Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

HB Hassler, B Probert, C Moore, E Lawson… - Microbiome, 2022 - Springer
Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in
species delineation, and now widely in microbiome studies. However, the gene suffers from …

Phylogenetic utility of rRNA ITS2 sequence-structure under functional constraint

W Zhang, W Tian, Z Gao, G Wang, H Zhao - International Journal of …, 2020 - mdpi.com
The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome
biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 …

[HTML][HTML] Comparative Analysis of the Mitochondrial Genomes of Three Species of Yangiella (Hemiptera: Aradidae) and the Phylogenetic Implications of Aradidae

L Ji, Z Jia, X Bai - Insects, 2024 - mdpi.com
Simple Summary Aradidae is a large family in Hemiptera, which feeds on mycelium, and its
phylogenetic status is not fully understood. Mitochondrial genome sequences can be used …

Senecavirus A enhances its adaptive evolution via synonymous codon bias evolution

S Zhao, H Cui, Z Hu, L Du, X Ran, X Wen - Viruses, 2022 - mdpi.com
Synonymous codon bias in the viral genome affects protein translation and gene
expression, suggesting that the synonymous codon mutant plays an essential role in …

Interaction of glucosamine with uracil and thymine: a computational study

A Srivastava, BK Pandey, S Gupta, S Mishra - Journal of Molecular …, 2022 - Springer
The present study delves into the interaction of the monomer of glucosamine with uracil and
thymine in vacuum and in different phases by density functional theory (DFT). Both the …

Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis

AF Magee, SK Hilton, WS DeWitt - Molecular biology and …, 2021 - academic.oup.com
Likelihood-based phylogenetic inference posits a probabilistic model of character state
change along branches of a phylogenetic tree. These models typically assume statistical …