scholarly journals Taxonomic Revisiting and Phylogenetic Placement of Two Endangered Plant Species: Silene leucophylla Boiss. and Silene schimperiana Boiss. (Caryophyllaceae)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 740
Author(s):  
Ahmed EL-Banhawy ◽  
Iman H. Nour ◽  
Carmen Acedo ◽  
Ahmed ElKordy ◽  
Ahmed Faried ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Epidermal Cells ◽  
Phylogenetic Study ◽  
Endangered Plant ◽  
Sinai Peninsula ◽  
Phylogenetic Placement ◽  
Bayesian Phylogenetic Analysis ◽  
Genus Silene ◽  
Sectional Classification

The genus Silene L. is one of the largest genera in Caryophyllaceae, and is distributed in the Northern Hemisphere and South America. The endemic species Silene leucophylla and the near-endemic S. schimperiana are native to the Sinai Peninsula, Egypt. They have reduced population size and are endangered on national and international scales. These two species have typically been disregarded in most studies of the genus Silene. This research integrates the Scanning Electron Microscope (SEM), species micromorphology, and the phylogenetic analysis of four DNA markers: ITS, matK, rbcL and psb-A/trn-H. Trichomes were observed on the stem of Silene leucophylla, while the S. schimperiana has a glabrous stem. Irregular epicuticle platelets with sinuate margin were found in S. schimperiana. Oblong, bone-shaped, and irregularly arranged epidermal cells were present on the leaf of S. leucophylla, while Silene schimperiana leaf has “tetra-, penta-, hexa-, and polygonal” epidermal cells. Silene leucophylla and S. schimperiana have amphistomatic stomata. The Bayesian phylogenetic analysis of each marker individually or in combination represented the first phylogenetic study to reveal the generic and sectional classification of S. leucophylla and S. schimperiana. Two Silene complexes are proposed based on morphological and phylogenetic data. The Leucophylla complex was allied to section Siphonomorpha and the Schimperiana complex was related to section Sclerocalycinae. However, these two complexes need further investigation and more exhaustive sampling to infer their complex phylogenetic relationships.

scholarly journals A Bayesian Phylogenetic Classification of Tupí-Guaraní

2015 ◽  
Vol 15 (2) ◽  
pp. 193 ◽  
Author(s):  
Lev Michael ◽  
Natalia Chousou-Polydouri ◽  
Keith Bartolomei ◽  
Erin Donnelly ◽  
Sérgio Meira ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Structure ◽  
Character Table ◽  
Loss Model ◽  
Phylogenetic Classification ◽  
Bayesian Phylogenetic Analysis ◽  
Binary Coding ◽  
Semantic Shift ◽  
Lexical Data

This paper presents an internal classification of Tupí-Guaraní based on lexical data from 30 Tupí-Guaraní languages and 2 non-Tupí-Guaraní Tupian languages, Awetí and Mawé. A Bayesian phylogenetic analysis using a generalized binary cognate gain and loss model was carried out on a character table based on the binary coding of cognate sets, which were formed with attention to semantic shift. The classification shows greater internal structure than previous ones, but is congruent with them in several ways.

The Tupí-Guaraní language family

Diachronica ◽  
2021 ◽  
Author(s):  
Fabrício Ferraz Gerardi ◽  
Stanislav Reichert
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Stochastic Algorithm ◽  
Language Family ◽  
Historical Sources ◽  
Bayesian Phylogenetic Analysis

Abstract Attempts to classify Tupí-Guaraní languages have so far been inconsistent with archaeological evidence and ignored information from historical sources. The case of Tupinambá is most illustrative in this regard. Using both Bayesian phylogenetic analysis and a stochastic algorithm that reconstructs phylogenetic trees by relying on maximum likelihood estimation, we suggest a new internal classification of the Tupí-Guaraní branch. The results of the analyses are in accordance with the most recent genetic research on Tupían populations and challenge previous classifications by suggesting, among others, that Tupinambá should not be considered a ‘Guaraní’ language.

The genus Agaricus in the Caribbean. Nine new taxa mostly based on collections from the Dominican Republic

Phytotaxa ◽  
2018 ◽  
Vol 345 (3) ◽  
pp. 219 ◽  
Author(s):  
LUIS A. PARRA ◽  
CLAUDIO ANGELINI ◽  
BEATRIZ ORTIZ-SANTANA ◽  
GERARDO MATA ◽  
CHRISTOPHE BILLETTE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dominican Republic ◽  
Intraspecific Variability ◽  
Virgin Islands ◽  
Its Sequences ◽  
Phylogenetic Study ◽  
Preliminary Study ◽  
The Caribbean ◽  
Taxonomic System

Field collections of Agaricus were collected in the Dominican Republic from 2009–2016 with the intent to evaluate the diversity in this genus, which was quasi-unknown in this country. In the same period, studies on tropical Agaricus revealed tropical clades that remained unclassified. A new taxonomic system of classification was developed, with the aim, inter alia, to integrate such tropical clades. A recent phylogenetic study, which included some samples from the Dominican Republic, revealed they belonged to three putative new sections. Our objective in this paper is to describe the species of Agaricus collected in this country and to classify them whitin the new taxonomic system, including formal descriptions of the three new sections to which they belong. A preliminary study indicated that the collections of the Dominican Republic belong either to a group of three related subgenera (Flavoagaricus, Minores, and Minoriopsis) or to the unrelated A. subg. Pseudochitonia. For the species of the three related subgenera, a phylogenetic analysis based on ITS sequences data reliably confirmed the classification of the species into five sections including the three new sections, which were well supported. For the collections of A. subg. Pseudochitonia, preliminary studies indicated that they all belonged to species of A. sect. Xanthodermatei without any doubt except for one species. This species was included in a multi-gene (ITS, LSU and tef-1α) phylogenetic analysis which confirmed placement in this section. Consequently, all the samples were included in a phylogenetic analysis based on ITS sequences and focusing on A. sect. Xanthodermatei. We noted an unusually high intraspecific variability in the ITS sequences of five of the 12 studied species. Fifteen taxa are described, among which three sections and six species are new for science: Agaricus sect. Kerrigania, Agaricus sect. Minoriopsis, Agaricus sect. Pantropicales, A. argenteopurpureus, A. candussoi, A. flavidodiscus, A. lodgeae, A. porphyropos and A. tephrolepidus. We report all these taxa from the Dominican Republic but the latter three species are also recorded from Puerto Rico, United States Virgin Islands, and Mexico, respectively.

The classification of the Tungusic languages

2020 ◽  
pp. 80-91
Author(s):  
Lindsay J. Whaley ◽  
Sofia Oskolskaya
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Relationships ◽  
Comparative Method ◽  
Bayesian Phylogenetic Analysis ◽  
Southern Branch ◽  
Basic Vocabulary ◽  
Cladistic Classification ◽  
Northern Branch

This chapter surveys previous attempts to classify the genetic relationships among the Tungusic languages. The set of sound correspondences that can be employed in this classification is examined and it is argued that, if one assumes binary branching for a cladistic classification, there are three plausible classifications that result from the application of the classical comparative method. Next, a Bayesian phylogenetic analysis of basic vocabulary is undertaken to determine whether that analysis provides any further evidence for which of the three classifications is preferred. The conclusion is that it does and that one of the best classifications of Tungusic places Manchu, Xibe, and Jurchen in a Southern Branch together with Udihe and Nanai complexes, and the Even-Evenki complex in a Northern Branch. Though our analysis does not exclude the most common classification in which the Manchuric branch separated first from all other Tungusic languages.

Pogostemon jaitapurensis (Lamiaceae), a new species from India based on morphological and molecular evidence

Phytotaxa ◽  
2021 ◽  
Vol 502 (1) ◽  
pp. 28-50
Author(s):  
ARUN NIVRUTTI CHANDORE ◽  
ASIF SHABODIN TAMBOLI ◽  
DEVIDAS BHAUSAHEB BORUDE ◽  
AVINASH RAMCHANDRA GHOLAVE ◽  
SANJAY PRABHU GOVINDWAR ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Phylogenetic Placement ◽  
Clade B ◽  
Close Relationship ◽  
Sectional Classification ◽  
A New Species

Based on morphological and molecular analyses, Pogostemon jaitapurensis is described and illustrated as a new species from Konkan region of Maharashtra, India. Present study added the molecular data of Indian endemic Pogostemon species of sect. Verticillatus and provide their phylogenetic placement. The bayesian and parsimony phylogenetic analyses conducted resolve Pogostemon into two clades, from them the new species belongs to Clade B and shows close relationship with species of sect. Verticillatus. A possible relationship between the new species and P. deccanensis and P. erectus, endemic to India, is also revealed by the phylogenetic analyses. Phylogenetically, the new species has been also placed in genus Pogostemon subg. Dysophyllus sect. Verticillatus. Sectional classification of these species is congruent with their phylogenetic positions.

scholarly journals Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 241
Author(s):  
Joon Moh Park ◽  
Jachoon Koo ◽  
Se Won Kang ◽  
Sung Hee Jo ◽  
Jeong Mee Park
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Nicotiana Benthamiana ◽  
Economic Value ◽  
Virulence Gene ◽  
Economic Losses ◽  
Herbaceous Perennials ◽  
Rhodococcus Fascians ◽  
Different Strains

Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Maroua Oueslati ◽  
Magdalena Mulet ◽  
Mohamed Zouaoui ◽  
Charlotte Chandeysson ◽  
Jorge Lalucat ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Pseudomonas Syringae ◽  
Ice Nucleation ◽  
Phylogenetic Study ◽  
Future Studies ◽  
Citrus Orchards ◽  
First Time ◽  
New Cultivars

Abstract The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 28
Author(s):  
Umaru Bangura ◽  
Jacob Buanie ◽  
Joyce Lamin ◽  
Christopher Davis ◽  
Gédéon Ngiala Bongo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sierra Leone ◽  
Small Mammal ◽  
Hemorrhagic Fever ◽  
Lassa Fever ◽  
Lassa Virus ◽  
Sierra Leonean ◽  
Bayesian Phylogenetic Analysis ◽  
Prevalent Species ◽  
Lineage Iv

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

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