bluuebunny/crossref_metadata_2025 huggingface dataset:
Deconstructing Survivin: comprehensive genetic analysis of Survivin function by conditional knockout in a vertebrate cell line
Authors: Yue Zuojun , Carvalho Ana , Xu Zhenjie , Yuan Xuemei , Cardinale Stefano , Ribeiro Susana , Lai Fan , Ogawa Hiromi , Gudmundsdottir Elisabet , Gassmann Reto , Morrison Ciaran G. , Ruchaud Sandrine , Earnshaw William C.
Published: October 2008

Survivin is a key cellular protein thought to function in apoptotic regulation, mitotic progression, or possibly both. In this study, we describe the isolation of two conditional knockouts of the survivin gene in chicken DT40 cells. DT40 cells lacking Survivin die in interphase after failing to complete cytokinesis. However, these cells show normal sensitivity to the chemotherapeutic agent etoposide. Expression of Survivin mutants against a null background to reassess the role of several key residues reveals that DT40 cells can grow normally if their sole Survivin is missing a widely studied cyclin-dependent kinase phosphorylation site or sites reportedly essential for binding to Smac or aurora B. Mutations in the nuclear export sequence or dimerization interface render cells temperature sensitive for growth. As an important caveat for other studies in which protein function is studied by transient transfection, three of the Survivin mutants fail to localize in the presence of the wild-type protein but do localize and indeed support life in its absence.
The pH sensor for flavivirus membrane fusion
Authors: Harrison Stephen C.
Published: October 2008

Viruses that infect cells by uptake through endosomes have generally evolved to “sense” the local pH as part of the mechanism by which they penetrate into the cytosol. Even for the very well studied fusion proteins of enveloped viruses, identification of the specific pH sensor has been a challenge, one that has now been met successfully, for flaviviruses, by Fritz et al. (Fritz, R., K. Stiasny, and F.X. Heinz. 2008. J. Cell Biol. 183:353–361) in this issue. Thorough mutational analysis of conserved histidine residues in the envelope protein of tick-borne encephalitis virus led Fritz et al. (2008) to identify a histidine at a key domain interface as the critical pH sensor; its protonation triggers the large-scale conformational rearrangement that induces fusion of viral and endosomal membranes.
Fatal NosocomialLegionella pneumophilaInfection Due to Exposure to Contaminated Water From a Washbasin in a Hematology Unit
Authors: Brûlet Alexandre , Nicolle Marie-Christine , Giard Marine , Nicolini Franck-Emmanuel , Michallet Mauricette , Jarraud Sophie , Etienne Jérôme , Vanhems Philippe
Published: October 2008

A fatal nosocomial infection withLegionella pneumophilaserogroup 5 occurred in a patient with leukemia. Isolates recovered from both the potable water supply and the patient showed an identical genomic profile. With no other exposure identified, the water from the washbasin was evidently the source of infection.
THEORIES AND METHODS IN DIFFERENT APPROACHES TO PHYLOGENETIC SYSTEMATICS
Authors: BROOKS DANIEL R. , WILEY E. O.
Published: October 2008

Abstract— Systematic techniques may be viewed as symbolic languages which have both surface structure (measures of descriptive adequacy) and deep structure (measures of explanatory adequacy). Phylogenetic systematics is not theory‐neutral because its deep structure embodies evolutionary assumptions. Pattern cladistics stands in relationship to phylogenetic systematics as a part to a whole and is indistinguishable from phylogenetic systematics unless an artificial dichotomy between surface structure and deep structure is maintained. Direct observation of ontogeny as a means of polarizing characters also stands as a part to a whole relative to outgroup comparisons. Direct observation of ontogeny does not resolve any cases that outgroup comparison fails to resolve, and outgroup comparison does resolve some cases where direct observation fails.
AN EMPIRICAL COMPARISON OF NUMERICAL WAGNER COMPUTER PROGRAMS
Authors: LUCKOW MELISSA , PIMENTEL RICHARD A.
Published: October 2008

Abstract— The performance of four computer programs that calculate Wagner trees (WAGNER 78, WAGPROC, PHYLIP, and PHYSYS) was compared for twenty‐five data sets. Eight combinations of algorithms and options were tried, including different methods of adding taxa, optimizing stem states, obtaining multiple trees, and branch swapping. Using the criterion of finding a minimum length tree, PHYSYS with the WAG.S option performed best, providing the shortest tree for twenty‐four of the twenty‐five data sets. WAGPROC with the GLOB option found sixteen minima for eighteen data sets, exceeding run time on the remaining seven. All other algorithm/options were less successful in providing minimum trees. In comparing the options we found that minimum homoplasy is not completely reliable in optimizing trees and that the brute force algorithm is helpful but not required for finding minimum trees. The advancement index criterion for adding taxa to a tree is more effective than adding taxa in their data file sequence. The success of the PHYSYS WAG.S option and the WAGPROC GLOB demonstrate that both multiple trees and branch swapping are necessary to produce a minimum length tree.
ON THE INDEPENDENCE OF SYSTEMATICS
Authors: BRADY RONALD H.
Published: October 2008

Abstract— Before the publication of On the Origin of Species the standing patterns of natural history—common plan, homology, ontogenetic parallelism, and the hierarchy of groups — were taken as indications of a biological order that had not yet been understood. Darwin covered all of these in chapter 13 of the Origin, arguing that his theory was the first to provide a reasonable explanation for the existence of such patterns. Since Darwin took these relations to be established by previous biology, and used them as evidence for the explanatory power of his theory, he was clearly of the opinion that they were independent of that theory. Although several modern figures have argued to the contrary, it seems that Darwin was right. The patterns listed above are recoverable from observation without reference to evolutionary theory, which theory may then be applied to provide an account of the processes by which they may have come about. That aspect of systematics concerned with the identification of the empirical patterns evidently constitutes a study prior to and independent of theories of process.
ONTOGENETIC SEQUENCES AND THE PHYLOGENETICS OF PARASITIC FLATWORM LIFE CYCLES
Authors: O'GRADY RICHARD T.
Published: October 2008

Abstract— Ontogenetic data can be used in phylogenetic analyses (1) as tests of character homology, (2) for polarizing transformation series, and (3) as characters themselves. The ontogenetic sequence of semaphoronts can change by addition, substitution, or deletion of stages which are either terminal or nonterminal. Outgroup comparisons can use life cycle data as well as morphological data to establish a general reference system of inferred genealogy, which can then be used to distinguish which of the six ontogenetic sequence changes has occurred in a particular phylogeny. A cladistic study of the parasitic platyhelminths suggests that the evolution of the Digenea involved a nonterminal addition of ontogenetic stages and a terminal addition of a second host to the ancestral life cycle. The evolution of the Cestoidea appears to have involved a terminal addition of ontogenetic stages and a nonterminal addition of a second host. The “complex life cycles” of the two groups are thus different in nature and etiology. Further cladistic analysis, within the Digenea, suggests that the plesiomorphic state of the intercalated ontogenetic stages was a miracidium‐sporocyst‐cercariae sequence. Rediae are concluded to have been intercalated between sporocysts and cercariae at a later point. The mutual exclusivity of rediae and daughter sporocysts in a life cycle is noted.
PHYLOGENY OF PRIMATES AND OTHER EUTHERIAN ORDERS: A CLADISTIC ANALYSIS USING AMINO ACID AND NUCLEOTIDE SEQUENCE DATA
Authors: GOODMAN MORRIS , CZELUSNIAK JOHN , BEEBER JUDITH E.
Published: October 2008

Abstract— Genealogical reconstructions carried out by the parsimony method on protein amino acid and DNA nucleotide sequence data are providing fresh evidence on cladistic branching patterns at taxonomic levels from the classes of Vertebrata and orders of Eutheria to the genera of Hominoidea. Minimum length trees constructed from amino acid sequence data group Mammalia with Archosauria (i.e., Aves plus Crocodilia), Amniota with Amphibia, and Tetrapoda with Teleostei. Within Mammalia, Edentata and Paenungulata (e.g., Proboscidea) appear as the most anciently separated from other eutherians. Another superordinal eutherian clade consists of Artiodactyla, Cetacea, and Perissodactyla. A third consistently contains Primates, Lagomorpha, and Tupaia. The cladistic positions of such orders as Carnivora, Chiroptera, Insectivora, and Rodentia are not well resolved by the currently still sparse body of sequence data. However, recent dramatic progress in the technology of gene cloning and nucleotide sequencing has opened the way for so enlarging the body of sequence data that it should become possible to solve almost any problem concerning the phylogenetic systematice of extant mammals. An example is provided by hominoid genera. Minimum length trees constructed from mitochondrial DNA nucleotide sequence data very strongly group Pan, Homo, and Gorilla into Homininae and then join Homininae and Ponginae (pongo) into Hominidae as the sister family of Hylobatidae (Hylobates). Resolution of the hominine trichotomy into two dichotomous branchings should be forthcoming as kilobase sequencing of nuclear genes progresses.
NEW QUESTIONS IN GENETICS AND EVOLUTION
Authors: KAUFFMAN STUART A.
Published: October 2008

Abstract— The use and misuse of the concept of “developmental constraints” in analyses of allometry, heterochrony, and quantitative genetics is examined. Allometric analysis constitutes an advantageous redescription but poses no constraining explanation; analysis of heterochronies does not by itself establish the existence of developmental constraints; quantitative genetic threshold theories fail to account for why arbitrary alternatives are not to be expected. A structuralist approach to constraints therefore warrants attention; examples involve phyllotaxis, echinoid morphology, shell patterns, metazoan gene regulation, and orthogenesis.
MAJOR CLADES OF THE ANGIOSPERMS
Authors: DAHLGREN ROLF , BREMER KÅRE
Published: October 2008

Abstract— Our knowledge of fundamental angiosperm interrelationships is still very incomplete. The absence of a narrowly circumscribed gymnosperm outgroup, ideally the sister group, makes character evaluation, necessary for a cladistic analysis, difficult. According to current views the superorder Magnoliiflorae with a number of other groups, for example the monocotyledons, may represent a complex of families near the base of the angiosperms. Interrelationships of groups within the monocotyledons are much better understood than those between groups within the dicotyledons. A cladogram of monocotyledon orders based on earlier work by R. Dahlgren, H. T. Clifford, and F. N. Rasmussen is presented. A data matrix for a sample of the angiosperms with 61 characters for 49 taxa, mostly magnoliifloran and related families, is presented. The characters are polarized mainly according to the current view that the primitive angiosperm morphotype is a woody dicotyledon with strobiloid flowers. As an alternative the matrix is adjusted following W. C. Burger's conjecture that the primitive angiosperm was a herbaceous monocotyledon with trimerous flowers. Both matrices were run in a computerized parsimony analysis, resulting in numerous equally parsimonious solutions. This result is illustrative of the great homoplasy in the available character information, and also of how little actually is known about fundamental angiosperm interrelationships or phylogeny.
SUMMARY OF GREEN PLANT PHYLOGENY AND CLASSIFICATION
Authors: BREMER KÅRE
Published: October 2008

Abstract— A cladogram of green plants involving all major extant groups of green algae, bryophytes, pteridophytes, and seed plants is presented. It is partly based on contributions by B. Mishler and S. Churchill, H. Wagner, and P. Crane. The relationships of green plants to other green organisms (Prochloron, euglenophytes) are discussed. The characters and subclades of the cladogram are briefly discussed, with an attempt to indicate weak points. The possibility of including some major extinct groups is considered. A cladistic classification consistent with the cladogram is presented. Grades are abandoned as taxa and major clades like the division Chlorophyta (green algae excluding micro‐monadophytes and charophytes sensu Mattox and Stewart), the division Streptophyta (charophytes + embryophytes), the subdivision Embryophytina (land plants or embryophytes), the superclass Tracheidatae (tracheophytes), and the class Spermatopsida (seed plants) are recognized.
THE MYTH OF OBJECTIVITY—POST‐HENNIGIAN DEVIATIONS
Authors: SÆTHER OLE A.
Published: October 2008

Abstract— The punctuated equilibrium speciation mode is an implied consequence of the deviation rule and the differences between cladograms and phylogenetic trees implicitly were recognized by Hennig. Neocladism and transformed cladism, however, both are contradictory to the view of Hennig. Neither of them will be consistent when parallel changes exceed informative unparallel changes, which in the real world there are many indications to believe they do. In three tables cladogenetic trends used in erecting three schemes of argumentation, on the specific, generic, and subfamily levels respectively, are analyzed and divided into: “objective” synapomorphies not allowing for outside parallelism or secondary change, subjective synapomorphies, and underlying synapomorphies. Evaluations based on the strictest criteria for asserting synapomorphy are possible only when comparing higher taxa of subfamily level and up. On the generic level trends showing outside parallelism can be rejected if all other possibly synapomorphic trends are included. On the specific level it is necessary to take all kinds of synapomorphies into consideration, including those showing outside parallelism. There may often be a preponderance of trends caused by parallel selection in taxa with specialized sexual and/or feeding behaviors, as exemplified by some chironomid male imagines and larvae. It is necessary to have knowledge of the nature of the different possible natural processes and try to explain these before undertaking estimations of patterns of kinship. The persistent intuitive and subjective element in phylogenetics was stressed by Hennig. Objectivity is a myth.
ON THE BOUNDARIES OF PHYLOGENETIC SYSTEMATICS
Authors: FARMS JAMES S.
Published: October 2008

Abstract— The parsimony criterion both measures the ability of genealogical hypotheses to explain observed similarities and corresponds to Hennig's principle of grouping by synapomorphy. Sæther's proposal of grouping according to homoiology is neither Hennigian nor justified on any other grounds. Criticisms by Felsenstein that parsimony analysis may be statistically inconsistent lead to an equivalent criticism of all statistical methods, and so are of no value for evaluating phylogenetic methods.
PARSIMONY AND CHARACTER WEIGHTING
Authors: SOBER ELLIOTT
Published: October 2008

Abstract— The likelihood justification of parsimony proposed in Sober (1983, 1984a) is applied to some problems posed by character weighting. An argument is provided for thinking that the point frequency of a character is not a good descriptor for parsimonious reconstructions of phylogeny. The idea that a good character will be conservative or nonadaptive is also examined from a likelihood point of view.
LIKELIHOOD AND PARSIMONY: COMPARISON OF CRITERIA AND SOLUTIONS
Authors: THOMPSON E. A.
Published: October 2008

Abstract— The merits of alternative approaches to the inference of evolutionary trees have been much discussed, but there have been few attempts to compare inferences systematically or to pinpoint the source of differences. The two major classes of approach are via likelihood inference under an evolutionary model and estimates based upon parsimony methods. Within the general class of likelihood approaches, there are differences depending upon the particular class of models considered. This paper makes comparisons of the characteristics of inferences for the case of quantitative variation (of allele frequencies, for example), concentrating on the case of very small numbers of populations where explicit solutions are possible, but also upon features which apply as well to inferences for larger groups of populations. The parsimony method of “minimum evolution” was proposed by Edwards and Cavalli‐Sforza (1964) to provide an approximation to the likelihood solution for an intractable model. In fact, its estimated phylogenies are closest to those of a more recent model of Felsenstein (1981) which, like parsimony, produces a fundamentally unrooted tree. Likelihood estimates based upon models involving an implicit or explicit root are radically different. These differ also from each other, depending upon whether or not the root is explicitly estimated, and upon whether or not a model for the fissioning of populations is included. Some general features of the comparisons can be summarized.
ORB WEBS IN “NON‐ORB WEAVING” OGRE‐FACED SPIDERS (ARANEAE: DINOPIDAE): A QUESTION OF GENEALOGY
Authors: CODDINGTON JONATHAN A.
Published: October 2008

Abstract— Observations of web spinning behavior in Costa Rican Dinopis sp. reveal the same behaviors synapomorphic for orb weavers: specifically frame, radius, non‐sticky spiral construction, and sticky spiral construction, as well as more detailed motor patterns. Dinopids are therefore highly derived orb weavers, although the behavioral data do not conclusively indicate whether they are more closely related to the uloborid or araneoid orb weavers. A cladogram of dinopids, uloborids, and araneoids is presented.
CONGRUENCE OF BOLITOGLOSSINE BIOGEOGRAPHY AND PHYLOGENY WITH GEOLOGIC HISTORY: PALEOTRANSPORT ON DISPLACED SUSPECT TERRANES?
Authors: Hendrickson Dean A.
Published: October 2008

Abstract— A vicariance hypothesis of New World biogeography involving transport of living biota on fragments of an ancestral landmass to present positions ranging from southern Alaska to northern South America is developed. Geological, as well as biogeographical, ecological, and systematic data from plethodontid salamanders provide correlative support for the model. Other groups appear to have similar biogeographic histories and, along with further geological data, could provide means of corroboration of this hypothesis. Active biotic dispersal between the American continents before Pliocene closure of the Panamanian isthmus may have been less prevalent than previously believed, and tectonic transport may have dispersed many organisms. If corroborated, geologists may be provided a new method of analyzing relationships among “suspect terranes” using phylogenetic analyses of living biota, and biologists may be required to reassess previous concepts of New World historical biogeography.
DISTANCE METHODS: A REPLY TO FARRIS
Authors: FELSENSTEIN JOSEPH
Published: October 2008

Abstract— Farris (1985) claimed that my assertions about unbiasedness and consistency of estimates of a phylogeny obtained by least squares fitting are in error. The counterexample he constructed violates the assumptions of additivity and independence of distances which were clearly stated in my earlier paper. As such it is not a valid counterexample. It is argued, contrary to Farris's claims, that one need not avoid nonmetric distances, and that one should avoid negative branch lengths in estimates of phylogenies from distance data. Statistical tests of clockness, and, to a limited extent, of alternative phylogenies can be constructed, and these are demonstrated by example. A computer program to infer phylogenies from distance matrices has been in free distribution by me for several years; it seems as effective as the program recently announced by Farris. Information on phylogenies is present in distance data, as in other kinds of data, and statistical methods can be developed to extract it.
DISTANCES AND STATISTICS
Authors: FARRIS JAMES S.
Published: October 2008

Abstract— Felsenstein's claim of approximate additivity for sequence differences is based on an unjustified model, as is his proposed nonadditive fitting method. His advocacy of the nonnegativity restriction on fitted branch lengths rests on the false premise that distances are additive. His proposed significance test confounds sampling error with departures from additivity and rests on false assumptions of additivity and of independence of distances. His additive fitting program lacks any useful facility for recognizing ambiguities in distance data.
HISTORICAL BIOGEOGRAPHY IN THE INDO‐PACIFIC: A CLADISTIC APPROACH
Authors: SCHUH RANDALL T. , STONEDAHL GARY M.
Published: October 2008

Abstract— The history of biogeographic theories about the Indo‐Pacific is reviewed. The methods of cladistic biogeography are introduced and 10 monophyletic groups of Miridae (Insecta: Heteroptera) are used to apply these methods in the Indo‐Pacific. The results are summarized and then combined with those of Duffels on cicadas. The results of most previous schemes are rejected on the basis of new results because the prior studies applied methods which failed to correctly interrelate areas of endemism within the Indo‐Pacific and between this and other regions. The composite biotic nature of New Guinea is stressed.

“it is the presence in and not the absence from land areas of organisms that calls for reasoned explanations” (Evans, 1959)
HEADS AND TAILS: A CHORDATE PHYLOGENY
Authors: MAISEY JOHN G.
Published: October 2008

Abstract— A cladistic analysis of chordates is presented, based on some 320 nested characters. All the principal higher taxa are defined by synapomorphies, including extinct acanthodians and placoderms. The data base draws broadly from adult anatomy (including osteological data for Recent and fossil taxa), embryology, physiology, and biochemistry. A conventional sequence of chordate higher taxa is generated (hemichordates, urochordates, cephalochordates, craniates). Among the craniates, cyclostomes are considered paraphyletic. Gnathostomes are monophyletic, but two fossil “agnathan” groups (galeaspids, osteostracans) are regarded as stem gnathostomes. Chondrichthyans and osteichthyans are monophyletic. New arguments for osteichthyan affinity of acanthodians are presented. The phylogenetic position of placoderms is still problematic, but they can no longer be perceived as stem chondrichthyans or even as “elasmobranchiomorphs.” Recent dipnoans and tetrapods are sister groups, but new paleontological discoveries refute many of their supposed osteological synapomorphies, thereby reopening the possibility of a closer relationship between tetrapods and osteolepiform rhipidistians.
HIGHER‐LEVEL RELATIONSHIPS OF THE RECENT EUTHERIAN ORDERS: MORPHOLOGICAL EVIDENCE
Authors: NOVACEK MICHAEL J. , WYSS ANDRÉ R.
Published: October 2008

Abstract— Diverse morphological evidence from both living and fossil taxa suggests several higher‐level groupings of the Recent orders of eutherian mammals. The strongest hypotheses closely relate rodents and lagomorphs within Glires, proboscideans and sirenians within Tethytheria, hyracoids and tethytheres within Paenungulata, chiropterans and dermopterans, and pholidotans and edentates. Somewhat weaker evidence supports groupings of Glires with macroscelideans, primates and tree‐shrews with bats and flying lemurs (Archonta), and all Eutheria excluding pangolins and edentates (Epitheria). There is some tenuous evidence for the monophyly of all modern ungulate orders (including cetaceans), and for the division between artiodactyls and other ungulates. Rather than providing only a confusing and unresolved picture of higher eutherian relationships, comparative morphology and paleontology offer some compelling hypotheses that comprise a framework for studies of macromolecular traits.
HISTORICAL VERSUS SELECTIONIST EXPLANATIONS IN EVOLUTIONARY BIOLOGY
Authors: Taylor Peter J.
Published: October 2008

Abstract— Evolutionary changes require historical explanations, yet these are limited by the evolutionary processes we entertain and investigate. Using phylogenetic analysis, adaptation and natural selection can be tested as historical claims, but this is appropriate only in those special cases where change follows the scheme of one character‐one function, singled out in new environmental circumstances. Systematic treatment of the evolutionary origin of characters (in particular, origin through ecological and developmental flexibility) lies outside the scope of selectionist explanations. Structural hypotheses about regularities in the directions of change, also analyzed phylogenetically, expand the scope of historical explanation to include the origin of characters, yet retain the view of organisms as passive and constrained objects of evolutionary change. Historical biology needs to encompass both the active responses of organisms and the construction by organisms of their own environments. For this to be realized will require changes in the concepts and practices of evolutionary biology, including a re‐examination of the Lamarckian theme that the active responses of organisms have evolutionary significance—the rarity of individual‐to‐individual transmission of “acquired” characters does not disprove the possibility of their frequency increasing in a population.
HOST‐PLANT RELATIONSHIPS IN THE PAPILIONIDAE (LEPIDOPTERA): PARALLEL CLADOGENESIS OR COLONIZATION?
Authors: Miller James S.
Published: October 2008

Abstract— Stepwise coevolution, as defined by Ehrlich and Raven (1964) and others, can be equated with parallel cladogenesis or association by descent (Mitter and Brooks, 1983). I review the insect/plant literature and discuss recent cladistic findings for the Papilionidae, and compare two contrasting theories: 1) that insect/host associations have evolved through parallel cladogenesis; or 2) that insects have ‘colonized’ their hosts subsequent to plant cladogenesis. I conclude that no documented examples of parallel cladogenesis between insects and plants are known. The swallowtail cladograms instead offer evidence in support of the second theory. They suggest that host association patterns in the Papilionidae have resulted from repeated colonization of plants belonging to a relatively small number of families. I discuss data which indicate that plant secondary chemicals have been important ‘barriers’ to colonization (sensu Ehrlich and Raven, 1964), and have in large part mediated host switching in the Papilionidae.
ON SPECIES and OTHER TAXA
Authors: Loevtrup Soeren
Published: October 2008

Abstract— It is argued that taxa, whether Linnaean or phylogenetic, belong to Popper's worlds 2 and 3, the worlds of knowledge, but that they represent entities residing in world 1, the world of objects, namely, classes of living beings. The Linnaean taxa are concepts, and thus untestable, whereas phylogenetic taxa are statements, the monophyletic taxa being true, and the paraphyletic and polyphyletic ones false statements. The taxa are neither strictly nor numerically universal statements, but probabilistic ones which cannot be falsified by single observations. It is suggested that the classical “species problem” is due to the fact that “species” has been used in three different senses. First, traditionally it has been assumed that the specific “essence” of an organism is that by which it is what it is. When we know the species, we know the organism. Second, the species are terminal taxa in the phylogenetic hierarchy. This implies that it is only a very small part of the “essence” of the organism which distinguishes the species. The remaining part characterizes the succession of superior taxa in the phylogenetic lineage which ends with the species in question. Third, the species has been regarded to be the “evolutionary unit.” This idea may be refuted for two reasons: (1) since concepts and statements cannot evolve, species cannot evolve either, and (2) it is generally in very small isolated populations that evolutionary innovations are first established. In Linnean systematics the superior taxa are allotted categorical rank. The fact that the classification is constrained by this conventional stipulation implies that the superior taxa are often man‐made artifacts. In the phylogenetic hierarchy, composed of monophyletic taxa, the ontological states of the taxa is completely independent of their numerical rank; the kingdom is as “real” as the species.
TRIBAL INTERRELATIONSHIPS OF THE ASTERACEAE
Authors: Bremer Kåre
Published: October 2008

Abstract— A cladistic analysis involving 27 tribes and subtribes of Asteraceae and 81 characters is presented. The terminal taxa are mainly those of present tribal classification, though some apparently poly‐ and paraphyletic tribes, notably the Mutisieae and the Inuleae, have been represented by sub‐tribal taxa. Characters are assembled from all available sources. Corolla types, styles and stamens have provided many characters. The Lobeliaceae are used as an outgroup and are considered as the most probable sister group of the Asteraceae. There is a basal dichotomy in the family, the Mutisieae‐Barnadesiinae being the monophyletic sister group of the remaining major, also monophyletic part of the family. The recent family division into two subfamilies about equal in size, the Cichorioideae and the Asteroideae, neither represents a basal dichotomy nor a sister group relationship within the Asteraceae. The Asteroideae are monophyletic and have their sister group within the paraphyletic Cichorioideae. Interrelationships among the cichorioid tribes are still unclear. The Lactuceae, Eremothamneae, Vernonieae and Liabeae may be one monophyletic group, and the Arctoteae, Carlineae, Echinopsideae and Cardueae another. The Mutisieae are a paraphyletic grade at the base of the family. Within the subfamily Asteroideae tribal interrelationships are also rather unclear. The Anthemideae and the Heliantheae sensu lato (including the Helenieae, Tageteae, Coreopsideae and all helenioid/helianthoid representatives sometimes placed in the Senecioneae) may be sister groups. The Heliantheae appear to be monophyletic and there is little support for the hypothesis that other tribes are derived from or have their sister group within the Heliantheae. The Astereae and the Eupatorieae may be sister groups, though a closer relationship between the Eupatorieae and the Heliantheae is possible. The Inuleae are a paraphyletic grade group at the base of the subfamily Asteroideae in the same way as the Mutiseae are a grade group at the base of the family.
CLADISTIC TESTS OF ADAPTATIONAL HYPOTHESES
Authors: Coddington Jonathan A.
Published: October 2008

Abstract— A cladistic viewpoint provides an historical definition of adaptation and an operational ecological test for evolutionary adaptations. Adaptation is apomorphic function promoted by natural selection, as compared with plesiomorphic function. Adaptation is thus a conditional, hierarchical, comparative term, like homology. Hypotheses of adaptation that do not specify levels of apomorphy are weak; they should refer to and explain the function at the level at which it is apomorphic with respect to the plesiomorphic (outgroup) condition. The adaptational hypothesis serves as a prior prediction in the comparison of the apomorphic function of the derived trait with the plesiomorphic function of the plesiomorphic trait serving as the null hypothesis. It is useful to distinguish whether hypotheses about characters identify selection as facilitating: 1) the origin of a character; 2) its maintenance; 3) neither; or 4) both. The latter two are uniformitarian and testable in a strong sense. The former two possibilities use ancillary arguments to protect the hypothesis of the role of natural selection in one way or another, but might still be tested by the weak criterion of plausibility. Given an hypothesis of both origin and maintenance due to selection, the test of adaptation may still be thwarted because only certain kinds of cladistic structure allow feasible tests. Few of the really classic and common examples of supraspecific adaptation survive this kind of cladistic test.
A Cladistic Analysis of the Genus Cyttaria (Fungi‐Ascomycotina)*
Authors: Crisci Jorge V. , Gamundi Irma J. , Cabello Marta N.
Published: October 2008

Abstract—Cyttaria Berkeley (Cyttariaceae, Cyttariales, Class Discomycetes), is a genus of eleven species, seven from South America and four from Australasia (Australia, Tasmania, and New Zealand). Cyttaria is a monophyletic genus defined by the following synapomorphies: fleshy to gelatinous stromata with endostromatic apothecia; and complete lack of fungal chitin in the cell walls, having instead β‐1–3‐glucan. All Cyttaria are exclusive parasites of Nothofagus species. A cladistic analysis of the genus was performed using 18 characters from macromorphology, micro‐morphology, and phenology. Polarity of characters is based on the outgroup comparison method (using the Class Discomycetes as a whole) and on the ontogenetic criterion. A hypothetical outgroup was constructed using all plesiomorphic states. Two equally parsimonious cladograms were produced, each with 40 steps and a consistency index of 0.70. These differed in the position of the South American species C. hookeri and C. johowii. In one cladogram, C. hookeri is the sister group to the rest of the genus, and in the other, both species form a monophyletic group (ascospores ovoid) that is the sister group of the rest of the genus. Our analysis of the two characters causing this difference (position of apothecia on stroma, and shape of ascospores) supports the latter hypothesis. In both cladograms, all of the Australasian species form a monophyletic group (thick ectostroma), and, within that, two subgroups are defined: C. gunnii‐C. pallida (papillae present), and C. nigra‐C. septentrionalis (ectostroma with black incrustations). The Australasian species form a monophyletic group (spermatangia absent) with C. berteroi, and this last group forms a monophyletic group (conidia absent) with C. espinosae. Cytlaria darwimi and C. exigua form another monophyletic group (very thick ectostroma). Excluding C. hookeri and C. johowii, C. hariotii is the sister group to the remaining eight species.
On the Information Content of Classifications
Authors: Mickevich M. F. , Platnick Norman I.
Published: October 2008

Abstract— The best fit estimate of the retrospective information content of a classification is argued to be the proportion of the maximal sum of informative subgroups to which each included taxon is assigned. The best fit estimate of the prospective information content of a classification is argued to be the proportion of fully resolved dadograms prohibited by that classification. Those (wo proportions are multiplied to provide a general information index that is sensitive to both the degree of resolution and the contents of individual subgroups. That index and the best fit considerations supporting it have implications for congruence studies, consensus indices, and the choice between Adams and Nelson consensus trees.
A Hypothesis‐Independent Method of Character Weighting for Cladistic Analysis
Authors: Sharkey Michael J.
Published: October 2008

Abstract— A hypothesis‐independent method of weighting cladistir characters, based on character compatibility, is proposed. The method is used in two fashions, to generate cladograms, and to select from multiple minimum length cladograms. To illustrate the techniques, published data on Hoplinema (Coleoptera) are reanalysed. The method is contrasted with other weighting techniques which arc generally found to be hypothesis dependent.
QUANTITATIVE CHARACTERS IN PHYLOGENETIC ANALYSIS
Authors: Chappill Jennifer A.
Published: October 2008

Abstract— When analysing phylogcnetic relationships at low laxonomic levels it is often the ease that many of the features that can be used to separate taxa show continuous variation. The theoretical and practical problems for the use of such quantitative characters in phylogenetic analysis arc examined. Three methods of coding continuous data into discrete characters are assessed in detail: simple gap‐coding, generalised gap‐coding and segment‐coding, a form of range‐coding. The methods are applied to a data set gathered for Eucatyptus L'Hérit. informal subgenus Symphyomyrtus section Maidenana (Myrtaceae). Each method is capable of distorting relative differences between taxa, but segment‐coding produces the least amount of distortion, provided the range of variation of the character is divided into a sufficient number of character states.

Continuous quantitative characters provide data for phylogenetic analysis that arc more noisy than those provided by discrete qualitative characters and should, therefore, only be used when the number of qualitative characters is insufficient for resolution of relationships. The results of such analyses should be recognised as provisional pending the discovery of more readily informative characters.
RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION
Authors: Smith Andrew B.
Published: October 2008

Abstract— 18S ribosomal RNA sequences from 11 echinoderms are analysed using parsimony to investigate phylogenetic relationships. Their estimated divergence limes range from less than 20 Ma to more than 550 Ma before present. Phylogenies based on 18S rRNA sequence data are compared with well‐established morphological phylogenies to discover at what evolutionary distance the two approaches start to produce incongruent results. Three regions of the 18S rRNA molecule are analysed separately and together, and paired and unpaired sites are also treated separately and combined.

Results show that a parsimony analysis of sequence data produces reliable results only when taxa have diverged more recently than about 100 Ma. At greater evolutionary distances (up to 250 Ma), paired nucleotides produce more reliable results than unpaired, while paired and unpaired data combined produce intermediate results. All trees within about 1% of the most parsimonious solution ought to be accepted. Transversions give results almost as reliable as paired regions though there were relatively few informative sites. The relationships of echinoderm classes, which diverged 450–550 Ma ago, are unresolved by 18S rRNA data.
SYSTEMATICS AND BIOGEOGRAPHY OF THE AUSTRALIAN “GREEN ASH” EUCALYPTS (MONOCALYPTUS)
Authors: Ladiges Pauline Y. , Newnham M. R. , Humphries C. J.
Published: October 2008

Abstract— A cladistic analysis of the “green ash” eucalypts, informal subgenus “Monocalyptus”, is presented‐ As a first step, ordination methods of principal coordinates analysis and multidimensional scaling delineated some terminal taxa. The cladistic analysis, applying parsimony methods to the unweighted data set, yielded 25 equally parsimonious trees, each with a consistency index of 0.57.

Farris' successive approximations approach to character weighting produced one tree with a consistency index of 0.74.

An informal classification of the group, superseries Eucalyptus, is based on that cladogram. The biogeographic history of superseries Eucalyptus is interpreted from the cladogram as having been caused by lour vicariant events in southeastern Australia, in combination with a suite of ecological features that overlie the biogeographic area‐pattern.
RECONSTRUCTING CHARACTER EVOLUTION ON POLYTOMOUS CLADOGRAMS
Authors: Maddison Wayne
Published: October 2008

Abstract— Algorithms to reconstruct character evolution on polytomous cladograms or phylogenetic trees have to date interpreted each polytomy literally, as if it were an event of multiple speciation, with multiple daughter species descending independently from a mother species, thus requiring any similarities shared by only some of these daughters to be accounted for by convergence. These algorithms are not appropriate when the polytomy is interpreted in the usual way, namely as representing uncertainty in the cladogram's resolution. New algorithms for both ordered and unordered characters are presented to reconstruct character evolution under the uncertain‐resolution interpretation of polytomies. These algorithms allow the cladogram to resolve itself so as to be favourable for the character whose evolution is being reconstructed. Because different characters may have different favourable resolutions, it is not possible in general to use these algorithms to determine the total parsimony of a polytomous cladogram (the number of evolutionary steps required over all characters by the cladogram), for which the only adequate approach is to find a most parsimonious dichotomous resolution of the cladogram.
A CLADISTIC TEST OF THE TAXON CYCLE AND TAXON PULSE HYPOTHESES
Authors: Liebherr James K. , Hajek Ann E.
Published: October 2008

Abstract— A species' habitat preference is intcrpretablc both as a response to present‐day conditions and as a result of evolutionary response to historical conditions. The taxon cycle and taxon pulse have been proposed as hypotheses that allow prediction of patterns of habitat specialization within a lineage. Both are based on common assumptions: (1) habitat specialization is largely irreversible in a lineage, (2) ecological specializations arise in a center of origin, and (3) dispersal events leading to current distributions can be ascertained. Eight taxa of Antillean, Mexican, and Central American Carabidae, for which cladistic hypotheses of relationship have been proposed, are used to test the generality of the taxon cycle and pulse. The patterns of habitat utilization predicted by the taxon cycle and taxon pulse hypotheses are tested by comparing cladistic transformations of habitat preference to randomly generated patterns of data generated under a null hypothesis. Evolutionary changes in habitat are interpreted using Camin‐Sokal coding, which assumes irreversible habitat shifts and a predetermined ecological ground state (assumptions of the taxon cycle and taxon pulse). An observed pattern is considered to demonstrate the taxon cycle or pulse when it results in an explanation of the habitat shifts that is more parsimonious than 95 % of the randomly generated patterns. Of the eight carabid groups, only one exhibits a statistically significant pattern supporting the taxon cycle and pulse. The failure of the taxon cycle and pulse as generally predictive hypotheses may be due to historical changes in climate that permit episodes of range expansion for species previously restricted to small ranges, and habitat shifts and specialization that do not progress in a linear transformation series.

Habitat shifts are also analyzed using Farris optimization, resulting in the most parsimonious transformation series of habitats, subject to a predefined ordering of habitats, while allowing reversals. Significance of an observed pattern of habitat shifts under Farris optimization implies habitat constancy relative to cladogenesis, and step‐wise changes in habitat preference. Two of the eight groups exhibit significant patterns of habitat utilization under Farris optimization, indicating that vicariance of areas of like habitat has been the predominant factor generating species diversity in these groups. The other groups do not exhibit habitat constancy, suggesting rapid changes in habitat preference relative to speciation.
ONTOGENY AND CHARACTER PHYLOGENY
Authors: Wheeler Quentin D.
Published: October 2008

Abstract— The doctrine of recapitulation was long ago exchanged for a view that ontogeny is orderly and recapitulates ancestral ontogenies. Only recently has the pattern of ontogeny, as a means for determining individual character phylogenies (polarities), been explicitly explored by Gareth Nelson and other cladists. Constraints on outgroup comparisons are suggested to apply to Nelson's rule equally, and the supposed distinction between “direct” and “indirect” methods is suggested to be nonexistent. Nelson's rule is concluded to measure character adjacency directly, but polarity indirectly. Nelson's (ontogenetic) rule is compared to the Outgroup Rule of Watrous and Wheeler, based on 60 postembryonic larval characters of three species of slime‐mold beetles of the genus Agathidium (onisemdes Palisot de Beauvois, pulchrum LeConte, aristerium Wheeler), and reference to larvae of Amsotoma basalts (Le Conte) as an outgroup. Polarities were hypothesized based on each rule and cladograms constructed with the microcomputer programs Henning86 (J. S. Farris) and CLADOS (K. C. Nixon). With levels of analytical error, or homoplasy, measured as the consistency index, the results were compared and the least homoplastic solutions preferred. It is concluded that the outgroup rule and Nelson's rule arc of about the same efficacy as criteria for polarity, and that each is ultimately justified on the basis of parsimony. The following hypothesis of relationships is accepted for the species studied: (Anisotoma basalts + (Agathidium oniscoides + (Agathidium pulchrum + Agathidium arislerium))).
Practice management: costing procedures*
Authors: CHANDLER E. A.
Published: October 2008

Costing procedures and their importance in small animal practice are reviewed together with previous literature on the subject. Fee‐setting scales are discussed, and detailed analysis tables of the costing of the sections of one veterinary hospital are given.

Résumé. On passe en revue les dépenses à engager et leur importance dans la pratique vétérinaire concernant les petits animaux, en mentionnant les données de la littératu reconcernant ces dépenses. On discute les barèmes et honoraires et on donne des tableaux détaillés se rapportant à l'analyse des dépenses engagées dans les départements d'un hôpital vétérinaire.

Zusammenfassung. Kostenrechnungsverfahren und ihre Bedeutung in der Kleintierpraxis werden zusammen mit früheren Veröffentlichungen über dieses Thema betrachtet. Massstäbe der Honorarfestsetzung werden besprochen und ins einzelne gehende analytische Tabellen der Abteilungskosten einer Tierklinik werden mitgeteilt.
Some aspects of pathology of the lower respiratory tract of the dog: review*
Authors: DONE S. H.
Published: October 2008

The limited literature on canine lung pathology is reviewed and the relative importance of canine pulmonary conditions is discussed.

Résumé. On passe en revue la littératwe peu abondante concernant la pathologie pulmonaire du chien et on discute l'importance relative des affections en question chez l'espèce canine.

Zusammenfassung. Die begrenzte Literatur über die Pathologie der Lunge des Hundes und die relative Bedeutung der Pulrnonalzustände beim Hund werden besprochen.
Clinical impressions of canine pulmonary disease*
Authors: ROHRBACH J. A.
Published: October 2008

The clinical methods of diagnosis are described and it is emphasized that their useful application increases with practice. Details are given of relevant cases seen during a period of 6 months. There were two cases of bronchitis, two cases of pulmonary congestion, secondary to cardiac insufficiency, one of inflammation due to migrating roundworm larvae and two cases of tumour metastasis.

Résumé. On décrit les méthodes cliniques de diagnostic et on souligne le fait que l'utilité de leur emploi augmente avec l'augmentation de la pratique. On donne des détails des cas caractéristiques observés au cours d'une période de 6 mois; il s'agissait de deux cas de bronchite, de deux cas de congestion pulmonaire secondaire à une insuffisance cardiaque, d'un cas d'inflammation due à la migration de larves d'Ascaris et de deux métatases de tumeurs.

Zusammenfassung. Die klinischen Methoden der Diagnose werden beschrieben, und es wird betont, dass mit zunehmender Praxis sich ihre erfolgreiche Anwendung verbessert. Einzelheiten über aufschlussreiche Fälle in einem Zeitraum von 6 Monaten werden angegeben. Es handelte sich um zwei Fälle von Bronchitis, zwei Fälle von Lungenstauung nach Herzinsuffizienz, einen von Entzündung infolge wandernder Fadenwurmlarven und zwei Fälle von metastatischem Tumor.