A Bayesian Phylogenetic Classification of Tupí-Guaraní

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.

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

Plants ◽

10.3390/plants10040740 ◽

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.

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The Tupí-Guaraní language family

Diachronica ◽

10.1075/dia.18032.fer ◽

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.

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Cladistic analysis of the tribe Torneutini Thomson (Coleoptera: Cerambycidae: Cerambycinae: Trachyderoinia)

Zootaxa ◽

10.11646/zootaxa.1062.1.1 ◽

2005 ◽

Vol 1062 (1) ◽

pp. 1 ◽

Cited By ~ 4

Author(s):

MARCELA LAURA MONNÉ ◽

DILMA SOLANGE NAPP

Keyword(s):

Phylogenetic Analysis ◽

Cladistic Analysis ◽

Morphological Characters ◽

Generic Level ◽

Phylogenetic Classification ◽

Genus Level ◽

First Time

A generic-level phylogenetic analysis of the tribe Torneutini Thomson, 1860 is presented based on 72 morphological characters for 39 terminal taxa of which, 31 are representatives of the Torneutini genera. The outgroup includes eight representatives from other tribes. A hypothesis of monophyly for supertribe Trachyderoinia Dupont, 1836 (sensu Fragoso, Monné and Seabra 1987) is presented for the first time. Torneutini, as currently recognized, was shown to be paraphyletic. In order to eliminate this condition, Bothriospilina Lane, 1950 is raised herein to tribe level. Torneutini, as herein defined, comprises the following genera in parenthetic notation: (Macellidiopygus (Psygmatocerus (Gigantotrichoderes (Spathopygus + Coccoderus) (Gnathopraxithea + Praxithea) (Torneutopsis (Torneucerus + Diploschema) (Torneutes (Dragomiris + Dragoneutes) (Thaumasus + Xenambyx)))))). The maintenance of Macellidiopygus in Torneutini needs further investigating. Bothriospilini Lane, 1950, new status, includes in parenthetic notation: ((Ranqueles + Scapanopygus) (Taygayba (Delemodacrys (Bothriospila + Timbaraba))) (Gnaphalodes (Knulliana + Chlorida)))). The position of Chrotoma is still no certain, and it is tentatively included in Bothriospilini. The results indicate that Bothriospilini is closely related to Trachyderini, Pyrestini and Basipterini. A phylogenetic classification of Trachyderoinia at tribe level, and of Torneutini and Bothriospilini at genus level, is proposed.

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A new phylogeny and phylogenetic classification for the Canthyloscelidae (Diptera: Psychodomorpha)

Canadian Journal of Zoology ◽

10.1139/z00-010 ◽

2000 ◽

Vol 78 (6) ◽

pp. 1067-1077 ◽

Cited By ~ 2

Author(s):

Dalton de Souza Amorim

Keyword(s):

Phylogenetic Analysis ◽

Middle Jurassic ◽

Sister Group ◽

Head Capsule ◽

Sister Group Relationship ◽

Phylogenetic Classification ◽

The Family

A new phylogeny and phylogenetic classification for the Canthyloscelidae (Diptera: Psychodomorpha) is presented. A phylogenetic analysis of the Scatopsoidea is performed. A sister-group relationship between the Canthyloscelidae and Scatopsidae is accepted and the monophyly of the Canthyloscelidae is corroborated, including the genera Exiliscelis, Synneuron, Hyperoscelis, and Canthyloscelis. An earlier phylogenetic analysis of the group is considered, in which Synneuron was accepted as the sister-group of the Scatopsidae and Exiliscelis was considered the sister-group of Synneuron + Scatopsidae. Some apomorphic similarities between the larvae of all genera of Canthyloscelidae, especially the reduction of the head capsule, are considered true synapomorphies. Exiliscelis is considered the sister-group of the rest of the family and is placed in a new subfamily, Exiliscelinae. In the Canthyloscelinae, Synneuron is the sister-group of Hyperoscelis + Canthyloscelis. A phylogenetic classification of the group is proposed. Prohyperoscelis rohdendorfi Kovalev, 1985, from the Middle Jurassic in Russia, is accepted as the sister-group of Canthyloscelis.

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Phylogenetic analysis of the Paulsoni species group (Decapoda : Alpheidae) from the American Pacific, with implications for the phylogenetic classification of the genus Synalpheus

Zootaxa ◽

10.11646/zootaxa.1744.1.2 ◽

2008 ◽

Vol 1744 (1) ◽

pp. 19 ◽

Cited By ~ 3

Author(s):

MARGARITA HERMOSO-SALAZAR ◽

MARY WICKSTEN ◽

JUAN J. MORRONE

Keyword(s):

Phylogenetic Analysis ◽

Cladistic Analysis ◽

Morphological Characters ◽

Species Group ◽

Natural Classification ◽

Phylogenetic Classification ◽

Species Groups

A cladistic analysis of 22 species of Synalpheus, represented primarily by species of the Paulsoni species group from the American Pacific and selected species from the Gambarelloides, Neomeris, Brevicarpus, and Biunguiculatus species groups was undertaken, based on 51 morphological characters. The Paulsoni species group proved to be paraphyletic, because species of the Neomeris, Brevicarpus, and Biunguiculatus species groups nested within it. It is proposed herein that in order to achieve a more natural classification, only two groups should be maintained within Synalpheus: Gambarelloides and Paulsoni, the latter in its broadest sense, treating the remaining species groups as synonyms.

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The classification of the Tungusic languages

The Oxford Guide to the Transeurasian Languages ◽

10.1093/oso/9780198804628.003.0007 ◽

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.

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

Pathogens ◽

10.3390/pathogens10020241 ◽

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.

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

Pathogens ◽

10.3390/pathogens10010041 ◽

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.

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

Biology ◽

10.3390/biology10010028 ◽

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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Case of Human Infestation with Dermanyssus gallinae (Poultry Red Mite) from Swallows (Hirundinidae)

Pathogens ◽

10.3390/pathogens10030299 ◽

2021 ◽

Vol 10 (3) ◽

pp. 299

Author(s):

Georgios Sioutas ◽

Styliani Minoudi ◽

Katerina Tiligada ◽

Caterina Chliva ◽

Alexandros Triantafyllidis ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Clinical Symptoms ◽

Skin Lesions ◽

Coi Gene ◽

Dermanyssus Gallinae ◽

Poultry Red Mite ◽

Human Form ◽

Bayesian Phylogenetic Analysis

Dermanyssus gallinae (the poultry red mite, PRM) is an important ectoparasite in the laying hen industry. PRM can also infest humans, causing gamasoidosis, which is manifested as skin lesions characterized by rash and itching. Recently, there has been an increase in the reported number of human infestation cases with D. gallinae, mostly associated with the proliferation of pigeons in cities where they build their nests. The human form of the disease has not been linked to swallows (Hirundinidae) before. In this report, we describe an incident of human gamasoidosis linked to a nest of swallows built on the window ledge of an apartment in the island of Kefalonia, Greece. Mites were identified as D. gallinae using morphological keys and amplifying the Cytochrome C oxidase subunit I (COI) gene by PCR. Bayesian phylogenetic analysis and median-joining network supported the identification of three PRM haplogroups and the haplotype isolated from swallows was identical to three PRM sequences isolated from hens in Portugal. The patient was treated with topical corticosteroids, while the house was sprayed with deltamethrin. After one week, the mites disappeared and clinical symptoms subsided. The current study is the first report of human gamasoidosis from PRM found in swallows’ nest.

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