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.

Sporastatia crassulata, a new species from the Altai Mountains with a key to Sporastatia and remarks on some additional species

2018 ◽  
Vol 50 (4) ◽  
pp. 439-450
Author(s):  
Lidia S. YAKOVCHENKO ◽  
Evgeny A. DAVYDOV
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Diversity ◽  
Central Asia ◽  
Type Specimen ◽  
New Combination ◽  
Altai Mountains ◽  
Additional Species ◽  
Sister Relationship ◽  
A New Species

AbstractSporastatia crassulata Yakovchenko & Davydov sp. nov. is described and a phylogenetic analysis (mtSSU) is presented, confirming its distinctness and indicating a sister relationship with S. testudinea. The species is unique among Sporastatia species in having a distinctly squamulose, thick, uneven thallus composed of convex, rounded squamules irregularly ascending in the central part of the thallus. The new combination Sporastatia karakorina (Poelt & Obermayer) Davydov & Yakovchenko is proposed. The type specimen of S. subasiatica was examined. A key to the six species of Sporastatia is given. Mountainous Central Asia appears to be the centre of species diversity and endemism for Sporastatia.

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.

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.

Pseudodactylaria fusiformis sp. nov. from freshwater habitat in China

Phytotaxa ◽  
2020 ◽  
Vol 446 (2) ◽  
pp. 95-102
Author(s):  
YONG-ZHONG LU ◽  
JING-YI ZHANG ◽  
CHUAN-GEN LIN ◽  
ZONG-LONG LUO ◽  
JIAN-KUI (JACK) LIU
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Latitudinal Gradient ◽  
Sequence Data ◽  
Distinct Species ◽  
Freshwater Fungi ◽  
Morphological Comparison ◽  
Sister Relationship ◽  
Freshwater Habitat ◽  
Phylogenetic Placement

Pseudodactylaria fusiformis sp. nov. was collected during an investigation of freshwater fungi along a north-south latitudinal gradient in the Asian region. Evidence for the new species is provided by morphological comparison and sequence data analysis. Pseudodactylaria fusiformis differs from other species in having hyaline conidiophores and fusiform, 0–1-septate hyaline conidia without a sheath. Phylogenetic analysis based on combined ITS and LSU sequence data was carried out to determine the phylogenetic placement of the species. Six Pseudodactylaria taxa clustered together and formed a monotypic clade representing the genus, and five species are well recognized. Pseudodactylaria fusiformis and P. camporesiana share a sister relationship and they are phylogenetically distinct species. A detailed description and illustration are provided, as well as the comparisons with similar taxa.

Phylogenetic analysis of the genera of endemic Hawaiian sap beetles (Coleoptera: Nitidulidae) based on morphology with redescription and key to the genera of endemic Hawaiian Nitidulidae

Zootaxa ◽  
2007 ◽  
Vol 1427 (1) ◽  
pp. 1-36 ◽  
Author(s):  
CURTIS EWING
Keyword(s):  
Phylogenetic Analysis ◽  
Single Species ◽  
Morphological Characters ◽  
External Morphology ◽  
Direct Connection ◽  
Undescribed Species ◽  
Additional Species ◽  
Incertae Sedis ◽  
Sap Beetles ◽  
Endemic Genera

The endemic Hawaiian sap beetles were originally placed in 13 genera in 1908; Apetasimus, Apetinus, Cillaeopeplus, Cyrtostolus, Eunitidula, Eupetinus, Gonioryctus, Goniothorax, Nesapterus, Nesopeplus, Nesopetinus, Notopeplus, and Orthostolus. Apetasimus, Cyrtostolus, Eunitidula, and Notopeplus were described for single species, with additional species later described for Apetasimus and three undescribed species known for Eunitidula from Oahu, Molokai, and West Maui. Nesopeplus and Nesopetinus have been previously shown to be junior synonyms of Prosopeus. The monophyly of the genera is tested using morphological characters, primarily of the male copulatory sac, in a parsimony framework. The results provide the rationale for reducing the number of endemic genera to six; Apetasimus (= Cyrtostolus + Orthostolus in part), Cillaeopeplus (= Notopeplus), Eupetinus (= Apetinus), Gonioryctus (= Eunitidula + Goniothorax + Nesapterus), Orthostolus s.s., and Prosopeus. Brachypeplus (= Cillaeopeplus) gracilis, a species endemic to Guam, was placed in the formerly Hawaiian endemic Cillaeopeplus in 1962. Examination of the types of all species of Cillaeopeplus shows no direct connection between B. gracilis and the Hawaiian taxa comprising the remainder of Cillaeopeplus. Brachypeplus gracilis is placed incertae sedis in Brachypeplus herein. The position of the endemic Hawaiian sap beetles within the nit idulid subfamily Cillaeinae is surveyed using exemplar species from 22 of 27 genera placed in Cillaeinae. Undescribed species from eastern Polynesia allied with Brachypeplus subgenus Selis are proposed as the closest relatives of the Hawaiian endemic sap beetles based on internal and external morphology.

A new species of the genus Lucasioides Kwon, 1993 (Isopoda, Oniscidea, Agnaridae) from Siberia, Russia

Zootaxa ◽  
2021 ◽  
Vol 4903 (1) ◽  
pp. 140-150
Author(s):  
KONSTANTIN B. GONGALSKY ◽  
PAVEL S. NEFEDIEV ◽  
ILYA S. TURBANOV
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
First Record ◽  
Morphological Characters ◽  
Molecular Data ◽  
Altai Mountains ◽  
The Family ◽  
Southwestern Siberia ◽  
A New Species ◽  
Preliminary Phylogenetic Analysis

A new species of the family Agnaridae, Lucasioides altaicus sp. nov., is described from the Altai Mountains, southwestern Siberia, based both on morphological characters and molecular data. This species is the first record of Lucasioides from Russia, whose location is the northernmost habitat of terrestrial isopods in indigenous habitats presently known to Eurasia. The diagnostic characters of the new species and a preliminary phylogenetic analysis within Agnaridae 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.

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