bluuebunny/crossref_metadata_2025 huggingface dataset:
TRANSITION TO A LAND FLORA: PHYLOGENETIC RELATIONSHIPS OF THE GREEN ALGAE AND BRYOPHYTES
Authors: MISHLER BRENT D. , CHURCHILL STEVEN P.
Published: October 2008

Abstract— Separate cladistic analyses of the green algae, liverworts, and hornworts are presented. Classificatory and evolutionary implications of these analyses, in addition to our previously published cladistic analyses of mosses and the embryophytes as a whole, are discussed. The embryophytes are monophyletic, and are part of a larger monophyletic group that includes some of the green algae (the “charophytes”). Important evolutionary transformations in the early phylogeny of the land plants include: (1) retention of the zygote on the haploid plant (gametophyte), with the sporophyte generation arising de novo by delaying meiosis, (2) independent elaboration of an elongate sporophyte in some liverworts, some hornworts, and in the moss‐tracheophyte clade, (3) independent origin of radial (axial) symmetry in the gametophyte in some liverworts and in the moss‐tracheophyte clade, (4) independent origin of leaves on the gametophyte in some liverworts and in mosses, and (5) the unique development of a branching sporophyte with multiple sporangia in the tracheophytes.
PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS
Authors: CRANE PETER R.
Published: October 2008

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen (“platy‐sperms”). Relationships between medullosans, cycads, and “platysperms” were not resolved, but within the “platysperm” clade conifers and cordaites (Cordaixylon, Mesoxylon) + Ginkgo form a monophyletic group (“coniferophytes”). The “higher platysperms” (glossopterids, Caytonia, corystosperms, Bennettitales, Pentoxylon, Gnetales, and angiosperms) are also monophyletic, but their relationship to “coniferophytes,” peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms (“anthophytes”) form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.
THE GENUS PEGOLETTIA (COMPOSITAE, INULEAE)
Authors: ANDERBERG ARNE
Published: October 2008

Abstract— The genus Pegolettia (Compositae, Inuleae) from Africa, Arabia, and the Middle East is revised. The nine recognized species, viz. P. lanceolata Harv., P. baccaridifolia Less., P. gariepina A. Anderb., P. oxyodonta DC., P. retrofracta (Thunb.) Kies, P. tenuifolia Bolus, P. plumosa M. D. Hend., P. pinnatilobata (Klatt) O. Hoffm. ex Dinter, and P. senegalensis Cass., are treated cladistically, and a cladogram is presented. The species are illustrated, and their distributions mapped. Hypotheses on the mode of speciation and the biogeography of the group including a model of area relationships in southern Africa are presented.
STATISTICAL COVARIANCE AS A MEASURE OF PHYLOGENETIC RELATIONSHIP
Authors: FORSTER MALCOLM R.
Published: October 2008

Abstract— The method of parsimony in phylogenetic inference is often taken to mean two things: (1) that one should favor the genealogical hypothesis that minimizes the required number of homoplasies (matchings of independently evolved derived character states), and (2) that symplesiomorphies (matchings of primitive character states) have little or no evidential value for phylogenetic relationship. This paper shows both theses to be false by undermining recent likelihood arguments for them and by providing a more secure likelihood proof of a new method, which is incompatible with both (1) and (2).
BIOGEOGRAPHY OF INDO‐PACIFIC CICADOIDEA: A TENTATIVE RECOGNITION OF AREAS OF ENDEMISM
Authors: DUFFELS J. P.
Published: October 2008

Abstract— The biogeography of the cicadas of the Indo‐Pacific is discussed in relation to paleogeography and compared with distribution patterns found in other groups of organisms. The cicadas show a low degree of endemism in the mainland of southeast Asia and the Greater Sunda Islands, and a high degree of endemism in Sulawesi, New Guinea, and the islands of the west Pacific. The biogeography of the cicadas of these regions with high endemism is analyzed for four groups: the subtribe Cosmopsaltriaria, the tribe Prasiini, the genus Baeturia, and the Pacific Cryptotympanini. A review of the paleogeography of the Indo‐Pacific, specifying the relevant barriers, island arcs, and land connections, is provided. The recognized areas of endemism are tentatively related to the geological history of the Indo‐Pacific. Areas of endemism are the Sulawesi Arcs and the Outer and Inner Melanesian Arcs. New Guinea appears to be a composite of areas of different origin: the central mountains of the Inner Melanesian Arc, the north‐coast mountains of the Outer Melanesian Arc, and the Vogelkop area, which is of uncertain origin. The Papuan Peninsula of New Guinea seems to be a zone of overlap between the Outer and the Inner Melanesian Arcs. The Pacific archipelagos of the Outer Melanesian Arcs (viz., the Bismarck Archipelago, Solomon Islands, Vanuatu, and the Fiji, Tonga, and Samoa Islands) represent distinct areas of endemism. The taxon‐area cladogram of the Cosmopsaltriaria gives some indication of the relationships among the areas of endemism. The discussion is extended to groups of bats, frogs, psocids, butterflies, and moths of the Melanesian Arcs, as their patterns of distribution seem equally relevant for the recognition of the biogeographic interrelationships in the Indo‐Pacific.
PATTERN CLADISTICS OR EVOLUTIONARY CLADISTICS?
Authors: HILL CHRISTOPHER R. , CAMUS JOSEPHINE M.
Published: October 2008

We can also put it like this. The introduction of an auxiliary hypothesis should always be regarded as an attempt to construct a new system; and this new system should then always be judged on the issue of whether it would, if adopted, constitute a real advance in our knowledge of the world—K. R. Popper.
THE CLADISTICS OF IDEAS (LEPIDOPTERA, DANAINAE)
Authors: Kitching I. J. , Vane‐Wright R. I. , Ackery P. R.
Published: October 2008

Abstract— Males of Idea tambusisiana, previously unstudied, lack the only known unequivocal synapomorphy associating the constituent members of Idea. Further cladistic analyses were performed on an expanded data matrix containing two characters alternatively coded in binary and multistate form. Two topologies were obtained of which one, in which I. tambusisiana remains internal to the genus, is accepted following consideration of information content and assessment of the supporting character states. A character analysis is also performed in which the problem of ambiguous charater state assignments to the internal nodes of the cladogram is examined. Biogeographic implications of the results are discussed with respect to areas of endemism in southeast Asia, the origin of Sulawesi (Celebes), and vicariance/dispersal models intended to explain the distribution of Idea species in relation to the Makassar Strait.
PARSIMONY ANALYSIS OF THE PHYLOGENY OF SOME OLIGOCHAETA (ANNELIDA) USING SPERMATOZOAL ULTRASTRUCTURE
Authors: Jamieson Barrie G. M. , Erseus Christer , Ferraguti Marco
Published: October 2008

Abstract— Quantitative and qualitative ultrastructural data from the spermatozoa of 11 oligochaete species, representing all orders (Tubificida, Lumbriculida, and Haplotaxida, yielded a single most parsimonious tree, using the Wagner‐tree (PAUP) method of Swofford (1984). The Haplotaxida (Haplotaxis through Megascolecidae) form a discrete monophyletic group, with inclusion, however, of the reproductively exceptional tubificidan Phreodrilus. Bythonomus, representing the Lumbriculidae, the phylogenetic position of which has been so controversial, forms the plesiomorphic sister group of the Haplotaxida, a position which is supported from other evidence. The Tubificida, represented by two tubificids (Rhizodrilus and Limnodriloides) and by the enchytraeid Lumbricillus, are plesiomorphic relative to the lumbriculid+haplotaxid assemblage and lie at the base of the tree, but all three appear mutually paraphyletic. Monophyly of the Tubificida cannot, however, be considered conclusively refuted from the small sample used. Lumbricillus appears to have the most plesiomorphic sperm in the investigated oligochaetes. The Megascolecidae (Amynthas and Fletcherodrilus) form the highest affinity and most apomor‐phic group. The implications of relative apomorphy of the Lumbriculida (Bythonomus) are profound. Branchiobdellids and leeches are generally regarded as sharing a common ancestry with lumbriculids and would, because of the revised position of the latter, cladistically constitute part of the Oligochaeta sensu lato.
THE NATURE OF CLADISTIC DATA
Authors: Pimentcl Richard A. , Riggins Rhonda
Published: October 2008

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non‐additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.
A CLADISTIC ANALYSIS OF LUCILIA CASS. (COMPOSITAE, INULEAE)
Authors: Freire Susana E.
Published: October 2008

Abstract— Lucilia is a South American genus with 23 species restricted to disjunct areas in southeastern Brazil and along the Andes. Lucilia is a monophyletic group defined by the co‐occurrence of six characters: herbaceous, alternate‐leaved, pappus with scabrid bristles fused at the base into a ring, style‐branches with sweeping hairs far down, capitula sessile, and aseptate‐flagellate hairs. A dadogram is presented using 41 morphological and anatomical characters arranged into 26 transformation series. The polarity of character states was determined by outgroup comparison with the genus Berroa. The cladistic analysis showed extensive parallel evolution in a number of the more conspicuous characters and produced four unresolved trichotomies. However, basing the hierarchy of Lucilia on the branching pattern produced by cladistic analysis results in a more natural and predicitive classification. Lucilia is divided into three sections, Lucilia, Intermedieae (sect, nov), and Lucilioides [divided into two subsections, Subspicata (subsect. nov.) and Lucilioides]. The latter subsection is subdivided into two series, Lucilioides (ser. nov.) and Paralucilia. The Brazilian species of section Lucilia (acutijolia, linearifolia, ferruginea, tmentosa, recurva, nitens, and flagelliformis) form the most primitive group within the genus. The more derived species of the genus, section lucilioides (plicatifolia, catamarcensis, burkartii, subspkata, lopezmirandae, alpina, pickeringii, piptolepis, santamca, chilensis, schultzii, longifolia, radians, lehmanni, pusilla) are found in the Andes L. eriophora (section Intermedieae) from central Chile bridges these two groups. An explanation for the distribution of the genus is given, based on the ecology of the species in relation to theories of the geologic and climatic history of South America. The present pattern has been determined by the age, geographical range, and vicissitudes of the habitat in which each group occurs. In the Brazilian species group, the habitat is old, and has remained relatively stable since well before the Pleistocene. In the Andean species group, the habitat is young and has undergone numerous rapid alterations since its inception at the end of the Pliocene.
A CLADISTIC ANALYSIS OF ANGOPHORA CAV. (MYRTACEAE)
Authors: Thiele Kevin , Ladiges Pauline Y.
Published: October 2008

Abstract— A cladistie analysis of Angophora Cav. used a data set dominated by quantitative morphological characters. These were coded into multistates using Generalized Gap‐Coding, and treated as ordered sequences of stales. The reasons for choosing an ordered over an unordered sequence are discussed. A branch and bound method yielded one minimal‐length, unrooted tree. Because of uncertainty in the position of the root, five cladograms were derived from the unrooted tree. The consensus cladogram comprises four main clades. The consensus cladogram was used for a biogeographic study using component analysis, which generated a single statement of relationships for five areas of eastern Australia. An infra‐generic classification of Angophora comprising four series corresponding to the four main clades, and two subseries, is presented. The following new names are published: Angophora series i>Floribundinae, series Subvelutininae, series Bakerinae. subseries Costntitac. Angophora leiocarpa: L. Johnson ex G. Leach) K. R. Thiele and P. Y. Ladiges and A.paludosa (G. Leach) K. R. Thiele and P. Y. Ladiges are published as new combinations.
A Cladistic Outline of the Eumycota
Authors: Tehler Anders
Published: October 2008

Abstract— A cladistic classification of fungi determined by a parsimony method with 21 terminal taxa and 51 characters is presented. Outgroup comparison with Oomycetes determined polarity assessments. The group Eumycota, including the traditional taxa Hyphochytriomycetes, Chytridio‐mycetes, Zygomycetes, Ascomycetes and Basidiomycetes, is defined by two synapomorphies, molecular weight of 25S RNA, and chitin cell walls. Some groups are supported as monophyletic; Eumycota, Amastigomycota, Dicaryomycotina, Ascomycetes, Protobasidiomycetes, Basidiomycetes, Euascomy‐cetidae, Hymenomycetidae and Homobasidiomycetales. The Hyphochytriomycota is the sister group to remaining groups. The Taphrinaceae and Saccharomycetaceae are more closely related to the Basidiomycetes than to any of the ascomycetous groups. In the absence of unique character sets groups such as the Mastigomycotina, Hemiascomycetes, Ustomycetes, Holobasidiomycetes, Heterobasidio‐mycetes, Phragmobasidiomycetes and the Teliomycetes cannot be maintained and are abandoned as paraphyletic. Characters and terminal taxa used for the analysis are defined and discussed.
PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM
Authors: de Queiroz Kevin , Donoghue Michael J.
Published: October 2008

Abstract— A tension has arisen over the primacy of interbreeding versus monophyly in defining the species category. Manifestations of this tension include unnecessary restriction of the concept of monophyly as well as inappropriate attribution of “species” properties, to “higher taxa”, and vice versa. Distinctions between systems (wholes) deriving their existence from different underlying. processes have been obscured by failure to acknowledge different interpretations of the concept of individuality. We identify interbreeding (resulting in populations) and evolutionary descent (resulting in monophyletic groups) as two processes of interest to phylogenetic systematists, and explore the relations between the systems resulting from these processes. In the case of sexual reproduction, populations of interbreeding organisms (regardless of whether they are monophyletic) exist as cohesive wholes and play a special role in phylogenetic systematics, being the least inclusive entities appropriate for use as terminal units in phylogenetic analysis of organismal relationships. Both sexual and asexual organisms form monophyletic groups. Accepting the reality and significance of both interbreeding and monophyly emphasizes that a conscious decision must be made regarding which phenomenon should be used to define the species category. Examination of species concepts that focus either on interbreeding or on common descent leads us to conclude that several alternatives are acceptable from the standpoint of phylogenetic systematics but that no one species concept can meet the needs of all comparative biologists.
RUST FUNGI AND HOST PLANT COEVOLUTION: DO PRIMITIVE HOSTS HARBOR PRIMITIVE PARASITES?
Authors: Hart Jeffrey A.
Published: October 2008

Abstract— The classical view of rust phylogeny is that rusts found on ferns and conifers are primitive, while rusts that parasitize angiosperms are advanced. This belief was based on the theory that primitive hosts harbor primitive parasites; that is, it assumed coevolution (co‐speciation) of hosts and parasites. A cladistic analysis of 30 genera and 28 characters representative of the major patterns of rust fungi diversity is presented. The results of this analysis suggest that tropical short‐cycle rusts on angiosperms form the cladistically basal group of rusts, while the rusts on conifers and ferns (Melampsoraceae sensu lato) form a nested terminal clade. These results suggest that rusts and their hosts have not undergone a long period of parallel cladogenesis (co‐speciation); host transfer has probably been at least as frequent as co‐speciation. The cladograms indicate evolutionary trends of spore stages and life history: urediniospores evidently preceded the evolution of aeciospores and pycniospores within Uredinales, and heteroecism is a derived condition which evolved at least several times. This study stresses the importance of making use of independent cladistic analyses of both host and parasite in order to test assumptions of coevolution and host transfer.
ON THE PHYLOGENY AND HIGHER CLASSIFICATION OF THE OLIGOCHAETA
Authors: Jamieson B. G. M.
Published: October 2008

Abstract— The 50 oligochaete taxa representing all families of “opisthoporous” oligochaetes (Aliuroididae, earthworms and aquatic “megadriles”) together with two representatives of the Haplotaxidac and three examples of “microdiles” were subjected to cladistic analysis using the PAUP program. Sixty‐eight characters used in the analyses were derived from a comprehensive range of somatic and genital systems. The optimal result, in terms of maximal number of characters and taxa and of parsimony, produced two trees (consistency index 0.362) differing only in the placement of the monotypic clade for the family Lumbriculidae. From a line originating from the presumed octogonadial ancestor, the following branches were derived, in sequence from the basal to most derived (new taxa asterisked): subclass Randiellata* (order Randiellida*, Randiellidae); subclass Tubificata* (order Tubificida, Tubincidae, Naididae computed and others not computed); subclass Lumbriculata* (order Lumbriculida, Lumbriculidae); superorder Haplotaxidea* (order Haplotaxida, Haplotaxidae); order Moniligastrida (Moniligastridae); suborder Alluroidina (Aliuroididae and Syngenodrilidae); cohort Aquamegadrili* (with, in succession, superfamilice Sparganophiloidea, Sparganophilidae; Biwadriloidea, Biwadrilidac, and Almoidca—Lutodrilidac and Almidae, including Criodrilus); superfamily Eudriloidea*, superfamily Lumbricoidea and, as the adelphotaxon of the latter, the superfamily Megascolecoidea. Intermediate nodes were given the following names, with the adelpholaxon through to the Megascolecoidea, M, in parentheses: subclass Diplotesticulata (Haplotaxidea—M); superorder Metagynopohora* (Moniligastrida—M); order Opisthopora (Alluroidina M); suborder Crassiclitellata* (Aquamegadrili — M); cohort Terrimegadrili* (Ocnerodriloidea M); unnamed (Eudriloidea M); unnamed (Lumbricoidea and Megascolecoidea). Recognition of the Randiellata, which alone were added intuitively and not computed, and the position of the Lumbriculata, are tentative. Location of the Lumbricoidea as the adelphotaxon of a restricted Megascoecloidea is heuristic, but the alternative depiction of lumbricoids in some analyses, as the adelphotaxon of an ocnerodrilid‐eudrilid‐megascolecoid clade (the conventional Megascolecoidea s. lat.), is not conclusively dismissed.
Speciational Evolution: a Phylogenetic Test With Allozymes in Sceloporus (Reptilia)
Authors: Mindell David P. , Sites Jack W. , Graur Dan
Published: October 2008

Abstract— The potential role of speciation in accelerating evolutionary divergence remains controversial. Earlier tests based on genetic and morphologic distances which indicated an absence of speciational evolution rely on problematic assumptions. We provide a phylogenetic test in which amounts of discrete character change relative to an outgroup are compared between sister taxa. Although this test is constrained by a need to assume similar extinction rates in groups compared, it provides conceptual improvements regarding monophyly, equal age of taxa, and distribution of homoplasy. Based on analysis of 68 informative allozyme characters for 19 lizard species in the genus Sceloporus, significant speciational evolution and punctuational change is, at least, a viable explanation for the distribution of observed character changes.
PHYLOGENY AND CLASSIFICATION OF THE PANDALOIDEA (CRUSTACEA, CARIDEA)
Authors: Christoffersen Martin L.
Published: October 2008

Abstract— A manual cladistic analysis, subsequently expanded with a PAUP computer analysis, was performed on 21 genera of the monophyletic taxon Pandaloidea. Morphological data were obtained from the literature for 146 of the 152 known species‐group taxa and from specimens belonging to 11 genera and 15 species—those of Pantomus parvulus extending the known range from the North Western Atlantic to Uruguay. The taxon Physetocaridoidca was synonymized with Pandaloidea, and the genus Pandalopsis with “Pandalus”. I have rejected reversal hypotheses indicated by the computer for four transformation series and chosen a final cladogram of slightly different topology which is six steps longer than the shortest tree. The cladogram for 20 terminal taxa is based on 108 apomorphic characters, resolved into 155 steps (72 synapomorphies and 83 homoplasies and reversals). The following sequenced phylogenctic classification is proposed: Pandaloidea; Pandalidae; Pantominae subfam.n.; Notopandalus [N. magnoculus]; Peripandalus [P. serratus]; Pantomus; P. ajfinis; P. parvulus; Pandalinae; Austropandalini trib.n.; Austropandalus [A. grayi]; Pandalina; P. brevirostris; P. profunda; Pandalini; Dichdopandalus; D. bonnieri; D. leptorerus; Pandalus: “Plcsionikidae” [“Plesionika”]; Heterocarpidae [Heterocarpus]; Heterocarpoididae fam.n. [Heterocarpoides] [H. levicarina]; Dorodoteidae fam.n. [Dorodotes] [D. reflexus]; Thalassocarididae; Chlorotocus; C. crassicornis; C. novaezelandiae; Chlorotocoides [C. spinicauda]; Thalassocaris;, T. obscura; T. crimia; T. lucida; Physetocandidae; Stylopandalus [S. richardi]; Chlorotocella; C. gracilis; C. leptorhjnehus; Physetocaris [P. microphthalma]; Chlorocurtis [C. jactans]; Anachlorocurtis [A, commensalis]; Miropandalus [M. hardingi]. Quotation marks indicate taxa of uncertain systematic status. Square brackets indicate redundant, phylogenetically uninformative, genus and species‐level taxa maintained in the classification to comply with the principle of binominal nomenclature.
A CLADISTIC ANALYSIS OF THE FAMILY TRISTIRIDAE (ORTHOPTERA, ACRIDOIDEA)
Authors: Cigliano Marfa Marta
Published: October 2008

Abstract— A cladistic analysis of the endemic South American family Tristiridae was performed using 29 characters from external morphology and the genitalia. Polarity of characters was based on the outgroup comparison method. One most parsimonious cladogram of 54 steps was obtained, from which a classification of the family Tristiridae was constructed. The analysis of phylogenetic relationships showed that the different kinds of characters define taxa at different levels in the cladogram. Those mostly from the phallic complex define suprageneric taxa while those from external morphology characterize genera. It is hypothesized that in Tristiridae differentiation of the phallic complex preceded differentiation of external morphology and that characters from the phallic complex arc less conservative than those from the external morphology.
FREQUENCY DISTRIBUTIONS OF LENGTHS OF POSSIBLE NETWORKS FROM A DATA MATRIX
Authors: Quesne Walter J. Le
Published: October 2008

Abstract— It is common practice to attempt to find the minimum length tree (also known as the Wagner tree) for a given data matrix on a group of OTUs (taxa). However, little study has been made of the pattern of frequency distributions when the lengths of all possible networks (unrooted trees) are taken into consideration. A published real data matrix with eight OTUs was compared with randomly generated data, when the former showed a much larger variance and very marked skewness. A number of published data matrices with a larger number of OTUs were studied by random selection of 10240 out of the possible trees: these were compared with 32 randomly generated data sets with 13 OTUs, using the same program. An algorithm has been found for calculation of the expected mean, variance and skewness for random binary data with up to 13 OTUs, based on the number of characters representing each type of partition of the OTUs. The calculation requires listing of the possible topologies and their relative weighting, which are tabulated.
EVOLUTIONARY MORPHOLOGY AND PHYLOGENY OF ARAGHNIDA
Authors: Shultz Jeffrey W.
Published: October 2008

Abstract— This paper reports results from a cladistic analysis of the 11 Recent arachnid orders. The polarities of 64 newly discovered and traditional characters were determined through outgroup comparisons that included Eurypterida, Xiphosura, Trilobita and Crustacea. A branch‐and‐bound algorithm was used to discover a single tree (consistency index 0–59). The relationships suggested by this analysis differ substantially from previous interpretations of arachnid phylogeny, and a new taxonomic system is introduced to accommodate these results. This analysis suggests that Arachnida is monophyletic and composed of two principal lineages, Micrura and Dromopoda. Possible synapomorphies of Micrura include a pygidmm, tntosternum, six principal lateral eyes, poorly sclerotized postgenital appendages, coxal gland orifices near leg 1, an array of micxotubules associated with the spermatozoan nucleus, and absence of coxal endites on the walking legs. The micruran orders appear to have the following relationships: (Palpigradi (Araneae (Amblypygi (I helyphonida, Schizomida)))) (Ricinulei, Acari). Possible synapomorphies of Dromopoda include transverse carapaeal furrows, greatly reduced prosomal sternum, prosomal endosternite with two segmental components, stomotheca, bicondylar femoropatellar and patellotibial joints and extensor muscles. The dromopodan orders appear to have the following relationships: Opiliones (Scorpioncs (Pscudo‐scorpiones, Solifugae)).
COMPONENT ANALYSIS: A VALIANT FAILURE?
Authors: Page Roderic D. M.
Published: October 2008

Abstract— Rerent criticisms of component analysis are based on misunderstandings of the relationship between component analysis, parsimony and consensus methods. These criticisms are rebutted, and the appropriateness of applying the Wagner parsimony criterion to the study of biogcography and co‐speciation is questioned. An alternative parsimony method, previously applied to mapping gene cladograms onto organism cladograms, is developed.
EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM
Authors: Mickevich M. F. , Weller S. J.
Published: October 2008

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies.

Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed.

Tracing the evolution of characters interests both systematists and non‐systematists alike. When character state trees (transmodal characters) are optimized on pre‐existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants.

Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.
Radiology of the normal canine thorax*
Authors: DOUGLAS S. W.
Published: October 2008

The interpretation of chest radiographs is dependent on good radiographic technique and on a knowledge of the normal radiological appearance of the component structures of the thoracic cavity (rib cage, pleural cavity, lungs, bronchial tree and mediastinum); these aspects are described.

Résumé. L'interprétation d'une radiographie thoracique dépend du perfectionnement de la technique radiographique et de la connaissance des aspects norrnaux radiologiques des formations complexes de la cavité thoracique (cage thoracique, cavité pleurale, poumons, arbre bronchique et médiastin); on décrit ces divers aspects.

Zusammenfassung. Die Interpretierung von Röntgenaufnahmen des Brustraums hängt von guten radiographischen Methoden und der Kenntnis der normalen radiologischen Erscheinung der den Brustraum erfüllenden Strukturen ab (Rippen, Pleuralraurn, Lungen, Bronchien und Mediastinum); diese Aspekte werden beschrieben.
Knockout mouse models for intestinal electrolyte transporters and regulatory PDZ adaptors: new insights into cystic fibrosis, secretory diarrhoea and fructose‐induced hypertension
Authors: Seidler Ursula , Singh Anurag , Chen Mingmin , Cinar Ayhan , Bachmann Oliver , Zheng Wen , Wang Jian , Yeruva Sunil , Riederer Brigitte
Published: October 2008

Knockout mouse models have provided key insights into the physiological significance of many intestinal electrolyte transporters. This review has selected three examples to highlight the importance of knockout mouse technology in unravelling complex regulatory relationships important for the understanding of human diseases. Genetic ablation of the cystic fibrosis transmembrane conductance regulator (CFTR) has created one of the most useful mouse models for understanding intestinal transport. Recent work has provided an understanding of the key role of the CFTR anion channel in the regulation of HCO3− secretion, and the important consequences that a defect in HCO3− output may have on the viscoelastic properties of mucus, on lipid absorption and on male and female reproductive function. The regulation of CFTR activity, and also that of the intestinal salt absorptive transporter NHE3, occurs via the formation of PSD95‐Drosophila homologue Discs‐large‐tight junction protein ZO‐1 (PDZ) adaptor protein‐mediated multiprotein complexes. The recent generation of knockout mice for three members of the sodium‐hydrogen regulatory factor (NHERF) family of PDZ adaptor proteins, namely NHERF1 (EBP50), NHERF2 (E3KARP) and NHERF3 (PDZK1), has helped to explain why NHERF1 is essential for both normal and mutant CFTR function. In addition, they have provided new insight into the molecular mechanisms of secretory diarrhoeas. Genetic ablation of members of the recently discovered Slc26 anion transporter gene family not only reproduced the phenotype of the genetic diseases that led to the discovery of the gene family, but also resulted in new insights into complex human diseases such as secretory diarrhoea, fructose‐induced hypertension and urolithiasis.
Are l‐glutamate and ATP cotransmitters of the peripheral chemoreflex in the rat nucleus tractus solitarius?
Authors: Accorsi‐Mendonça Daniela , Bonagamba Leni G. H. , Leão Ricardo M. , Machado Benedito H.
Published: October 2008

Peripheral chemoreflex activation in awake rats or in the working heart–brainstem preparation (WHBP) produces sympathoexcitation, bradycardia and an increase in the frequency of phrenic nerve activity. Our focus is the neurotransmission of the sympathoexcitatory component of the chemoreflex within the nucleus of the tractus solitarius (NTS), and recently we verified that the simultaneous antagonism of ionotropic glutamate and purinergic P2 receptors in the NTS blocked the pressor response and increased thoracic sympathetic activity in awake rats and WHBP, respectively, in response to peripheral chemoreflex activation. These previous data suggested the involvement of ATP and L‐glutamate in the NTS in the processing of the sympathoexcitatory component of the chemoreflex by unknown mechanisms. For a better understanding of these mechanisms, here we used a patch‐clamp approach in brainstem slices to evaluate the characteristics of the synaptic transmission of NTS neurons sending projections to the ventral medulla, which include the premotor neurons involved in the generation of the sympathetic outflow. The NTS neurons sending projections to the ventral medulla were identified by previous microinjection of the membrane tracer dye, 1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine perchlorate (DiI), in the ventral medulla and the spontaneous (sEPSCs) and tractus solitarius (TS)‐evoked excitatory postsynaptic current (TS‐eEPSCs) were recorded using patch clamp. With this approach, we made the following observations on NTS neurons projecting to the ventral medulla: (i) the sEPSCs and TS‐eEPSCs of DiI‐labelled NTS neurons were completely abolished by 6,7‐dinitroquinoxaline‐2,3(1H,4H)‐dione (DNQX), an antagonist of ionotropic non‐NMDA glutamatergic receptors, showing that they are mediated by L‐glutamate; (ii) application of ATP increased the frequency of appearance of spontaneous glutamatergic currents, reflecting an increased exocytosis of glutamatergic vesicles; and (iii) ATP decreased the peak of TS‐evoked glutamatergic currents. We conclude that L‐glutamate is the main neurotransmitter of spontaneous and TS‐evoked synaptic activities in the NTS neurons projecting to the ventral medulla and that ATP has a dual modulatory role on this excitatory transmission, facilitating the spontaneous glutamatergic transmission and inhibiting the TS‐evoked glutamatergic transmission. These data also suggest that ATP is not acting as a cotransmitter with L‐glutamate, at least at the level of this subpopulation of NTS neurons studied.
Murein Hydrolase Activity in the Surface Layer of
Lactobacillus acidophilus
ATCC 4356
Authors: Prado Acosta Mariano , Palomino María Mercedes , Allievi Mariana C. , Rivas Carmen Sanchez , Ruzal Sandra M.
Published: October 2008

We describe a new enzymatic functionality for the surface layer (S-layer) of
Lactobacillus acidophilus
ATCC 4356, namely, an endopeptidase activity against the cell wall of
Salmonella enterica
serovar Newport, assayed via zymograms and identified by Western blotting. Based on amino acid sequence comparisons, the hydrolase activity was predicted to be located at the C terminus. Subsequent cloning and expression of the C-terminal domain in
Bacillus subtilis
resulted in the functional verification of the enzymatic activity.
Influence of High Pressure on the Dimerization of ToxR, a Protein Involved in Bacterial Signal Transduction
Authors: Linke Kai , Periasamy Nagarajan , Ehrmann Matthias , Winter Roland , Vogel Rudi F.
Published: October 2008

High hydrostatic pressure (HHP) is suggested to influence the structure and function of membranes and/or integrated proteins. We demonstrate for the first time HHP-induced dimer dissociation of membrane proteins in vivo with
Vibrio cholerae
ToxR variants in
Escherichia coli
reporter strains carrying
ctx
::
lacZ
fusions. Dimerization ceased at 20 to 50 MPa depending on the nature of the transmembrane segments rather than on changes in the ToxR lipid bilayer environment.
Moraxella catarrhalis
M35 Is a General Porin That Is Important for Growth under Nutrient-Limiting Conditions and in the Nasopharynges of Mice
Authors: Easton Donna M. , Maier Elke , Benz Roland , Foxwell A. Ruth , Cripps Allan W. , Kyd Jennelle M.
Published: October 2008

Moraxella catarrhalis
is a gram-negative respiratory pathogen that is an important causative agent for otitis media and exacerbations of chronic obstructive pulmonary disease. We have previously predicted the outer membrane protein M35 to be a general porin, and in the current study, we have investigated the function of M35 and its importance for survival of
M. catarrhalis
in vivo. Lipid bilayer experiments reveal that refolded M35 functions as a channel that is typical of gram-negative bacterial porins. M35 forms wide and water-filled channels with a single-channel conductance of about 1.25 nS in 1 M KCl solution and has only a small selectivity for cations over anions. When the in vitro growth characteristics of two M35 deletion mutant strains of
M. catarrhalis
were compared to the wild-type parent isolates, the growth of the mutant strains was inhibited only under nutrient-poor conditions. This growth defect could be eliminated by additional glutamic acid, but not additional aspartic acid, glycine, sucrose, or glucose. The mutant strains compensated for the lack of M35 by enhancing their uptake of glutamic acid, and this enhanced rate of glutamic acid uptake was attributed to the compensatory upregulation of a protein of approximately 40 kDa. M35 was also found to be essential for nasal colonization of mice, demonstrating that its presence is essential for survival of
M. catarrhalis
in vivo. These results suggest that M35 is a general porin that is necessary for the uptake of important energy sources by
M. catarrhalis
and that it is likely that M35 is an essential functional protein for in vivo colonization.
Hierarchical Regulation of Photosynthesis Gene Expression by the Oxygen-Responsive PrrBA and AppA-PpsR Systems of
Rhodobacter sphaeroides
Authors: Gomelsky Larissa , Moskvin Oleg V. , Stenzel Rachel A. , Jones Denise F. , Donohue Timothy J. , Gomelsky Mark
Published: October 2008

In the facultatively phototrophic proteobacterium
Rhodobacter sphaeroides
, formation of the photosynthetic apparatus is oxygen dependent. When oxygen tension decreases, the response regulator PrrA of the global two-component PrrBA system is believed to directly activate transcription of the
puf
,
puh
, and
puc
operons, encoding structural proteins of the photosynthetic complexes, and to indirectly upregulate the photopigment biosynthesis genes
bch
and
crt
. Decreased oxygen also results in inactivation of the photosynthesis-specific repressor PpsR, bringing about derepression of the
puc
,
bch
, and
crt
operons. We uncovered a hierarchical relationship between these two regulatory systems, earlier thought to function independently. We also more accurately assessed the spectrum of gene targets of the PrrBA system. First, expression of the
appA
gene, encoding the PpsR antirepressor, is PrrA dependent, which establishes one level of hierarchical dominance of the PrrBA system over AppA-PpsR. Second, restoration of the
appA
transcript to the wild-type level is insufficient for rescuing phototrophic growth impairment of the
prrA
mutant, whereas inactivation of
ppsR
is sufficient. This suggests that in addition to controlling
appA
transcription, PrrA affects the activity of the AppA-PpsR system via an as yet unidentified mechanism(s). Third, PrrA directly activates several
bch
and
crt
genes, traditionally considered to be the PpsR targets. Therefore, in
R. sphaeroides
, the global PrrBA system regulates photosynthesis gene expression (i) by rigorous control over the photosynthesis-specific AppA-PpsR regulatory system and (ii) by extensive direct transcription activation of genes encoding structural proteins of photosynthetic complexes as well as genes encoding photopigment biosynthesis enzymes.
HPrK Regulates Succinate-Mediated Catabolite Repression in the Gram-Negative SymbiontSinorhizobium meliloti
Authors: Pinedo Catalina Arango , Gage Daniel J.
Published: October 2008

The HPrK kinase/phosphatase is a common component of the phosphotransferase system (PTS) of gram-positive bacteria and regulates catabolite repression through phosphorylation/dephosphorylation of its substrate, the PTS protein HPr, at a conserved serine residue. Phosphorylation of HPr by HPrK also affects additional phosphorylation of HPr by the PTS enzyme EI at a conserved histidine residue.Sinorhizobium melilotican live as symbionts inside legume root nodules or as free-living organisms and is one of the relatively rare gram-negative bacteria known to have a gene encoding HPrK. We have constructedS. melilotimutants that lack HPrK or that lack key amino acids in HPr that are likely phosphorylated by HPrK and EI. Deletion ofhprKinS. melilotienhanced catabolite repression caused by succinate, as did an S53A substitution in HPr. Introduction of an H22A substitution into HPr alleviated the strong catabolite repression phenotypes of strains carrying ΔhprKorhpr(S53A) mutations, demonstrating that HPr-His22-P is needed for strong catabolite repression. Furthermore, strains with ahpr(H22A) allele exhibited relaxed catabolite repression. These results suggest that HPrK phosphorylates HPr at the serine-53 residue, that HPr-Ser53-P inhibits phosphorylation at the histidine-22 residue, and that HPr-His22-P enhances catabolite repression in the presence of succinate. Additional experiments show that ΔhprKmutants overproduce exopolysaccharides and form nodules that do not fix nitrogen.
A Unique GTP-Dependent Sporulation Sensor Histidine Kinase in
Bacillus anthracis
Authors: Scaramozzino Francesca , White Andrea , Perego Marta , Hoch James A.
Published: October 2008

The
Bacillus anthracis
BA2291 gene codes for a sensor histidine kinase involved in the induction of sporulation. Genes for orthologs of the sensor domain of the BA2291 kinase exist in virulence plasmids in this organism, and these proteins, when expressed, inhibit sporulation by converting BA2291 to an apparent phosphatase of the sporulation phosphorelay. Evidence suggests that the sensor domains inhibit BA2291 by titrating its activating signal ligand. Studies with purified BA2291 revealed that this kinase is uniquely specific for GTP in the forward reaction and GDP in the reverse reaction. The G1 motif of BA2291 is highly modified from ATP-specific histidine kinases, and modeling this motif in the structure of the kinase catalytic domain suggested how guanine binds to the region. A mutation in the putative coiled-coil linker between the sensor domain and the catalytic domains was found to decrease the rate of the forward autophosphorylation reaction and not affect the reverse reaction from phosphorylated Spo0F. The results suggest that the activating ligand for BA2291 is a critical signal for sporulation and in a limited concentration in the cell. Decreasing the response to it either by slowing the forward reaction through mutation or by titration of the ligand by expressing the plasmid-encoded sensor domains switches BA2291 from an inducer to an inhibitor of the phosphorelay and sporulation.
The Genome of
Burkholderia cenocepacia
J2315, an Epidemic Pathogen of Cystic Fibrosis Patients
Authors: Holden Matthew T. G. , Seth-Smith Helena M. B. , Crossman Lisa C. , Sebaihia Mohammed , Bentley Stephen D. , Cerdeño-Tárraga Ana M. , Thomson Nicholas R. , Bason Nathalie , Quail Michael A. , Sharp Sarah , Cherevach Inna , Churcher Carol , Goodhead Ian , Hauser Heidi , Holroyd Nancy , Mungall Karen , Scott Paul , Walker Danielle , White Brian , Rose Helen , Iversen Pernille , Mil-Homens Dalila , Rocha Eduardo P. C. , Fialho Arsenio M. , Baldwin Adam , Dowson Christopher , Barrell Bart G. , Govan John R. , Vandamme Peter , Hart C. Anthony , Mahenthiralingam Eshwar , Parkhill Julian
Published: October 2008

Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease.
Burkholderia cenocepacia
infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates.
B. cenocepacia
strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although
B. cenocepacia
strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of
B. cenocepacia
rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of
B. cenocepacia
, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.