How to resolve cryptic species of polypores: an example in Fomes by Ursula Peintner, Regina Kuhnert-Finkernagel, Viana Wille, Franco Biasioli, Anton Shiryaev, Claudia Perini

“…A detailed examination of a number of different Fomes strains that had been collected and isolated from different habitats in Italy and Austria confirmed the presence of distinct lineages in the Fomes fomentarius clade. Our zero hypothesis was that the Mediterranean strains growing on Quercus represent a species which can be delimited based on morphological and physiological characters when they are evaluated in statistically relevant numbers. …”
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Genetic Diversity of Echinococcus granulosus in Southwest China Determined by the Mitochondrial NADH Dehydrogenase Subunit 2 Gene by Jiahai Wang, Ning Wang, Dandan Hu, Xiuqin Zhong, Shuxian Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang

“…We detected 19 haplotypes, which formed a distinct clade with the standard sheep strain (G1). Hence, all 51 isolates were identified as E. granulosus sensu stricto (G1–G3). …”
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Phylogeny and taxonomy of Nigroporus (Polyporales, Basidiomycota) with four new species from Asia and Oceania by Xiang-Lin Li, Yu-Cheng Dai, Zhan-Bo Liu, Yu-Han Jiang, Hong-Gao Liu, Yuan Yuan

“…The 2-gene (ITS+nLSU) analysis of the Steccherinaceae indicated that the four new species nested in the Nigroporus clade. The 3-gene (ITS+nLSU+TEF1) analysis of the genus Nigroporus showed that N. australianus formed a monophyletic lineage, N. subvinosus was sister to N. austroasianus and N. yunnanensis, and N. austroasianus was sister to N. yunnanensis. …”
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Anthracophyllum sontraense (Omphalotaceae, Agaricales), A New Species from Danang, Vietnam by Trung Thanh Nguyen, Hanh Hong Do, Toan Nguyen-Sy, Uyen Thi Diem Huynh, Nguyen Thi Lam Hai, Thi Thanh Tam Phan, Thi Thu Hoai Nguyen, Do Tan Khang, Phu Thi Tran

“…The phylogenetic analyses based on the combined internal transcribed spacer (ITS) and Large Subunit (LSU) molecular markers of ribosomal RNA genes revealed that the two specimens clustered in a single clade at species level with all tested Anthracophyllum species with strong bootstrap support of 99%. …”
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Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex by Harald Bernhard, Hana Petržílková, Barbora Popelářová, Kamil Ziemkiewicz, Karolina Bartosik, Marcin Warmiński, Laura Tengo, Henri Gröger, Luciano G. Dolce, Cameron D. Mackereth, Ronald Micura, Jacek Jemielity, Eva Kowalinski

“…Abstract Kinetoplastids are a clade of eukaryotic protozoans that include human parasitic pathogens like trypanosomes and Leishmania species. …”
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Molecular Detection of Anaplasma phagocytophilum in Small Mammals and Infesting Ticks in Laikipia County, Kenya by Erick Titus Mosha, Joseph K. N. Kuria, Moses Otiende, Isaac Lekolool

“…Comparison was also made with a known pathogenic A. phagocytophilum variant HA and a nonpathogenic variant 1 that were clustered into a distinctive clade different form haplotypes detected in this study. …”
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New insights into the stipitate hydnoid fungi Sarcodon, Hydnellum, and the formerly informally defined Neosarcodon, with emphasis on the edible species marketed in Southwest China by Di Wang, Hui Feng, Jie Zhou, Tian-Hai Liu, Zhi-Yuan Zhang, Ying-Yin Xu, Jie Tang, Wei-Hong Peng, Xiao-Lan He

“…In the present molecular analyses, four distinct clades were recovered and strongly supported: Hydnellum, Neosarcodon, Phellodon and Sarcodon. …”
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Genome variability of domestic tomato varieties: data from AFLP analysis by A. V. Kulakova, E. A. Dyachenko, A. V. Shchennikova, O. N. Pyshnaya, E. A. Dzhos

“…Analysis of the amplification spectra placed wild tomato accessions into separate clades. Sister clades included cultivars of FSCV breeding resistant to drought and/or cold and, in part, to late blight, Alternaria, Septoria, tobacco mosaic virus and blossom end rot, as well as tomato accessions not characterized according to these traits, which suggests that they have resistance to stress factors. …”
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Integrating phylogeographic and phenotypic evidence to delimit deep evolutionary lineages in the Dryophytes japonicus species complex, with an assessment of their conservation need... by Amaël Borzée, Yikweon Jang, Siti N. Othman, Jordy Groffen, Irina V. Maslova, Zoljargal Purevdorj, Kiyomi Yasumiba, Tomohiko Shimada, Yoonjung Yi, Natalya Alekseevna Schepina, Desiree Andersen, Yoonhyuk Bae, Ikuo Miura, Christophe Dufresnes

“…Earlier studies on the northeast Asian treefrog, Dryophytes japonicus, identified a deep Mio-Pliocene diversification; however, phenotypic assessments were lacking, and the taxonomic identity of the identified clades is under debate. In this study, we assessed the genetic, genomic, morphological, and acoustic diversity and differentiation within the D. japonicus complex to propose taxonomic arrangements and assess taxon-specific threats for each defined clade. …”
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Comparative analysis of genetic polymorphism in <i>Rhaponticum carthamoides</i> (Asteraceae) populations by ISSR markers in the Altai Republic by E. V. Zhmud, I. N. Kuban, A. A. Achimova, M. B. Yamtyrov, O. V. Dorogina

“…The analysis showed that individual plants from five cenopopulations (CP) were distributed into three groups of similarity on the dendrogram. A separate clade was formed by plant samples from two CPs of the Katun Nature Reserve (KNR). …”
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<i>Phytophthora</i> Species and Their Associations with Chaparral and Oak Woodland Vegetation in Southern California by Sebastian N. Fajardo, Tyler B. Bourret, Susan J. Frankel, David M. Rizzo

“…<i>cadmea</i> (subclade 7a), <i>P</i>. taxon ‘oakpath’ (subclade 8e, first reported in this study), and several clade-6 species, including <i>P. crassamura</i>. …”
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Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa by Feifei Liu, Shuaifei Chen, Maria A. Ferreira, Runlei Chang, Mohammad Sayari, Aquillah M. Kanzi, Brenda D. Wingfield, Michael J. Wingfield, David Pizarro, Ana Crespo, Pradeep K. Divakar, Z. Wilhelm de Beer, Tuan A. Duong

“…Alectoria sarmentosa is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi.…”
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Avian influenza overview September–December 2024 by European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian Influenza, Leonidas Alexakis, Hubert Buczkowski, Mariette Ducatez, Alice Fusaro, Jose L. Gonzales, Thijs Kuiken, Karl Ståhl, Christoph Staubach, Olov Svartström, Calogero Terregino, Katriina Willgert, Miguel Melo, Lisa Kohnle

“…The risk of infection with currently circulating avian A(H5) influenza viruses of clade 2.3.4.4b in Europe remains low for the general public in the European Union/European Economic Area (EU/EEA). …”
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Biogeographic Insights Into the Late Miocene Diversification of the Giant Deep‐Ocean Amphipod Eurythenes by Carolina E. González, Johanna N. J. Weston, Reinaldo Rivera, Marcelo Oliva, Rubén Escribano, Osvaldo Ulloa

“…The resulting phylogenetic tree reveals a diverse clade, with a common ancestor originating around 11.81 Ma. …”
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A novel approach to analyzing the evolution of SARS-CoV-2 based on visualization and clustering of large genetic data compactly represented in operative memory by A. Yu. Palyanov, N. V. Palyanova

“…It is in good correspondence with phylogenetic trees (usually based on 3–4 thousand of genome variant representatives), but is built over millions of genomes, shows more details and is independent of the type of lineage/clade classification.…”
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Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling by Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui, Jun Cao

“…A phylogenetic analysis revealed that they could be further divided into four, three, and two clades, respectively. The distribution of protein motifs and gene structures among members of the same clade exhibited notable similarity. …”
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A soft tick vector of Babesia sp. YLG in Yellow-legged gull (Larus michahellis) nests by Bonsergent, Claire, Vittecoq, Marion, Leray, Carole, Jouglin, Maggy, Buysse, Marie, McCoy, Karen D., Malandrin, Laurence

“…YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studied Babesia sp. …”
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Morphological and phylogenetic features of the Crimean population of <i>Juniperus deltoids</i> R.P. Adams by A. O. Lantushenko, O. O. Korenkova, A. A. Syrovets, Ya. V. Meger, P. A. Korenkov, O. M. Shevchuk

“…The sequences obtained in this work formed a clade with J. deltoides samples 9430 and 9431 (BAYLU) growing in Turkey, which makes it possible to assign the samples studied to J. deltoides.…”
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Decoding mpox: a systematic review and meta-analysis of the transmission and severity parameters of the 2022–2023 global outbreak by Adriana Buitrago-Lopez, Zulma M Cucunubá, Candida Diaz Brochero, Laura Cristina Nocua-Báez, Jorge Alberto Cortes, Kelly Charniga

“…CFR estimates varied by geographical region and were higher in Africa, in countries linked with clade I. Our results contribute to a better understanding of mpox dynamics, and the development of mathematical models to assess the impact of current and future interventions.…”
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Analysis of marker substitutions in A/chicken/Astrakhan/2171-1/2020 H5N8 isolate of avian influenza virus recovered in the Astrakhan Oblast by N. G. Zinyakov, A. V. Andriyasov, Ye. V. Ovchinnikova, A. A. Kozlov, P. D. Zhestkov, D. B. Andreychuk, I. A. Chvala

“…Phylogenetic analysis of nucleotide sequences of hemagglutinin gene segment (848–1105 bp ORF) allowed A/chicken/Astrakhan/2171-1/2020 H5N8 isolate to be classified to highly pathogenic avian influenza virus genetic clade 2.3.4.4. Comparative analysis of genome segments using available databases showed that A/chicken/Astrakhan/2171-1/2020 H5N8 virus related to А/Н5 avian influenza virus isolates detected in the Russian Federation in 2016–2020. …”
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