scholarly journals MOLECULAR PHYLOGENY OF LEIOGNATHIDAE IN THE WATERS OF PERHENTIAN ISLANDS, TRENGGANU, MALAYSIA

2008 ◽  
Vol 33 (2) ◽  
pp. 139-144
Author(s):  
Seah Ying Giat ◽  
Mazlan Abd. Ghaffar ◽  
Gires Usup
Keyword(s):  
Organ System ◽  
The Other ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Light Organ ◽  
Mitochondrial Rrna ◽  
Good Marker ◽  
Molecular Phylogenetic ◽  
Mitochondrial Rdna ◽  
Trawl Surveys

Several series of trawl surveys were carried out in the waters of Perhentian Islands using commercial trawlers. 16S mitochondrial rRNA gene sequences were used to infer the phylogenetic relationships among nine morphospecies of leiognathids. The results showed that the genus Leiognathus is paraphyletic, whereas Gazza secutor, Photoplagios, Photopectoralis and Nuchequula are monophyletic. The molecular phylogenetic posions of the leiognathids studied were identical with morphological delineation, except for Photoplagios stercorarius. Branch of P. stercorarius was placed between Photoplagios spp. clade and clade of Secutor and Gazza. P. stercorarius was more affiliated to genus Photoplagios morphologically however have slight different features of light organ system compared with others three Photoplagios sp. caught in this study. It is probable that two distinct subclades occur in genus Photoplagios. Leiognathus equulus formed the base of the other leiognathids. Leiognathus splendens and Leiognathus jonesi formed a sister taxa to Photopectoralis species. Gazza formed a sister taxa to Secutor and Nuchequula formed a sister taxa to the group of trifurcation but toth with low bootstrap support. This study has shown that 16S mitochondrial rDNA is a good marker for phylogenetic analysis of the Leiognathidae.

scholarly journals Molecular phylogenetic assessment of Spirobranchus kraussii-complex (Annelida: Serpulidae) from the Japanese Archipelago

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11746
Author(s):  
Genki Kobayashi ◽  
Ryutaro Goto
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Nucleotide Sequences ◽  
The Other ◽  
Its2 Region ◽  
Rrna Gene ◽  
Molecular Phylogenetic

Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex.

scholarly journals Molecular Phylogeny and Global Diversity of the Genus Haploporus (Polyporales, Basidiomycota)

2021 ◽  
Vol 7 (2) ◽  
pp. 96
Author(s):  
Meng Zhou ◽  
Yu-Cheng Dai ◽  
Josef Vlasák ◽  
Yuan Yuan
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Geographic Range ◽  
Rrna Gene ◽  
Pore Surface ◽  
Mitochondrial Rrna ◽  
Molecular Phylogenetic

Phylogeny and taxonomy of the genus Haploporus were carried out based on a larger number of samples covering a wider geographic range including East Asia, South Asia, Europe, and America, and the species diversity of the genus is updated. Four species, Haploporus bicolor, H. longisporus, H. punctatus and H. srilankensis, are described as new species based on morphology and molecular phylogenetic analyses inferred from the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), and the small subunit mitochondrial rRNA gene (mtSSU). Haploporus bicolor is characterized by the distinctly different colors between the pore surface and the tubes, small pores measuring 5–7 per mm, and narrow basidiospores measuring 10.5–11.9 × 4.5–5 µm; H. longisporus differs from other species in the genus by its large pores measuring 2–3 per mm, hyphae at dissepiment edge with simple septum, and the long basidiospores (up to 22 µm); H. punctatus is distinguished by its cushion-shaped basidiocarps, wide fusiform cystidioles with a simple septum at the tips, the absence of dendrohyphidia and the cylindrical to slightly allantoid basidiospores measuring 9–10.8 × 3.8–5 µm; H. srilankensis is characterized by its perennial habit, small pores measuring 4–5 per mm, dextrinoid skeletal hyphae, the presence of cystidioles and dendrohyphidia. An identification key to accepted species of Haploporus is provided.

scholarly journals First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lampet Wongsaroj ◽  
Ratmanee Chanabun ◽  
Naruemon Tunsakul ◽  
Pinidphon Prombutara ◽  
Somsak Panha ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Organic Fertilizer ◽  
The Other ◽  
Organic Fertilizers ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Physiochemical Properties ◽  
Nutrient Profiles ◽  
Soil Recovery ◽  
Local Farmers

AbstractNortheastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson’s correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.

scholarly journals Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

2018 ◽  
Vol 63 (2) ◽  
pp. 45-64 ◽  
Author(s):  
Jolanta Miadlikowska ◽  
Nicolas Magain ◽  
Carlos J. Pardo-De la Hoz ◽  
Dongling Niu ◽  
Trevor Goward ◽  
...  
Keyword(s):  
High Specificity ◽  
Molecular Data ◽  
Fungal Species ◽  
Bootstrap Support ◽  
Phenotypic Traits ◽  
Phylogenetic Structure ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
High Bootstrap ◽  
Phylogenetic Revision

AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.

scholarly journals A NEW CRYPTIC SPECIES OF BUSH FROG (AMPHIBIA: ANURA: Raorchestes) FROM THE SOUTHERN EASTERN GHATS, INDIA

2020 ◽  
pp. 164-173
Author(s):  
Gaurang G. Gowande ◽  
S.R. Ganesh ◽  
Zeeshan A. Mirza
Keyword(s):  
New Species ◽  
Species Level ◽  
Eastern Ghats ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Upper Eyelid ◽  
Phylogenetic Reconstructions ◽  
Molecular Phylogenetic ◽  
Mitochondrial 16S Rrna Gene ◽  
The Western Ghats

A new cryptic lineage of bush frogs of the genus Raorchestes from the understudied Eastern Ghats of India is described. Molecular phylogenetic reconstructions using mitochondrial 16S rRNA gene sequences suggest that the new species belongs to the Raorchestes charius clade, is sister to the allopatric R. charius of the Western Ghats and support the species-level distinctiveness of the lineage. The new species morphologically resembles R. charius from which it can be distinguished using the following characters: narrower head (HW/SVL 0.31 vs 0.34–0.36), wider inter upper eyelid (IUE/SVL 0.14–0.16 vs 0.11–0.13), greater maximum upper eyelid width (UEW/SVL 0.10–0.12 vs 0.06–0.09) and shorter thigh (TL/SVL 0.32–0.43 vs 0.44–0.51). Acoustic observations from the breeding males further corroborate the distinct specific status of the new species. The discovery of this new species of bush frog from an understudied landscape suggests that additional extensive surveys in the Eastern Ghats would yield several more amphibian lineages yet unknown to science.

scholarly journals Sedum formosanum subsp. miyakojimense (Crassulaceae), a new subspecies from Miyako-jima Island of the Ryukyu Islands, Japan

PhytoKeys ◽  
2020 ◽  
Vol 148 ◽  
pp. 51-70
Author(s):  
Takuro Ito ◽  
Chih-Chieh Yu ◽  
Masatsugu Yokota ◽  
Goro Kokubugata
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
The Other ◽  
Ryukyu Islands ◽  
Morphological Comparison ◽  
Molecular Analyses ◽  
New Subspecies ◽  
The Ryukyu Islands ◽  
Molecular Phylogenetic ◽  
Axillary Branches

We re-examined the taxonomic status of plants treated as Sedum formosanum (Crassulaceae) from Miyako-jima Island of the Ryukyu Islands, Japan, using morphological comparison and molecular phylogenetic analyses with related species. In morphology, plants from Miyako-jima Island bore a close resemblance to the other plants of S. formosanum, but differed in being perennial, polycarpic, and having lateral axillary branches. Molecular analyses based on ITS of nrDNA and six regions of cpDNA sequencing indicated that the Miyako-jima plants formed a distinct subclade. This subclade was part of a polytomy with three other subclades comprising nine taxa endemic to Taiwan and S. formosanum from other areas, including the type locality. Therefore, we propose and describe the Miyako-jima plants as a new subspecies, Sedum formosanum subsp. miyakojimense.

scholarly journals Dicranum ignatovii sp. nova (Dicranaceae, Bryophyta) from the Far East

2018 ◽  
Vol 12 (1) ◽  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Far East ◽  
Integrative Taxonomy ◽  
Rrna Gene ◽  
Unique Combination ◽  
Leaf Lamina ◽  
Kurile Islands ◽  
The Far East ◽  
Molecular Phylogenetic

The new species Dicranum ignatovii Tubanova & Fedosov is described from Sakhalin, South Kurile Islands and the Khabarovsk Territory based on the approach of integrative taxonomy. The species is characterized by the unique combination of (1) short leaves with broadly acute apex, (2) slightly recurved distal leaf lamina, (3) short-rectangular to transverse rectangular distal leaf cells, (4) proximal leaf cells abruptly shortened distally and thus occupying only the basalmost leaf portion, (5) costa ending before apex, and (6) presence of flagelliform branchlets in upper leaf axils. Based on nrITS 1, 2 & 5.8 rRNA gene sequences, molecular phylogenetic analysis was carried out. As a result, three studied specimens were found in a well supported clade, nested in a weakly supported clade where D. acutifolium, D. caesium, D. bardunovii, D. angustum, D. bonjeanii, D. scoparium and D. brevifolium were also found.

Reassignment of Six Polyalthia Species to the New Genus Maasia (Annonaceae): Molecular and Morphological Congruence

2008 ◽  
Vol 33 (3) ◽  
pp. 490-494 ◽  
Author(s):  
Johan B. Mols ◽  
Paul J. A. Keßler ◽  
Steven H. Rogstad ◽  
Richard M. K. Saunders
Keyword(s):  
New Genus ◽  
Complex Form ◽  
The Other ◽  
Monophyletic Group ◽  
Bootstrap Support ◽  
Molecular Phylogenies

Recently published molecular phylogenies of the Annonaceae have confirmed the long-held hypothesis that the large paleotropical genus Polyalthia is polyphyletic. Species previously assigned to Polyalthia are now known to belong to up to six distinct, generally well-supported clades. Three members of a group of six species previously referred to as the Polyalthia hypoleuca complex form a monophyletic group (with 99% bootstrap support) that is only distantly related to the other species of Polyalthia sampled. Putative morphological synapomorphies are assessed, and justification provided for validating a new generic name, Maasia. Six species names in the Polyalthia hypoleuca complex are accordingly transferred to Maasia: M. discolor, M. glauca, M. hypoleuca, M. multinervis, M. ovalifolia, and M. sumatrana.

Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 15-25
Author(s):  
Hervé Philippe ◽  
Anne Chenuil ◽  
André Adoutte
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Reconstruction ◽  
Cambrian Explosion ◽  
Bootstrap Support ◽  
Time Interval ◽  
Short Time Interval ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

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