Figure 3: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12095985 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Maximum Likelihood ◽

Southern Africa ◽

Type Species ◽

Phylogenetic Analyses ◽

Coi Gene ◽

Bootstrap Support ◽

Tree Search ◽

The Past ◽

Cytochrome Oxidase I Gene ◽

I Gene

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Fig.3 Maximum-likelihood phylogram based on partial sequences of the COI gene. Bootstrap support values were attained using a heuristic tree search and 1000 replicates. Numbers following locality names represent SAIAB catalogue numbers and GenBank accession numbers (in brackets). The shaded boxes enclose well-supported clades that were identified as populations of Mesobola brevianalis in the past. The scale bar represents the number of base substitutions per site.</div>

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Figure 2: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12095988 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Cytochrome Oxidase ◽

Southern Africa ◽

Morphometric Analysis ◽

Type Species ◽

Phylogenetic Analyses ◽

Cytochrome Oxidase I ◽

Cytochrome Oxidase I Gene ◽

I Gene

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Fig 2. Truss network used for morphometric analysis, defined by ten landmarks A–J.</div>

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Table 1: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12096003.v1 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome Oxidase ◽

Southern Africa ◽

Type Species ◽

Phylogenetic Analyses ◽

Cytochrome Oxidase I ◽

Cytochrome Oxidase I Gene ◽

I Gene ◽

Locality Information

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Table 1. Sample catalogue numbers and locality information for specimens from which DNA was extracted for phylogenetic analysis.</div>

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Table 1: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12096003 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome Oxidase ◽

Southern Africa ◽

Type Species ◽

Phylogenetic Analyses ◽

Cytochrome Oxidase I ◽

Cytochrome Oxidase I Gene ◽

I Gene ◽

Locality Information

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Table 1. Sample catalogue numbers and locality information for specimens from which DNA was extracted for phylogenetic analysis.</div>

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Figure 2: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12095988.v1 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Cytochrome Oxidase ◽

Southern Africa ◽

Morphometric Analysis ◽

Type Species ◽

Phylogenetic Analyses ◽

Cytochrome Oxidase I ◽

Cytochrome Oxidase I Gene ◽

I Gene

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Fig 2. Truss network used for morphometric analysis, defined by ten landmarks A–J.</div>

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Pengujian Dua Pasang Primer Universal Untuk Amplifikasi Gen Cytochrome Oxidase I Copepoda

Jurnal MIPA ◽

10.35799/jm.4.1.2015.6912 ◽

2015 ◽

Vol 4 (1) ◽

pp. 93

Author(s):

Thalita C. P. Sumampow

Keyword(s):

Cytochrome Oxidase ◽

Cryptic Species ◽

Dna Barcoding ◽

Cytochrome Oxidase I ◽

Coi Gene ◽

Universal Primer ◽

Cytochrome Oxidase I Gene ◽

I Gene

Copepoda merupakan zooplankton kaya manfaat dengan diversitas yang sangat tinggi dan terdiri dari banyak spesies kriptik. Identifikasi cepat, akurat, dan hemat dapat dilakukan dengan menggunakan teknik DNA Barcoding. Kesuksesan teknik tersebut sangat dipengaruhi oleh penggunaan primer yang tepat. Tujuan penelitian ini adalah untuk menguji kemampuan dua pasang primer universal, yakni LCO1490-HCO2198 dan FF2d-FR1d, mengamplifikasi gen COI Copepoda. Dalam penelitian ini, pasangan primer LCO1490-HCO2198 tidak berhasil mengamplifikasi gen target. Sekuens-sekuens hasil amplifikasi menggunakan pasangan primer FF2d-FR1d diidentifikasi melalui BLAST. Hasil yang diperoleh menunjukan bahwa sekuens-sekuens tersebut memiliki persentase kemiripan sebesar 92% dengan bakteri Pandoraea pnomenusa. Melalui hasil yang didapatkan disimpulkan bahwa kedua pasangan primer universal LCO1490-HCO2198 dan FF2d-FR1d tidak cukup spesifik untuk amplifikasi gen cytochrome oxidase I Copepoda.Copepoda is a very beneficial and highly diverse zooplankton with many cryptic species. A fast, reliable, and affordable identification can be done through DNA Barcoding. The success of this technique is affected by the usage of correct primers. The aim of this research was to test the ability of two universal primer pairs, which were LCO1490-HCO2198 and FF2d-FR1d, amplifying COI gene of Copepoda. In this research, LCO1490-HCO2198 primer pairs weren’t able to amplify COI gene of Copepoda. Sequences which were successfully amplified using FF2d-FR1d primer pairs were identified through BLAST. The result shows that the sequences are 92% similar to bacteria named Pandoraea pnomenusa. It can be concluded that both primer pairs are not specific enough to amplify cytochrome oxidase I gene of Copepoda.

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Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.056697-0 ◽

2014 ◽

Vol 64 (Pt_4) ◽

pp. 1406-1411 ◽

Cited By ~ 27

Author(s):

Melissa Dsouza ◽

Michael W. Taylor ◽

Jason Ryan ◽

Andrew MacKenzie ◽

Kirill Lagutin ◽

...

Keyword(s):

Type Species ◽

Total Phospholipid ◽

Phylogenetic Analyses ◽

Bootstrap Support ◽

Rrna Gene ◽

Total Lipid Extract ◽

Strictly Aerobic ◽

Content Type ◽

Link Type ◽

Gamma Irradiated

A novel bacterium, strain BrT, was isolated from gamma-irradiated soils of the Britannia drift, Lake Wellman Region, Antarctica. This isolate was rod-shaped, endospore forming, Gram-stain-variable, catalase-positive, oxidase-negative and strictly aerobic. Cells possessed a monotrichous flagellum. Optimal growth was observed at 18 °C, pH 7.0 in PYGV or R2A broth. The major cellular fatty acid was anteiso-C15 : 0 (63.4 %). Primary identified lipids included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Total phospholipid was 60 % (w/w) of the total lipid extract. MK-7 was the dominant isoprenoid quinone. The genomic DNA G+C content was 55.6 mol%. Based on 16S rRNA gene sequence similarity, strain BrT clusters within the genus Paenibacillus with similarity values ranging from 93.9 to 95.1 %. Phylogenetic analyses by maximum-likelihood, maximum-parsimony and neighbour-joining methods revealed that strain BrT clusters with Paenibacillus daejeonensis (AF290916), Paenibacillus tarimensis (EF125184) and Paenibacillus pinihumi (GQ423057), albeit with weak bootstrap support. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, we propose that strain BrT represents a novel species, Paenibacillus darwinianus sp. nov. The type strain is BrT ( = DSM 27245T = ICMP 19912T).

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Phylogenetic placement of Iodosphaeriaceae (Xylariales, Ascomycota), designation of an epitype for the type species of Iodosphaeria, I. phyllophila, and description of I. foliicola sp. nov.

Fungal Systematics and Evolution ◽

10.3114/fuse.2021.08.05 ◽

2021 ◽

Author(s):

A.N. Miller ◽

M. Réblová

Keyword(s):

Maximum Likelihood ◽

Type Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Monophyletic Group ◽

Its Sequence ◽

Phylogenetic Placement ◽

Wide Range ◽

Single Genus

The Iodosphaeriaceae is represented by the single genus, Iodosphaeria, which is composed of nine species with superficial, black, globose ascomata covered with long, flexuous, brown hairs projecting from the ascomata in a stellate fashion, unitunicate asci with an amyloid apical ring or ring lacking and ellipsoidal, ellipsoidal-fusiform or allantoid, hyaline, aseptate ascospores. Members of Iodosphaeria are infrequently found worldwide as saprobes on various hosts and a wide range of substrates. Only three species have been sequenced and included in phylogenetic analyses, but the type species, I. phyllophila, lacks sequence data. In order to stabilize the placement of the genus and family, an epitype for the type species was designated after obtaining ITS sequence data and conducting maximum likelihood and Bayesian phylogenetic analyses. Iodosphaeria foliicola occurring on overwintered Alnus sp. leaves is described as new. Five species in the genus form a well-supported monophyletic group, sister to the Pseudosporidesmiaceae in the Xylariales. Selenosporella-like and/or ceratosporium-like synasexual morphs were experimentally verified or found associated with ascomata of seven of the nine accepted species in the genus. Taxa included and excluded from Iodosphaeria are discussed.

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Reinertia, a New Subgenus of the Genus Aedes Meigen and Its Type Species Aedes (Reinertia) suffusus (Diptera: Culicidae), Newly Recorded From Bhutan

Journal of Medical Entomology ◽

10.1093/jme/tjaa277 ◽

2021 ◽

Author(s):

Pradya Somboon ◽

Thanari Phanitchakun ◽

Jassada Saingamsook ◽

Rinzin Namgay ◽

Ralph E Harbach

Keyword(s):

Male Genitalia ◽

Type Species ◽

Phylogenetic Analyses ◽

Strong Support ◽

Molecular Data ◽

Coi Gene ◽

Maxillary Palpus ◽

Mitochondrial Coi ◽

New Subgenus ◽

Tree Hole

Abstract A new subgenus, Reinertia Somboon, Namgay & Harbach, of the genus Aedes Meigen and its type species, Ae. suffusus Edwards, are described from specimens reared from larvae and pupae found in a tree hole in Bhutan. The scutum of the adults is mostly covered with narrow pale falcate scales. The proboscis, maxillary palpus, tibiae, and tarsi are dark-scaled. The gonocoxite of the male genitalia bears a unique setose basomesal sclerite. The larva closely resembles larvae of the subgenus Downsiomyia Vargus in having setae 4–6-C with numerous branches and inserted more or less on level with seta 7-C, abdominal seta 12-I is present and the comb is composed of 6–10 spine-like scales arranged in an irregular row. Surprisingly, Reinertia shares features of the adult habitus, male genitalia, and larva with the Palearctic subgenus Dahliana Reinert, Harbach & Kitching. However, in phylogenetic analyses of the mitochondrial COI gene of species representing 38 subgenera of Aedes and six other genera of the tribe Aedini Neveu-Lemaire, Reinertia was not associated with Dahliana or Downsiomyia. In both maximum likelihood and Bayesian analyses of the data, Ae. suffusus was recovered as the weakly supported sister of a clade composed of five species of the subgenus Protomacleaya Theobald. In the absence of strong support, and because Protomacleaya is an unnatural group of species that resemble each other phenetically by virtue of what they lack, Ae. suffusus cannot be placed in the subgenus Protomacleaya. Thus, the morphological and molecular data attest the uniqueness of Ae. suffusus and its recognition as a monobasic subgeneric lineage.

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Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

PLoS ONE ◽

10.1371/journal.pone.0231367 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0231367

Author(s):

Jessica M. Vélez ◽

Reese M. Morris ◽

Rytas Vilgalys ◽

Jessy Labbé ◽

Christopher W. Schadt

Keyword(s):

Maximum Likelihood ◽

Cryptic Species ◽

Populus Trichocarpa ◽

Phylogenetic Analyses ◽

The United States ◽

Bootstrap Support ◽

Rrna Gene ◽

Cenococcum Geophilum ◽

Phylogenetic Groups ◽

Globally Distributed

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

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