypothesis about evolutionary events and phylogenetic relationships. Different characters are used for each gene: (1) presence/absence, (2) orientation, and (3) relative position. The relative position of a particular gene inside the genome is the pair of genes surrounding it. The relative position character represents all the positions of a gene in the sampled genomes. It is coded as a multistate character. Our coding method has a priori variable cost implications on operators such as inversion, transposition, and gene loss/gain, which we discuss. The overall approach best fits the “duplication, random loss” evolutionary model. The coding method allows the reconstitution of a possible hypothetical common ancestor genome at each node of the tree. This reconstitution is based on the character states’ optimization; it comes down to choosing, among all possible optimizations, the optimization compatible with a complete genome topology at each internal node. The multistate coding of gene relative position, which is an undeniable advantage of this method, permits this reconstitution.
Basal subtribes of the Nymphidiini (Lepidoptera: Riodinidae): phylogeny and myrmecophily
Authors: Hall Jason P.W. , Harvey Donald J. 
Published: July 2005

AbstractThree cladistic analyses, based predominantly on adult morphology, are presented for myrmecophilous riodinid butterflies in the tribe Nymphidiini. The first is a species‐level analysis of all 22 species recognized here in Aricoris (=Audre auctt.) using 27 characters. The second is a species‐level analysis of all 24 species recognized here in Synargis using 53 characters. The third is a generic‐level analysis of all six genera (Aricoris, Ariconiasn. gen., Lemonias, Thisbe, Juditha, and Synargis) recognized here as belonging in the basal clades of the Nymphidiini (=Lemoniadina auctt.) using 17 characters, with members of the Theopeina and Nymphidiina included with the ingroup to assess the monophyly of subtribes. Almost all characters are illustrated. The first analysis indicates that Aricoris consists of five monophyletic species groups, with the relationship ((constantius gr.colchis gr.)+(chilensis gr.(aurinia gr.+epulus gr.))), and contains the type species of Eiseleia and Audre, which are synonymized with Aricoris (n. syns.). The second analysis indicates that Synargis consists of four monophyletic species groups, with the relationship (phliasus gr.(regulus gr.+(pittheus gr.+abaris gr.))), and contains the type species of Ematurgina and Thysanota, which are synonymized with Synargis (n. syns.). The third analysis indicates that the Lemoniadina, or basal clades of the Nymphidiini, are paraphyletic with respect to the Theopeina and Nymphidiina, with the generic relationship ((Aricoris+Ariconias)+(((Lemonias+Thisbe)+(Juditha+Synargis))+(Theopeina+Nymphidiina))). We therefore restrict the Lemoniadina to include Lemonias, Thisbe, Juditha, and Synargis and provide the name Aricorina n. subtribe for Aricoris and Ariconias. All nymphidiine subtribes are characterized and a synonymic checklist for the Aricorina and Lemoniadina is presented. A “supertree” composed of the species‐level phylogenies derived here for Aricoris and Synargis, and those derived elsewhere for Ariconias, Lemonias, Thisbe, and Juditha, is used to map the distribution of larval host plant and attending ant taxa and the occurrence of aphytophagy. Observed patterns are discussed.
Distinguishing “or” from “and” and the case for historical identification
Authors: Kluge Arnold G 
Published: July 2005

AbstractThe adequacy of a probabilistic interpretation must be judged according to the nature of the event, or thing, being inferred. For example, conditional (frequency) probability is not admissible in the inference of phylogeny, because basic statements of common ancestry do not fulfill the requirements of the relations specified by the probability calculus. The probabilities of the situation peculiar to the time and place of origin of species are unique. Moreover, according to evolutionary theory, an event of species diversification is necessarily unique, because species are parts of a replicator continuum—species arise from ancestral species. Also, these probabilities cannot be ascertained, because the relevant situation cannot be repeated—it is unique. Finally, the applicability of conditional (frequency) probability is denied, because events of common ancestry have already occurred—there is nothing to predict. However, hypotheses of species relationships can be identified objectively according to the degree to which they have survived simultaneous testing with critical evidence, not with generally confirming evidence. The most parsimonious hypothesis of species relationships represents the least disconfirmed, best supported, proposition among the alternatives being compared. That hypothesis does not, however, deserve any special epistemological status beyond serving as the focus of the next round of testing.
Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes
Authors: Brooks Daniel R , McLennan Deborah A 
Published: July 2005

AbstractDowling recently compared the empirical properties of Brooks parsimony analysis (BPA) and the leading method for studying phylogenetic aspects of coevolution, reconciled tree analysis (using the computer program TreeMap), based on a series of simulations. Like the majority of authors who have compared BPA with other methods, however, Dowling considered only the form of BPA proposed in 1981 and did not take into account various modifications of the method proposed from 1986 to 2002. This leaves some doubt as to the robustness of his assessments of both the superiority of BPA and its shortcomings. We provide a précis of the principles of contemporary BPA, including ways to implement it algorithmically, using either Wagner algorithm‐based or Hennigian argumentation‐based approaches, followed by an empirical example. Our study supports Dowling's fundamental conclusions about the superiority of primary BPA relative to TreeMap. However, his conclusions about the shortcomings of BPA due to inclusive ORing (i.e., the production of ghost taxa) are incorrect, as secondary BPA eliminates inclusive ORing from the method. Secondary BPA provides a more complete account of the evolutionary associations between the parasite groups and their hosts than does primary BPA, without sacrificing any indirectly generated information about host phylogeny. Secondary BPA of two groups of nematodes inhabiting Great Apes shows that TreeMap analysis underestimated the amount of cospeciation in the evolution of the nematode genus Enterobius.
Countering concerted homoplasy
Authors: Harris Simon R , Wilkinson Mark , Marques Antonio C 
Published: July 2005

AbstractConcerted homoplasy is a concern in phylogenetics because of its potential to generate strong but misleading evidence of relationships. Marques and Gnaspini (Cladistics 17, 371–381, 2001) proposed a method of recoding characters suspected of concerted homoplasy that avoids problems associated with their wholesale exclusion or inclusion. Here we show that the proposed method is analytically equivalent to excluding the recoded characters.
The problem of characters susceptible to parallel evolution in phylogenetic analysis: a reply to Marquès and Gnaspini (2001) with emphasis on cave life phenotypic evolution
Authors: Desutter‐Grandcolas Laure , D’Haese Cyrille , Robillard Tony 
Published: July 2005

AbstractMarquès and Gnaspini [Cladistics 17 (2001) 371–381] analyzed the problem of the phylogenetic treatment of characters submitted to parallel evolution. Their proposal aimed at preserving the potential phylogenetic significance of supposedly homoplastic characters and considering them for phylogeny reconstruction. As an example, they used the troglobiomorphic features of animals restricted to caves; according to their preliminary hypothesis of homoplasy, troglobitic animals would exhibit a particular phenotype, referred to as troglobiomorphic, which they would acquire under similar selective pressures from the subterranean environment. We examined Marquès and Gnaspini's approach not from the point of view of its technical flaws, but from the point of view of the authors’ basic assertions on the treatment of troglobiomorphic characters and more generally the inclusion/exclusion/transformation of characters prior to phylogenetic analysis. In the present paper, we argue that this approach is invalidated by the repeated use of ad hoc hypotheses, which are supported neither by an existing phylogenetic pattern nor by available data. We consequently contest the adequateness of this approach with a cladistic analysis of historical questions.