Irina A. Milyutina

PHYLOGENY OF NEMATODA AND CEPHALORHYNCHA DERIVED FROM 18S RDNA

Abstract. 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.

Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes

This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome.

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

Abstract The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5·8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fast-evolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5·8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.

Support from DNA data for a narrow species concept in Schistidium (Grimmiaceae, Musci)

Abstract A study of ITS1 of 28 specimens of eight species of Schistidium from well-separated populations in Russia and northwest Europe revealed that there are very big differences between species (up to 16 substitutions and 256 indels), whereas within the species differences in DNA there are very few (none to four substitutions and none to six indels). These results strongly support the narrow species concept in Schistidium. Schistidium papillosum is represented by two quite distinct genotypes and probably needs further splitting.

Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis

TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in Arabidopsis thaliana is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5′-terminal miR390 target site.

Analysis of 18S rRNA gene sequences suggests significant molecular differences between Macrodasyida and Chaetonotida (Gastrotricha).

Partial 18S rRNA gene sequences of four macrodasyid and one chaetonotid gastrotrichs were obtained and compared with the available sequences of other gastrotrich species and representatives of various metazoan phyla. Contrary to the earlier molecular data, the gastrotrich sequences did not comprise a monophyletic group but formed two distinct clades, corresponding to the Macrodasyida and Chaetonotida, with the basal position occupied by the sequences of Tetranchyroderma sp. and Xenotrichula sp., respectively. Depending on the taxon sampling and methods of analysis, the two clades were separated by various combinations of clades Rotifera, Gnathostomulida, and Platyhelminthes, and never formed a clade with Nematoda. Thus, monophyly of the Gastrotricha is not confirmed by analysis of the presently available molecular data.

ITS and morphology tell different histories about the species of the Sciuro-hypnum reflexum complex (Brachytheciaceae, Bryophyta)

Abstract Morphology and ITS relationships are compared for 111 Sciuro-hypnum specimens, 95 of which belong to S. curtum, S. hylotapetum, or the S. reflexum complex. In the latter, S. reflexum is probably ancestral. Within the S. reflexum complex ITS haplotype relationships are congruent with morphology for S. brotheri, S. dovrense, S. glaciale, and S. ornellanum, and support the recognition of the two new species S. sinolatifolium and S. sichuanicum, whereas incongruence occurs for several species. In an ITS haplotype context, S. tromsoeense and S. latifolium are resolved as polyphyletic, and S. altaicum, some specimens of S. oedipodium, and S. curtum–S. starkei intermediates cannot be distinguished from S. reflexum. Sciuro-hypnum fuegianum is molecularly identical and morphologically similar to S. glaciale, and is considered conspecific with the latter. There is no evidence to suggest that ITS a priori is more reliable than morphology, and we therefore suggest that the abundant incongruent patterns reflect either 1) a young age in terms of number of generations in relation to the rate of ITS differentiation and associated incomplete lineage sorting and occasional hybridization events, 2) a faster rate of morphological than ITS evolution, 3) the existence of many lineages that are propagated by selfing, or 4) regional differences in extinction rates during the Pleistocene glaciations. However, additional information is required to decide which of these is/are most important. Finally, S. squarrosum, a morphologically distinct species that molecularly belongs outside the S. reflexum complex, is described as new.

[Phylogeny of the genus Lophozia (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F].

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongata, and Obtusifolium obtusum based on combined nuclear ITS1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. A low level of genetic divergence of geographically distant forms was demonstrated.

The phylogeny of Schistidium (Bryophyta, Grimmiaceae) based on the primary and secondary structure of nuclear rDNA internal transcribed spacers

Phylogeny of Schistidium (Bryophyta, Grimmiaceae) was studied by comparing the nucleotide sequences of internal transcribed spacers ITS1-2 of nuclear rDNA and the trnT-trnD region of chloroplast DNA. Phylogenetic trees constructed based on nuclear and chloroplast sequences were consistent, comprising a basal grade and two large clades. Morphological characteristics specific for these clades were described. Secondary structures of ITS1 and ITS2 Schistidium species were modeled using thermodynamic criteria. Four different structures of the longest ITS1 hairpin were identified. These results were used to analyze possible paths of Schistidium evolution. Characteristics of the ITS2 secondary structure support the two major clades recognized in the phylogenetic trees.

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.