Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods by A. Yu. Pronozin, A. A. Paulish, E. A. Zavarzin, A. Yu. Prikhodko, N. M. Prokhoshin, Yu. V. Kruchinina, N. P. Goncharov, E. G. Komyshev, M. A. Genaev

“…Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. …”
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The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013–2014 Has Significant Implications for the Epidemiology of the Virus in the Region... by Victor V. Nikiforov, Sergey A. Noskov, Alexander V. Sprygin, Mohammad Abed Alhussen, Anastasia S. Krylova, Taisia V. Erofeeva, Svetlana N. Fomina, Svetlana R. Kremenchugskaya, Fedor I. Korennoy, Maxim V. Patrushev, Ilya A. Chvala, Tamara K. Mayorova, Stepan V. Toshchakov

“…The accessibility of genetic data will facilitate a more comprehensive delineation of FMDV phylogeny on a global scale. In this study, we investigated the FMDV strains circulating in Russia during the 2013–2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences. …”
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Structure and metabolic function of spatiotemporal pit mud microbiome by Zhihua Li, Chi Zhao, Zhenyu Mao, Fengju Zhang, Ling Dong, Chuan Song, Yao Chen, Xin Fu, Zonghua Ao, Yanfei Xiong, Qin Hui, Weizhi Song, Petri Penttinen, Suyi Zhang

“…In this study, we used a combination of metagenomic analysis and chemical derivatization LC–MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples. …”
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Genome polymorphism of the synthetic species xTrititrigia cziczinii Tsvel. inferred from AFLP analysis by A. A. Trifonova, K. V. Boris, L. V. Dedova, V. A. Melnik, L. P. Ivanova, N. P. Kuzmina, S. V. Zavgorodniy, V. P. Upelniek

“…The new species is a good object for fundamental research in the field of genetics, phylogeny and evolution of cereals (Poaceae). However, there were practically no genetic studies of ×T. cziczinii. …”
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Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone by Jianping Jiang, Astrid V. Cienfuegos-Galletd, Tengfei Long, Gisele Peirano, Tingyu Chu, Johann D. D. Pitout, Barry N. Kreiswirth, Liang Chen

“…The molecular epidemiology, population structure, and time phylogeny were investigated. The virulome, resistome, and mobilome were analyzed, and the recombination in the capsular region was studied. …”
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Genomic epidemiology and phenotypic characterization of Staphylococcus aureus isolated from atopic dermatitis patients in South China by Chao Yang, Xiaowei Chen, Min Li, Wenchang Yuan, Shunguang Li, Dexing Han, Junhui Feng, Haimin Luo, Minling Zheng, Jiaqi Liang, Cha Chen, Pinghua Qu, Song Li

“…From China and global perspectives, we analyzed S. aureus’s genomic epidemic traits, phylogeny, and population structure in AD skin. These findings contribute to understanding S. aureus-host interactions and genomic diversity in AD.…”
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Relationship of the gene pool of the Khants with the peoples of Western Siberia, Cis-Urals and the Altai-Sayan Region according to the data on the polymorphism of autosomic locus a... by V. N. Kharkov, N. A. Kolesnikov, L. V. Valikhova, A. A. Zarubin, M. G. Svarovskaya, A. V. Marusin, I. Yu. Khitrinskaya, V. A. Stepanov

“…A detailed phylogenetic analysis of various Y-chromosome haplogroups made it possible to describe and clarify the differences in the phylogeny and structure of individual ethnospecific sublines, to determine their relationship, traces of population expansion in the Khanty gene pool. …”
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Perspektywiczne kierunki rozwoju biologii człowieka w Polsce, ze szczególnym uwzględnieniem auksologii by Napoleon Wolański, Anna Siniarska

“…However, the main accent which included anthropogenesis, rasogenesis, and ethnogenesis has changed into mechanisms of adaptation to changing environment (also understood as living conditions and social surroundings) during ontogeny, and causes the mechanisms of evolution (phylogeny is recapitulated during the first phases of ontogeny).…”
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Genomic detection of Panton-Valentine Leucocidins encoding genes, virulence factors and distribution of antiseptic resistance determinants among Methicillin-resistant S. aureus iso... by Masoud A. Juma, Tolbert Sonda, Boaz Wadugu, Davis Kuchaka, Mariana Shayo, Petro Paulo, Patrick Kimu, Livin E. Kanje, Melkiory Beti, Marco Van Zwetselaar, Blandina Mmbaga, Happiness Kumburu

“…Virulence genes were detected using virulenceFinder 2.0, while resistance genes were detected by ResFinder 4.1, and phylogenetic relatedness was determined by CSI Phylogeny 1.4 tools. Results Out of the 80 MRSA isolates analyzed, 11 (14%) were found to harbor LukS-PV and LukF-PV, pvl-encoding genes in their genome; therefore pvl-positive MRSA. …”
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Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae by Qian Qin, Yanjing Dong, Jialong Chen, Bo Wang, Yuxin Peng, XinPeng Zhang, Xiaoyun Wang, Jinxiang Zeng, Guoyue Zhong, Shouwen Zhang, Xiaolang Du

“…Conclusion This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research.…”
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Identification of <i>Bacillus anthracis</i> Strains from Animal Cases in Ethiopia and Genetic Characterization by Whole-Genome Sequencing by Abebe Olani, Domenico Galante, Matios Lakew, Bayeta Senbeta Wakjira, Getnet Abie Mekonnen, Tesfaye Rufael, Tsegaye Teklemariam, Wondwosen Kumilachew, Shimalis Dejene, Ayele Woldemeskel, Adanech Wakjira, Getachew Abichu, Baye Ashenafi, Nigatu Kebede, Aklilu Feleke Haile, Fufa Dawo Bari, Laura Del Sambro, Tadesse Eguale

“…The five sequenced strains were compared to one Ethiopian <i>B. anthracis</i> genome and the other 29 <i>B. anthracis</i> genomes available in the global genetic databases to determine their phylogeny. The genomes of the strains were also analyzed to detect the presence of antimicrobial resistance and virulence genes. …”
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Elevation gradient effects on grassland species diversity and phylogenetic in the two-river source forest region of the Altai Mountains, Xinjiang, China by Jing Che, Jing Che, Mao Ye, Mao Ye, Qingzhi He, Qingzhi He, Guoyan Zeng, Guoyan Zeng, Miaomiao Li, Miaomiao Li, Weilong Chen, Weilong Chen, Xiaoting Pan, Xiaoting Pan, Jiaorong Qian, Jiaorong Qian, Yexin Lv, Yexin Lv

“…The study analyzes the patterns of species composition, diversity, and phylogeny across different elevation gradients and explores their relationships with key environmental factors. …”
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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? by Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch

“…Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). …”
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Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus by Gang Wang, Yuanyuan Wang, Lianfu Chen, Hongbo Wang, Lin Guo, Xuan Zhou, Meijie Dou, Baiyu Wang, Jingxian Lin, Lei Liu, Zhengchao Wang, Youjin Deng, Jisen Zhang

“…By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. …”
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Isolation and Characterization of Indigenous <i>Acetobacter</i> Strains from Cashew Apple and Their Potential Use in Vinegar Production by Yaya Anianhou Ouattara, Doudjo Soro, Kouakou Romain Fossou, Ahou Cinthia Ines Yebouet, Ismael Abraham Cissé, Dogbo Marius Akissi, Adolphe Zézé, Emmanuel Assidjo, Kouassi Benjamin Yao

“…Physiological and biochemical tests followed by 16S rRNA gene analysis and phylogeny were used for isolate characterization. Moreover, their acetic acid production capacity was assessed. …”
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Proteasome inhibition enhances oncolytic reovirus therapy in multiple myeloma independently of its direct cytotoxic effects by Ada Alice Dona, Theophilus Tandoh, Lokesh Nigam, Mahmoud Singer, Enrico Caserta, Mariam Murtadha, Yinghui Zhu, Milad Moloudizargari, Preeti Sharma, Ottavio Napolitano, Janet Winchester, Arnab Chowdhury, Alex Pozhitkov, James F. Sanchez, Hawa Vahed, Guido Marcucci, Matt Coffey, Gerard Nuovo, Douglas W. Sborov, Flavia Pichiorri, Craig C Hofmeister

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Comparative genomics of Aspergillus nidulans and section Nidulantes by Sebastian Theobald, Tammi Vesth, Jane L. Nybo, Jens C. Frisvad, Inge Kjærbølling, Stephen Mondo, Kurt LaButti, Sajeet Haridas, Robert Riley, Alan A. Kuo, Asaf A. Salamov, Jasmyn Pangilinan, Anna Lipzen, Maxim Koriabine, Mi Yan, Kerrie Barry, Alicia Clum, Ellen K. Lyhne, Elodie Drula, Ad Wiebenga, Astrid Müller, Ronnie J.M. Lubbers, Roland S. Kun, Ana Carolina dos Santos Gomes, Miia R. Mäkelä, Bernard Henrissat, Blake A. Simmons, Jon K. Magnuson, Jakob B. Hoof, Uffe H. Mortensen, Paul S. Dyer, Michelle Momany, Thomas O. Larsen, Igor V Grigoriev, Scott E. Baker, Ronald P. de Vries, Mikael R. Andersen

“…In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. …”
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Révision de l’espèce Homo erectus (Dubois, 1893) by Valéry Zeitoun

“…Ignoring which of the most discriminant parameters allow the reconstruction of phylogeny, all the measurements existing between every reference points are taken into account. …”
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A taxonomic summary and revision of Rozella (Cryptomycota) by Peter M. Letcher, Martha J. Powell

“…Determined in molecular phylogenies to be the earliest diverging lineage in kingdom Fungi, Rozella currently nests among an abundance of environmental sequences in phylum Cryptomycota, superphylum Opisthosporidia. …”
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treeducken: An R package for simulating cophylogenetic systems by Wade Dismukes, Tracy A. Heath

“…Abstract Cophylogenetic methods describe discordance between non‐independent phylogenies. Simulation is necessary for testing cophylogenetic methods, but few simulators exist that are capable of generating data under explicit and biologically meaningful models. …”
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