Integrative systematics and ecology of a new deep-sea family of tanaidacean crustaceans.

A new family of paratanaoidean Tanaidacea - Paranarthrurellidae fam. nov. - is erected to accommodate two genera without family classification (Paratanaoidea incertae sedis), namely Armatognathia Kudinova-Pasternak, 1987 and Paranarthrurella Lang, 1971. Seven new species of Paranarthrurella and two of Armatognathia are described from material taken in different deep-sea areas of the Atlantic and Pacific oceans. The type species of Paranarthrurella - P. caudata (Kudinova-Pasternak, 1965) - is redescribed based on the paratype. The genus Cheliasetosatanais Larsen and Araújo-Silva, 2014 originally classified within Colletteidae is synonymised with Paranarthrurella, and Arthrura shiinoi Kudinova-Pasternak, 1973 is transferred to Armatognathia. Amended diagnoses of Armatognathia and Paranarthrurella genera are given. Choosing characters for distinguishing and defining both genera was supported by Principal Component Analysis. Designation of the new family is supported by molecular phylogenetic analysis of COI and 18S datasets. The distribution of all species currently included in the new family was visualised and their bathymetric distribution analysed.

Dictamen de Mariano de la Paz Graells sobre la obra herpetológica de Eduardo Boscá: análisis de una evaluación científica del siglo XIX / Mariano de la Paz Graells pronouncement on the herpetological works of Eduardo Boscá: analysis of a XIX century scientific evaluation

Se analiza y da a conocer una evaluación científica solicitada por el naturalista Eduardo Boscá a la Dirección General de Instrucción Pública en 1891 en la que pide le sean valoradas sus publicaciones sobre zoología de anfibios y reptiles, aparecidas entre 1877 y 1883. La evaluación la realiza Mariano de la Paz Graells en 1893 por encargo de la Real Academia de Ciencias mediante un extenso y crítico Dictamen inédito. A través de las críticas del informe podemos conocer los estándares reales de calidad entonces exigibles en taxonomía y faunística, no fácilmente deducibles de publicaciones ni de correspondencia epistolar. El Dictamen se encuadra en la historia biográfica de los científicos implicados, y en el desarrollo de la herpetología y la biodiversidad ibero-balear (AU)

A scientific evaluation, requested by the naturalist Eduardo Boscá to the Spanish Dirección General de Instrucción Pública in 1891, is made known and analyzed. In this request, Boscá asks for an evaluation of his zoological publications dealing with amphibians and reptiles, completed between 1877 and 1883. The evaluation is made by the Spanish Real Academia de Ciencias through an unpublished comprehensive and critical Dictum written by Mariano de la Paz Graells in 1893. Through this Dictum we can perceive the real quality standards then required for taxonomy and faunistics, information not easily inferable from publications or mail correspondence. The analysis of this Dictum is here framed in the biographical history of the scientists involved, and also in the development of herpetology and Ibero-Balearic biodiversity (AU)

Development and characterization of microsatellite loci of Microglanis cottoides (siluriformes: pseudopimelodidae) and cross-species amplification

Thirteen microsatellite loci were isolated and characterized in Microglanis cottoides. Of these, two were monomorphic and 11 were polymorphic. These polymorphic loci tested on 24 individuals from a wild population produced a total of 108 different alleles, with levels of variability high, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. A high combined probability of paternity exclusion value and a low probability combined genetic identity value obtained show that the set of loci described herein displays good suitability for paternity studies and differentiation of M. cottoides. Additionally, all thirteen microsatellite primers developed for M. cottoides were tested in four other Pseudopimelodidae species and successful cross-species amplification was achieved for the majority of loci.

Treze loci microssatélites foram isolados e caracterizados em Microglanis cottoides. Destes, dois foram monomórficos e 11 foram polimórficos. Estes loci polimórficos foram testados em 24 indivíduos de uma população selvagem e produziram um total de 108 alelos diferentes, com níveis de variabilidade alta, variando de 2 a 20, com uma média de 8,3 alelos por locus. A heterozigosidade observada e esperada variou de 0,125 a 0,958 e 0,119 a 0,931, respectivamente. Um elevado valor de exclusão de paternidade e um baixo valor de identidade genética foram obtidos, demostrando que o conjunto de loci descritos no presente trabalho exibe boa aplicabilidade no estudo de parentesco e diferenciação populacional em M. cottoides. Adicionalmente, os treze primers de microssatélites desenvolvidos para M. cottoides foram testados em outras quatro espécies de Pseudopimelodidae e a transferabilidade foi obtida para a maioria dos loci.

[Karyofunds of Chironomus plumosus (L.) (Diptera, Chironomidae). V. terminal and interstitial populations].

The study of polytene chromosomes of Chironomus plumosus from Rybinsk reservoir, its inflows and surrounding water bodies allow to mark out two type's of population. Terminal populations--presented by karyoforms with concrete limited composition of genotype combinations and zygotic arm combinations, which adapted to specific complex of the habitat factors. The immediate exchange of genes between different terminal populations is absent (even they placed in nearness) from allochronie of life cycles and impossibility of larvae-immigrants to finish ontogenesis in unfit for they habitat conditions. Interstitial populations inhabit the biotopes, where the karyoforms of two or more terminal populations can to finish ontogenesis and to reproduce. The genetic exchange between terminal population implement through interstitial populations.

Understanding of evolution may be improved by thinking about people.

The theory of evolution is poorly understood in the population at large, even by those with some science education. The recurrent misunderstandings can be partly attributed to failure to distinguish between processes which individual organisms undergo and those which populations undergo. They may be so pervasive because we usually explain evolutionary ideas with examples from non-human animals, and our everyday cognition about animals does not track individuals as distinct from the species to which they belong. By contrast, everyday cognition about other people tracks unique individuals as well as general properties of humans. In Study 1, I present experimental evidence that categorization by species occurs more strongly for non-human animals than for other people in 50 British university students. In Study 2, I show, in the same population, that framing evolutionary scenarios in terms of people produces fewer conceptual errors than when logically identical scenarios are framed terms of non-human animals. I conclude that public understanding of evolution might be improved if we began instruction by considering the organisms which are most familiar to us.

The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla.

BACKGROUND: Molecular clock dates, which place the origin of animal phyla deep in the Precambrian, have been used to reject the hypothesis of a rapid evolutionary radiation of animal phyla supported by the fossil record. One possible explanation of the discrepancy is the potential for fast substitution rates early in the metazoan radiation. However, concerted rate variation, occurring simultaneously in multiple lineages, cannot be detected by "clock tests", and so another way to explore such variation is to look for correlated changes between rates and other biological factors. Here we investigate two possible causes of fast early rates: change in average body size or diversification rate of deep metazoan lineages. RESULTS: For nine genes for phylogenetically independent comparisons between 50 metazoan phyla, orders, and classes, we find a significant correlation between average body size and rate of molecular evolution of mitochondrial genes. The data also indicate that diversification rate may have a positive effect on rates of mitochondrial molecular evolution. CONCLUSION: If average body sizes were significantly smaller in the early history of the Metazoa, and if rates of diversification were much higher, then it is possible that mitochondrial genes have undergone a slow-down in evolutionary rate, which could affect date estimates made from these genes.

[Animals (Animalia) in system of organisms. 2. Phylogenetic understanding of animals].

The development of systematics in last decade has shown that typological classifications of five-six Kingdoms is not adequate for describing the diversity of organisms. Information from the sequences of small subunit rRNA is not sufficient to reconstruct the position of eukaryotes on the phylogenetic tree due to the effect of long branches. Totally new reconstruction of eukaryotic phylogeny was built upon the analysis of many new molecular markers. Evolution of eukaryotes had two mainstreams. One has been connected with diversification of ancestral biciliate forms (Bikonta). Sister-group of Bikonta (Unikonta) includes some originally uniciliate amoebae and moulds (Amoebozoa), and uniciliate eukaryotes with posterior cilium (Opisthokonta). The taxon Opisthokonta unites Fungi, Nuclearimorpha, Mesomycetozoa, Choanozoa and Metazoa. The latter three groups or only Metazoa are attributes to animals. The following differentiation of the groups used in systematic for the description of diversity of organisms is proposed. (1) Taxon is a group which is defined on the basis of ancestry: taxon includes all species descended from one ancestor. Taxon differs from logic classes of typology at an ontologic level. Taxon arises and exists, and its composition and occupied niches can constantly change; taxon can flourish or, on the contrary, fade up to full disappearance. Thus, the predicative characteristic of taxon, including characters which are considered significant, are not absolute. It is significant only at the moment of consideration. But characters (synapomorphies) are important as the practical tool for discerning taxa at given time period. Taxa unite species into unique classification. This understanding of taxon corresponds to monophyletic group sensu Willi Hennig. (2) Class of organisms is a group which is defined on the basis of characters: class includes all species having the given character. The class is only a logic object. Unlike taxa grouping species into classes may be through different and crossed classifications. Inside the given category of groups it is possible to distinguish: (2.1) Level of the organization (grade) described by the differences on the levels of organization: for example prokaryotic and eukaryotic levels of the organization. Eukaryotes can be divided into unicellular (Protoctista, Protista) and multicelluar (tissue-specific-Histonia) forms. (2.2) Types of the organization distinguishing groups of one level: for example, amoedoid type (Sarcodina), naked (Gymnamoebia), and testate (Testacea) amoebas. (2.3) Taxonomic groups as set-theoretical approximations of taxa. (2.4) Groups of the mixed nature. For example, Haeckel has recognized Protophyta and Protozoa describing the unicellular level of the organization inside plants and animals accordingly. Protozoa in Cavalier-Smith's system (2002, 2004) is also an example of groups of the mixed nature.

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

[Animals (Animalia) in the system of organisms. 1. Typological systems].

Since times of Aristotle animals were considered as a group, opposing to plants. The last were distinguished by two characters. Plants as distinct from animals live the attached way of a life and all nutrients receive from a substratum on which live and from the surrounding air. Animals live an active way of life and exist due to digestion. Fungi at such definition belong to plants. Only in second half of XX centuries due to works of Whittaker and of Tachtadjan fungi have received the separate status equally with plants and animals. In this new system of a plant embraced either oxygenic phototrophs, or photosynthetic eukaryotes. The traditional characters distinguishing animals from plants and fungi are in detail analysed. Many of them appeared formal, not reflecting the structure of relationship. Comparing heterotrophs some authors saw in absorptive nutrition the main difference of fungi from animals. However on mechanisms of receipt of substances in a cell fungi, animals and plants do not differ. Phagocytosis and pinocytosis (clathrin-mediated endocytosis), considered as the most characteristic feature of animals, are revealed both in fungi, and in plants. On photosynthetic activity plants form heterogeneous group, differing on primary and secondary plastids. The last besides have the various origin connected to symbiogenesis of the host cell with red or green algae. Heterotrophy cannot be considered as a uniting attribute of fungi and animals. It is essentially different and focused on diverse food sources. Evolution of animals is connected to perfection of structure of a plasmatic membrane and saturation by its molecules allowing a cell, and through it all organism to be guided in an environment and adequally to be up to external irritants. At a cellular level animals use the various mechanisms of cellular activity connected to moving of cells, their combination in aggregates and complexes or, on the contrary, separation in new cellular configurations. The complex of cellular adaptations connected to the analysis of external signals and adequate response to them of cells, underlies the phenomenon of irritability. At a cellular level irritability is mediated through work of the actin apparatus. Lamarck in "Philosophie zoologique" considered irritability as the main distinctive feature of animals. Evolution of plants and fungi went in a direction of development of a secondary metabolism. The secondary metabolism, concerning synthesis of protective substances, is peculiar to all sedentary organisms, including the animals.

[Towards a simple logic in the determination of biological groups: the species and supraspecific groups]. / Hacia una lógica simple en la determinación de grupos biológicos: la especie y los grupos supraespecíficos.

In this paper we discuss about the utility of the species concept as real definition, particularly the Mayr concept. We propose a method for the logical separation of taxa based in the statements of the logical mathematics and the application of the sets theory to the concepts in systematic. We attempt to provide an objective methodology for the interpretation of natural groups in biology including the species as a basic group in evolution. We introduce the concept of the hypothetical ancestor as a mathematical possibility derived from the use of matrix calculations for non square matrix.

Information extraction from full text scientific articles: where are the keywords?

BACKGROUND: To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant. RESULTS: In this work we addressed those questions showing that the keyword content of the different sections of a standard scientific article (abstract, introduction, methods, results, and discussion) is very heterogeneous. CONCLUSIONS: Although the abstract contains the best ratio of keywords per total of words, other sections of the article may be a better source of biologically relevant data.

Developmental constraints in a comparative framework: a test case using variations in phalanx number during amniote evolution.

Constraints are factors that limit evolutionary change. A subset of constraints is developmental, and acts during embryonic development. There is some uncertainty about how to define developmental constraints, and how to formulate them as testable hypotheses. Furthermore, concepts such as constraint-breaking, universal constraints, and forbidden morphologies present some conceptual difficulties. One of our aims is to clarify these issues. After briefly reviewing current classifications of constraint, we define developmental constraints as those affecting morphogenetic processes in ontogeny. They may be generative or selective, although a clear distinction cannot always be drawn. We support the idea that statements about constraints are in fact statements about the relative frequency of particular transformations (where 'transformation' indicates a change from the ancestral condition). An important consequence of this is that the same transformation may be constrained in one developmental or phylogenetic context, but evolutionarily plastic in another. In this paper, we analyse developmental constraints within a phylogenetic framework, building on similar work by previous authors. Our approach is based on the following assumptions from the literature: (1) constraints are identified when there is a discrepancy between the observed frequency of a transformation, and its expected frequency; (2) the 'expected' distribution is derived by examining the phylogenetic distribution of the transformation and its associated selection pressures. Thus, by looking for congruence between these various phylogenetic distribution patterns, we can test hypotheses about constraint. We critically examine this approach using a test case: variation in phalanx-number in the amniote limb.

[The problem of individuality in taxonomy]. / Problema individnosti v taksonomii.

The ideas of wholeness of superorganism units consist of three constituents: 1) emergeness of properties of the whole; 2) structureness; 3) separability of the whole. Emergeness is a character of both integrated and complex units. Integrated units in strict sense are those that consist of functionally different parts. Species but not super-specific taxa are integrated units. The ideas of unity are based on formula "unity is an aggregation of shape and matter". In taxonomy the idea of archaetype can be used as a shape. Superspecific taxa but not species are recognized as unitary units in taxonomy. Unitary but not integrated units can be considered as individuals.

Ribbon worm relationships: a phylogeny of the phylum Nemertea.

We present the most extensive phylogenetic analysis to date, to our knowledge, of higher-level nemertean relationships, based on sequence data from four different genes (the nuclear genes for nuclear large subunit rRNA (28S rRNA) and histone H3 (H3), and the mitochondrial genes for mitochondrial large subunit rRNA (16S rRNA) and cytochrome c oxidase subunit I (COI)). Well-supported clades are, in general, compatible with earlier, more limited, analyses, and current classification is largely in agreement with our results, although there are some notable exceptions. Bdellonemertea (represented by Malacobdella) is found to be a part of Monostilifera, and Polystilifera is the monophyletic sister group to Monostilifera. Cratenemertidae is the sister group to the remaining monostiliferans (including Malacobdella), a group to which we apply the new name Distromatonemertea. Heteronemertea is monophyletic and forms a clade with Hubrechtella; for this clade we introduce the name Pilidiophora. Finally, Pilidiophora and Hoplonemertea (with Malacobdella) form a monophyletic group, and we introduce the name Neonemertea to refer to this group. Palaeonemertea is found to be non-monophyletic and basal among nemerteans.