Morphological Diversity of Gracilaria blodgettii Harvey 1853 (Gracilariaceae, Rhodophyta) from Sarawak, Malaysian Borneo by Ruhana Hassan, Muhammad Nur Arif Othman, Mohd Nasarudin Harith, Amir Shah Ruddin Md Sah

“…However, based on 672 bp CO1-5P gene sequence analysis, all the three species were identified as G. blodgettii; besides, low genetic divergence values (0.17%–0.34%) were scored between samples in this study with the same species in GenBank. In the phylogenetic trees, all samples in this study group together with other G. blodgettii have high bootstrap values; thus, this species is monophyletic. …”
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Molecular Characterization and Antibacterial Potential of Endophytic Fungal Isolates from Selected Mangroves along the Coastline of Kenya by Teresia Nyambura Wacira, Huxley Mae Makonde, Carren Moraa Bosire, Cromwell Mwiti Kibiti

“…The isolates in the inferred phylogenetic trees were affiliated with the genus Aspergillus. …”
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An Active-Learning Framework for Educating Medical Students on SARS-CoV-2 Variants and COVID-19 Epidemiology [version 1; peer review: 2 approved] by Samiksha Prasad, Amanda J Chase

“…Qualitative data yielded positive feedback for the session, notably in students' ability to interpret phylogenetic trees and understand the role of variants. …”
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Cadophora species from marine glaciers in the Qinghai-Tibet Plateau: an example of unsuspected hidden biodiversity by Bingqian Zhang, Xiaoguang Li, Guojie Li, Qi-Ming Wang, Manman Wang

“…As one of the most frequently encountered genera, the Cadophora isolates were studied in detail. Two phylogenetic trees were constructed: one was based on the partial large subunit nrDNA (LSU) to infer taxonomic placement of our isolates and the other was based on multi-locus sequences of LSU, ITS, TUB and TEF-1α to investigate more exact phylogenetic relationships between Cadophora and allied genera. …”
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Isolation and characterization of a novel lytic phage K14-2 infecting diverse species of the genus Klebsiella and Raoultella by Seomin Kang, Jeong-Eun Han, Young-Sik Choi, In-Chul Jeong, Jin-Woo Bae, Jin-Woo Bae, Jin-Woo Bae

“…The phage with the highest genomic similarity to K14-2 was vB_KpM-Milk. Phylogenetic trees constructed based on the major capsid protein revealed that the phage belonged to the genus Slopekvirus of the Straboviridae family. …”
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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

“…Phylogenetic analysis showed congruence in the topology of the phylogenetic trees constructed using the complete genome and VP1 gene sequence, clearly demonstrating that the isolates analyzed belong to two distinct genetic lineages: A/SEA97 in the Far East and Iran-05 in the North Caucasus. …”
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Molecular Epidemiology of Human Norovirus Variants from Outbreaks in Zhejiang Province, China, during 2021 by Yi Sun, Yongjuan Yuan, Haiyan Mao, Lingxuan Su, Qiong Ge, Jian Gao, Changping Xu, Liming Gong

“…Furthermore, the whole genomes of positive samples were sequenced, enabling the characterization of both nucleotide and amino acid differences within the virus. Finally, phylogenetic trees were constructed to further analyze and understand the genetic relationships among the detected viruses. …”
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Mitochondrial genome insights into the phylogenetics and biogeographic evolution of snow trout (Cyprinidae, Schizothorax) in the Tien Shan Mountains by Akbarjon Rozimov, Yufan Wang, Min Wang, Ming Zou, Jobir Sobirov, Erkin Karimov, Bakhtiyor Kholmatov, Jörg Freyhof, Sirojiddin Namozov, Chongnv Wang, Xinxin Li, Baocheng Guo

“…We classified Schizothorax sp. as a valid independent species based on comprehensive phylogenetic trees and DNA barcode genetic distance. The dramatic uplift of the Tien Shan Mountains during the Late Miocene to the Pliocene, followed by periods of isolation on its eastern and western flanks, has driven extensive speciation, contributing to the rich diversity observed today. …”
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Analysis of bacterial genetic diversity in biofloc by using ARDRA 16S-rRNA gene by , Widanarni, Dewi Nurhayati, Dinamella Wahjuningrum

“…The 16S-rRNA gene of the isolates was then cut using HaeIII (5’-GG↓CC) and HhaI (5’-GCG↓C) restriction enzymes resulting an ARDRA pattern which was further used as the binary data for the construction of phylogenetics tree that was used to estimate the group of bacteria. …”
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Characterizations of cytokines and viral genomes in serum of patients with Dabie bandavirus infection by Zefeng Dong, Man Yuan, Yueping Xing, Hongkai Zhang, Qiang Shen

“…The sequencing process was performed using a Nanopore GridION X5 instrument. Phylogenetic trees for the L, M, and S segments of Dabie bandavirus were constructed using the maximum likelihood (ML) method in MEGA 11 software, with the bootstrap value set at 1,000.ResultsAll 10 patients with Dabie bandavirus infection exhibited a severe clinical course, resulting in three fatalities. …”
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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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Host-symbiont-gene phylogenetic reconciliation by Menet, Hugo, Trung, Alexia Nguyen, Daubin, Vincent, Tannier, Eric

“…It handles the possibility of ghost lineages as well as temporary free-living symbionts. Given three phylogenetic trees, we devise a Monte Carlo algorithm which samples evolutionary scenarios of symbionts and genes according to an approximation of their likelihood in the model. …”
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Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae by Xinbi Jia, Jiaqi Wei, Yuewen Chen, Chenghong Zeng, Chan Deng, Pengchen Zeng, Yufei Tang, Qinghong Zhou, Yingjin Huang, Qianglong Zhu

“…Furthermore, the maximum likelihood-based phylogenetic trees constructed from complete chloroplast genomes and protein-coding sequences presented similar topologies. …”
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A survey of the Sli gene in wild and cultivated potato by Mercedes Ames, Andy Hamernik, William Behling, David S. Douches, Dennis A. Halterman, Paul C. Bethke

“…DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. …”
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Identification and Pathogenicity of <i>Fusarium</i> Species from Herbaceous Plants on Grassland in Qiaojia County, China by Yanzhu Gao, Zhixiao Zhang, Mei Ji, Sangzi Ze, Haodong Wang, Bin Yang, Lianrong Hu, Ning Zhao

“…Through morphological means and based on ITS, <i>RPB2</i>, and <i>TEF-1</i> gene sequences, we compared and constructed polygenic phylogenetic trees to classify and identify the <i>Fusarium</i> species. …”
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Is The SARS-CoV2 Evolved in Human Being: A prospective Genetic Analysis by Salvatore Dimonte, Paywast Jamal Jalal, Hiwa Abdulrahman Ahmad, Safa Bakr Karim, Taib Ahmed Hama Soor, Salar Ibrahim Ali, Muhammed Babakir-Mina, Francesco Greco

“…An attempt has been made to investigate the epidemiological study of this new contagious virus using molecular biology techniques. The phylogenetic trees for all human coronaviruses with the novel Coronavirus have been built using a several complete amino acid sequences of the four known structural proteins, S (spike), E (envelope), M (membrane), and N (nucleocapsid). …”
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The Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya by Richard Nyamota, Earl A. Middlebrook, Hussein M. Abkallo, James Akoko, Francis Gakuya, Lillian Wambua, Bernard Ronoh, Isaac Lekolool, Athman Mwatondo, Mathew Muturi, Bernard Bett, Jeanne M. Fair, Andrew W. Bartlow

“…The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest. …”
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Morphological and Molecular Characterization of Trichoderma Isolates from Vegetable Crop Rhizospheres in Nepal [version 2; peer review: 1 approved, 2 approved with reservations] by Arvind Kumar Keshari, Suraj Baidya, Aashaq Hussain Bhat, Ram B. Khadka, Puja Jaiswal

“…Results The morphological characteristics and phylogenetic trees for both regions provided a clear species resolution, with four main clades: Harzianum, Viride, Brevicompactum and Longibrachiatum with 12 species T. harzinaum, T. afroharzianum, T. lentiforme, T. inhamatum, T. camerunense, T. azevedoi, T. atroviride, T. asperellum, T. asperelloides, T. koningii, T. longibrachiatum and T. brevicompactum and nine species as a new country record. …”
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Prevalence and phylogenetic analysis of cytomegalovirus (Orthoherpesviridae: <i>Cytomegalovirus: Cytomegalovirus humanbeta5</i>) genetic variants from children and immunocompromise... by Ol’ga E. Van’kova, Nina F. Brusnigina, Nadezhda A. Novikova

“…The genetic diversity of CMV was assessed for two variable genes: UL55(gB) and UL73(gN), using NGS technology on the Illumina platform. Phylogenetic trees were constructed in the MEGA X program, the reliability of the cluster topology on the trees was confirmed using the rapid bootstrap method based on the generation of 500 pseudo-replicas. …”
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The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera by Wei Yu, Xiao-Juan Li, Zhen Lv, Li-E Yang, De-Li Peng

“…To investigate the phylogenetics of P. paradoxum and its related genera, we first sequenced, assembled, and annotated the chloroplast genome of two subspecies of P. paradoxum in China and reconstructed the phylogenetic trees. Due to the lack of samples of P. paradoxum subsp. franchetianum from Japan, this study only analyzed and discussed P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei. …”
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