We consider the problem of the minimum number of phylogenetic trees it would take to display all splits in a given set, a problem related to k-compatibility. A set of trees that displays every single possible split is termed a universal tree set. In this note, we find the universal incompatibility U(n), the minimal size of a universal tree set for n taxa. By normalising incompatibility using U(n), one can then compare incompatibility of split systems across different numbers of taxa. We demonstrate this application by comparing two SplitsTree networks derived from archaeal genomes, with different numbers of taxa.
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http://dx.doi.org/10.1007/s11538-021-00911-6 | DOI Listing |
Mol Phylogenet Evol
January 2025
Department of Life Science, Tunghai University, Taichung, Taiwan; Center for Ecology and Environment, Tunghai University, Taichung, Taiwan. Electronic address:
Taiwan, a relatively young continental island, harbors a high proportion of endemic phasmids, reflecting its unique evolutionary history. However, a comprehensive phylogenetic framework to clarify these phasmids is still lacking. In this study, we sequenced ten of eleven valid genera and two undescribed species of Taiwanese phasmids (total 16 species) using the genome-skimming approach.
View Article and Find Full Text PDFComput Biol Med
January 2025
National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India. Electronic address:
The biotransformation of drugs by enzymes from the human microbiome can produce active or inactive products, impacting the bioactivity and function of these drugs inside the human host. However, understanding the biotransformation reactions of drug molecules catalyzed by bacterial enzymes in human microbiota is still limited. Hence, to characterize drug utilization capabilities across all the microbial phyla inside the human gut, we have used a knowledge-based approach to develop HgutMgene-Miner software which predicts xenobiotic metabolizing enzymes (XMEs) through genome mining.
View Article and Find Full Text PDFPlants (Basel)
January 2025
Estonian Literary Museum, 51003 Tartu, Estonia.
Finnish North Karelia is a region with a rich cultural history of ethnomedicinal plant use, shaped by centuries of interactions among various ethnic groups. This study identified both similarities and divergences between local Finns, Karelians war refugees, and individuals of mixed origin compared to historical records. Based on 67 semi-structured interviews, we documented the use of 43 medicinal plant taxa from 25 families, of which 31 remain in use.
View Article and Find Full Text PDFPlants (Basel)
January 2025
Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, 12900 Prague, Czech Republic.
Species are disappearing worldwide, and changes in climate and land use are commonly assumed to be the most important causes. Organisms are counteracting the negative effects of environmental factors on their survival by evolving various defence strategies, which positively affect their fitness. Here, the question addressed is: can evolution shape these defence strategies so that they positively affect the fitness of an organism? This question is complex and depends on the taxa and environmental factors.
View Article and Find Full Text PDFMicroorganisms
January 2025
Hunan Provincial Key Laboratory of Agroecological Engineering, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology.
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