scholarly journals The diversity of the Polytrichopsida—a review

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
NEIL BELL ◽  
ISURU KARIYAWASAM ◽  
JORGE FLORES ◽  
JAAKKO HYVÖNEN
Keyword(s):  
Phylogenetic Analysis ◽  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Phylogenetic Analyses ◽  
Molecular Taxonomy ◽  
Whole Cells ◽  
Phylogenetic Hypotheses ◽  
Ancestral Type

The class Polytrichopsida are a phylogenetically isolated moss lineage of around 200 species. The nematodontous peristome found in most species has a fundamentally different structure from the arthrodontous peristome of the Bryopsida and may be independently evolved from an ancestral type of spore dehiscence apparatus. Within the class generic circumscriptions and relationships are now fairly confidently resolved and more or less congruent with the most developed pre-molecular taxonomy. Drawing on previously published datasets, we conducted a phylogenetic analysis of a novel matrix of terminals representing diversity across the Polytrichopsida. The class comprises 17 extant genera and two known only from fossils. Most of these are numerically small, the most notable exception being Pogonatum with over 50 species. Considering current phylogenetic hypotheses in the light of morphology and global distributions, Alophosia, Bartramiopsis and Lyellia, the earliest diverging lineages according to recent phylogenetic analyses, appear to be relicts, with scattered and disjunct distributions. All of these genera lack peristomes, while all later originating lineages have nematodontous peristomes developed from bundles of “u-shaped” whole cells. The genus Dawsonia, sister to all other peristomate taxa, differs in its unique peristome composed of long, bristle-like teeth arranged in concentric layers. Many members of some traditional genera found to be polyphyletic in recent studies are part of a southern hemisphere grade and only distantly related to the superficially similar northern hemisphere species with which they were historically classified. A large apical clade including eight genera accounts for the majority of the diversity, these being most speciose in northern temperate regions or the Asian tropics. Many of the Polytrichopsida are relatively large plants with well-developed vasculature and a “pseudo-mesophyll” capable of supporting relatively high rates of photosynthesis in moist, well-illuminated environments. With ten described species, Cenozoic fossils of Polytrichopsida are fairly numerous compared with other mosses. Records of fossils from older sediments have been rare, but recently several well-preserved fossils of Polytrichopsida have been found, most of which still await detailed description.

scholarly journals Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11737
Author(s):  
Cristian B. Canales-Aguirre ◽  
Peter A. Ritchie ◽  
Sebastián Hernández ◽  
Victoria Herrera-Yañez ◽  
Sandra Ferrada Fuentes ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Ancestral Population ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
The Tropics ◽  
Two Populations

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

Preliminary considerations on phylogeny of Simuliidae Genera from Southern Hemisphere (Insecta, Diptera)

Zootaxa ◽  
2007 ◽  
Vol 1643 (1) ◽  
pp. 39-68 ◽  
Author(s):  
LEONARDO H. GIL-AZEVEDO ◽  
MARILZA MAIA-HERZOG
Keyword(s):  
Phylogenetic Analysis ◽  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Morphological Characters ◽  
Data Matrix ◽  
Phylogenetic Hypothesis

In this paper, the first phylogenetic hypothesis for the 13 Southern Hemisphere genera of Simuliidae is proposed, through a cladistic approach. In order to investigate the position of those genera representatives of five Northern Hemisphere genera were also included in the analyses as outgroups. The study was based on a data matrix with 33 terminal taxa and 119 morphological characters of adult, pupa and larva. The phylogenetic analysis under equal weights resulted in four most parsimonious trees, with similar topologies and 349 steps (CI = 49; RI = 68). The analyses showed that all Southern Hemisphere genera of Simuliidae are closer to Simuliini than to Prosimuliini. According to our analyses, Araucnephia Wygodzinsky & Coscarón and Paracnephia Rubtsov are polyphyletic, and Gigantodax Enderlein and Crozetia Davies are monophyletic. It is possible also to recognize the following groups (A. iberaensis Coscarón & Coscarón-Arias + Lutzsimulium s.l. d’Andretta & d’Andretta); ((Simulium Latreille + Metacnephia Crosskey) (Cnesiamima Wygodzinsky & Coscarón (Paraustrosimulium Wygodzinsky & Coscarón + Austrosimulium Tonnoir))); and ((Paracnephia of Australia + Cnesia Enderlein) (Pedrowygomyia Coscarón & Miranda-Esquivel + Gigantodax Enderlein)).

scholarly journals A Phylogenetic Analysis of Salix (Salicaceae) Based on matK and Ribosomal DNA Sequence Data

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
T. M. Hardig ◽  
C. K. Anttila ◽  
S. J. Brunsfeld
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Lineage Sorting ◽  
Data Set ◽  
Infrageneric Classification ◽  
Dna Sequence Data ◽  
Phylogenetic Hypotheses ◽  
High Degree

The genus Salix has proven a fertile taxon for a host of evolutionary and ecological studies, yet much work remains in the development of a definitive phylogenetic context for those studies. We performed phylogenetic analyses, using both maximum likelihood and maximum parsimony techniques, of chloroplast-encoded matK and nuclear-encoded ribosomal DNA (rDNA) gene sequences, gathered from specimens deemed representative of the existing subgeneric classification, with the objective of identifying and elaborating the phylogenetic relationships within Salix. Comparisons between the two phylogenetic hypotheses indicate a high degree of polyphyly in the matK-based phylogeny. This we attribute to the effects of hybridization, introgression, and lineage sorting. Comparisons with previous molecule-based phylogenetic hypotheses indicate a fair degree of congruence and all are unanimous in placing Chosenia arbutifolia within the genus Salix. The phylogenetic analysis of our ITS data set has produced results that generally support the most-recent infrageneric classification.

Alpha-Effect, Current and Kinetic Helicities for Magnetically Driven Turbulence, and Solar Dynamo

2000 ◽  
Vol 179 ◽  
pp. 387-388
Author(s):  
Gaetano Belvedere ◽  
V. V. Pipin ◽  
G. Rüdiger
Keyword(s):  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Convection Zone ◽  
Solar Surface ◽  
Momentum Transport ◽  
Angular Momentum Transport ◽  
Magnetic Buoyancy ◽  
Alpha Effect ◽  
Current Helicity

Extended AbstractRecent numerical simulations lead to the result that turbulence is much more magnetically driven than believed. In particular the role ofmagnetic buoyancyappears quite important for the generation ofα-effect and angular momentum transport (Brandenburg & Schmitt 1998). We present results obtained for a turbulence field driven by a (given) Lorentz force in a non-stratified but rotating convection zone. The main result confirms the numerical findings of Brandenburg & Schmitt that in the northern hemisphere theα-effect and the kinetic helicityℋkin= 〈u′ · rotu′〉 are positive (and negative in the northern hemisphere), this being just opposite to what occurs for the current helicityℋcurr= 〈j′ ·B′〉, which is negative in the northern hemisphere (and positive in the southern hemisphere). There has been an increasing number of papers presenting observations of current helicity at the solar surface, all showing that it isnegativein the northern hemisphere and positive in the southern hemisphere (see Rüdigeret al. 2000, also for a review).

The Hemispheric Sign Rule of Current Helicity during the Rising Phase of Cycle 23

2000 ◽  
Vol 179 ◽  
pp. 303-306
Author(s):  
S. D. Bao ◽  
G. X. Ai ◽  
H. Q. Zhang
Keyword(s):  
Solar Cycle ◽  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Active Regions ◽  
Hemispheric Preference ◽  
Current Helicity

AbstractWe compute the signs of two different current helicity parameters (i.e., αbestandHc) for 87 active regions during the rise of cycle 23. The results indicate that 59% of the active regions in the northern hemisphere have negative αbestand 65% in the southern hemisphere have positive. This is consistent with that of the cycle 22. However, the helicity parameterHcshows a weaker opposite hemispheric preference in the new solar cycle. Possible reasons are discussed.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

2021 ◽  
pp. 1-11
Author(s):  
Andrea Highfield ◽  
Angela Ward ◽  
Richard Pipe ◽  
Declan C. Schroeder
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Dunaliella Salina ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Hypersaline Environments ◽  
Rdna Its ◽  
Β Carotene ◽  
Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

scholarly journals First results of low frequency electromagnetic wave detector of TC-2/Double Star program

2005 ◽  
Vol 23 (8) ◽  
pp. 2803-2811 ◽  
Author(s):  
J. B. Cao ◽  
Z. X. Liu ◽  
J. Y. Yang ◽  
C. X. Yian ◽  
Z. G. Wang ◽  
...  
Keyword(s):  
Electromagnetic Wave ◽  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Geomagnetic Storms ◽  
Low Frequency ◽  
Wave Detector ◽  
Ion Cyclotron Waves ◽  
Satellite Platform ◽  
Ion Cyclotron ◽  
First Results

Abstract. LFEW is a low frequency electromagnetic wave detector mounted on TC-2, which can measure the magnetic fluctuation of low frequency electromagnetic waves. The frequency range is 8 Hz to 10 kHz. LFEW comprises a boom-mounted, three-axis search coil magnetometer, a preamplifier and an electronics box that houses a Digital Spectrum Analyzer. LFEW was calibrated at Chambon-la-Forêt in France. The ground calibration results show that the performance of LFEW is similar to that of STAFF on TC-1. The first results of LFEW show that it works normally on board, and that the AC magnetic interference of the satellite platform is very small. In the plasmasphere, LFEW observed the ion cyclotron waves. During the geomagnetic storm on 8 November 2004, LFEW observed a wave burst associated with the oxygen ion cyclotron waves. This observation shows that during geomagnetic storms, the oxygen ions are very active in the inner magnetosphere. Outside the plasmasphere, LFEW observed the chorus on 3 November 2004. LFEW also observed the plasmaspheric hiss and mid-latitude hiss both in the Southern Hemisphere and Northern Hemisphere on 8 November 2004. The hiss in the Southern Hemisphere may be the reflected waves of the hiss in the Northern Hemisphere.

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