Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Comparison of in vitro decomposition of bryophytic and tracheophytic plant material

The fossil record of bryophytes is generally poor and infertile plants attributable to liverworts and mosses could also be thalloid vascular plant gametophytes or herbaceous lycophytes respectively. The paucity of the bryophytic record could be the result of relatively rapid degradation of bryophytic material in comparison to that of vascular plants, the absence of lignified cells in bryophytes sustaining this belief. However, certain organs of bryophytes are as robust as those of vascular plants (e.g. spores) and the hydroxybenzofuran polymers produced by some mosses could be of similar preservational resistance to lignins. A simplistic experiment to test the relative resistance to decay of bryophytic material has been undertaken. Its findings suggest that bryophytic plant material has a similar preservational potential to that of a selected vascular plant, particularly in organic rich sediments. This result may be construed to imply that bryophytes were indeed less abundant in the preservational environments of the Coal Measures than might be expected on the basis of current palaeoenvironmental reconstructions.     

Échinodermes de l'Ordovicien supérieur (Ashgill) de Sardaigne et d'Algérie

Research on the influence of sea level variations on the benthic faunas have been carried out in the Upper Ordovician of Sardinia. Study of the depositional facies and sequence analysis of the upper part (Lower Ashgill) of the Portixeddu Formation led to the identification of the sedimentary environments. Cystoids and crinoids are associated to bryozoans and brachiopods in most levels. The numerical analysis of associations and megaguilds shows that crinoids and cystoids have a higher frequency in the proximal and median facies of the upper offshore. The columnal association characterized by Conspectocrinus celticus and the coronoid Mespilocystites tregarvanicus has been discovered in the upper part of the formation. This material and complementary samples from Upper Ordovician of Sardinia and Kabylia (Algeria) bring additional data on the systematic and show the wide distribution of this fauna outside of the Ibero-armorican domain. The distribution of this echinoderm association supports a palaeogeographical position of the Ibero-armorican domain and Sardinia within the north gondwanan margin during the Lower Palaeozoic.     

Des Miliolacea aux Alveolinacea (grands foraminifères): la faune du Crétacé supérieur et du Tertiaire inférieur du Chiapas (S.E. Mexique)

Found in Chiapas (South-East of Mexico), Praealveolina michaudi nov. sp. and Chubbina jamaicensis (of Campanian-Maestrichtian age) are described, both evolved from Nummoloculina sp. while Raadshoovenia guatemalensis (upper Paleocene-lower Eocene) arises from Quinqueloculina. We precisely analyze and modelize the nepionic coiling during the evolutionary change from Miliolacea to Alveolinacea. During ontogenesis as well as during phylogenesis, quinqueloculine coiling progresses to streptospiral and then to planispiral chamber arrangement with the increase of volume of embryo and of chambers. Appearance of these large foraminifers are understood as a consequence of the rise of K-strategies in their mode of life, following the development of photosynthetic symbioses.     

人工合成多样性突变文库研究进展*

突变文库的构建是定向进化研究过程中一个关键步骤,主要利用天然存在的系统或者人工合成的分子技术来产生多样性核酸分子文库,为制备和筛选具有一定特性的蛋白酶、多肽、人工抗体等提供庞大的遗传基因库,也可用于合成生物学中相关基因元件的研究与筛选,为目标生物制品的高效工业化生产提供动力。随着对突变文库构建技术研究的日益深入,各种文库构建策略相继被开发出来,并在生物能源、生物化工、生物医药、生物试剂和食品工业等方面得到了广泛的应用。然而,定向进化中的文库构建策略多有不同,各种突变文库构建技术的核心方法也在不断创新。主要介绍近年来实验室中人工合成多样性文库的前沿技术,并对文库构建技术在自动化和智能化方向的发展进行了展望。     

A phylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl

A phylogenetic analysis of 123 morphological characters of basal waterfowl (Aves: Anseriformes) and other selected avian orders confirmed that the screamers (Anhimae: Anhitn-idae) are the sister-group of other waterfowl (Anseres), and that the magpie goose (Anseranatidae: Anseranas semipalmata) is the sister group of other modern waterfowl exclusive of screamers (Anatidae sensu stricto). The analysis also supports the traditional hypothesis of the gallinaceous birds (Galliformes) as the sister group of the Anseriformes. Presbyornis, a fossil from the early Eocene of Wyoming and averred by Olson & Feduccia as showing that the Anseriformes were derived from shorebirds (Charadriiformes), was found to represent the sister group of the Anatidae. Associated hypotheses by Olson & Feduccia concerning the implications of Presbyornis for the phylogenetic relationships of flamingos (Phoenicopteriformes), the position of the Anhimidae within the waterfowl, relationships among modern Anatidae, and a plausible evolutionary scenario for waterfowl also are rejected. Analyses revealed that cranial characters were critical to the establishment of the Galliformes as the sister group of the Anseriformes; exclusion of the Anhimidae, especially in combination with Anseranas, also undermined the support for this inference. Placement of Presbyornis as the sister group of the Anatidae casts doubt on the role suggested by Feduccia of ‘transitional shorebirds' in the origin of modern avian orders, and calls into question the concept of ‘fossil mosaics’. The phylogenetic hypothesis is used to reconstruct an evolutionary scenario for selected ecomorphological characters in the galliform-anseriform transition, to predict the most parsimonious states of these characters for Presbyornis, and to propose a phylogenetic classification of the higher-order taxa of waterfowl. This re-examination of Presbyornis also is used to exemplify the fundamental methodological shortcomings of the intuitive approach to the reconstruction of phylogenetic relationships.     

L’habitat en grotte au Néolithique : vers une estimation de l’intensité des occupations

The archaeological excavation of the cave of the Gardon has brought to light a dilated and nearly continuous stratigraphy for the Neolithic era. The analysis of lithic industry has showed the existence of variations between those neolithic layers, which are independents of the technological processes of tools productions. Four criteria allow us to characterize the occupation’s type of each layer. Compared to the excavations data and to sedimentological analysis, these results allow us to display the evolution of the intensity of occupations of the cave throughout the whole Neolithic.     

The Natural Host Range of Steinernema and Heterorhabditis spp. and Their Impact on Insect Populations

The natural host range of entomopathogenic nematodes of the genera Steinernema and Heterorhabditis can be defined as the range of insects which indigenous nematode populations use for propagation. Information on the natural host range is rare. However, based on records of insects found to be naturally infected with nematodes, some conclusions regarding the natural host range of some Steinernema spp. and Heterorhabditis spp. are presented. Reports of indigenous nematode populations impacting on insect populations can be divided between relatively balanced, long-lasting nematode-host associations and unbalanced, short-lasting epizootics. Examples of the augmentation and inoculative introduction of nematodes in agriculture and forestry ecosystems are presented. Based on current knowledge, nematode reproduction strategies are discussed and indications of the risk involved in the release of non-indigenous nematodes are given.     

Concentration of 17 trace elements in serum and whole blood of plains viscachas (Lagostomus maximus) by ICP-MS, their reference ranges, and their relation to cataract

The reference ranges of the trace elements Al, As, Be, B, Cd, Co, Cu, Fe, Mn, Mo, Ni, Pb, Li, Rb, Se, Sr, and Zn were determined by inductively coupled plasma-mass spectrometry (ICP-MS) in sera of a group of free-ranging plains viscachas of the pampa grasslands of Argentina. The values were compared with those of a small group of captive plains viscachas of the Zurich Zoo with diabetes and bilateral cataracts. In addition, a method for digestion of whole-blood samples is described for the trace element determination. Significant differences in the concentration of trace elements in the two groups of animals are discussed. No correlation was found between the levels of selenium and of other trace elements compared to the formation of cataracts.     

A Species-specific Monoclonal Antibody System for Detecting the Remains of Field Slugs, Deroceras reticulatum (Muller) (Mollusca: Pulmonata), in Carabid Beetles (Coleoptera: Carabidae)

The field slug, Deroceras reticulatum (Muller), is probably the most damaging and widespread species of slug, causing severe economic losses in a broad range of crops in temperate zones throughout the world. Investigations into the role of predation in the population dynamics of this species required a biochemical system which was capable of identifying the remains of this slug in the crop contents of predators, and distinguishing them from those of other molluscs. A monoclonal antibody was developed (IgM isotype). This was capable of separating, in an enzyme-linked immunosorbent assay, D. reticulatum from the related D. caruanae (Pollonera) and all molluscs and other invertebrates tested, with the unexpected exceptions of New Zealand flatworms, Artioposthia triangulata (Deny) and the millipede Polymicrodon polydesmoides (Leach). Characterization of the antibody and assay demonstrated that the system could clearly detect as little as 11.6 ng of D. reticulatum protein in 200 mu l of buffer. Slug remains could be identified as such in the crops of the carabid predator Pterostichus melanarius Illiger for 38.1 h, while the antibody-antigen reaction declined to half of that measured immediately following consumption, after 12.9 h. A practical and highly sensitive system was therefore developed, using the first species-specific monoclonal antibody available for the investigation of predation on slugs.     

Freeliving nematodes from the Salton Sea

Thirteen species, or putative species, of freeliving nematodes are recorded from a variety of habitats in the hypersaline Salton Sea, the largest inland lake in California. This doubles the number of species of multicellular invertebrates known to occur in the lake. All species are referable to known marine genera, and are regarded as having a marine coastal origin. The range of taxa present is representative of the full taxonomic spread found in marine coastal habitats, suggesting that a wide range of marine nematode taxa are capable of adapting to the hypersaline conditions. The broad spectrum of feeding types present suggests that nematodes play a variety of ecological roles within the lake.     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

Apostatic selection on prey that match the background

There is good experimental evidence that predators often remove disproportionately more of the common prey types. This 'apostatic selection' could maintain colour polymorphisms within prey species. In nature, morphs of many species appear to match components in the background, but most of the experiments that have tested apostatic selection have used prey that were conspicuous. In work described in this paper, wild birds at one site were presented a random order of 51 experiments. Seventeen frequencies of orange and grey pastry prey were presented on each of three types of background: a hessian sheet scattered with either orange and grey stones (the 'matching' background), or lilac and yellow stones, or green stones (two sorts of 'control' background). Each experiment consisted of four trials in succession and the numbers of the two colours eaten in each trial were recorded when about half the total prey had been eaten. Two methods of graphical analysis revealed that apostatic selection occurred on the prey on all three backgrounds, but was strongest in the grey/orange one. This last result must have been caused by some effect of the match between prey and background colour, and behavioural explanations are suggested. It is unclear whether the prey were exhibiting 'crypsis' or 'masquerade'.     

Pandanus subg. Martellidendron (Pandanaceae) part II: revision of sect. Martellidendron Pic. Serm. in Madagascar

This paper provides a taxonomic revision of Pandanus sect. Martellidendron , which so far comprises six species of which only one is known from both staminate and pistillate plants. Research in herbaria and in the field in Madagascar has provided the data on which a revision of the unclear taxonomy of this section can be based. Based on micromorphology, architecture and phytogeography, the number of these dioecious species is reduced. One new species (P. gallinarum Callmander) from the Biosphere reserve of Mananara-North on the east coast is described, and P. karaka Martelli is transferred to this section 30 years after it was assigned to section Dauphinensia. A key to all species of subg. Martellidendron is provided. Finally, the important role of the section for the understanding of the phylogeny of the Pandanaceae is discussed in the context of Indian Ocean biogeography.     

Iberia: bridge or cul-de-sac? implications of the Iberian record for the debate on the middle to upper palaeolithic transition

Recent discoveries and dating of materials from Spain and Portugal for the period between c. 40–30 kya highlight the fact that the Iberian Peninsula is a microcosm of the complex mosaic of conditions that characterized the middle to upper palaeolithic and Neanderthal to Cro-Magnon transitions. They would tend to suggest that the replacement of one way of life by another was suggest that the replacement of one way of life by another was far from rapid, abrupt or simple, and they call into question the “out of Africa” invasionist scenario. Although Iberia seems to have been a “bridge” between Africa and the rest of Europe during certain times (notably at the time of the first colonization(s) of Europe, perhaps in the late Lower Pleistocene, as suggested by the discoveries at Atapuerca), at other times it seems to have been cut off from Africa. Despite the presence of Aurignacian technology in Cantabria and Catalonia since 40 kya, the continued persistence of Neanderthals and of Mousterian technology for over 10 ky in southern Iberia would seem to belie the superiority and African origin of upper palaeolithic Cro-Magnon. Furthermore, even in northern Spain, where the taxonomic identity of the makers of the early Aurignacian remains unknown, the nature of the technological transition was variable: abrupt in Catalonia and gradual in Cantabria. Added to the rest of the record, which includes Neanderthals apparently making Chatelperronian tools in France, Szeletian tools in Hungary and later Aurignacian tools in Croatia, a complete lack of any fossils in definite association with early Aurignacian anywhere, evidence of subsistence and technological change during the Mousterian in certain regions of Europe, scant evidence for cultural differentiation between Neanderthals and early anatomically modern humans (Skhul & Qafzeh) in Israel, growing (albeit limited) evidence for middle palaeolithic artistic or ornamental activity, and evidence for considerable, on-going change in technology and subsistence during the upper palaeolithic, the Iberian record strongly argues for a long, uneven transition from middle to upper palaeolithic lifeways- not a simple, abrupt invasion of Europe out of Africa.     

Effect of Herbivore Density, Timing of Attack and Plant Community on Performance of Creeping Thistle Cirsium arvense (L.) Scop. (Asteraceae)

Creeping thistle, Cirsium arvense (L.) Scop. (Asteraceae), is one of the most serious weeds in ecological compensation areas (within-field or border refugia) in Europe. Since conventional weed control measures are restricted in compensation areas, augmenting indigenous agents for biological control of the weed may be a feasible alternative. In this paper, we studied the effect of density of the shield beetle, Cassida rubiginosa Muller (Coleoptera, Chrysomelidae), and two vegetation types typical for ecological compensation areas, on the performance of creeping thistle plants in an open field experiment. Early-season larval feeding had no measurable effect on creeping thistle growth, while late-season feeding significantly reduced shoot growth. These findings were attributed to higher feeding rates of the herbivores at higher ambient temperatures late in the season. Defoliation had a strong effect on the above-ground performance of C. arvense plants, but not on the below-ground performance. In contrast, the plant community affected all below-ground performance parameters measured, but only some of the above-ground performance parameters of creeping thistle. A combination of high levels of plant competition and herbivory by C. rubiginosa larvae led to 50% mortality in C. arvense plants during the growing season. We conclude that augmentation of indigenous herbivores of C. arvense in combination with breaking up the root system by tillage and the establishment of a highly competitive plant community of beneficial herbs may be a feasible way to control this problematic weed in ecological compensation areas.     

The sperm, a neuron with a tail: 'neuronal' receptors in mammalian sperm

A number of plasma membrane receptor types originally thought to be specific to neurons have been found in other somatic cells. More surprisingly, the mammalian sperm and neuron appear to share many of these 'neuronal' receptors. The morphology, chromosome number, genomic activity, and functions of those two cell types are as unlike as any two cells in the body, but they both achieve their highly disparate goals with the aid of a number of the same receptors. Exocytosis in neurons and sperm is essential to the functions of these cells and is strongly influenced by similar receptors. 'Neuronal' receptor types in sperm may also play a role in the control of sperm motility (a function of course not shared by neurons). This review will consider the evidence for the presence of sperm plasma membrane 'neuronal' receptors and for their significance to mammalian sperm function. The persuasiveness of the evidence varies depending on the receptor being considered, but there is strong experimental support for the presence and importance of a number of 'neuronal' receptors in sperm.     

Synthesis and anticancer activity of novel bisindolylhydroxymaleimide derivatives with potent GSK-3 kinase inhibition

Synthesis and biological evaluation of a series of novel indole derivatives as anticancer agents is described. A bisindolylmaleimide template has been derived as a versatile pharmacophore with which to pursue chemical diversification. Starting from maleimide, the introduction of an oxygen to the headgroup (hydroxymaleimide) was initially investigated and the bioactivity assessed by screening of kinase inhibitory activity, identifying substituent derived selectivity. Extension of the hydroxymaleimide template to incorporate substitution of the indole nitrogens was next completed and assessed again by kinase inhibition identifying unique selectivity patterns with respect to GSK-3 and CDK kinases. Subsequently, the anticancer activity of bisindolylmaleimides were assessed using the NCI-60 cell screen, disclosing the discovery of growth inhibitory profiles towards a number of cell lines, such as SNB-75 CNS cancer, A498 and UO-31 renal, MDA MB435 melanoma and a panel of leukemia cell lines. The potential for selective kinase inhibition by modulation of this template is evident and will inform future selective clinical candidates.