Molecular identification of stone loaches of Choman River system, Tigris Basin, based on the Cytochrome b gene with an overview of the Cobitoidea Superfamily

AbstractMolecular data and phylogenetic relationships of four Choman loaches species (Oxynoemacheilus chomanicus, O. zagrosensis, O. kurdistanicus and Turcinoemacheilus kosswigi) recently morphologically described from western Iran were evaluated with 64 species from the Cobitoidea superfamily based on their cytochrome b sequences to exhibit the placement of the Choman loaches species within the Cobitoidea superfamily. A comparative analysis of Kimura-2-parameter (K2P) distances was accomplished using sequence divergences of Cobitoidea to calculate intra and interspecific in superfamily, family and genus taxa. The average intraspecific K2P genetic distances of Choman loaches species was 0.005 whereas this value was 0.016 for the Cobitoidea superfamily. Molecular phylogenetic relationships were assessed using Maximum likelihood and Bayesian methods. Dendrograms obtained by these methods revealed all four Choman loaches species as distinct species among other reported Nemacheilidae Spp. These species were clustered with Oxynoemacheilus and Turcinoemacheilus genera within other species in the Nemacheilidae family. The phylogenetic analysis revealed that Cobitoidea superfamily consists of nine families ((Gyrinocheilidae + Botiidae) + ((Catostomidae + Vaillentellidae) + ((Nemacheilidae + Cobitidae) + ((Ellopostomidae + Gastromyzontidae) + Balitoridae)))) and indicated Nemacheilidae is a valid and distinct family from Balitoridae.

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Revision of Hygrochilus (Orchidaceae: Epidendroideae: Aeridinae) and a molecular phylogenetic analysis

Phytotaxa ◽

10.11646/phytotaxa.159.4.2 ◽

2014 ◽

Vol 159 (4) ◽

pp. 256 ◽

Cited By ~ 5

Author(s):

MING-HE LI ◽

GUO-QIANG ZHANG ◽

ZHONG-JIAN LIU ◽

SI-REN LAN

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Maximum Likelihood ◽

Bayesian Methods ◽

New Combination ◽

Molecular Phylogenetic Analysis ◽

Molecular Phylogenetic ◽

A New Species

Hygrochilus and Sedirea are genera of orchids with only three species endemic to Asia. An analysis of ITS and five plastid regions using parsimony, maximum likelihood, and Bayesian methods obtain clear evidence that Sedirea is nested within and should be considered synonymous with Hygrochilus. We adopt a broadly defined Hygrochilus characterized by possession of four pollinia. A new combination, namely, Hygrochilus japonica, and a new species, namely, Hygrochilus tsii (Orchidaceae: Epidedroideae: Aeridinae), are proposed.

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Phylogenetic analysis of lysine, threonine and butanol strain-producers

Faktori eksperimental'noi evolucii organizmiv ◽

10.7124/feeo.v21.853 ◽

1970 ◽

Vol 21 ◽

pp. 288-292

Author(s):

O. O. Tigunova ◽

G. S. Andriiash ◽

N. Ye. Beiko ◽

S. M. Shulha

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Maximum Likelihood ◽

16S Rrna ◽

Phylogenetic Relationships ◽

Clostridium Acetobutylicum ◽

Genomic Dna ◽

Agarose Gel ◽

Brevibacterium Flavum ◽

Mutant Strains

Aim. Identify and confirm the taxonomic position of the obtained mutant strains Brevibacterium sp. IMB B-7447, Brevibacterium flavum IMB B-7446 and Clostridium acetobutylicum IMB B-7407 (IFBG C6H). Methods. A fragment of genomic DNA from agarose gel using «Macherey-Nagel NucleoSpin Extract» was isolated according to the instructions of the producer and sequenced. Comparative analysis using the program «BLAST-online» was done. Phylogenetic dendrograms using methods Neighbour joining and Maximum likelihood were created. Results. Dendrograms of phylogenetic relationships of studied strains and related strains of databases «GenBank» were constructed. Conclusions. Found that homology of Brevibacterium sp. 90 and Brevibacterium sp. IMB B-7447 is 98 %, and stains B. flavum TH7 and B. flavum IMB B-7446 classified to species C. glutamicum. Strain C. acetobutylicum IMB B-7407 (IFBG C6H) been reclassified to C. pasteurianum IFBG C6H. Keywords: genes 16S rRNA, dendrogram, stains-produsers.

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A Polyphasic Characterisation of Tetradesmus almeriensis sp. nov. (Chlorophyta: Scenedesmaceae)

Processes ◽

10.3390/pr9112006 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2006

Author(s):

Sara Turiel ◽

Jose Antonio Garrido-Cardenas ◽

Cintia Gómez-Serrano ◽

Francisco Gabriel Acién ◽

Lorenzo Carretero-Paulet ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Maximum Likelihood ◽

Distinct Species ◽

Molecular Data ◽

Optimal Conditions ◽

Unique Combination ◽

Bayesian Approaches ◽

Morphological And Molecular Data ◽

Scenedesmus Almeriensis

The microalga Tetradesmus almeriensis, previously known as Scenedesmus almeriensis, has been isolated and cultivated as a highly productive, fast-growing strain known as a natural source of different products of commercial interest, including bioactive compounds such as lutein. This strain produces up to 40 g·m−2·day−1 of lutein under optimal conditions and is highly recommendable for outdoor production in temperate and warm climates, showing maximal performance at temperatures up to 35 °C with no photo-inhibition taking place with irradiances greater than 1000 μE·m−2·s−1. Morphological and molecular data allow its assignment to the Chlorophycean genus Tetradesmus. The new species can be distinguished from similar Tetradesmus taxa due to its unique combination of features that are seen under light microscopy. We present herein a robust and comprehensive phylogenetic analysis of T. almeriensis, together with several additional Scenedesmaceae species, using a combination of maximum likelihood and Bayesian approaches. Our results confirm T. almeriensis as a distinct species consistently clustering with other Scenedesmaceae.

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Molecular data support the placement of the enigmatic Cheguevaria as a subfamily of Lampyridae (Insecta: Coleoptera)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz073 ◽

2019 ◽

Vol 187 (4) ◽

pp. 1253-1258 ◽

Cited By ~ 1

Author(s):

Vinicius S Ferreira ◽

Oliver Keller ◽

Marc A Branham ◽

Michael A Ivie

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Maximum Likelihood ◽

18S Rrna ◽

Molecular Data ◽

Molecular Phylogenetic Analysis ◽

Incertae Sedis ◽

Maximum Likelihood Approach ◽

Molecular Phylogenetic ◽

Likelihood Approach

Abstract Since the description of the genus Cheguevaria as incertae sedis (Lampyridae), the placement of these beetles has been uncertain. This study is the first to address the placement of this genus based on a molecular phylogenetic analysis. We used three genes (18S rRNA, rrnl mitochondrial DNA and cox1 mitochondrial DNA) and a maximum likelihood approach with W-IQ-TREE to support Cheguevaria as a member of the Lampyridae and recognize it as the sole genus in the new subfamily Cheguevariinae stat. nov.

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Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin & Cochran, 1963 (Anura: Brachycephaloidea)

Zootaxa ◽

10.11646/zootaxa.4514.4.3 ◽

2018 ◽

Vol 4514 (4) ◽

pp. 487

Author(s):

ANDRÉS R. ACOSTA-GALVIS ◽

JEFFREY W. STREICHER ◽

LUIGI MANUELLI ◽

TRAVIS CUDDY ◽

RAFAEL O. DE SÁ

Keyword(s):

Phylogenetic Analysis ◽

New World ◽

Taxonomic Revision ◽

Phylogenetic Inference ◽

Genetic Distances ◽

Molecular Phylogenetic Analysis ◽

Phylogenetic Placement ◽

Molecular Phylogenetic ◽

First Time

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered Niceforonia nana nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus Hypodactylus in the synonymy of Niceforonia to resolve the paraphyly and place Niceforonia in the subfamily Hypodactylinae. Based on our revised concept of the genus Niceforonia we conducted preliminary morphological comparisons using specimens and literature descriptions. Finally, Nicefornia nana is quite divergent from other species of Niceforonia (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted.

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Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

Bulletin of Entomological Research ◽

10.1017/s0007485308005828 ◽

2008 ◽

Vol 98 (5) ◽

pp. 499-507 ◽

Cited By ~ 13

Author(s):

H.C. Zhang ◽

G.X. Qiao

Keyword(s):

Phylogenetic Analysis ◽

Molecular Phylogeny ◽

Host Specificity ◽

Nuclear Gene ◽

Molecular Data ◽

Molecular Phylogenetic Analysis ◽

Phylogenetic Study ◽

Primary Host ◽

Molecular Phylogenetic Study ◽

Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

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Rhodocybe formosa (Agaricales, Entolomataceae): new collections, molecular data and synonymy, and Rhodocybe griseonigrella comb. nov.

Phytotaxa ◽

10.11646/phytotaxa.255.1.3 ◽

2016 ◽

Vol 255 (1) ◽

pp. 34 ◽

Cited By ~ 1

Author(s):

ALFREDO VIZZINI ◽

BERNARDO PICILLO ◽

ENRICO ERCOLE ◽

JORDI VILA ◽

MARCO CONTU

Keyword(s):

Phylogenetic Analysis ◽

Distinct Species ◽

Molecular Data ◽

Its Sequences ◽

European Species ◽

Molecular Comparison

Rhodocybe formosa (sect. Rhodocybe), a species so far known only from Spain, is here reported from Italy. A detailed description, including also macrophotographs, microphotographs and drawings together with a phylogenetic analysis of the ITS sequences, are provided. According to the molecular comparison of the type collections, R. minutispora, a species recently described on the basis of collections from Spain, is a synonym of R. formosa. Clitopilus griseonigrellus is recognized as a distinct species and recombined in Rhodocybe. A key to the European species of Rhodocybe sect. Rhodocybe is provided.

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New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges

Zootaxa ◽

10.11646/zootaxa.5052.3.3 ◽

2021 ◽

Vol 5052 (3) ◽

pp. 353-379

Author(s):

JULIO C.C. FERNANDEZ ◽

MARIANELA GASTALDI ◽

GERMÁN ZAPATA-HERNÁNDEZ ◽

LUIS M. PARDO ◽

FABIANO L. THOMPSON ◽

...

Keyword(s):

New Species ◽

Phylogenetic Relationships ◽

Morphological Characters ◽

Molecular Data ◽

Southern Chile ◽

Deep Waters ◽

Molecular Phylogenetic ◽

Molecular Phylogenies ◽

Taxonomic Studies ◽

Phylogenetic Affinities

Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.

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Molecular phylogenetic relationships of Metastrongylus nematodes with emphasis on specimens from domestic pigs in Vietnam

Journal of Helminthology ◽

10.1017/s0022149x21000353 ◽

2021 ◽

Vol 95 ◽

Author(s):

N.V. Tuyen ◽

N.T.K. Lan ◽

P.N. Doanh

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Molecular Data ◽

Global Scale ◽

Single Infection ◽

Parasitic Nematodes ◽

Nucleotide Sequence Data ◽

Wild Boars ◽

Domestic Pigs ◽

Molecular Phylogenetic

Abstract Lungworms of the genus Metastrongylus are parasitic nematodes in the respiratory tract of swine. Although they infect both wild boars and domestic pigs, studies on Metastrongylus infections in wild boars in Europe, the Americas and Africa are numerous, while those in domestic pigs are few. There are several studies analysing the molecular phylogenetic relationships of few individual Metastrongylus species with other nematode taxa, but there are no studies on the phylogenetic relationships of species within the genus Metastrongylus. In Southeast Asia, reports on swine lungworms are extremely scarce and do not include any nucleotide sequence data. Therefore, the aim of the present study is to survey Metastrongylus infection in domestic pigs raised in Dien Bien Province, Northern Vietnam, and to analyse the molecular phylogenetic relationships of Metastrongylus species. Based on morphological and molecular data, we identified two species: Metastrongylus apri and Metastrongylus pudendotectus. The prevalence of the former species was found to be significantly higher than the latter one (24.1% vs. 2.3%). We observed pigs exhibiting a coinfection with the two lungworm species or a single infection with only M. apri. However, we did not observe any pigs being infected with just M. pudendotectus. Vietnamese Metastrongylus specimens showed slight morphological and molecular differences compared to those from other countries. The molecular analyses revealed a close genetic relationship between M. apri and Metastrongylus salmi, while both these species were far distant from M. pudendotectus. The present study highlights the needs for further studies to clarify the morphological features and ecological and phylogenetic relationships of Metastrongylus species at the global scale.

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Debating phylogenetic relationships of the scleractinian Psammocora: molecular and morphological evidences

Contributions to Zoology ◽

10.1163/18759866-07601004 ◽

2007 ◽

Vol 76 (1) ◽

pp. 35-54 ◽

Cited By ~ 66

Author(s):

Francesca Benzoni ◽

Fabrizio Stefani ◽

Jaroslaw Stolarski ◽

Michel Pichon ◽

Guillaume Mitta ◽

...

Keyword(s):

Molecular Phylogeny ◽

Phylogenetic Relationships ◽

Molecular Data ◽

Genetic Distances ◽

The Other ◽

Congeneric Species ◽

Genetic Affinity ◽

Phylogenetic Structure ◽

Skeletal Structures ◽

The Family

The phylogenetic relationships of the scleractinian genus Psammocora with the other genera traditionally included in the family Siderastreidae and some Fungiidae are assessed based on combined skeletal and molecular data. P. explanulata differs from the other examined congeneric species (P. contigua, P. digitata, P. nierstraszi , P. profundacella, P. superficialis, and P. stellata) in possessing interstomatous septa between adult corallites, costae, and in having continuous buttress-like structures joining septal faces (i.e., fulturae) which typically occur in fungiids. These characters are shared with Coscinaraea wellsi but not with the remainder of the examined siderastreids (the congeneric C. columna, and Anomastraea irregularis, Horastrea indica, Pseudosiderastrea tayamai, Siderastrea savignyana) whose septa are interconnected by typical synapticulae. Most of the examined species form septa with distinct transverse groups of centers of calcification, a biomineralization pattern typical of the Robusta clade. The observations on skeletal structures corroborate the results of the ITS2 and 5.8S molecular phylogeny. C. wellsi and P. explanulata are phylogenetically very close to each other and show closer genetic affinity with the examined Fungiidae (Halomitra pileus, Herpolitha limax, Fungia paumotensis, and Podabacia crustacea) than with the other species in the genera Psammocora and Coscinaraea, or with any other siderastreid. Our results show that neither Psammocora nor Coscinaraea are monophyletic genera. The high genetic distances between the species of Siderastreidae, especially between Pseudosiderastrea tayamai and Siderastrea savignyana on one side and the other genera on the other, suggest a deep divergence in the phylogenetic structure of the family.

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