The Anthropocene and the biodiversity crisis: an eco-evolutionary perspective by Jarne, Philippe

“…This crisis does not only affect the ecological dynamics of biodiversity, but also its evolutionary dynamics, including genetic diversity, an aspect that is generally neglected. …”
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The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation by Kevin S. Blake, Yao-Peng Xue, Vincent J. Gillespie, Skye R. S. Fishbein, Niraj H. Tolia, Timothy A. Wencewicz, Gautam Dantas

“…This suggests mechanism-specific selection by each tetracycline generation; however, the evolutionary dynamics of this remain unclear. Here, we evaluate 24 recombinant Escherichia coli strains expressing tetracycline resistance genes from each mechanism (efflux pumps, ribosomal protection proteins, and enzymatic inactivation) in the context of each tetracycline generation. …”
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Geographic variation in abundance and diversity of Acinetobacter baumannii Vieuvirus bacteriophages by Dafne Arellano-Maciel, Juan Manuel Hurtado-Ramírez, Laura Carolina Camelo-Valera, Santiago Castillo-Ramírez, Alejandro Reyes, Gamaliel López-Leal

“…Specifically, Vieuvirus-related phages were frequently identified in isolates from Thailand, Mexico, China, and South Korea, which show the geographic prevalence of A. baumannii prophages.DiscussionThis study highlights the importance of considering geographic factors to fully understand prophage diversity and their significant role in the evolutionary dynamics of A. baumannii.…”
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From threats to solutions: A literature review of climate adaptation in anadromous salmon and trout by Lisa G. Crozier, Jared E. Siegel

“…In conclusion, our findings identify strengths and gaps in the research investigating the role of evolutionary dynamics in the face of climate change. By capitalizing on new tools for sequencing, genomic analysis, and automated field data collection, we can establish baselines for tracking evolutionary responses to climate change. …”
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Differential Evolutionary Constraints in the Evolution of Chemoreceptors: A Murine and Human Case Study by Ricardo D’Oliveira Albanus, Rodrigo Juliani Siqueira Dalmolin, José Luiz Rybarczyk-Filho, Mauro Antônio Alves Castro, José Cláudio Fonseca Moreira

“…We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes in Mus musculus, Homo sapiens, and Rattus norvegicus. …”
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Whole genome sequences of nine Taylorella equigenitalis strains isolated in the Czech Republic between 1982-2021: Molecular dating suggests a common ancestor at the time of Roman E... by Matěj Hrala, Petr Andrla, Juraj Bosák, Pavla Fedrová, Amir Mugutdinov, Renata Karpíšková, Kateřina Nedbalcová, Jitka Raichová, Martin Faldyna, Petr Hořín, David Šmajs

“…While previous studies have analyzed this organism for various parameters, the evolutionary dynamics of this pathogen, including the emergence of antibiotic resistance, remains unresolved. …”
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Chromosome-level genome assembly and annotation of Japanese anchovy (Engraulis japonicus) by Shufang Liu, Le Wang, Ruixiang Wang, Huan Wang, Ang Li, Changting An, Zining Meng, Zhimeng Zhuang

“…However, the lack of genomic resources hampers our understanding of its genetic diversity and differentiation, as well as the evolutionary dynamics. Here, we firstly report a complex chromosome-level genome assembly of E. japonicus with a large size of 1.4 Gb, with features of high repetitive sequences (54.9%), high heterozygosity (2.3%) and a number of protein-coding genes (24,405). …”
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Revisiting Key Entry Routes of Human Epidemic Arboviruses into the Mainland Americas through Large-Scale Phylogenomics by Túlio De Lima Campos, Ricardo Durães-Carvalho, Antonio Mauro Rezende, Otávio Valério de Carvalho, Alain Kohl, Gabriel Luz Wallau, Lindomar José Pena

“…Here, we applied robust phylogenomic methods to trace the evolutionary dynamics of these arboviruses with special focus on Brazil, the epicenter of these triple epidemics. …”
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Search for differentially methylated regions in ancient and modern genomes by D. D. Borodko, S. V. Zhenilo, F. S. Sharko

“…Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. …”
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Using RAD-seq to identify and differentiate the medicinal herb Scrophularia ningpoensis and its adulterants by Lei Guo, Xia Wang, Hong Li, Mengli Zhou, Liqin Liu, Ruihong Wang, Pan Li

“…Conclusions This study successfully identified S. ningpoensis and the three adulterants, enriched the genomic information of Scrophularia species, and contributed to a more profound understanding of the evolutionary dynamics within this genus. Furthermore, it offers novel insights and methodologies for the identification of medicinal plants.…”
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Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress by Dan Huang, Jingqiu Liao, Jose Luis Balcazar, Mao Ye, Ruonan Wu, Dongsheng Wang, Pedro J. J. Alvarez, Pingfeng Yu

“…Abstract Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. …”
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Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback by Sylvestre, Florent, Aubin-Horth, Nadia, Bernatchez, Louis

“…Moreover, studying gene expression in species with recently established sex chromosomes can help understand the evolutionary dynamics of gene loss and dosage compensation. …”
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In silico characterization of defense system hotspots in Acinetobacter spp. by Wenjing Yi, Ning Zhu, Zhihan Peng, Xiao Chu, Haotian Sun, Lei Song, Zhimin Guo, Arnab Pain, Zhaoqing Luo, Qingtian Guan

“…These findings provide critical insights into the genetic organization of phage defense systems, contributing to a broader understanding of bacterial immunity and the evolutionary dynamics that shape Acinetobacter genomes. This knowledge lays the foundation for developing targeted interventions  to combat antibiotic resistance Acinetobacter baumannii.…”
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RNA Virus Discovery Sheds Light on the Virome of a Major Vineyard Pest, the European Grapevine Moth (<i>Lobesia botrana</i>) by Humberto Debat, Sebastian Gomez-Talquenca, Nicolas Bejerman

“…These results underscore the existence of a complex virome within <i>L. botrana</i> and lay the foundation for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses in the <i>L. botrana</i>–vineyard ecosystem.…”
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Can Cryptogonimids of the Same Genus Influence Each Other’s Level of Genetic Variation? by Ekaterina S. Tokarskaya, Yulia V. Tatonova, Haneef Ahmed Amissah, Polina G. Shumenko, Mikhail Yu. Shchelkanov

“…To uncover the dynamics driving these observations, we propose the approach of expanding sampling, broader genetic marker analyses, and investigations of varied host populations that could elucidate the complexities of the <i>Exorchis</i> species genetic variability and evolutionary dynamics.…”
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The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems by Murielle Richard, Alexandre Garreau, Elvire Bestion, Julien Cucherousset, Jose M. Montoya, Simon Blanchet

“…Here, we present the Aquatic Metatron, a unique mesocosm facility providing a large‐scale experimental resource to study the combined effects of global change components, in particular climate change and habitat fragmentation, on the ecological and evolutionary dynamics of aquatic ecosystems. The Aquatic Metatron consists of 144 mesocosms of 2 m3 each that can be connected to each other with aquatic corridors, and—for a subset of them—with aerial corridors. …”
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Phage WO diversity and evolutionary forces associated with Wolbachia-infected crickets by Qing-Chen Luo, Yue-Yuan Li, Ye-Song Ren, Xiao-Hui Yang, Dao-Hong Zhu

“…To examine the diversity and evolutionary dynamics of phage WO, we conducted a screening for the presence of phage WO in Wolbachia-infected cricket species from China.MethodsThe presence of phage WO was detected using a PCR-based methodology. …”
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Life-history traits, pace of life and dispersal among and within five species of Trichogramma wasps: a comparative analysis by Guicharnaud, Chloé, Groussier, Géraldine, Beranger, Erwan, Lamy, Laurent, Vercken, Elodie, Dahirel, Maxime

“…Knowing about such life-history strategies may be especially important for understanding eco-evolutionary dynamics, as these trait syndromes may constrain trait variation or be correlated with other traits. …”
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Epidemiological and genetic charateristics of Vibrio vulnificus from diverse sources in China during 2012–2023 by Dongling Long, Min Li, Lingchao Ma, Jiewen Huang, Chao Lv, Yiwen Chen, Zile Cheng, Chang Liu, Huitao Huang, Xiaokui Guo, Chao Yang, Yongzhang Zhu

“…These findings provide new insights into the ecological and evolutionary dynamics of V. vulnificus.…”
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Insight into the codon usage patterns and adaptation of Tembusu Virus by Fucheng Guo, Huiming Tan, Jinjin Yang, Rumin Jia, Ruichen Wang, Lie Wu, Fengzhi Pan, Kai Kang, Weitian Xie, Youquan Li, Kewei Fan

“…Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. Phylogenetic and compositional analyses consistently classify TMUV into four evolutionary lineages—Clusters 1, 2, 3, and ancestral TMUV—with Cluster 2 emerging as the dominant lineage. …”
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