scholarly journals Juniperus excelsa s. str. in crimea – differentiation and history inferred from genetic and morphological markers

2021 ◽  
Vol 63 (4) ◽  
pp. 276-288
Author(s):  
Małgorzata Mazur ◽  
Katarzyna A. Jadwiszczak ◽  
Agnieszka Bona ◽  
Yuliya Krasylenko ◽  
Oleg Kukushkin ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Geographic Location ◽  
Morphological Differentiation ◽  
Species Range ◽  
Internal Transcribed Spacer Region ◽  
Crimean Peninsula ◽  
Molecular Features ◽  
Juniperus Excelsa ◽  
Close Relationship

Abstract Juniperus excelsa s. str. (Greek juniper) in Crimea is a relic species on the limits of its range, and represents the Mediterranean flora in the Sub-Mediterranean part of the peninsula. Its origin and history in this area remains unresolved. We aimed to analyze phylogeny and potential demographic expansion of the juniper in the Crimea as well as to study its morphological differentiation. We analyzed plant material from 59 trees inhabiting eight populations. Genetic variation assessments were based on the four non-coding chloroplast DNA (cpDNA) fragments and the nuclear internal transcribed spacer region ITS1-5,8S-ITS2 (ITS). To examine the morphological differentiation, eight measured/counted traits of cones, seeds, and shoots were chosen and eight ratios were calculated. Morphological parameters were compared using ANOVA, Student’s t test, discrimination analysis and Kruskal-Wallis and U Mann-Whitney tests. Two cpDNA fragments were polymorphic and, in total, 10 cpDNA haplotypes were found. Haplotype diversity (Hd) ranged from 0.0 to 0.9. Based on both cpDNA and ITS sequences variation, phylogenetic analyses revealed a close relationship of the Crimean junipers to the individuals from other parts of the species range. In general, our molecular results confirmed the low level of genetic differentiation of J. excelsa individuals inhabiting different parts of the species range, likely resulting from a common ancestry. Only slight morphological differences were found between populations with different geographic location or habitat. The analyzes showed the distinctness of the populations from the southern part of the coast. Some unique morphological and molecular features of southern coastal populations imply that they are remnants of Late Pleistocene abundant forests. We suggest that the recent fragmentation of the Juniperus populations in the Crimean Peninsula could have arisen during the Atlantic period of the Holocene.

Divergence, diversity and species of the Australasian Callitris (Cupressaceae) and allied genera: evidence from ITS sequence data

2003 ◽  
Vol 16 (4) ◽  
pp. 505 ◽  
Author(s):  
M. G. Pye ◽  
P. A. Gadek ◽  
K. J. Edwards
Keyword(s):  
Strong Evidence ◽  
Internal Transcribed Spacer ◽  
New Caledonia ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequence ◽  
Internal Transcribed Spacer Region ◽  
Diverse Range ◽  
26S Rdna ◽  
Close Relationship

Callitris Vent. is the most speciose of the Southern Hemisphere genera of Cupressaceae, occupying a diverse range of habitats within Australia and New Caledonia and is closely allied to Actinostrobus Miq. and the monotypic New Caledonian genus Neocallitropsis Florin. Results of phylogenetic analyses of 18S–26S rDNA internal transcribed spacer region sequences for representatives of 12 of the 18 currently recognised species of Callitris, two of the three Actinostrobus species and the single known species of Neocallitropsis help to clarify major lineages and relationships in this group. ITS data provide strong evidence against the monophyly of Callitris as currently circumscribed, with the strongest evidence being for the inclusion of the New Caledonian monotypic species Neocallitropsis pancheri (Carriere) de Laubenfels. This species shares a close relationship with C. sulcata (Parl.) Schltr. Three representatives of Actinostrobus are monophyletic and are placed in a polytomy with C.�drummondii (Parl.) F.Muell., although indels provide some support for the early divergence of Actinostrobus in this group. Remaining sampled members of Callitris form a weakly supported clade, with C. macleayana (F.Muell.) F.Muell. sister to a highly robust core Callitris. Relationships within this core Callitris are unresolved; however, the following seven lineages are supported: C. rhomboidea R.Br. ex Rich.; C. muelleri (Parl.) F.Muell., C. oblonga Rich. and C. endlicheri (Parl.) F.M. Bailey; C. gracilis R.T. Baker, C. glaucophylla Thompson & Johnson and C.�tuberculata R.Br. ex R.T. Baker & Smith; C. intratropica Baker & Smith; and C. columellaris F.Muell. There has been a marked increase in the rate of divergence of ITS sequences during the evolution of those populations assigned to C. intratropica, which perhaps reflects speciation processes within this widely distributed group.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Racial Differences in Esophageal Squamous Cell Carcinoma: Incidence and Molecular Features

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Shirui Chen ◽  
Kai Zhou ◽  
Liguang Yang ◽  
Guohui Ding ◽  
Hong Li
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Cancer ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Racial Differences ◽  
Squamous Cell ◽  
Geographic Location ◽  
Molecular Features ◽  
Genome Wide ◽  
White Patients

The incidence and histological type of esophageal cancer are highly variable depending on geographic location and race/ethnicity. Here we want to determine if racial difference exists in the molecular features of esophageal cancer. We firstly confirmed that the incidence rate of esophagus adenocarcinoma (EA) was higher in Whites than in Asians and Blacks, while the incidence of esophageal squamous cell carcinoma (ESCC) was highest in Asians. Then we compared the genome-wide somatic mutations, methylation, and gene expression to identify differential genes by race. The mutation frequencies of some genes in the same pathway showed opposite difference between Asian and White patients, but their functional effects to the pathway may be consistent. The global patterns of methylation and expression were similar, which reflected the common characteristics of ESCC tumors from different populations. A small number of genes had significant differences between Asians and Whites. More interesting, the racial differences of COL11A1 were consistent across multiple molecular levels, with higher mutation frequency, higher methylation, and lower expression in White patients. This indicated that COL11A1 might play important roles in ESCC, especially in White population. Additional studies are needed to further explore their functions in esophageal cancer.

Origin of euconodont elements

1993 ◽  
Vol 67 (4) ◽  
pp. 640-654 ◽  
Author(s):  
Hubert Szaniawski ◽  
Stefan Bengtson
Keyword(s):  
Morphological Differentiation ◽  
Ontogenetic Development ◽  
Evolutionary Development ◽  
Posterior Edge ◽  
Upper Cambrian ◽  
Close Relationship

Primitive euconodont elements from the Upper Cambrian of Sweden are investigated histologically and compared with co-occurring elements of paraconodonts. The proposed close relationship between the two groups is confirmed. Typical euconodont and paraconodont elements are bridged by intermediate forms. The ontogenetic development of the early euconodont elements shows striking similarities to the evolutionary development from paraconodonts to euconodonts, suggesting that evolution generally followed a peramorphic pattern (“recapitulation”). The conodont crown originated through extension of the growth lamellae around the whole element, accompanied by stronger mineralization. The first denticulation in Proconodontus arose when a jagged posterior edge in juvenile specimens was enhanced by the subsequent deposition of growth lamellae, a process comparable to the regeneration of broken tips. The most primitive euconodont elements probably erupted from the epithelium earlier in ontogeny than in more advanced forms. After the appearance of the phosphatic crown, conodont elements underwent a very rapid morphological differentiation. Cordylodus may have arisen from Proconodontus serratus.

scholarly journals Characterization and Establishment of a Novel EBV Strain Simultaneously Associated With Nasopharyngeal Carcinoma and B-Cell Lymphoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Fenggang Yu ◽  
Nicholas L. Syn ◽  
Yanan Lu ◽  
Qing Yun Chong ◽  
Junyun Lai ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Phylogenetic Analyses ◽  
Human Tumor ◽  
B Cell Lymphoma ◽  
Asia Pacific ◽  
B Lymphoma ◽  
Barr Virus ◽  
Molecular Features ◽  
Geographical Regions ◽  
Epstein Barr

Epstein-Barr virus (EBV)—the prototypical human tumor virus—is responsible for 1–2% of the global cancer burden, but divergent strains seem to exist in different geographical regions with distinct predilections for causing lymphoid or epithelial malignancies. Here we report the establishment and characterization of Yu103, an Asia Pacific EBV strain with a highly remarkable provenance of being derived from nasopharyngeal carcinoma biopsy but subsequently propagated in human B-lymphoma cells and xenograft models. Unlike previously characterized EBV strains which are either predominantly B-lymphotropic or epitheliotropic, Yu103 evinces an uncanny capacity to infect and transform both B-lymphocytes and nasopharyngeal epithelial cells. Genomic and phylogenetic analyses indicated that Yu103 EBV lies midway along the spectrum of EBV strains known to drive lymphomagenesis or carcinogenesis, and harbors molecular features which likely account for its unusual properties. To our knowledge, Yu103 EBV is currently the only EBV isolate shown to drive human nasopharyngeal carcinoma and B-lymphoma, and should therefore provide a powerful novel platform for research on EBV-driven hematological and epithelial malignancies.

scholarly journals Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

2021 ◽  
Author(s):  
Blessing Amaka Ezeonuegbu ◽  
Dauda Abdullahi Machido ◽  
Clement Z. Whong ◽  
Wisdom S. Japhet ◽  
Clement Ameh Yaro ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Industrial Effluent ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Likelihood Method ◽  
Internal Transcribed Spacer Region ◽  
Fungal Isolates ◽  
Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

A new species of Cleistocybe (Agaricales, Basidiomycota) from the Tibetan Plateau, China

Phytotaxa ◽  
2018 ◽  
Vol 336 (3) ◽  
pp. 286 ◽  
Author(s):  
HONG-MEI WU ◽  
JIA-QI LUO ◽  
KE WANG ◽  
RUN-CHAO ZHANG ◽  
YI LI ◽  
...  
Keyword(s):  
New Species ◽  
Tibetan Plateau ◽  
Phylogenetic Analyses ◽  
Morphological Observation ◽  
Morphological Description ◽  
The Tibetan Plateau ◽  
Sequence Analyses ◽  
The North ◽  
Close Relationship ◽  
A New Species

During field expeditions to the Tibetan Plateau, a collection of an undescribed species with several basidiomes was found. Morphological observation and DNA sequence analyses of the collection revealed a close relationship with Cleistocybe vernalis, the type species of the genus Cleistocybe. Therefore, a new species is proposed for the fungus with full morphological description accompanied by phylogenetic analyses. The discovery of the species extends the reported distribution of the genus from the north of America and Europe to Asia.

scholarly journals Eutypa, Eutypella, and Cryptovalsa Species (Diatrypaceae) Associated with Prunus Species in South Africa

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1402-1409 ◽  
Author(s):  
Providence Moyo ◽  
Ulrike Damm ◽  
Lizel Mostert ◽  
Francois Halleen
Keyword(s):  
South Africa ◽  
Phylogenetic Analyses ◽  
Fruit Trees ◽  
Fungal Species ◽  
Stone Fruit ◽  
Prunus Species ◽  
Internal Transcribed Spacer Region ◽  
Eutypa Lata ◽  
Eutypa Dieback ◽  
Prunus Spp

Stone fruit trees (Prunus spp.) are economically important fruit trees cultivated in South Africa. These trees are often grown in close proximity to vineyards and are to a large extent affected by the same trunk disease pathogens as grapevines. The aim of the present study was to determine whether stone fruit trees are inhabited by Diatrypaceae species known from grapevines and whether these trees could act as alternative hosts for these fungal species. Isolations were carried out from symptomatic wood of Prunus species (almond, apricot, cherry, nectarine, peach, and plum) in stone fruit growing areas in South Africa. Identification of isolates was based on phylogenetic analyses of the internal transcribed spacer region and β-tubulin gene. Forty-six Diatrypaceae isolates were obtained from a total of 380 wood samples, from which five species were identified. All five species have also been associated with dieback of grapevine. The highest number of isolates was found on apricot followed by plum. No Diatrypaceae species were isolated from peach and nectarine. Eutypa lata was the dominant species isolated (26 isolates), followed by Cryptovalsa ampelina (7), Eutypa cremea (5), Eutypella citricola (5), and Eutypella microtheca (3). First reports from Prunus spp. are E. cremea, E. citricola, and E. microtheca. Pathogenicity tests conducted on apricot and plum revealed that all these species are pathogenic to these hosts, causing red-brown necrotic lesions like those typical of Eutypa dieback on apricot.

An expanded concept of Madisonia including miscellaneous species of Pleurothallidinae (Orchidaceae): evidence from molecular analysis

Phytotaxa ◽  
2021 ◽  
Vol 505 (1) ◽  
pp. 71-84
Author(s):  
ERIC DE CAMARGO SMIDT ◽  
A. L. V. TOSCANO DE BRITO ◽  
ANNA VICTORIA SILVÉRIO R. MAUAD ◽  
NICOLÁS GUTIÉRREZ MORALES
Keyword(s):  
Molecular Analysis ◽  
Amazon Basin ◽  
Phylogenetic Analyses ◽  
Monotypic Genus ◽  
Phylogenetic Information ◽  
Close Relationship ◽  
The Caribbean ◽  
Taxonomic Studies ◽  
Expanded Concept ◽  
New Nomenclatural Combinations

Prior taxonomic studies in subtribe Pleurothallidinae have suggested a close relationship between miscellaneous species featuring long-repent, segmented rhizomes, abbreviated ramicauls, few-flowered inflorescences, and flowers with partially connate sepals and trilobed lip. The lack of phylogenetic information for most species has prevented further conclusions or changes in their taxonomy; and as a result, they are currently assigned to several unrelated genera: Anathallis, Madisonia, Pabstiella, Pleurothallis, Sansonia and Specklinia. We performed phylogenetic analyses using nuclear (nrITS) and five plastid (matK, psbD-trnT, rps16-trnQ, trnH-psbA and trnS-trnG) markers and demonstrated that these species form an isolated clade which requires generic recognition. The name Madisonia, previously a monotypic genus endemic of the Amazon basin, is re-circumscribed and expanded to include nine species distributed in the Atlantic Rainforest and the Caribbean. Eight new nomenclatural combinations are proposed.

Amanita submelleialba sp. nov. in section Amanita from northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 513 (2) ◽  
pp. 129-140
Author(s):  
YUAN S. LIU ◽  
JIAN-KUI LIU ◽  
PETER E. MORTIMER ◽  
SAISAMORN LUMYONG
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Line Drawing ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Nuclear Rdna ◽  
Internal Transcribed Spacer Region ◽  
Northern Thailand ◽  
Extant Species ◽  
Distinct Lineage

Amanita submelleialba sp. nov. in section Amanita, is described from northern Thailand based on both multi-gene phylogenetic analysis and morphological evidences. It is characterized by having small to medium-sized basidiomata; a yellow to yellowish pale pileus covering pyramidal to subconical, white to yellow white volval remnants; globose stipe base covered conical, white to yellow white volval remnants; fugacious subapical annulus; and absent clamps. Multi-gene phylogenetic analyses based on partial nuclear rDNA internal transcribed spacer region (ITS), partial nuclear rDNA larger subunit region (nrLSU), RNA polymerase II second largest subunit (RPB2), partial translation elongation factor 1-alpha (TEF1-α) and beta-tubulin gene (TUB) indicated that A. submelleialba clustered together with A. elata and A. mira, but represented as a distinct lineage from other extant species in section Amanita. The detailed morphological characteristics, line-drawing illustration and comparisons with morphologically similar taxa are provided.

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