bluuebunny/crossref_metadata_2025 huggingface dataset:
Reliable multicast for the Grid: a case study in experimental computer science
Authors: Nekovee Maziar , Barcellos Marinho P , Daw Michael
Published: July 2005

In its simplest form, multicast communication is the process of sending data packets from a source to multiple destinations in the same logical multicast group. IP multicast allows the efficient transport of data through wide-area networks, and its potentially great value for the Grid has been highlighted recently by a number of research groups. In this paper, we focus on the use of IP multicast in Grid applications, which require high-throughput reliable multicast. These include Grid-enabled computational steering and collaborative visualization applications, and wide-area distributed computing. We describe the results of our extensive evaluation studies of state-of-the-art reliable-multicast protocols, which were performed on the UK's high-speed academic networks. Based on these studies, we examine the ability of current reliable multicast technology to meet the Grid's requirements and discuss future directions.
Towards a Grid infrastructure to support integrative approaches to biological research
Authors: Gavaghan D.J , Simpson A.C , Lloyd S , Mac Randal D.F , Boyd D.R.S
Published: July 2005

This paper discusses the scientific rationale behind the e-Science project,
Integrative Biology
, which is developing mathematical modelling tools, HPC-enabled simulations and an underpinning Grid infrastructure to provide an integrative approach to the modelling of complex biological systems. The project is focusing on two key applications to validate the approach: the modelling of heart disease and cancer, which together are responsible for over 60% of deaths in the United Kingdom. This paper provides an overview of the project, describes the initial prototype architecture and discusses the long-term scientific aims.
A practical toolkit for computational steering
Authors: Pickles S.M , Haines R , Pinning R.L , Porter A.R
Published: July 2005

Computational steering refers to the real-time interaction of a scientist with their running simulation code. Despite the many benefits associated with computational steering, its uptake to date has been limited. In this paper we discuss the reasons for this and how the computational steering library and associated tools developed as part of the RealityGrid project aim to tackle them. We describe the functionality of the steering library and the use of Grid services in constructing a generic, dynamic architecture for discovering, steering and connecting visualization software to running simulations. The use of on-line visualization for providing feedback to the scientist is described, including the ways in which it may be enhanced through tools such as Chromium and Access Grid. Finally, we illustrate the flexibility of our approach by describing the functionality that has been added to various simulation codes as part of the RealityGrid project.
Improving scientists' interaction with complex computational–visualization environments based on a distributed grid infrastructure
Authors: Kalawsky R.S , O'Brien J , Coveney P.V
Published: July 2005

The grid has the potential to transform collaborative scientific investigations through the use of closely coupled computational and visualization resources, which may be geographically distributed, in order to harness greater power than is available at a single site. Scientific applications to benefit from the grid include visualization, computational science, environmental modelling and medical imaging. Unfortunately, the diversity, scale and location of the required resources can present a dilemma for the scientific worker because of the complexity of the underlying technology. As the scale of the scientific problem under investigation increases so does the nature of the scientist's interaction with the supporting infrastructure. The increased distribution of people and resources within a grid-based environment can make resource sharing and collaborative interaction a critical factor to their success. Unless the technological barriers affecting user accessibility are reduced, there is a danger that the only scientists to benefit will be those with reasonably high levels of computer literacy. This paper examines a number of important human factors of user interaction with the grid and expresses this in the context of the science undertaken by RealityGrid, a project funded by the UK e-Science programme. Critical user interaction issues will also be highlighted by comparing grid computational steering with supervisory control systems for local and remote access to the scientific environment. Finally, implications for future grid developers will be discussed with a particular emphasis on how to improve the scientists' access to what will be an increasingly important resource.
Scientific Grid computing
Authors: Coveney Peter V
Published: July 2005

We introduce a definition of Grid computing which is adhered to throughout this Theme Issue. We compare the evolution of the World Wide Web with current aspirations for Grid computing and indicate areas that need further research and development before a generally usable Grid infrastructure becomes available. We discuss work that has been done in order to make scientific Grid computing a viable proposition, including the building of Grids, middleware developments, computational steering and visualization. We review science that has been enabled by contemporary computational Grids, and associated progress made through the widening availability of high performance computing.
Integrating epidemiology and genetic association: the challenge of gene–environment interaction
Authors: Kraft Peter , Hunter David
Published: July 2005

Recent advances in human genomics have made it possible to better understand the genetic basis of disease. In addition, genetic association studies can also elucidate the mechanisms by which ‘non-genetic’ exogenous and endogenous exposures influence the risk of disease. This is true both of studies that assess the marginal effect of a single gene and studies that look at the joint effect of genes and environmental exposures. For example, gene variants that are known to alter enzyme function or level can serve as surrogates for long-term biomarker levels that are impractical or impossible to measure on many subjects. Evidence that genetic variants modify the effect of an established risk factor may help specify the risk factor's biologically active components. We illustrate these ideas with several examples and discuss design and analysis challenges, particularly for studies of gene–environment interaction. We argue that to increase the power to detect interaction effects and limit the number of false positive results, large sample sizes will be needed, which are currently only available through planned collaborative efforts. Such collaborations also ensure a common approach to measuring variation at a genetic locus, avoiding a problem that has led to difficulties when comparing results from genetic association studies.
Genetic analysis of Pten and Tsc2 functional interactions in the mouse reveals asymmetrical haploinsufficiency in tumor suppression
Authors: Ma Li , Teruya-Feldstein Julie , Behrendt Nille , Chen Zhenbang , Noda Tetsuo , Hino Okio , Cordon-Cardo Carlos , Pandolfi Pier Paolo
Published: July 2005

The role of tumor suppressor haploinsufficiency in oncogenesis is still poorly understood. The PTEN and TSC2 tumor suppressors function to antagonize mTOR (mammalian target of rapamycin) activation by Akt; hence, compound heterozygous inactivation ofPtenandTsc2in the mouse may in principle exacerbate the tumor phenotypes observed in the single mutants in a reciprocal manner. In contrast, we found that whileTsc2heterozygosity unmasksPtenhaploinsufficiency in growth and tumor suppression, tumorigenesis inTsc2+/-mutants is surprisingly not accelerated byPtenheterozygosity, even though mTOR activation is cooperatively enhanced by compoundPten/Tsc2heterozygosity. We show that the wild-type alleles of bothPtenandTsc2are retained in prostate tumors from bothPten+/-andPten+/-Tsc2+/-mice, whereas TSC-related tumor lesions are invariably associated withTsc2loss of heterozygosity (LOH) in bothTsc2+/-andPten+/-Tsc2+/-mice. These findings demonstrate that inactivation ofTSC2is epistatic toPTENin the control of tumor initiation and progression and, importantly, that bothPtenandTsc2are haploinsufficient for suppression of tumorigenesis initiated byPtenheterozygosity, while neitherPtennorTsc2is haploinsufficient for repression of carcinogenesis arising fromTsc2heterozygosity, providing a rationale for the differential cancer susceptibility of the two human conditions associated withPTENorTSC2heterozygous mutations.
Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis
Authors: Onouchi Hitoshi , Nagami Yoko , Haraguchi Yuhi , Nakamoto Mari , Nishimura Yoshiko , Sakurai Ryoko , Nagao Nobuhiro , Kawasaki Daisuke , Kadokura Yoshitomo , Naito Satoshi
Published: July 2005

Expression of the Arabidopsis CGS1 gene that codes for cystathionine γ-synthase is feedback regulated at the step of mRNA stability in response to S-adenosyl-L-methionine (AdoMet). A short stretch of amino acid sequence, called the MTO1 region, encoded by the first exon of CGS1 itself is involved in this regulation. Here, we demonstrate, using a cell-free system, that AdoMet induces temporal translation elongation arrest at the Ser-94 codon located immediately downstream of the MTO1 region, by analyzing a translation intermediate and performing primer extension inhibition (toeprint) analysis. This translation arrest precedes the formation of a degradation intermediate of CGS1 mRNA, which has its 5′ end points near the 5′ edge of the stalled ribosome. The position of ribosome stalling also suggests that the MTO1 region in nascent peptide resides in the ribosomal exit tunnel when translation elongation is temporarily arrested. In addition to the MTO1 region amino acid sequence, downstream Trp-93 is also important for the AdoMet-induced translation arrest. This is the first example of nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in eukaryotes. Furthermore, our data suggest that the ribosome stalls at the step of translocation rather than at the step of peptidyl transfer.
A model of bidirectional synaptic plasticity: From signaling network to channel conductance
Authors: Castellani Gastone C. , Quinlan Elizabeth M. , Bersani Ferdinando , Cooper Leon N. , Shouval Harel Z.
Published: July 2005

In many regions of the brain, including the mammalian cortex, the strength
of synaptic transmission can be bidirectionally regulated by cortical activity
(synaptic plasticity). One line of evidence indicates that long-term synaptic
potentiation (LTP) and long-term synaptic depression (LTD), correlate with the
phosphorylation/dephosphorylation of sites on the
α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor
subunit protein GluR1. Bidirectional synaptic plasticity can be induced by
different frequencies of presynaptic stimulation, but there is considerable
evidence indicating that the key variable is calcium influx through
postsynaptic N-methyl-d-aspartate (NMDA) receptors. Here,
we present a biophysical model of bidirectional synaptic plasticity based on
[Ca2+]-dependent phospho/dephosphorylation of the GluR1
subunit of the AMPA receptor. The primary assumption of the model, for which
there is wide experimental support, is that the postsynaptic calcium
concentration, and consequent activation of calcium-dependent protein kinases
and phosphatases, is the trigger for phosphorylation/dephosphorylation at
GluR1 and consequent induction of LTP/LTD. We explore several different
mathematical approaches, all of them based on mass-action assumptions. First,
we use a first order approach, in which transition rates are functions of an
activator, in this case calcium. Second, we adopt the Michaelis-Menten
approach with different assumptions about the signal transduction cascades,
ranging from abstract to more detailed and biologically plausible models.
Despite the different assumptions made in each model, in each case, LTD is
induced by a moderate increase in postsynaptic calcium and LTP is induced by
high Ca2+ concentration.
Glucose injections into the dorsal hippocampus or dorsolateral striatum of rats prior to T-maze training: Modulation of learning rates and strategy selection
Authors: Canal Clinton E. , Stutz Sonja J. , Gold Paul E.
Published: July 2005

The present experiments examined the effects of injecting glucose into the
dorsal hippocampus or dorsolateral striatum on learning rates and on strategy
selection in rats trained on a T-maze that can be solved by using either a
hippocampus-sensitive place or striatum-sensitive response strategy.
Percentage strategy selection on a probe trial (Pcrit) administered
after rats achieved criterion (nine of 10 correct choices) varied by group.
All groups predominately exhibited a response strategy on a probe trial
administered after overtraining, i.e., after 90 trials. In experiment 1, rats
that received intrahippocampal glucose injections showed enhanced acquisition
of the T-maze and showed increased use of response solutions at
Pcrit compared with that of unimplanted and artificial cerebral
spinal fluid (aCSF)-treated groups. These findings suggest that glucose
enhanced hippocampal functions to accelerate the rate of learning and the
early adoption of a response strategy. In experiment 2, rats that received
intrastriatal glucose injections exhibited place solutions early in training
and reached criterion more slowly than did aCSF controls, with learning rates
comparable to those of unoperated and operated-uninjected controls. Relative
to unoperated, operated-uninjected and glucose-injected rats, rats that
received intrastriatal aCSF injections showed enhanced acquisition of the
T-maze and increased use of response solutions at Pcrit. The
unexpected enhanced acquisition seen after striatal aCSF injections suggests
at least two possible interpretations: (1) aCSF impaired striatal function,
thereby releasing competition with the hippocampus and ceding control over
learning to the hippocampus during early training trials; and (2) aCSF
enhanced striatal functioning to facilitate striatal-sensitive learning. With
either interpretation, the results indicate that intrastriatal glucose
injections compensated for the aCSF-induced effect. Finally, enhanced
acquisition regardless of treatment was accompanied by rapid adoption of a
response solution for the T-maze.
A different recruitment of the lateral and basolateral amygdala promotes contextual or elemental conditioned association in Pavlovian fear conditioning
Authors: Calandreau Ludovic , Desmedt Aline , Decorte Laurence , Jaffard Robert
Published: July 2005

Convergent data suggest dissociated roles for the lateral (LA) and
basolateral (BLA) amygdaloid nuclei in fear conditioning, depending on whether
a discrete conditioned stimulus (CS)–unconditional stimulus (US) or
context–US association is considered. Here, we show that pretraining
inactivation of the BLA selectively impaired conditioning to context. In
contrast, inactivation of the LA disrupted conditioning to the discrete tone
CS, but also either impaired or enhanced contextual conditioning, depending on
whether the context was in the foreground or in the background. Hence, these
findings refine the current model of the amygdala function in emotional
learning by showing that the BLA and the LA not only differentially contribute
to elemental and context–US association, but also promote, through their
interaction, the most relevant of these two associations.
Child Labour and Resistance to Change
Authors: Bellettini Giorgio , Ceroni Carlotta Berti , Ottaviano Gianmarco I. P.
Published: July 2005

We study the interaction between technological innovation, investment in human capital and child labour. In a two‐stage game, first firms decide on innovation, then households decide on education. In equilibrium the presence of inefficient child labour depends on parameters related to technology, parents' altruism and the diffusion of firms' property. Child labour is due either to firms' reluctance to innovate or to households' unwillingness to educate, or both. In some cases, compulsory schooling laws or a ban on child labour are welfare‐reducing, whereas a subsidy for innovation is the right tool to eliminate child labour and increase welfare.
Social Welfare Orderings: A Life‐Cycle Perspective
Authors: Abul Naga Ramses H.
Published: July 2005

Life‐cycle theories emphasize the fact that consumption is allocated intertemporally, on the basis of a long‐term concept of resources that differs from household income. Because life‐cycle income is unobserved, the distribution of this variable cannot be recovered. It is shown that, within a suitably defined class, a predictor of life‐cycle income based on household income and expenditure entails a distribution dominated in a social welfare sense by the distribution of life‐cycle incomes. A predictor constructed from socio‐demographic variables induces a distribution that welfare‐dominates the distribution of life‐cycle incomes.
Unhappiness and Crime: Evidence from South Africa
Authors: Powdthavee Nattavudh
Published: July 2005

This paper is the first of its kind to study quality of life responses of crime victims. Using cross‐sectional data from the OHS97 survey of South Africa, it is shown that victims report significantly lower well‐being than the non‐victims, ceteris paribus. Happiness is lower for non‐victimized respondents currently living in higher crime areas. However, some evidence is found that criminal victimization hurts, but hurts less if regional crime rate on our reference group is high.
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.
PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET
Authors: Mickevich M.F. , Lipscomb Diana
Published: July 2005

Abstract— When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious. For some systematists, choosing among alternative transformation series for the same set of taxa is equivalent to attaining trees with shorter length and minimal homoplasy. Homoplasy is shown to be composed of hierarchical discordance and scattering, which are recognized and described for the first time. Neither the consistency nor retention indices can be used in assessing different theories of multistate character transformation because both are affected by the shape of the transformation series rather than the character state distribution on a tree. Fits of transformations to a tree are better assessed by comparing the transformation to the cladogram character and the nearest neighbor network. Nearest neighbor networks are graphical representations of the nearest neighbor matrix. Transformations with the closest greatest number of matches between cladogram characters and the least complexity in the nearest neighbor network are preferred. These transformations are shown to make the fewest number of ad hoc statements and hence to be the most parsimonious. A means for obtaining cladogram characters and nearest neighbor matrices using a widely distributed microcomputer program is presented.
PHYLOGENETIC RELATIONSHIPS AMONG THE CHROMISTA: A REVIEW AND PRELIMINARY ANALYSIS
Authors: Williams David M.
Published: July 2005

Abstract— It is now well established that the algae do not constitute a monophyletic group. A number of brown and golden algae are related to various heterotrophic protists, which have recently been characterized and described as a kingdom, the Chromista. The kingdom was defined primarily by two ultrastructural features: the presence of tubular, tripartite hairs (mastigonemes) on the surface of at least one flagellum, and the presence of a chloroplast endoplasmic reticulum. This included the watermoulds which, although they lack chloroplasts, do have mastigonemes. In addition, a number of heterotrophic flagellates also possess mastigonemes and should therefore be considered in the determination of interrelationships. This paper presents a cladistic analysis that focuses on 79 ultrastructural, cytological and biochemical characters. The unpigmented taxa appear at the base of the cladogram, suggesting a single origin for the chromophytic chloroplast. The crytomonads and Eustigmatophyta, usually considered primitive taxa, are sister to all the chrysophycean taxa which, with the exception of two monotypic genera and the Sarcinochrysidales, are monophyletic. The Prymnesiophyta, Bacillariophyta and Phaeophyta form a monophylectic group.
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.
ON MISSING ENTRIES IN CLADISTIC ANALYSIS
Authors: Platnick Norman I. , Griswold Charles E. , Coddington Jonathan A.
Published: July 2005

Abstract The exact algorithms of two commonly used parsimony programs, Hennig86 by J. S. Farris and PAUP by D. Swofford, sometimes produce different solutions, and sometimes produce resolutions that are not supported by the data being analysed. The discrepancies apparently involve the treatment of missing entries, which can currently represent unknown data, inapplicable character and/or polymorphic taxa. Each of those potential sources of ambiguity is logically (if not computationally) different; with regard to binary characters, unknown data could be either 0 or 1, inapplicable characters are neither 0 nor 1 and polymorphisms are both 0 and 1. Resolutions that cannot be supported by any possible combination of known state attributions should either be flagged as such or suppressed entirely.
“ALL TREE HISTOGRAMS” AND THE EVALUATION OF CLADISTIC EVIDENCE: SOME AMBIGUITIES
Authors: Novacek Michael J.
Published: July 2005

Abstract— Inspection of trees of varying lengths (by the option ALL TREES, which produces a histogram for tree lengths in PAUP 3.0) has been used to evaluate cladistic data and results. For example, a result may be judged more effective if the groups supported in the most parsimonious tree are preserved in trees that require increasingly greater amounts of homoplasy. Evaluation of grouping purely on the basis of this stability criterion ignores other highly relevant aspects of cladistic results. In particular, some data sets may incorporate additional taxa that introduce homoplasy to the shortest tree in a manner that concurrently allows for a revised understanding of character optimization patterns. These taxa may render groups preserved in the shortest tree less stable, but this result is not necessarily deficient if the homoplasy underlying such instability reveals possible character state changes for the given taxa irretrievable from the original matrix. The hypothetical example described here is relevant to so called “stem”, “basal” or “plesiomorphic sister” taxa that are commonly considered in studies of both fossil and extant taxa.
THREE‐TAXON STATEMENTS: A MORE PRECISE USE OF PARSIMONY?
Authors: Nelson Gareth , Platnick Norman I.
Published: July 2005

Abstract— Binary characters can be represented in data matrices by the three‐taxon statements they imply. Transforming characters into three‐taxon statements may increase the sensitivity of parsimony to differences in the fit of data to alternative cladograms. Extrapolation of the technique to multistate features allows semi‐additive characters to be coded accurately. In many cases, analysis of the transformed data produces fewer equally parsimonious solutions than does analysis of the raw data. In other cases, additional equally parsimonious solutions, or even different solutions, may be produced; in those cases, the results appear to accommodate information from a larger number of characters than do the results from raw data.
THE CLADISTICS OF AMAURIS BUTTERFLIES: CONGRUENCE, CONSENSUS AND TOTAL EVIDENCE
Authors: Vane‐Wright R.I. , Schulz S. , Boppré M.
Published: July 2005

Abstract— Two data sets for 10 species of African milkweed butterflies (Nymphalidae, Danainae: one Danaus, two Tirumala, seven Amauris) have been analysed cladistically, separately and in combination. One data set comprised 32 morphological characters, the other comprised 68 chemical compounds from male scent organs. Analysed separately, the two data sets produced six similar but non‐identical minimum‐length solutions. Analysed together, the combined data set of 100 characters produced a single minimum‐length tree, identical to one of the three solutions for the morphological data set. The combined data produced a more informative result than congruence comparisons based on strict or combinable component consensus analysis. These results, together with re‐analysis of a morphological data set for all 15 species of Amauris (which produced 12 minimum‐length solutions), permit increased resolution of the existing classification of this Afrotropical genus, including the formal recognition of two subgenera, Amauris (Amauris) Hübner, and Amauris (Amaura) Geyer (stat. rev.). The fit of uniquely derived, unreversed chemical characters to the tree raises the possibility that stepwise additive evolution of semiochemicals may have occurred during cladogenesis of these mimetic butterflies. The implications for chemoecology and speciation are briefly discussed.
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.
CONGRUENCE BETWEEN SUPERPOSITIONAL AND PHYLOGENETIC PATTERNS: COMPARING CLADISTIC PATTERNS WITH FOSSIL RECORDS
Authors: Norell Mark A. , Novacek Michael J.
Published: July 2005

Abstract— As the only direct evidence of past organismic history, the fossil record has always figured importantly in the reconstruction of phylogeny. But the incomplete nature of the fossil record has also been cited as a basis for claiming that fossils play only a secondary role in developing phylogenetic hypotheses that encompass extant taxa. The reliability of fossil data in such applications is a function of the degree of fit between superpositional relationships and the sequence of phylogenetic events. Thirty‐eight vertebrate cases are examined for the fit between age data based on fossil first occurrences and phylogenetic results based on cladistic analysis. A general correspondence between superpositional and cladistic information is observed, although the degree of fit varies widely among cases. Horses, certain other ungulates, synapsids and basal archosaurs, which show very high correlations, are taxa characterized by an abundance of superpositional and cladistic data. Other groups, such as primates, show very poor correlations because certain major clades have either unreasonably short fossil durations or no fossil record at all. Correlations are also diminished when either fossil records or cladistic sequences are poorly resolved. In most cases, cladistic resolution was observed to exceed superpositional resolution. Correlations can be enhanced by more precise (e.g. radiometric) age dates, but these also place a high expectation on the fit between fossil first occurrence and cladistic results. Stratigraphic occurrence does not always provide a precise reflection of independently derived phylogenies, but the correspondence between age and cladistic information is remarkably high in a notable number of vertebrate examples.
ARTHROPOD PHYLOGENY: A COMBINED APPROACH
Authors: Wheeler Ward C. , Cartwright Paulyn , Hayashi Cheryl Y.
Published: July 2005

Abstract— Ribosomal and ubiquitin protein coding sequence data are generated from 20 arthropods and five close relatives. These molecular data are combined with morphological characters derived from the literature to approach arthropod phylogenetics from the perspective of total evidence. Trilobita were included in the analysis through morphological comparison alone. The overall data strongly support arthropod monophyly. Recent molecular analyses which have yield different results are shown to have been based on few characters, few taxa or both. The most parsimonious explanation of the data is (Annelida + (Onychophora + (Trilobita + Chelicerata) + (Crustacea + (Myriapoda + Hexapoda))))). The data are largely concordant both internally among data sets and externally with previous cladistic anatomical analyses.
ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH
Authors: Goloboff Pablo A.
Published: July 2005

Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non‐iterative and does not require independent estimations of weights. It is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as a logical implication of the trees being compared. The “fittest” trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy.
PHYLOGENETIC RELATIONSHIPS AMONG PAPER WASP SOCIAL PARASITES AND THEIR HOSTS (HYMENOPTERA: VESPIDAE; POLISTINAE)
Authors: Carpenter James M. , Strassmann Joan E. , Turillazzi Stefano , Hughes Colin R. , Solís Carlos R. , Cervo Rita
Published: July 2005

Abstract— Cladistic analyses of data from allozyme polymorphisms in paper wasp social parasites and their hosts do not support the hypothesis that social parasites are most closely related to their hosts. Electrophoretic data are adduced for nine species of Polistes, including all three known species of social parasites (Sulcopolistes) and their hosts. Three different coding methods are investigated; in no case do the social parasites cluster most closely with their hosts. Rather, there is limited evidence that they form a monophyletic group. However, formal taxonomic recognition of Sulcopolistes is not justified, as it renders Polistes sensu stricto paraphyletic. Although the social parasites are not most closely related to their hosts, hosts and parasites belong in the same subgenus and share many characteristics that may have facilitated the exploitation and deception practised by the parasites on the hosts.
CLADISTIC REAPPRAISAL OF NEOTROPICAL STENODERMATINE BAT PHYLOGENY
Authors: Lim Burton K.
Published: July 2005

Abstract— Several phylogenies have been proposed for neotropical stenodermatine fruit‐eating bats (Phyllostomidae), based on detention, external morphology, osteology and chromosomes. However, these previous analyses did not incorporate fully the idea that relationships should be identified based solely on shared derived characteristics. A critique of past methodology and results, and an alternative phylogeny using a morphological data set supplemented with karyotypic information, is presented. In my analysis, there appear two main lineages. The eight genera of white‐shouldered bats form a monophyletic clade based on three synapomorphies (white patch of fur on shoulders, lack of a palatial extension with varying degrees of emargination and modified upper incisors); previous work suggested a paraphyletic relationship for this group. Furthermore, the monophyly of the four genera endemic to the Antilles is supported by two synapomorphies, suggesting a common origin as opposed to a multiple invasion for these genera. The appearance of the derived 2n = 30 and FN = 56 standard karyotype suggests that the morphologically distinct Sturnira forms the sister taxon to the remaining genera which are united by the synapomorphy of white facial stripes. This supports the inclusion of Sturnira within the stendodermatines and not in its own monotypic higher‐level taxon. My results do not refute the traditional systematic view of Artibeus (including Dermanura, Koopmania and Enchisthenes) being monophyletic, and supports Mesophylla and Vampyressa being distinct non‐sister genera.
CLADISTICS: WHAT'S IN A WORD?
Authors: Kluge Arnold G. , Wolf Alan J.
Published: July 2005

Abstract—Cladistics has changed considerably with the availability of new methods and sources of data, and the increasing realization that cladograms are relevant to all manner of historical questions. Criticisms of, and justifications for, consensus hypotheses in phylogenetic inference are reviewed. The conclusion is overwhelmingly against taxonomic congruence which deliberately seeks consensus propositions. The total evidence approach is not so burdened. A preference for suboptimal cladograms is also critized, as is the protocol for mapping characters of special interest onto a phylogenetic hypothesis derived from other evidence. The bootstrap and jackknife resampling techniques are questioned because their underlying assumptions are violated and they are sensitive to character frequencies. These findings suggest that cladistics is being redefined in ways that contradict the practices and principles responsible for its pre‐eminence in phylogenetic inference.
CHARACTER REMOVAL AS A MEANS FOR ASSESSING STABILITY OF CLADES
Authors: Davis Jerrold I.
Published: July 2005

Abstract—The stability of each clade resolved by a data set can be assessed as the minimum number of characters that, when removed, cause resolution of the clade to be lost; a clade is regarded as having been lost when it does occur in the strict consensus tree. The clade stability index (CSI) is the ratio of this minimum number of characters to the number of informative characters in the data set. The CSI of a clade can range from 0 (absence from the consensus tree of the complete data set) to 1 (all informative characters must be removed for the clade to fail to be resolved). Minimum character removal scores are discoverable by a procedure known as successive character removal, in which separate cladistic analyses are conducted of all possible data sets derived by the removal of individual characters and character combinations of successively increasing number.
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).
CLADISTICS AND FAMILY LEVEL CLASSIFICATION OF THE GENTIANALES
Authors: Struwe Lena , Albert Victor A. , Bremer Birgitta
Published: July 2005

Abstract— The most recent classification of the angiosperm order Gentianales (Thorne, 1992) includes four principal families: Apocynaceae, Gentianaceae, Loganiaceae, and Rubiaceae. Ever since Bentham (1857) the status of Loganiaceae has been questioned, and several segregates of that family have been proposed both before and after his treatment. In this study we present cladistic results that show Loganiaceae, sensu lato, to be a paraphyletic group definable only by plesiomorphies, with members showing closest relationships to other families of the order. As the impact of different character‐state representations of polymorphic terminals remains largely untested, our morphological and phytochemical data were analysed both with restricted polymorphism coding as well as with the monomorphic “subtaxon” recoding method of Nixon and Davis (1991). Both approaches yield highly compatible results, and we here discuss a new classification of the Gentianales based on (i) monophyletic groups identified by outgroup analysis, and (ii) the maximal portrayal of evidence provided by subtaxon polymorphism recoding. Most prominently, the Loganiaceae sensu lato are divided into four segregate families, two previously named (Loganiaceae sensu stricto and Strychnaceae), and two defined as a result of this study (Gelsemiaceae, L. Struwe & V. A. Albert, stat. nov. and Geniostomaceae, L. Struwe & V. A. Albert, fam. nov.). Apocynaceae (incl. Asclepiadaceae), Gentianaceae (incl. Loganiaceae—Potalieae), and Rubiaceae remain as monophyletic families. Outgroup analysis supports both the monophyly of the Gentianales as well as the exclusion from the order of Buddleja, Desfontainia, Plocosperma, Polypremum, and Retzia (all Loganiaceae sensu Leeuwenberg and Leenhouts).
A NOVEL METHOD FOR ECONOMICAL DIAGNOSIS OF CLADOGRAMS UNDER SANKOFF OPTIMIZATION
Authors: Wheeler Ward C. , Nixon Kevin
Published: July 2005

Abstract— A method is proposed to recode certain phylogenetic cost matrices in order to lessen the computational burden involved in the search for parsimonious cladograms. Multistate characters with complex costs among character states are converted to unordered multistate and binary variables with differential weights. These new variables can be optimized efficiently. The method has applications in cases where character states are distributed hierarchically and symmetrically. Cases of “inapplicable” states in morphology, and transition‐transversion weighting in molecular sequence data are discussed this light.
PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)
Authors: Sundberg Per , Hylbom Richard
Published: July 2005

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty‐five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum. An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo‐ and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy‐two equally most parsimonious cladograms were found; the consistency index was low but tree‐length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.
NOTHOFAGUSAND PACIFIC BIOGEOGRAPHY
Authors: Linder H. Peter , Crisp Michael D.
Published: July 2005

Abstract —Gondwanan biogeography, particularly the relationships between southern South America, New Zealand, Australia, New Guinea and New Caledonia, has been much studied.Nothofagusis often used as the “test taxon”, and many papers have been directed at usingNothofagusto explain Gondwanan biogeography. Cladistic biogeographers, working on plant material, have generally failed to find congruence among taxa expected from the southern Pacific disjunctions. New morphological and molecular data on the phytogeny ofNothofagushave re‐opened the issue, and we analysed these data to construct a new hypothesis of the biogeography of the genus. We assembled all plant taxa for which we could find reasonably robust phylogenetic hypotheses, and sought a parsimonious biogeographical pattern common to all. Two analyses, based on different assumptions, produced the same general areacladogram. We use the general area‐cladogram, in conjunction with the fossil record ofNothofagusto construct a historical scenario for the evolution of the genus. This scenario indicates extensive extinction, but also suggests that Australia has a more recent relationship to New Zealand than to southern South America. This is not congruent with the current geological theories, nor with the patterns evident from insect biogeography. We suggest that concordant dispersal is an unlikely explanation for this pattern, and propose that the solution might be found in alternative geological hypotheses.
ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE
Authors: Siddall Mark E.
Published: July 2005

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re‐investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.
RECONSTRUCTING THE HISTORY OF HOST‐PARASITE ASSOCIATIONS USING GENERALISED PARSIMONY
Authors: Ronquist Fredrik
Published: July 2005

Abstract — In reconstructing the history of host‐parasite associations, it is necessary to consider several different processes, such as cospeciation and host switching, that may affect an association. A simple reconstruction method is to maximise the number of host‐parasite cospeciations. However, maximum cospeciation reconstruction may require the postulation of a large number of other kinds of events, such as parasite extinction or exclusion from certain hosts. A more sophisticated method associates each kind of event with a cost or weight which is inversely related to the likelihood of that kind of event occurring. I present a method of the latter type that distinguishes between two different processes: host tracking, of which cospeciation is a special case, and host switching. Given a relative weight for these two types of events, it is possible to convert the host phytogeny into a cost matrix, allowing for host switching, and use generalised‐parsimony algorithms to find minimum‐cost reconstructions of the history of the host‐parasite association. Different relative switch weights give different minimum‐cost reconstructions; the optimal switch weight can be found by maximising the fit between the tracking events and the parasite phytogeny, controlling for the number of postulated switches. As an empirical application of the method, data on an association between pocket gophers and their parasitic chewing lice were re‐examined. Although these data have been extensively analysed previously, the generalised parsimony approach throws new light on the history of the association.