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N B Petrov

Publications and source records attributed to N B Petrov.

At least 19 recordsLinked to original sources
PubMed2002

[Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules].

The current phase of molecular phylogenetics can be named the 18S rRNA gene era, which is now approaching the end. To date, almost all phyla of metazoans and many taxa of protists are represented in databases of 18S rRNA gene sequences. The elements of the phylogenetic tree of Metazoa inferred from 18S rRNA genes are characterized by unequal validity: some of them seem to be well grounded; others are not adequately supported, and probably will be revised later. The validity of phylogenetic reconstruction is influenced by two main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate; (2) deficit of phylogenetically informative characters. A method for overcoming these difficulties is suggested in addition to known tools: using phylogenetic markers that are stable within individual taxa and evolve by punctuated equilibrium. These markers are least influenced by the convergence caused by a high evolution rate of the entire gene. The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evolution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates (Bilateria + Rhombozoa + Orthonectida + Myxozoa + Cnidaria + Placozoa and Echinodermata + Hemichordata) and some major taxa of Nematoda.

Animals↗
PubMed2001

The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication.

In order to ascertain a phylogenetic position of the freshwater amitochondriate amoeboflagellate Pelomyxa palustris its small subunit (SSU) rRNA gene was amplified and sequenced. It was shown to be 3502 bp long. The predicted secondary structure of its rRNA includes at least 16 separate expansion zones located in all the variable regions (V1-V9), as well as in some conservative gene regions. Most insertions are represented by sequences of low complexity that have presumably arisen by a slippage mechanism. Relatively conservative, uniformly positioned motifs contained in regions V4 and V7, as well as in some others, made it possible to perform folding. In maximum likelihood, maximum parsimony, and neighbor-joining trees, P. palustris tends to cluster with amitochondriate and secondary lost mitochondria amoebae and amoeboflagellates Entamoeba, Endolimax nana, and Phreatamoeba balamuthi, comprising together with them and aerobic lobose amoebae Vannella, Acanthamoeba, Balamuthia, and Hartmannella a monophyletic cluster. Another pelobiont, Mastigamoeba invertens, does not belong to this cluster. No specific similarity was discovered between the SSU rRNA of P. palustris and amitochondriate taxa of 'Archezoa': Diplomonada, Parabasalia, Microsporidia. Pelomyxa palustris SSU rRNA does not occupy a basal position in the phylogenetic trees and could be ascribed to the so-called eukaryotic 'crown' group if the composition of the latter were not so sensitive to the methods of tree building. Thus, molecular and morphological data suggest that P. palustris represents a secondarily modified eukaryotic lineage.

Amoeba↗
PubMed2001

The "Linh Duong" Pseudonovibos spiralis (Mammalia, Artiodactyla) is a new buffalo.

The controversial phylogenetic position of the recently described South-East Asian endemic bovid, Pseudonovibos spiralis, was evaluated on the basis of phylogenetic analyses of originally obtained nearly complete 12S mitochondrial rDNA sequences for this species and Bubalus bubalis and 26 sequences of Bovidae from the Genbank using Cervus elaphus (Cervidae) as outgroup. In most of the phylogenetic analyses performed using PAUP 4.0 (maximum parsimony, maximum likelihood and neighbour-joining), Bovidae consisted of two major clades: Bovinae including the tribes Bovini, Tragelaphini and Boselaphini, and Antilopinae + Caprinae, incorporating all other bovids. In most trees P. spiralis fell within the buffalos (subtribe Bovina) between Bubalus and Syncerus. Therefore, our phylogenetic analyses of bovid mitochondrial 12S rRNA gene sequences suggest the close relationship of this enigmatic species with the buffalos and its placement within the subtribe Bovina.

Animals↗
PubMed1998

Secondary structure of some elements of 18S rRNA suggests that strongylid and a part of rhabditid nematodes are monophyletic.

Analysis of the secondary structure of 18S rRNA molecules in nematodes revealed some new traits in the secondary structure peculiar to their hairpin 17. Some of them are characteristic of all the nematodes, whereas others are characteristic exclusively of the order Rhabditida. The loss of a nucleotide pair in the highly conservative region of hairpin 17 distinguishes 18S rRNA of the Strongylida and some species of the Rhabditida from other nematodes and, moreover, from all other organisms. Hence, it is possible to regard the Strongylida and a part of the Rhabditida including Caenorhabditis elegans as a new monophyletic taxon.

Animals↗
PubMed1998

Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA.

Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa.

Animals↗
PubMed1988

[Processing of the results of experiments on molecular DNA-DNA hybridization by using the Elektronika BZ-34 programmable microcomputer].

The programs for microcomputer "Electronika" BZ-34 permitting to compute the molecular DNA-DNA hybridization data with thermal stability duplex analysis have been developed. The proper different programs are offered for analysis of results obtained in different conditions of DNA hybridization. These programs are especially useful for accelerated calculation of large series of experimental data.

DNA↗
PubMed1985

[Comparison of different methods of introducing a label into the DNA of microorganisms].

Different methods of isotope introduction into plasmid and chromosomal DNA have been compared. The efficiency of label introduction into DNA was estimated by the results of DNA--DNA hybridisation and by the thermostability of hybrid duplexes. Using the enzymatic methods of label introduction levels of DNA specific radioactivity and label binding in homologous and heterologous reactions were close. DNA labeled by the method of enzymatic methylation forms more thermostable hybrid duplexes than "nick-translation" DNA. The advantages of enzymatic methods of label introduction for creating a microorganism reference DNA bank are discussed.

Bacillus subtilis↗
PubMed1980

[Determination of the degree of ribosomal genes conservativity in some invertebrate species].

DNA-RNA hybridization was used to determine the degree of similarity of ribosomal genes in some invertebrate species. The degree of similarity of the nucleotide sequences of the ribosomal genes in various classes of Echinodermata appeared to be the same as in different invertebrate types. The base sequence mismatch in hybrid rRNA-DNA molecules did not exceed 10%, even when species from different invertebrate types were compared. The results obtained suggest that the changes in common rRNA structures occurred at a very low rate in the course of a long time period (more than 600 million years).

Animals↗
PubMed1977

[Mutagenic process in bacteriophage T4B after long-term exposure to a mutagen].

Bacteriophage T4B was continuously passed on solid media in the presence of 5-bromodeoxyuridine in two simultaneous experiments. The subsitutions of amino acids were registered, and in one of the experiments biological changes were revealed in non-optimal conditions. Calculations has shown that the number of amino acid substitutions observed corresponds to at least 140--200 fixed mutations. The possibility of the mutation fixation via selection is discussed and their relative neutrality is suggested.

Amino Acids↗
PubMedDate not supplied

[Primary structure of hairpin 35 and 48 small rRNA is proof that Trefusiidae is a subtaxon of marine Enoplida (Nemotoda)].

A rare nucleotide substitution was found in the evolutionarily conserved loop of hairpin 35 of the 18S rRNA gene of marine free-living nematode, Trefusia zostericola (Nematoda: Enoplida). The same substitution was found in all the marine Enoplida studied but not in other nematodes. Such a molecular synapomorphy indicates that marine enoplids are more closely related to T. zostericola than to freshwater Triplonchida. Maximum parsimony, neighbor-joining, and maximum likelihood analyses of complete nucleotide sequences of the gene, with the heterogeneity of nucleotide sites in evolution rates taken into account, support this conclusion. Hence, the hypothesis of particular primitiveness of Trefusiidae among nematodes should be rejected. Phylogenies based on molecular data support the morphological reduction of metanemes in Trefusiidae. Alongside with the unique change in hairpin 35 loop among marine Enoplida (including T. zostericola), hairpin 48 is also modified by a rare transversion which could be found among Mesorhabditoidea nematodes, in related genera Pelodera, Mesorhabditis, Teratorhabditis, Parasitorhabditis, Crustorhabditis, and Distolabrellus, and in 11 orders of Rhodophyta. Rare mutations in hairpins 35 and 48 tend to be fixed correlatively in evolution and could be found in all the Acanthocephala species. X-Ray data show that these regions (H31 and H43, in alternative nomenclature) are spatially brought together in native ribosomes. The nature and distribution of molecular autoapomorphies in phylogenetic trees of high-rank taxa are discussed.

Animals↗
PubMedDate not supplied

[Molecular evidence of regression in evolution of metazoa].

Molecular data permit to construct phylogenetic trees independently of morphological characters. It allows to consider their evolution without the frames of a priori hypothesis of regularities of morphological evolution and independently of palaeontological data. Cladistic analysis of elements of secondary structure of varible areas V7 and V2 in 18S rRNA with different Protozoa as "external" groups shows that Bilateria + Cnidaria are monophyletic, Ctenophora and Porifera are early derivatives of Metazoa, Trichoplax (Placozoa) is a form related to Cnidaria, while Rhombozoa, Orthonectida and Myxozoa were branched within Bilateria. Morphological reduction with losses of any organs and tissues took place many times in early evolution of Metazoa and Bilateria not only in parasitic species. It occurred both at early and late stages of embryonic development and differentiation. Two alternative scenario of morphological degeneration in Trichoplax and the way of their testing are suggested. The similarity of Ctenophora and Calcarea is discussed. Meridional or oblique position of the third cleavage furrow of ovule can be considered as an evidence of their origin from common ancestor.

Animals↗
PubMedDate not supplied

[Phylogeny of protostome moulting animals (Ecdysozoa) inferred from 18 and 28S rRNA gene sequences].

Reliability of reconstruction of phylogenetic relationships within a group of protostome moulting animals was evaluated by means of comparison of 18 and 28S rRNA gene sequences sets both taken separately and combined. Reliability of reconstructions was evaluated by values of the bootstrap support of major phylogenetic tree nodes and by degree of congruence of phylogenetic trees inferred by various methods. By both criteria, phylogenetic trees reconstructed from the combined 18 and 28S rRNA gene sequences were better than those inferred from 18 and 28S sequences taken separately. Results obtained are consistent with phylogenetic hypothesis separating protostome animals into two major clades, moulting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, Crustacea + Hexapoda) and unmoulting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, Sipuncula). Clade Cephalorhyncha does not include nematomorphs (Nematomorpha). Conclusion was taken that it is necessary to use combined 18 and 28S data in phylogenetic studies.

Animals↗