scholarly journals Placolecis kashmirensis sp. nov. (Lichenized Ascomycota, Catillariaceae) from Azad Jammu & Kashmir, Pakistan

2021 ◽  
Vol 58 ◽  
Author(s):  
Robina Kousar ◽  
Rizwana Zulfiqar ◽  
Abdul Nasir Khalid
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Identification Key ◽  
Jammu And Kashmir ◽  
Generic Position

Placolecis kashmirensis sp. nov. is described from Azad Jammu and Kashmir, Pakistan. It is characterized by a yellowish-brown thallus, hyaline, broadly ellipsoid ascospores, a relatively taller hymenium and pear-shaped pycnidia. The generic position is confirmed by a phylogenetic analysis based on nrITS sequences. Description, a phylogenetic tree, and identification key for all the known Placolecis species are provided.

Morphological characteristics of water mite larvae of the genus Arrenurus Duges, 1834, with notes on the phylogeny of the genus and an identification key

Zootaxa ◽  
2008 ◽  
Vol 1765 (1) ◽  
pp. 1 ◽  
Author(s):  
ANDRZEJ ZAWAL
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Principal Components ◽  
Maximum Parsimony ◽  
Morphological Characteristics ◽  
Identification Key ◽  
Individual Species ◽  
Water Mite ◽  
Components Analysis ◽  
Mp Method

The larval characteristics of 42 European Arrenurus species are provided, based on earlier descriptions. Diagnostic characters are elucidated. The division of the genus into the subgenera Arrenurus s. str., Micrarrenurus, Megaluracarus, Micruracarus, and Truncaturus has been retained. Principal Components Analysis (PCA) and phylogenetic analysis using the Maximum Parsimony (MP) method were used to construct a phylogenetic tree of the genus. Recommendations on changes to the traditional subgeneric systematics are given, concerning mainly the subgenera Micruracarus and Truncaturus as well as subgeneric allocation of Arrenurus nobilis Neuman which is transferred from Arrenurus s. str. to Micruracarus. An identification key, supplemented with diagnostic descriptions of individual species, is supplied.

Rhizocarpon smaragdulum, a new monosporic yellow-thalline species and some additional species of the genus Rhizocarpon from the Altai Mountains (Siberia)

2017 ◽  
Vol 49 (5) ◽  
pp. 457-466 ◽  
Author(s):  
Evgeny A. DAVYDOV ◽  
Lidia S. YAKOVCHENKO
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Altai Mountains ◽  
Additional Species ◽  
Sister Relationship

AbstractRhizocarpon smaragdulum Davydov & Yakovchenko sp. nov. is described and a phylogenetic analysis (ITS, mtSSU) is presented, confirming its distinctiveness and indicating a sister relationship with R. suomiense and R. subgeminatum. The species is unique among yellow Rhizocarpon species in having a single hyaline ascospore per ascus. The phylogenetic tree suggests that the number of ascospores per ascus has been reduced in Rhizocarpon more than once during the course of its evolution. Two new distributional records are also reported: Rhizocarpon atroflavescens is new for Siberia and R. norvegicum is new for the Altai Mountains. Rhizocarpon norvegicum in this region grows on rocks and is also lichenicolous on Acarospora bullata.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

CONTRIBUTIONS TO THE KNOWLEDGE OF CAMBODIAN CYPERACEAE

2019 ◽  
Vol 76 (2) ◽  
pp. 197-220
Author(s):  
K. Tremetsberger ◽  
S. Hameister ◽  
D. A. Simpson ◽  
K.-G. Bernhardt
Keyword(s):  
Phylogenetic Analysis ◽  
Southeast Asia ◽  
Phylogenetic Tree ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Sequences ◽  
Cryptic Variation ◽  
The Family ◽  
History Of ◽  
Rapid Radiations

To date, there are very few sequence data for Cyperaceae from mainland Southeast Asia. The aim of the present study was to contribute nuclear ribosomal internal transcribed spacer (ITS) sequences of selected species of Cambodian Cyperaceae to the overall phylogeny of the family. We generated ITS sequences of 38 accessions representing 26 species from Cambodia and used these sequences for phylogenetic analysis together with similar sequences from the National Center for Biotechnology Information GenBank. Our results corroborate recent phylogenetic work in the family and largely confirm established tribal relationships. The backbone of the phylogenetic tree of species-rich genera that have undergone rapid radiations is often weakly resolved (e.g. in Fimbristylis and in the C4 clade of Cyperus). Cryptic variation was revealed in the taxonomically difficult group of Fimbristylis dichotoma, with samples of this taxon appearing in two distinct clades within Fimbristylis. Further addition of geographically spread accessions of taxa will improve our understanding of the complex biogeographical history of the genera in the family. Eleocharis koyamae Tremetsb. & D.A.Simpson is proposed as a new name for E. macrorrhiza T. Koyama.

Molecular characterization of small and medium segments of Crimean-Congo hemorrhagic fever virus in Turkey

2020 ◽  
Vol 15 (4) ◽  
pp. 247-254
Author(s):  
Murat Karamese ◽  
Erkan Ozmen ◽  
Hakan Aydin ◽  
Mehmet Ozkan Timurkan ◽  
Mesud Fakirullahoglu
Keyword(s):  
Infectious Disease ◽  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Molecular Characterization ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Crimean Congo Hemorrhagic Fever ◽  
Hemorrhagic Fever Virus ◽  
Relationship Of

Aim: The objective was to investigate the genotypic relationship of S and M segments in Crimean-Congo hemorrhagic fever virus (CCHFV) by phylogenetic analysis in 25 patients from seven endemic cities in Turkey. Materials & methods: A total of 25 samples from patients with CCHF were included between 2012 and 2015. Phylogenetic tree analyses were inferred using MEGA version-6.0 and distances were calculated by Kimura’s 2-parameter. Results: Phylogenetic analysis showed that all isolated viruses (n = 25) were in the predicted clades such as clade V- Europe-1 regarding both S and M segments of the CCHFV. Conclusion: Further epidemiological, molecular and phylogenic studies should be performed in both reservoir animals/vectors and humans to determine the incidence of tick-borne infectious disease and to help to develop vaccines for prevention of the disease.

A taxonomic review and phylogeny of the genera Hoplopisthius Senna, 1892 and Carcinopisthius Kolbe, 1892 (Coleoptera: Brentidae, Hoplopisthiini)

Zootaxa ◽  
2010 ◽  
Vol 2516 (1) ◽  
pp. 1 ◽  
Author(s):  
ANTOINE MANTILLERI
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Parsimony ◽  
New Guinea ◽  
Morphological Characters ◽  
Identification Key ◽  
Generic Level ◽  
Australian Species ◽  
Taxonomic Review ◽  
One New Species

The genera Hoplopisthius and Carcinopisthius are reviewed. All the species are redescribed and illustrated and an updated identification key and distributional maps are provided. One new species from New Guinea is described (Hoplopisthius maximus n. sp.) and two new synonymies are proposed: Hoplopisthius celebensis Kolbe, 1892 = H. trichemerus Senna, 1892, n. syn. and Carcinopisthius lamingtoni Damoiseau, 1987 = C. forcipitiger Damoiseau, 1987, n. syn. Phylogenetic analysis using PAUP (maximum parsimony) was performed using 25 morphological characters of adults. This analysis shows the group Hoplopisthius + Carcinopisthius is monophyletic, but Carcinopisthius alone is paraphyletic. Nomenclatural changes at the generic level are made to reconcile nomenclature and phylogeny: Hoplopisthius is preserved; Carcinopisthius is downgraded to the rank of subgenus for the two oriental species H. oberthueri and H. fruhstorferi; and Pseudotaphroderes is resurrected as a third subgenus and includes all New-Guinean and Australian species.

Roussoella guttulata (Roussoellaceae, Pleosporales), a novel bambusicolous ascomycete from Thailand

Phytotaxa ◽  
2020 ◽  
Vol 471 (3) ◽  
pp. 221-233
Author(s):  
JING-YI ZHANG ◽  
RUNGTIWA PHOOKAMSAK ◽  
SARANYAPHAT BOONMEE ◽  
KEVIN D. HYDE ◽  
DONG-QIN DAI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Tree ◽  
Full Description ◽  
Distinct Lineage ◽  
Thin Walled ◽  
Multigene Phylogenetic Analysis

Roussoella guttulata sp. nov. (Roussoellaceae) was found on bamboo culms collected in the northeast of Thailand. Roussoella guttulata differs from other species in having immersed, gregarious, black pseudoascostromata, single and central ostiole with periphyses, thin-walled peridium composed of cells of textura angularis to textura prismatica and yellowish brown ascospores. The multigene phylogenetic analysis shows that the new species forms a distinct lineage basal to R. hysterioides, R. japanensis, R. scabrispora and R. verrucispora. The new species is compared with closely related Roussoella species. A full description, color photo plates and a phylogenetic tree to show the placement of the new species are provided.

scholarly journals Legume Symbiotic Nitrogen Fixation byβ-Proteobacteria Is Widespread inNature

2003 ◽  
Vol 185 (24) ◽  
pp. 7266-7272 ◽  
Author(s):  
Wen-Ming Chen ◽  
Lionel Moulin ◽  
Cyril Bontemps ◽  
Peter Vandamme ◽  
Gilles Béna ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nitrogen Fixation ◽  
Phylogenetic Tree ◽  
Phylogenetic Diversity ◽  
Symbiotic Nitrogen Fixation ◽  
The Other ◽  
Gene Sequences ◽  
Free Living ◽  
Initial Discovery ◽  
Different Strains

ABSTRACT Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the β-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating thatβ -proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial β-proteobacteria (β-rhizobia) are very similar to those of rhizobia from theα -subclass (α-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. Theβ -rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered β-rhizobial sequences in two nodA lineages intertwined with α-rhizobial sequences. On the other hand, theβ -rhizobia were grouped with free-living nitrogen-fixingβ -proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that β-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.

Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis

Paleobiology ◽  
1997 ◽  
Vol 23 (1) ◽  
pp. 1-19 ◽  
Author(s):  
William C. Clyde ◽  
Daniel C. Fisher
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Ad Hoc ◽  
Retention Indices ◽  
Significant Loss ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Phylogenetic Hypotheses ◽  
Morphologic Data

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

scholarly journals 336 PHYLOGENETIC RELATIONSHIPS OF CELERY AND ITS WILD RELATIVES BASED ON RESTRICTION FRAGMENT LENGTH POLYMORPHISMS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 478f-478
Author(s):  
Gordon M. Huestis ◽  
Carlos F. Quiros
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Chloroplast Dna ◽  
Southern Hemisphere ◽  
Fragment Length ◽  
Wild Species ◽  
Phylogenetic Relationships ◽  
Wild Relatives ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Phylogenetic relationships of seven Apium species, including three horticultural types of A. graveolens, were assayed for RFLPs using cDNA, chloroplast DNA, and rDNA probes. Most of the probes had been previously mapped in celery. The three horticultural types of A. graveolens were found to be less polymorphic than the wild species and in phylogenetic analysis they clustered together. The wild species formed a cluster on the dendrogram corresponding to their origin in the southern hemisphere. A. nodiflorum, a wild species from Ethiopia formed a branch on the phylogenetic tree apart from all other species. This, along with morphological considerations, suggests that A. nodiflorum should be reclassified outside the genus Apium.

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