scholarly journals Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

2019 ◽  
Author(s):  
Hong-Rui Zhang ◽  
Ran Wei ◽  
Qiao-Ping Xiang ◽  
Xian-Chun Zhang
Keyword(s):  
Substitution Rate ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Basal Clade ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses ◽  
The Stability

AbstractSelaginellaceae has been repeatedly proved as monophyly by previous studies with only one genus being recognized. However, the subgeneric classification has been debated during the recent decades. Furthermore, phylogenetic position of the newly identified sanguinolenta group has not been resolved, varying depending on the datasets and analysis methods. We carried out the phylogenomic analyses of twenty-six species from Selaginellaceae with ten species being newly sequenced and three species representing the sanguinolenta group. Four of the ten newly sequenced plastomes are assembled into the complete molecules, whereas the other six species are only assembled into five to sixteen contigs owing to high numbers of repeats. The phylogenetic framework from our study is basically congruent with the subgeneric classification of Weststrand and Korall (2016b). The position of sanguinolenta group was resolved as the basal clade in subg. Stachygynandrum, which support the position β proposed by Weststrand and Korall (2016a), also supported by the morphological characters of dimorphic vegetative leaves, monomorphic sporophylls and intermixed sporangial arrangements. Both values of dS, dN and GC content in Selaginellaceae plastomes were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). The correlation analysis showed that the elevated synonymous substitution rate was significantly correlated with the high GC content in Selaginellaceae. Besides, the values of dS and dN differs significantly between branches in the phylogenetic tree of Selaginellaceae. We propose that both high GC content and the extensive RNA editing sites contributed to the elevated substitution rate in Selaginellaceae, and all of these three factors could influence the stability of phylogenetic topology of Selaginellaceae.

scholarly journals Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

2017 ◽  
Author(s):  
E. Figuet ◽  
M. Ballenghien ◽  
N. Lartillot ◽  
N. Galtier
Keyword(s):  
Body Mass ◽  
Substitution Rate ◽  
Evolutionary Biology ◽  
Gc Content ◽  
Evolutionary Process ◽  
Synonymous Substitution ◽  
Molecular Data ◽  
Large Species ◽  
Data Set ◽  
Peer Community

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100042).Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.

Five new morphological types of virgulate and microcotylous xiphidiocercariae based on morphological and molecular phylogenetic analyses

2019 ◽  
Vol 94 ◽  
Author(s):  
S.V. Shchenkov ◽  
S.A. Denisova ◽  
G.A. Kremnev ◽  
A.A. Dobrovolskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
The Family ◽  
Family Level ◽  
Molecular Phylogenetic ◽  
Morphological And Molecular Data ◽  
First Time

Abstract The phylogenetic position of most xiphidiocercariae from subgroups Cercariae virgulae and Cercariae microcotylae remains unknown or unclear, even at the family level. In this paper, we studied the morphology and molecular phylogeny of 15 microcotylous and virgulate cercariae (11 new and four previously described ones). Based on morphological and molecular data, we suggested five distinct morphological types of xiphidiocercariae, which are a practical alternative to Cercariae virgulae and Cercariae microcotylae subgroups. Four of these types correspond to actual digenean taxa (Microphallidae, Lecithodendriidae, Pleurogenidae and Prosthogonimidae), while the fifth is represented by Cercaria nigrospora Wergun, 1957, which we classified on the basis of molecular data for the first time. We reassessed the relative importance of morphological characters used for the classification of virgulate and microcotylous cercariae, and discussed the main evolutionary trends within xiphidiocercariae. Now stylet cercariae can be reliably placed into several sub-taxa of Microphalloidea on the basis of their morphological features.

Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae)

2006 ◽  
Vol 37 (4) ◽  
pp. 405-418 ◽  
Author(s):  
Andrew Brower ◽  
Niklas Wahlberg ◽  
Thomas Simonsen ◽  
Rienk de Jong
Keyword(s):  
Phylogenetic Relationships ◽  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Nuclear Genes ◽  
Total Evidence ◽  
Monophyletic Clade ◽  
Gene Coi ◽  
Phylogenetic Hypotheses ◽  
The Stability

AbstractWe examine the phylogenetic relationships among 29 species of Argynnini based on 141 previously published morphological characters and new data from the mitochondrial gene COI and the two nuclear genes EF-1a and wingless. We investigate the stability and robustness of the resulting phylogenetic hypotheses through various combinations of the 4 functionally separate datasets. Increasing the number of datasets in combined analyses led to increased support for clades, sometimes substantially. We find that the tribe Argynnini is a well-supported, robust, monophyletic clade with the following internal subtribal structure: (Euptoietina (Yrameina (Boloriina Argynnina))). Our analyses support the classification of argynnine species into six robust and stable genera: Euptoieta, Yramea, Boloria, Issoria, Brenthis and Argynnis. We suggest that for moderate amounts of data, a total evidence approach is always best.

Paepalanthus fabianeae (Eriocaulaceae): A New Microendemic Species from a Morphologically Coherent Clade

2020 ◽  
Vol 45 (4) ◽  
pp. 794-801
Author(s):  
Caroline Oliveira Andrino ◽  
Marcelo Fragomeni Simon ◽  
Jair Eustáquio Quintino Faria ◽  
André Luiz da Costa Moreira ◽  
Paulo Takeo Sano
Keyword(s):  
New Species ◽  
Iucn Red List ◽  
Phylogenetic Position ◽  
Similar Species ◽  
Infrageneric Classification ◽  
Espinhaço Range ◽  
Nuclear Its ◽  
Two Populations

Abstract—We describe and illustrate Paepalanthus fabianeae, a new species of Eriocaulaceae from the central portion of the Espinhaço Range in Minas Gerais, Brazil. Previous phylogenetic evidence based on analyses of nuclear (ITS and ETS) and plastid (trnL-trnF and psba-trnH) sequences revealed P. fabianeae as belonging to a strongly supported and morphologically coherent clade containing five other species, all of them microendemic, restricted to the Espinhaço range. Due to the infrageneric classification of Paepalanthus being highly artificial, we preferred not assigning P. fabianeae to any infrageneric group. Paepalanthus fabianeae is known from two populations growing in campos rupestres (highland rocky fields) in the meridional Espinhaço Range. The species is characterized by pseudodichotomously branched stems, small, linear, recurved, and reflexed leaves, urceolate capitula, and bifid stigmas. Illustrations, photos, the phylogenetic position, and a detailed description, as well as comments on habitat, morphology, and affinities with similar species are provided. The restricted area of occurrence allied with threats to the quality of the habitat, mainly due to quartzite mining, justifies the preliminary classification of the new species in the Critically Endangered (CR) category using the guidelines and criteria of the IUCN Red List.

Three new species, two new genera, and new family Biphragmosagittidae (Сhaetognatha) from Southwest Pacific Ocean

2011 ◽  
Vol 20 (1) ◽  
pp. 161-173
Author(s):  
A.P. Kassatkina
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characters ◽  
The Body ◽  
New Order ◽  
New Genera ◽  
New Family ◽  
The Family ◽  
Three New Species

Resuming published and own data, a revision of classification of Chaetognatha is presented. The family Sagittidae Claus & Grobben, 1905 is given a rank of subclass, Sagittiones, characterised, in particular, by the presence of two pairs of sac-like gelatinous structures or two pairs of fins. Besides the order Aphragmophora Tokioka, 1965, it contains the new order Biphragmosagittiformes ord. nov., which is a unique group of Chaetognatha with an unusual combination of morphological characters: the transverse muscles present in both the trunk and the tail sections of the body; the seminal vesicles simple, without internal complex compartments; the presence of two pairs of lateral fins. The only family assigned to the new order, Biphragmosagittidae fam. nov., contains two genera. Diagnoses of the two new genera, Biphragmosagitta gen. nov. (type species B. tarasovi sp. nov. and B. angusticephala sp. nov.) and Biphragmofastigata gen. nov. (type species B. fastigata sp. nov.), detailed descriptions and pictures of the three new species are presented.

Influence of internal and external risks on sustainability of financial system of Аltai krai

2018 ◽  
Vol 35 (4) ◽  
pp. 133-136
Author(s):  
R. N. Ibragimov
Keyword(s):  
Sustainable Development ◽  
Financial Stability ◽  
Management Strategy ◽  
Financial System ◽  
Risk Management Strategy ◽  
The Sustainable Development ◽  
The Stability ◽  
The Impact

The article examines the impact of internal and external risks on the stability of the financial system of the Altai Territory. Classification of internal and external risks of decline, affecting the sustainable development of the financial system, is presented. A risk management strategy is proposed that will allow monitoring of risks, thereby these measures will help reduce the loss of financial stability and ensure the long-term development of the economy of the region.

DEVELOPMENT OF THE BASIC CRITERIA FOR RUSSIAN COASTS TYPIFICATION

2017 ◽  
Author(s):  
Рубен Косян ◽  
Ruben Kosyan ◽  
Viacheslav Krylenko ◽  
Viacheslav Krylenko
Keyword(s):  
Coastal Zone ◽  
Coastal Area ◽  
Economic Activity ◽  
Basic Information ◽  
Dynamic Features ◽  
Static State ◽  
Evolutionary Features ◽  
Coastal Features ◽  
The Stability

There are many types of coasts classifications that indicate main coastal features. As a rule, the "static" state of the coasts is considered regardless of their evolutionary features and ways to further transformation. Since the most part of the coastal zone studies aimed at ensuring of economic activity, it is clear that the classification of coast types should indicate total information required by the users. Accordingly, the coast classification should include the criterion, characterizing as dynamic features of the coast and the conditions and opportunities of economic activity. The coast classification, of course, should be based on geomorphological coast typification. Similar typification has been developed by leading scientists from Russia and can be used with minimal modifications. The authors propose to add to basic information (geomorphological type of coast) the evaluative part for each coast sector. It will include the estimation of the coast changes probability and the complexity of the coast stabilization for economic activity. This method will allow to assess the dynamics of specific coastal sections and the processes intensity and, as a result – the stability of the coastal area.

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

scholarly journals Can Vaccination Trigger Autoimmune Disorders? A Meta-Analysis

Vaccines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 821
Author(s):  
Marek Petráš ◽  
Ivana Králová Lesná ◽  
Jana Dáňová ◽  
Alexander M. Čelko
Keyword(s):  
Meta Analysis ◽  
Autoimmune Disorders ◽  
Risk Of Bias ◽  
Extensive Literature ◽  
Primary Analysis ◽  
Measures Of Association ◽  
Assessment Development ◽  
Extensive Literature Search ◽  
The Stability

Vaccination as an important tool in the fight against infections has been suggested as a possible trigger of autoimmunity over the last decades. To confirm or refute this assumption, a Meta-analysis of Autoimmune Disorders Association With Immunization (MADAWI) was conducted. Included in the meta-analysis were a total of 144 studies published in 1968–2019 that were available in six databases and identified by an extensive literature search conducted on 30 November 2019. The risk of bias classification of the studies was performed using the Newcastle–Ottawa Quality Assessment Scale. The strength of evidence was assessed using the Grading of Recommendations Assessment, Development, and Evaluation. While our primary analysis was conducted in terms of measures of association employed in studies with a low risk of bias, the robustness of the MADAWI outcome was tested using measures independent of each study risk of bias. Additionally, subgroup analyses were performed to determine the stability of the outcome. The pooled association of 0.99 (95% confidence interval, 0.97–1.02), based on a total of 364 published estimates, confirmed an equivalent occurrence of autoimmune disorders in vaccinated and unvaccinated persons. The same level of association reported by studies independently of the risk of bias was supported by a sufficient number of studies, and no serious limitation, inconsistency, indirectness, imprecision, and publication bias. A sensitivity analysis did not reveal any discrepancy in the primary result. Current common vaccination is not the cause of any of the examined autoimmune disorders in the medium and long terms.

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