[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.

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.

Molecular phylogeny.

The avalanche of molecular sequence data from a wide variety of organisms and genes makes the construction and testing of evolutionary trees a widespread and demanding activity. We present the most recent advances in the interpretation of molecular data, as well as recent phylogenetic results affecting both molecular evolutionary biology and other areas of biological research.

Early evolution and the origin of eukaryotes.

Our understanding of evolutionary relationships in the eukaryotic world has been revolutionized by molecular systematics. Phylogenies based upon comparisons of rRNAs define five major eukaryotic assemblages plus a series of paraphyletic protist lineages. Comparison of conserved genes that were duplicated prior to the divergence of eubacteria, archaebacteria, and eukaryotes, positions the root of the universal tree within the eubacterial line of descent. In this review a novel model is presented which uses the rRNA and protein based phylogenies to describe the evolutionary origins of eukaryotes.

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.

Animal phylogeny: root and branch surgery.

Our view of how-many phyla relate to each other is being radically revised by molecular phylogenetics. For example, arthropods and annelids are no longer placed together, but are now considered to be in separate clades. The new tree has important ramifications for developmental biology and genomics.

Animal evolution. The end of the intermediate taxa?

Contrary to general belief, there has not been a reliable, global phylogeny of animals at hand within the past few decades. Recent progress in molecular phylogeny is rapidly changing the situation and has provided trees that constitute a reference frame for discussing the still controversial evolution of body plans. These trees, once purged of their possible artefacts, have already yielded confirmation of traditional, anatomically based, phylogenies as well as several new and quite significant results. Of these, one of the most striking is the disappearance of two superphyla (acoelomates such as flatworms, pseudocoelomates such as nematodes) previously thought to represent grades of intermediate complexity between diploblasts (organisms with two germ layers) and triploblasts (organisms with three germ layers). The overall image now emerging is of a fairly simple global tree of metazoans, comprising only a small number of major branches. The topology nicely accounts for the striking conservation of developmental genes in all bilaterians and suggests a new interpretation of the 'Cambrian explosion' of animal diversity.

[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.

[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.

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.

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.

Comments on the taxonomic status of Ikeda taenioides (Ikeda, 1904) with some amendments in the classification of the phylum Echiura.

Examination of thin sections of trunk wall in an old specimen of Ikeda taneioides from Misaki, Sagami Bay revised previous false information about the wall musculature, actually consisting of outer circular, middle longitudinal, and inner-most oblique layers, like all other echiurans. This finding, together with the reexamination of relevant museum specimens, led to some taxonomic changes. These include that the definition of the genus Ikeda was amended to be a senior synonym of Prashadus; the family Ikedidae was regarded as a junior synonym of the family Echiuridae; and the order Heteromyota, erected virtually for I. taenioides, was abolished. Non-discovery of males and some other features in the amended genus Ikeda were noted with reference to its possible relationship with the family Bonelliidae.

Classification of organisms: living and fossil.

The classification advanced herein provides a framework to which any organism can be readily placed and offers comprehensive coverage of the entire biological spectrum. The viruses are incorporated as a kingdom of organisms and a rationale advanced for a 6-kingdom system. Many seldom-classified fossil organisms are included, with a significant number of them classified at an advanced level. Individual phyla are recognized for the fossil genera Tribrachidium, Amiskwia, Dinomischus, Anomalocaris, Tullimonstrum, Hallucigenia, Opabinia and Pikaia. Other seldom-recognized phyla include viruses, conularids, loriciferans, tentaculites, hyoliths, scleritophores, myzostomans, acorn worms, conodonts, monoblastozoans and volborthellids. The notion that failures (geologically) cannot be phyla is rejected. A system of kingdom-related and rank-related suffixes is incorporated with the flexible opportunity, if deemed necessary, to advance or reduce taxa by re-suffixing. Other features of the complete classification of Anderson (Classification of Organisms: Living and Fossil, Golden Crowns Press, Lancaster, OH, 1992) include the elimination of duplicate taxa, incorporation of geologic ranges and number of species for many groups, and extensive usage of common names, which are completely indexed.

Biodiversity: molecular biological domains, symbiosis and kingdom origins.

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and 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.

[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.

[The problem of archetype and current biology]. / Problema arkhetipa i sovremennaia biologia.

Two ideas of homology--transformational and taxic--are used in biology. The first one deals with homology of different structures from morphological point of view, the second one--with the homology of characters. The main question of taxic homology is: in what cases the same character is not identical in two different species? Transformational homologies are determined according the archaetype, taxic ones--according inheritance from the common ancestor of comparing taxa. Archaetype is an idea of an organism from the position of its components. Archaetype should be distinguished from the type character, i.e. the description of an organism combining general and special features. The main idea of archaetype is an idea of coherence of characters describing morphological organization. Archaetype was considered by Owen as mechanical construction. As a matter of fact, the organism is a dynamic system Its dynamic nature can be demonstrated by the conception of module organization of living systems. In the framework of this conception archaetype is a description of an organism from constructive position, focused on the characters of the parts reflecting ontogenetic and evolutionary autonomy. The progress in developmental genetics in understanding of genetic mechanisms of spatial structure formation during the last years opens the wide perspectives in interpretation of archaetype idea. Homeobox family of genes of Hox complex is especially interesting from this point of view. They are characterized by colinearity: spatial and temporal sequence of their expression is corresponding to their order in chromosome. As it was shown by several experiments, changes in the level and sequence of expression of Hox genes result in the changes of archaetype. The discovery of homological genes determining non homological morphological structures in non related groups is a new challenge to morphologists studying the problem of homologies. The disagreements on this subject are connected with non critical use of transformational (archaetypical) and taxic approximations. From transformational positions, eyes of vertebrates and invertebrates are homological, although they have different structure. At the same time, if we specify what type of eyes we are considered, the results will change. Thus, compound eyes of insects and bivalve mollusk Arca are not homological because they originated independently from forms without compound eyes.

[Distribution of the species-specific lifespan in various taxonomic animal groups]. / Raspredelenie vidovoi prodolzhitel'nosti zhizni v razlichnykh taksonomicheskikh gruppakh zhivotnykh.

A distribution of specific lifespan has been studied in different taxonomic groups of animals. A positive skewness has been observed in animal kingdom as well as in smaller taxonomic groups. The skewness is higher in groups with relatively short lifespan (Insecta, Rotatoria, Mollusca). A coefficient of variation and excess is also higher in the above groups. A comparison of these coefficients with paleontological age of the group allows to conclude that evolutionary progress of animals was accompanied by the increase in skewness, variation and excess of specific lifespan distribution.