To shape a cell: an inquiry into the causes of morphogenesis of microorganisms.

We recognize organisms first and foremost by their forms, but how they grow and shape themselves still largely passes understanding. The objective of this article is to survey what has been learned of morphogenesis of walled eucaryotic microorganisms as a set of problems in cellular heredity, biochemistry, physiology, and organization. Despite the diversity of microbial forms and habits, some common principles can be discerned. (i) That the form of each organism represents the expression of a genetic program is almost universally taken for granted. However, reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading. Cellular form is generated by a web of interacting chemical and physical processes, whose every strand is woven of multiple gene products. The relationship between genes and form is indirect and cumulative; therefore, morphogenesis must be addressed as a problem not of molecular genetics but of cellular physiology. (ii) The shape of walled cells is determined by the manner in which the wall is laid down during growth and development. Turgor pressure commonly, perhaps always, supplies the driving force for surface enlargement. Cells yield to this scalar force by localized, controlled wall synthesis; their forms represent variations on the theme of local compliance with global force. (iii) Growth and division in bacteria display most immediately the interplay of hydrostatic pressure, localized wall synthesis, and structural constraints. Koch's surface stress theory provides a comprehensive and quantitative framework for understanding bacterial shapes. (iv) In the larger and more versatile eucaryotic cells, expansion is mediated by the secretion of vesicles. Secretion and ancillary processes, such as cytoplasmic transport, are spatially organized on the micrometer scale. The diversity of vectorial physiology and of the forms it generates is illustrated by examples: apical growth of fungal hyphae, bud formation in yeasts, germination of fucoid zygotes, and development of cells of Nitella, Closterium, and other unicellular algae. (v) Unicellular organisms, no less than embryos, have a remarkable capacity to impose spatial order upon themselves with or without the help of directional cues. Self-organization is reviewed here from two perspectives: the theoretical exploration of morphogens, gradients, and fields, and experimental study of polarization in Fucus cells, extension of hyphal tips, and pattern formation in ciliates. Here is the heart of the matter, yet self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm.     

Egg capsule dimensions as a taxonomic criterion in the digenean family transversotrematidae

Egg capsule morphometrics of the ectoparasitic digenean Transversotrema patialense are examined. Capsule width, but not length, shows age-dependency over the ovigerous life span of the fluke at 24°C. Capsule length is normally distributed. A comparison between 7 species of the family Transverso-trematidae indicates that the published data on egg dimensions are inadequate for statistical analyses. Simple methods for strengthening the role of egg capsule dimensions in numerical taxonomy are suggested.     

A cladistic phylogeny of the family Patellidae (Mollusca: Gastropoda)

A phylogenetic hypothesis for the patellid limpets is reconstructed by cladistic analysis of morphological characters from 37 species, representing all but one of the living members of the family. Characters included in the analysis are derived from shell shape and microstructure, headfoot and pallial complex, radula and sperm. The species fall into four clades, providing the basis for a new phylogenetic classification into four monophyletic genera: Helcion (four species; southern Africa), Cymbula (eight species; southern Africa, eastern Atlantic, southern Indian Ocean), Scutellastra (17 species; southern and southwestern Africa, Australia, Indo-West Pacific, Eastern Pacific) and Patella (nine species; northeastern Atlantic and Mediterranean). The analysis suggests sister-group relationships between Helcion and Cymbula, and between Scutellastra and Patella. In combination with present-day patterns of geographical distribution, this phylogenetic hypothesis is used to discuss the historical biogeography of the Patellidae. Scutellastra may have originated in southern Africa and dispersed across the Pacific, or alternatively may be a primitively Tethyan group. Both Helcion and Cymbula appear to have originated in southern Africa, but three Cymbula species have dispersed respectively to northwest Africa, St Helena and the southern Indian Ocean. The patellids of the northeastern Atlantic form a single clade, Patella (including P. pellucida), which may have arrived by northward dispersal of an ancestor from southern Africa, or possibly by vicariance of a widespread ancestral Tethyan distribution. The known fossil record of patellids is too fragmentary to permit choice between these alternatives.     

Phylogeny and classification of the Digenea (Platyhelminthes: Trematoda)

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history.     

Phylogenetic position of the family Trichodontidae (Teleostei: Perciformes), with a revised classification of the perciform suborder Cottoidei

The phylogenetic relationships of the family Trichodontidae and suborder Cottoidei (and zoarcoid Bathymasteridae) are reconstructed morphologically. The monophyly of the Trichodontidae, Cottoidei, and Zoarcoidei is unambiguously supported by 14 synapomorphies, including 1 newly recognized (and also 4 synapomorphies when ACCTRAN is accepted). It is assumed that the Trichodontidae is deeply nested within the Cottoidei, and the family and Cottoidea plus Cyclopteroidea have a sister relationship, supporting a previously inferred molecular phylogenetic hypothesis. We propose that the Trichodontidae is placed into the cottoid superfamily Trichodontoidea.     

The phylogeny and classification of Scaphopoda (Mollusca): an assessment of current resolution and cladistic reanalysis

The first cladistic analysis of phylogeny in the class Scaphopoda (Steiner 1992a,1996) examined relationships among family and selected sub-family taxa using morphological data. A preferred/ consensus tree of relationships illustrated monophyly of the orders Dentaliida and Gadilida, partial resolution among dentaliid families, and complete resolution among gadilid taxa. However, several alternative replications of the analysis, including use of a revised data matrix, did not produce the reported tree number or level of resolution; in all cases, monophyly of the Dentaliida was not supported by strict consensus of resultant parsimonious trees. Reanalysis, using unordered characters and outgroup rooting, only clearly resolves monophyly of the Gadilida and the sister relationship of the Entalinidae with the remaining gadilid families. These analyses emphasize the need for more comparative data and thorough parsimony analysis in scaphopod cladistic phylogenetics, as relationships in this class are still some way from resolution.     

Comparative biology and the importance of cladistic classification: a case study from the sensory biology of squamate reptiles

Evolutionary taxonomy has all but succumbed to cladistic methodology, but it continues to exert considerable influence in the realm of higher classification. Some systematists accept cladistic methods in phylogeny inference, but allow paraphyly in formal classifications. Most important, however, many traditional classifications based on paraphyletic groups (e.g. 'Reptilia') remain in force, deeply entrenched in the literature. Cladists have argued that such paraphyletic classifications can mislead comparative biologists into false evolutionary generalizations, but this assertion has rarely, if ever, been supported by example. This paper provides a case study, illustrating in detail the influence of a traditional paraphyletic classification of squamate reptiles on the historical development of ideas regarding the evolution of sensory modes (chemoreception vs. vision) in the group. The paraphyletic classification is shown to have led to false generalizations and incorrect conclusions stemming directly from the fact that the classification did not reflect accurately the phylogeny of Squamata, particularly the cladistic relationships of Gekkota. This study provides direct evidence that evolutionary generalization must be rooted in the branching pattern of phylogeny and not the potentially arbitrary categorical ranks of traditional taxonomies. It further supports recent calls for a truly phylogenctic taxonomy that has as its philosophical core the concept of descent.     

On the systematic position of the family Gyrinidae (Coleoptera: Adephaga)

Various characters of adult and larval members of Adephaga and Cupedidae were analyzed, and suggest that Gyrinidae are the sister-group of the remaining Adephaga, and are not closely related to the remaining aquatic Adephaga. The aquatic families Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae seem to form a well founded monophyletic unit. The following characters are considered as synapomorphies of Adephaga excluding Gyrinidae: bifurcate condition of the muscle (= M.) tentoriopraementalis inferior, reduction of hypopharynx, strongly developed prosternal process, reduction in size and specialized modification of the ventral sclerite of the mesothorax, strongly developed mesofurcal arms, a high mesopleural ridge, globular mesocoxae restricted to rotatory movements, invaginated sternum VIII (coxostemum), the strongly curved base of the median lobe of the aedeagus, which articulates with the parameres, the rotated position of the aedeagus in repose, fusion of the larval clypeolabrum with the frons and reduction of the larval lacinia. Mesal shifting of M. episterno-coxalis prothoracis, and the fusion of the apical portions of the malpighian tubules of either side are considered as synapomorphies of Adephaga excluding Rhysodidae and Gyrinidae. Lateral reduction of the meta “sternal” transverse ridge and the presence of the subcubital setal binding patch of the hind wing are considered as synapomorphic characters of Trachypachidae, Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae. We postulate that the metacoxal fusion occurred independently in gyrmids and the common ancestor of Trachypachidae, Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae. Consequently we consider this character state as another synapomorphy of Trachypachidae and Hydradephaga excluding Haliplidae and Gyrinidae. The following characters are considered as synapomorphies of Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae: Loss of tactile setae on the head capsule, metafurcal origin on the intercoxal wall, expansion of the intercoxal wall, elongation of the subcubital setal binding patch, loss of Mm. furca-coxale anterior and posterior, reduction of the larval abdominal segments IX and X, and the shifting of the uropmphi onto the ventral side of segment VIII. Presence of M. tentorio-mandibularis and M. stipitopalpalis intemus are certainly primitive features of adult gyrinids but the distribution of these character states among most members of Adephaga is yet unclear. Chemical defence gland constituents point towards a very isolated position of Gyrinidae. The old age of the group, documented by a larva found in upper Permian deposits, may support the hypothesis of a sister-group relation-ship between Gyrinidae and the remainder of Adephaga.     

An alternative hypothesis on the phylogenetic position of the family dactylopteridae (pisces: Teleostei), with a proposed new classification

The phylogenetic position of the family Dactylopteridae is inferred cladistically. The family lacks a close relationship with the Scorpaeniformes, owing to the posterior extension of the infraorbital in the former not being homologous with the scorpaeniform suborbital stay. Monophyly of the Dactylopteridae and percoid family Malacanthidae is supported by 20 synapomorphies, the former having a sister relationship with the malacanthid genusHoplolatilus supported by three synapomorphies. The former Dactylopteridae plus Malacanthidae are redefined as a percoid family. Dactylopteridae. being subdivided into the following four subfamilies: Branchiosteginae (includingBranchiostegus andLopholatilus), Malacanthinae (Caulolatilus andMalacanthus), Hoplolatilinae subfam. nov. (Hoplolatilus) and Dactylopterinae (Dactylopterus andDactyloptena).     

Systematic position and phylogenetic relationships of the family Omphalometridae (Digenea, Plagiorchiida) inferred from partial lsrDNA sequences

The phylogenetic relationships and systematic position of the digenean genus Omphalometra Looss, 1899 and several other closely related genera, have always been controversial and opinions of different authors on the systematic rank and content of this group have varied greatly. Molecular analysis based on the partial sequences of the large subunit ribosomal DNA gene of representatives of the genera Omphalometra, Rubenstrema and Neoglyphe as well as previously published sequences of members of five families of Plagiorchioidea, has demonstrated: (1) close phylogenetic relationships between these three genera, and (2) a strong support of their position within the family Plagiorchiidae as a well-defined separate clade considered here as a subfamily Omphalometrinae. Molecular data do not support the close affinities of the members of Omphalometrinae and genus Opisthioglyphe as has been suggested by majority of previous authors. Among Omphalometrinae, Omphalometra flexuosa (a parasite of moles, Talpidae) occupies a basal position in relation to Rubenstrema exasperatum and Neoglyphe locellus (both parasitic in shrews, members of the more evolutionary advanced family Soricidae). An extremely low level of lsrDNA sequence divergence between Neoglyphe and Rubenstrema suggests very close phylogenetic relationships of these two genera. Results of the molecular analysis are briefly discussed in comparison with the previously published systems.     

Shamanism and ritual in South America: an inquiry into Amerindian shape-shifting

Using ethnographic material on the Chachi, an Amerindian group in Northwest Ecuador, this article attempts to develop a renewed understanding of shamanism and ritual among so-called 'indigenous peoples' in South America, in both lowland and highland areas. I show that the human domain and that of spirits are always equivalent. It is also suggested that shamanic curing and many other forms of ritual can fruitfully be understood as instances of metamorphosis. In order to explore this argument I develop the notion of 'shape-shifting'.  

Résumé

Utilisant des matériaux ethnographiques sur les Chachi, groupe amérindien de la côte pacifique équatorienne, cet article tente de développer une compréhension renouvelée du chamanisme et des rituels des peuples indigènes de l'Amérique du Sud, à la fois dans les basses terres et dans les Andes. L'auteur explique pourquoi le domaine de l'humain et celui des esprits sont toujours équivalents. Il suggère ensuite que l'on gagne à comprendre les thérapies chamaniques et beaucoup d'autres formes rituelles comme des faits de métamorphose. Pour étayer cet argument, il développe la notion de « changement de forme >>.     

On the Proteaceae—the evolution and classification of a southern family*

A scheme of phylogeny in the Proteaceae is derived from analysis of new and previously available data on morphological, anatomical and chromosomal characters. The probable attributes of a common ancestor are indicated and it is concluded that the family has no close relatives, although it possibly diverged early from the Rosiflorean line. Chromosomal evolution has been complex, with early polyploidy, repeated dysploid reductions and great change in chromosome size, from a probable base of x = 7. Habit, wood anatomy, leaf form and sequence, chemical features, inflorescences, pollination and pericarp anatomy are discussed in relation to adaptation, phylogeny, parallelism and convergence. Distribution is analysed ecogeographically and in relation to the fossil record and chronology of continental movement. Ancestors of major groups may have differentiated before the break-up of Gondwanaland. Early members of almost all tribes were probably trees of mesothermic closed forests; xeromorphic characters found in many modern genera are secondary and of multiple origin in Australia, South Africa, New Caledonia and to a lesser degree in South America. The Proteaceae, with 75 genera, are divided into 5 subfamilies (3 new) comprising 14 tribes, further subdivided into 33 units of subtribal level. New genera described are Toronia, Acidonia, Pycnonia, Triunia, Malagasia, Athertonia, Virotia, Floydia.     

Transfer of the digenean trematode Transversohelmins borneoensis Fischthal & Kuntz in the Microphallidae family

Examination of the holotype and sole paratype of the digenean Transversohelmins borneoensis Fischthal & Kuntz, 1973 revealed a copulatory apparatus of the 'elasmocotyle' type that is characteristic of the family Microphallidae and tribe Basantisiini. The genus is described and figured as far as the specimens allow; it does not match any of the other genera of the tribe (Microphalloides and Queenslandisia). Microphalloides ovariolobatus Ke, 1978 is considered to be a synonym of the species T. borneoensis.     

Phylogeny and systematics of the Proterodiplostomidae Dubois, 1936 (Digenea: Diplostomoidea) reflect the complex evolutionary history of the ancient digenean group

The Proterodiplostomidae Dubois, 1936 is a relatively small family of diplostomoidean digeneans parasitising the intestines of reptilian hosts associated with freshwater environments in tropical and subtropical regions. The greatest diversity of proterodiplostomids is found in crocodilians, although some parasitise snakes and turtles. According to the most recent revision, the Proterodiplostomidae included 17 genera within 5 subfamilies. Despite the complex taxonomic structure of the family, availability of testable morphology-based phylogenetic hypotheses and ancient hosts, molecular phylogenetic analyses of the group were practically lacking. Herein, we use novel DNA sequence data of the nuclear lsrRNA gene and mitochondrial cox1 gene from a broad range of proterodiplostomid taxa obtained from crocodilian, fish, and snake hosts on four continents to test the monophyly of the family and evaluate the present morphology-based classification system of the Proterodiplostomidae in comparison with the molecular phylogeny. This first detailed phylogeny for the Proterodiplostomidae challenges the current systematic framework. Combination of molecular phylogenetic data with examination of freshly collected quality specimens and re-evaluation of morphological criteria resulted in a number of systematic and nomenclatural changes along with a new phylogeny-based classification of the Proterodiplostomidae. As the result of our molecular and morphological analyses: (i) the current subfamily structure of the Proterodiplostomidae is abolished; (ii) three new genera, Paraproterodiplostomum n. g., Neocrocodilicola n. g. and Proteroduboisia n. g., are described and Pseudoneodiplostomoides Yamaguti, 1954 is restored and elevated from subgenus to genus level; (iii) two new species, Paraproterodiplostomum currani n. g., n. sp. and Archaeodiplostomum overstreeti n. sp., are described from the American alligator in Mississippi, USA. Comparison of the structure of terminal ducts of the reproductive system in all proterodiplostomid genera did not support the use of these structures for differentiation among subfamilies (or major clades) within the family, although they proved to be useful for distinguishing among genera and species. Our study includes the first report of proterodiplostomids from Australia and the first evidence of a snake acting as a paratenic host for a proterodiplostomid. A key to proterodiplostomid genera is provided. Questions of proterodiplostomid-host associations parasitic in crocodilians are discussed in connection with their historical biogeography. Our molecular phylogeny of the Proterodiplostomidae closely matches the current molecular phylogeny of crocodilians. Directions for future studies of the Proterodiplostomidae are outlined.

     

水生植物排水草科的系统学位置

长期以来,小型水生植物类群排水草科（Hydate Uaceae）一直被认为是单子叶植物。最近的分子系统学研究表明,该科应隶属于基部被子植物（Basal Angiosperm）,和睡莲类植物为姐妹群。分类学家对该类群进行了系统修订,合并了该科的2个属,现有1属12种植物。对该科的深入研究正引起生物学家的广泛兴趣：