scholarly journals Molecular Phylogeny of Polyporales from Bafut Forest, Cameroon and Their Importance to Rural Communities

2019 ◽  
Vol 10 (2) ◽  
pp. 1
Author(s):  
Tonjock Rosemary Kinge ◽  
Azinue Clementine Lem ◽  
Seino Richard Akwanjoh
Keyword(s):  
Phylogenetic Analysis ◽  
Rural Communities ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationship ◽  
Local Communities ◽  
Medicinal Species ◽  
Forest Reserves ◽  
Phylogenetic Studies ◽  
Ctab Method ◽  
Relationship Of

The polyporales are a large order of pore fungi within the Basidiomycota (Kingdom Fungi). They are mostly found on decay wood with some edible and medicinal species and others causing diseases of trees. In Cameroon, the knowledge on the phylogeny of polyporales is limited, their historical uses as food, medicine, source of income and the sociological impacts are apparently threatened due to slow ethnomycology research drive. The aim of this study was to identify and determine the phylogenetic relationship of polyporales in the Bafut forest and document its uses to the local communities. DNA was extracted using CTAB method and amplified using primers ITS 1 and ITS4. Their identities were determined in GeneBank using BLAST and a phylogenetic analysis was done using MEGA version 7. For ethnomycological studies, a total of 180 semi structured questionnaires were used to collect information on traditional knowledge in four communities around the Bafut forest. Results from phylogenetic studies showed that, ten species were identified and belonged to seven genera comprising of the Microporus, Hexagonia, Ganoderma, Trametes, Favolus, Steccherinum and Cymatoderma which formed 7 independent monophyletic groups. Ethnomycological findings revealed that, polypores are used as food and medicine within these communities. Microporus xanthopus and Microporus vernicipes were used as food and medicine while all Trametes species were reported to be only medicinal. The Bafut people commonly called mushrooms “Boh” and those that grow on wood “Boh ti”. They usually differentiate the edible and nonedible mushroom using the term “yi kworu” and “yi tekworu”. Thus “Boh yi kworu” and “Boh yi tekworu” respectively. This study represents the first on the identification, phylogeny and uses of polyporales to the communities around the Bafut forest reserves and helps in their conservation.

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

2020 ◽  
Vol 34 (1) ◽  
pp. 101 ◽  
Author(s):  
Ryutaro Goto ◽  
James Monnington ◽  
Marija Sciberras ◽  
Isao Hirabayashi ◽  
Greg W. Rouse
Keyword(s):  
Molecular Phylogeny ◽  
Deep Sea ◽  
Sister Group ◽  
Molecular Data ◽  
Monterey Bay ◽  
Phylogenetic Studies ◽  
Littoral Zones ◽  
Family Level ◽  
Relationship Of ◽  
The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

Molecular phylogeny and taxonomy of Fibroporia (Basidiomycota) in China

Phytotaxa ◽  
2015 ◽  
Vol 203 (1) ◽  
pp. 47 ◽  
Author(s):  
YUAN-YUAN CHEN ◽  
HAI-JIAO LI ◽  
Bao-Kai Cui
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Brown Rot ◽  
Molecular Data ◽  
Its Rdna ◽  
Pore Surface ◽  
Hyphal System ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Close Relationship

Taxonomic and phylogenetic studies on the Chinese species of Fibroporia were carried out. Fibroporia albicans sp. nov. is described and illustrated on the basis of collections originating from Jiangxi and Xizang provinces, based on morphology and phylogenetic analysis of ITS rDNA sequences. Morphologically, it is characterized by resupinate, annual basidiocarps, white to cream-colored pore surface when fresh, becoming cream to cream-buff upon drying, small pores (6–8 per mm), presence of white to cream rhizomorphs, a dimitic hyphal system with clamped generative hyphae, fusoid cystidioles, and oblong to ellipsoid basidiospores; moreover, it causes a brown rot. Molecular data suggested a close relationship between Fibroporia albicans and F. citrina. Six species of Fibroporia form a monophyletic entity with 100% MP and 1.00 BPP supports. An identification key to the Chinese species of Fibroporia is provided.

Referral of Miacis jepseni Guthrie to Oödectes Wortman, and an assessment of phylogenetic relationships among early Eocene Miacidae (Mammalia: Carnivora)

1997 ◽  
Vol 71 (6) ◽  
pp. 1172-1178 ◽  
Author(s):  
Ronald E. Heinrich
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Phylogenetic Relationships ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Early Eocene ◽  
Relationship Of ◽  
Early Cenozoic

A phylogenetic analysis was conducted to address evolutionary relationships among the earliest members of the Miacidae (one of two early Cenozoic carnivoran families) and to ascertain the position of an ambiguous taxon, “Miacis” jepseni, with respect to the genera Miacis, Uintacyon, Vulpavus, Vassacyon, and Oödectes. The results of this analysis indicate that “Miacis” jepseni should be referred to the genus Oödectes, and both genus and currently included species are rediagnosed. The phylogenetic relationship of Oödectes to other miacids, and relationships among early Eocene miacids more generally, however, are less well resolved. Support is found for sister taxon relationships between Miacis and Vulpavus and between Uintacyon and Vassacyon, and it is suggested that this latter clade is the sister taxon to all other members of Miacidae.

Identification of nuclear low-copy genes and their phylogenetic utility in rosids

Genome ◽  
2014 ◽  
Vol 57 (10) ◽  
pp. 547-554 ◽  
Author(s):  
Baohua Wang ◽  
Yan Zhang ◽  
Peipei Wei ◽  
Miao Sun ◽  
Xiaofei Ma ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Nuclear Data ◽  
Single Copy ◽  
Orthologous Sequence ◽  
Phylogenetic Studies ◽  
Single Copy Nuclear Gene ◽  
Relationship Of ◽  
Consistent Support

By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eukaryotic orthologous groups) database, most of which were first used for phylogenetic analysis of angiosperms. The orthologous sequence datasets from completely sequenced genomes of rosids were assembled for the resolution of the position of the COM (Celastrales–Oxalidales–Malpighiales) clade in rosids. Our analysis revealed strong and consistent support for CM topology (the COM clade as sister to the malvids). Our results will contribute to further exploring the underlying cause of conflict between chloroplast, mitochondrial, and nuclear data. In addition, our study identified a few novel nuclear molecular markers with potential to investigate the deep phylogenetic relationship of plants or other eukaryotic taxonomical groups.

scholarly journals Phylogenetic Study of African Combretaceae R. Br. based on rbcL Sequence

2019 ◽  
Vol 25 (2) ◽  
pp. 170-177
Author(s):  
Alfred Ossai Onefeli ◽  
Vidmantas Stanys
Keyword(s):  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Economic Value ◽  
Composite Index ◽  
Evolutionary Genetics ◽  
Phylogenetic Study ◽  
Medicinal Species ◽  
Multiple Sequence ◽  
Relationship Of

Combretaceae is an angiosperm family of high economic value. However, there is dearth of information on the phylogenetic relationship of the members of this family using ribulose biphosphate carboxylase (rcbL) gene. Previous studies with electrophoretic-based and morphological markers revealed that this family is phylogenetically complex. In the present study, 79 sequences of rbcL were used to study the phylogenetic relationship among the members of Combretaceae of African origin with a view to provide more information required for the utilization and management of this family. Multiple Sequence alignment was executed using the MUSCLE component of Molecular Evolutionary Genetics Version X Analysis (MEGA X). Transition/Transversion ratio, Consistency index, Retention Index and Composite Index were also determined. Phylogenetic trees were constructed using Maximum parsimony (MP) and Neighbor joining methods. The alignment of rcbL in the family Combretaceae shows 0.59 for both variation and parsimony sites with the overall mean distance of 0.71. Result shows that the genera Combretum, Terminalia are polyphyletic, while Conocarpus, Quisqualis and Meiostemon are monophyletic. Findings from this study can be applied to the scientific classification of the African Combretaceae, especially where morphological and electrophoretic-based molecular delimitation have failed. rbcL from this family can also be used as barcodes against drug adulteration of the medicinal species.

scholarly journals Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and variations in shell form due to geography

2017 ◽  
Author(s):  
Chee-Chean Phung ◽  
Pooi-San Heng ◽  
Thor-Seng Liew
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationship ◽  
Species Differences ◽  
Shell Height ◽  
Nuclear Gene ◽  
Land Snails ◽  
Shell Form ◽  
Geographical Variations ◽  
Colour Patterns ◽  
Relationship Of

Leptopoma is a species rich genus with approximately 100 species documented according to shell morphology and animal anatomy. Many of the Leptopoma species are described in terms of shell size, shape, sculpture and colour patterns of a small number of examined materials. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. Over the last decade, more than 900 collection lots consisting of more than 4000 Leptopoma specimens have been obtained in Sabah and deposited in BORNEENSIS at Universiti Malaysia Sabah. Access to this collection gave us the opportunity to examine the geographical variations in shell forms and the phylogenetic relationship of Leptopoma species in Sabah. The phylogenetic relationship of three Leptopoma species was first estimated by performing maximum likelihood and Bayesian analysis based on mitochondrial genes (16S and COI) and nuclear gene (ITS-1). After this, a total of six quantitative shell characters (i.e. shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height and width) and three qualitative shell characters (i.e. shell colour patterns, spiral ridges, and dark ring band in aperture) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e. Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with one of the shell characters (i.e. shell spiral ridges) in the current morphological-based classification. Other qualitative and quantitative shell characters were incongruent with the Leptopoma species phylogeny. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to intra-species differences between populations from different locations. This study provides an initiation to resolve the taxonomy conundrum for the remaining 100 little known Leptopoma species from other regions and highlights a need to assess variations in shell characters before they could be used in species classification.

Comparative mitogenomes and phylogenetic analysis reveal taxonomic relationship of genera Teredorus and Systolederus (Orthoptera, Tetrigoidea)

Zootaxa ◽  
2021 ◽  
Vol 5027 (1) ◽  
pp. 127-135
Author(s):  
XUEJUAN LI ◽  
YUXIN LIU ◽  
LILIANG LIN
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Phylogenetic Relationship ◽  
Morphological Characteristics ◽  
Mitochondrial Genomes ◽  
Taxonomic Relationship ◽  
Mitochondrial Sequences ◽  
Relationship Of

The genera Teredorus and Systolederus belong to Tetriginae and Metrodorinae respectively. However, species within these two genera have strikingly similar features, made it difficult to identify clearly by morphological characteristics. In this study, we sequenced the mitochondrial genomes (mitogenomes) of two Teredorus species, and compared them with Systolederus mitochondrial sequences. The sequenced mitogenomes of T. hainanensis and T. bashanensis are 14,946 bp and 14,775 bp in size, respectively. The A+T content of mitogenomes is 76.2% (T. hainanensis) and 74.0% (T. bashanensis). Comparative analysis showed that mitochondrial sequences and structure were similar within these two genera. The results of K2P distances and phylogenetic analysis revealed that Systolederus and Teredorus might be likely considered as one genus of Teredorus. It will provide important resources for further understanding of the taxonomy and phylogenetic relationship of Systolederus and Teredorus.  

scholarly journals Phylogenetic analysis of perfect repeats in the genomes of unicellular cyanobacteria

2005 ◽  
Vol 3 (2) ◽  
pp. 15-21
Author(s):  
Lidia E Mikheeva ◽  
Yuri L Orlov ◽  
Nikolay A Kolchanov ◽  
Sergey V Shestakov
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Molecular Phylogeny ◽  
Genome Organization ◽  
Whole Genome ◽  
Ecological Genomics ◽  
Close Phylogenetic Relationship ◽  
Complete Genomes ◽  
Relationship Of ◽  
Close Genetic Relationship

We have fulfilled in silico research of number, structure, distribution and location of direct and inverted repeated sequences in eight complete genomes of unicellular cyanobacteria. Analysis of whole genome repeats has shown utility of this approach for purposes of molecular phylogeny and ecological genomics. Comparative analysis of nonrandom repeats patterns has allowed: 1) to confirm the close genetic relationship of two Prochlorococcus marinus strains (MED4 and SS120) that have reduced genomes and inhabit the econiches with different light intensities; 2) to suggest the close phylogenetic relationship of genomes Prochlorococcus marinus MIT9313 and Synechococcus WH8102 that significantly differ by sets of lightharvesting photosystem; 3) to  reveal specific differences in genome organization between marine and freshwater cyanobacteria.

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