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Molecular insight on phylogeny and systematics of the Lophoziaceae, Scapaniaceae, Gymnomitriaceae and Jungermanniaceae
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... This variety is distinct from var. turgida in often acuminate and occasionally dentate leaf lobes vs. often blunt to rounded lobes. Published molecular data have suggested diversity within T. quinquedentata-complex, thus careful study should be implemented in course of infraspecific diversity and reliability of previously described infraspecific taxa (Vilnet et al., 2010). The similarity of specimen 5-20 LE B-0028202 counts up to 99.8% in ITS1-2 and trnL-F (Vilnet et al., 2010, Konstantinova et al., 2020b Oncophorus integerrimus 1f,1i: along streams banks, on wet soil in dwarf shrub-herb-moss tundra, in the crevice of stones in stony area. ...
... Published molecular data have suggested diversity within T. quinquedentata-complex, thus careful study should be implemented in course of infraspecific diversity and reliability of previously described infraspecific taxa (Vilnet et al., 2010). The similarity of specimen 5-20 LE B-0028202 counts up to 99.8% in ITS1-2 and trnL-F (Vilnet et al., 2010, Konstantinova et al., 2020b Oncophorus integerrimus 1f,1i: along streams banks, on wet soil in dwarf shrub-herb-moss tundra, in the crevice of stones in stony area. 4 records: 3-20 LE B-0021834, 7-20 LE B-0021835, 9-20 LE B-0021770, 13-20 LE B- 1b,1i,1h,2a,2b: in the crevice of stone and on stones of rocky outсrops, in forb-moss tundra, along lake bank, associated with Distichium capillaceum, Flexigtrichum flexicaule,Tortella fragilis,[18][19][20]etc. ...
... This specimen resembles Scapania hyperborea Jørg. by morphology, but sequence similarity achieved 99.5% in ITS1-2 and 99.7% in trnL-F with multiplied sampled S. irrigua(Vilnet et al., 2010) that lies in the level of infraspecific variability and attend tested specimen to S. irrigua. !S. ligulifolia R. M. Schust. ...
The paper provides data on mosses and liverworts of the islands of south-eastean of the Barents Sea: Yuzhny Island of Novaya Zemlya, Vaygach and Matveev islands based on 700 identifications of mosses and 200 identifications of liverworts. The annotated list includes 173 species and one variety of mosses and 52 species and nine infraspecific taxa of liverworts, including insufficiently known Blepharostoma trichophyllum hybrib 1, Barbilophozia rubescens, Saccobasis polita var. arctica, Trilophozia quinquedentata var. grandiretis. Among them, 17 species and one variety of mosses and 13 species, two varieties and two forms of liverworts are reported for the first time for Novaya Zemlya, 66 species of mosses, and 16 species and one variety of liverworts for the first time for Yuzhny Island, 14 species of mosses, and six species, two varieties and one form of liverworts are reported for the first time for Vaygach Island. The first data of bryophytes of Matveev Island are obtained: 44 species of mosses, and 11 species and one variety of liverworts are recorded. For every species, data on localities, frequency, and habitats are provided. New combinations are published for Mesoptychia gillmanii f. orbiculata (R. M. Schust.) Potemkin, comb. nov., and Trilophozia quinquedentata var. grandiretis (H. Buch et S. W. Arnell) Potemkin, comb. nov.
... Schiffn. [7] or, more recently, M. patens (N. Kitag.) ...
... Thus, the synonymy of M. ustulata with M. sprucei was justified with the existence of intermediate cell sizes [20], the merger of M. ramosa with M. funckii was justified with the suggestion of the former being 'a large-celled modification (probably polyploid)' of the latter [31], and the synonymy of M. pygmaea and M. badensis received no justification at all [32,33]. On the other hand, the molecular support for the recognition of M. aquatica, as advocated by Vilnet et al. [7] and later authors, might be based on the neglect of cryptic diversity within the morphs corresponding to those taxa. European plants corresponding to M. emarginata and M. aquatica (both those selected by us and those deposited in GenBank by previous authors other than Vilnet et al. [7] and Bakalin et al. [3]) show either no differences at all or a different signal from ITS and plastid data (cf. ...
... On the other hand, the molecular support for the recognition of M. aquatica, as advocated by Vilnet et al. [7] and later authors, might be based on the neglect of cryptic diversity within the morphs corresponding to those taxa. European plants corresponding to M. emarginata and M. aquatica (both those selected by us and those deposited in GenBank by previous authors other than Vilnet et al. [7] and Bakalin et al. [3]) show either no differences at all or a different signal from ITS and plastid data (cf. Figure 1, Figures S1 and S2), and at the same time, they are molecularly clearly different from the plants (of mostly Russian provenance) sequenced under that name, despite us employing the most characteristic morphs corresponding to both taxa. ...
A new species of Marsupella sect. Ustulatae Müll. Frib. ex R.M. Schust. is described following an integrated morphological and molecular–phylogenetic study which examined the recently found dioicous plants growing epilithically on acidic substrates in several mountain ranges of Portugal between Peneda-Gerês in the north and Serra da Monchique in the extreme south. Employed molecular markers (plastid trnF–trnT region and nuclear ribosomal ITS) confirmed the distinctness of the lineage from other currently recognized species in the section, and furthermore, previously neglected diversity within M. sprucei (Limpr.) Bernet was signaled. Although not yet confirmed outside Portugal, the newly reported species is probably not rare in the region and has likely been overlooked as M. funckii (F. Weber & D. Mohr) Dumort. or M. profunda Lindb. in the past.
... Dumort., after the transfer of alien elements to other genera and even families [12,13], turned out to be a relatively small genus, encompassing, according to the latest list, 16 species [14]. Meanwhile, (1) the species status of some of these species may be questioned, and (2) Lophozia longiflora (Nees) Schiffn is regarded, in the latter list, as a possible synonym of L. guttulata (Lindb.) A. Evans, which was shown to be an independent taxon by Vilnet et al. [15]. To this number must also be added the species that have been described more recently: ...
Lophozia pallida, the commonly used name for a rare and little-known Sino-Himalayan species, was found to be a synonym of Lophozia dubia, a forgotten and previously misinterpreted species known in Indonesia. A comparative study of herbarium materials and our collections made it possible to ‘extend’ the distribution of Lophozia s. str. southward to Indonesia. The description of oil bodies from the species is provided for the first time. The position of the species in the Lophozia phylogenetic system demonstrates its clear differences from the morphologically similar Lophozia guttulata and its phylogenetic relationship with the Japanese–Korean Lophozia koreana.
... The general topology of the trees we obtained were in agreement with those presented by Vilnet et al. [9], Shaw et al. [10], Bakalin et al. [11], and Bakalin et al. [8]. In both Bayesian phylogenetic trees (Figures 1 and 2), the target specimen Konstantinovia sp. ...
The exploration of liverworts on Bering Island (the westernmost Aleutians) has revealed plants assigned to the recently described and previously monotypic Konstantinovia, previously known only from Yunnan Province of China, and belonging to the bigeneric Obtusifoliaceae. The collected plants are described here as Konstantinovia beringii sp. nov. The known localities of two species of Konstantinovia are separated by more than 6000 km, while the presence of the genus on the Commander Islands is probably a relict. Phylogenetic examination of both collected specimens and new material from other related families resulted in the construction of a fairly well-supported phylogenetic tree for the entire Cephaloziellaceae s.l. + Scapaniaceae s.l. clade. The constructed trees have confirmed the previously stated assumption that it is necessary to segregate one more family within this superclade, described here as Oleolophoziaceae fam. nov.
... Based on the data available in GenBank, we also included three accessions of Scapania compacta (Roth) Dumort. from Germany, Spain, and the United Kingdom and two accessions of Scapania spitsbergensis from Norway and Buryatiya Republic (originally studied by Vilnet et al. [8], Heinrichs et al. [2]); two specimens of S. crassiretis from Primorsky Territory were used as an outgroup for tree rooting. Specimen voucher details, including GenBank accession numbers, are listed in Table 1. ...
This paper addresses the genetic delimitation of narrowly distributed Scapania magadanica and broadly circumpolar S. kaurinii. The phylogenetic trees based on maximum likelihood and Bayesian inference constructed for one of the most informative loci (ITS1‒2) showed that Scapania magadanica was deeply nested within the clade of S. kaurinii. The comparison of the obtained topologies with known strong morphological dissimilarities of two taxa has led to the understanding that this approach does not work. The latter may be due to a widespread variable tentatively ‘ancestral’ species (S. kaurinii) having no joint molecular synapomorphies that would delimit it from the locally distributed derived taxon (S. magadanica). Therefore, the relationships of these two species were evaluated using molecular genetic distances with the Neighbor Net split network and TCS haplotype network. The obtained data have confirmed the speculation above, and it is possible to assume that when the S. magadanica lineage split, S. kaurinii already occupied a rather wide range, which could limit further gene flow among its remote populations.
Tritomaria koreana is transferred to Lophozia based on molecular studies involving material from the type locality. Within Lophozia, the species belongs to the early diverging branch sister to other taxa of the genus and is so distinctly morphologically different from congeners that the morphological circumscription of the genus should be revised based on the ability to develop 1) deep, pink-colored unicellular polygonal gemmae, 2) very unequally bilobed leaves, 3) leaves shaped and inserted as in Tritomaria exsecta. There are 5 morphologically distant species of Lophozia, four of which were described within the last decade and belong to the branches sister to the main bulk of taxa of the genus. All of these early diverging taxa are distributed on the geographical fringes of the area for the genus, whereas the geographical centre of the genus is occupied by widely distributed, morphologically intergrading and genetically closely related taxa of questionable taxonomic rank belonging to the L. ventricosa complex and its closest allies.
On the basis of phylogenetic analysis, the family Scapaniaceae Mig. is emended to include only the genus Scapania (Dumort.) Dumort. emend. Potemkin. The genus Macrodiplophyllum (H. Buch) Perss. is recognized as a subgenus in Scapania. The new combinations Scapania subgenus Macrodiplophyllum (H. Buch) Potemkin and Scapania plicata (Lindb.) Potemkin are provided. A new family, Diplophyllaceae Potemkin, with two genera, Diplophyllum (Dumort.) Dumort. and Douinia ii. Buch, is segregated from the Scapaniaceae as a group of different origins resulting in a different morphology. Douinia is distinguished as a genus derived from Diplophyllum and its rank as a subfamily is rejected. The distinctive characters of Delavayella Steph. are discussed. Segregation of Delavayellaceae R.M. Schust, and Blepharidophyllaceae (R.M. Schust.) R.M. Schust. from the Scapaniaceae is supported.
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
The phylogenetic system and classification of the family Scapaniaceae Mig. emend. Potemkin as a whole are presented for the first time. The classification of the family is significantly revised. Scapaniaceae is classified with 87 recent and one fossil species in 18 sections and three subgenera of one genus, Scapania (Dumort.) Dumort. emend. Potemkin. Subgenus Scapania has 82 species in 18 sections, subgenus Macrodiplophyllum (H. Buch) Potemkin has three species, and subgenus Macroscapania R.M. Schust. has two species. Earlier distinguished subgenera Plicaticalyx Müll. Frib. and Ascapania Grolle are merged in the sectio Plicaticalyx (Müll. Frib.) Potemkin, comb. & stat. nov., of the subgenus Scapania. The taxonomic composition of many sections is considerably revised, and the species composition of all infrageneric groups is listed in a systematic arrangement. Alteration of the species composition and/or species differentiation (including keys) of the sections Ciliatae Grolle, Gracilidae H. Buch, Nemorosae (Müll. Frib.) H. Buch, Planifoliae (Müll. Frib.) Potemkin, Plicaticalyx, Scapania, and Verrucosae Potemkin of the subgenus Scapania as well as of the subgenera Macrodiplophyllum and Macroscapania are provided. New sections are described for Scapania karl-muelleri Grolle (Grolleoscapania Potemkin, sect. nova) and for S. schljakovii Potemkin and S. himalayica Müll. Frib. (Muelleria Potemkin, sect. nova). A number of new synonyms and index for identification of taxonomic position of mentioned taxa of Scapania are provided.
Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles. Availability: SeqState runs on all major computer platforms and is downloadable for free from http:// www. nees. uni-bonn. de/ downloads/ SeqState, together with documentation and sample data files, or can be requested from the author.