China
Africa
Explore chapters and articles related to this topic
An Overview of Parasite Diversity
Published in Eric S. Loker, Bruce V. Hofkin, Parasitology, 2023
Eric S. Loker, Bruce V. Hofkin
To help us better characterize and understand biodiversity, enter the discipline of phylogenetics referring to the study of the evolutionary relationships among organisms based on molecular sequence data or morphological traits. These relationships are conveniently depicted with the use of evolutionary trees. Phylogenetics is often involved in making and evaluating hypotheses about historical patterns of descent and can be thought of as part of a broader subject called systematics, which refers to the study of the diversification of life on Earth, including the relationships among organisms over time. Evolutionary trees are constructed using algorithms that assess the degrees of similarity in DNA or RNA nucleotide sequences or in protein amino acid sequences in the organisms being compared. Many trees are also constructed based on morphological characters or a combination of morphology and sequence data. The optimal ways to construct trees remain a topic of vigorous and ongoing debate, with entire professional societies and journals devoted to the topic.
A Brief Introduction to Virology
Published in Rae-Ellen W. Kavey, Allison B. Kavey, Viral Pandemics, 2020
Rae-Ellen W. Kavey, Allison B. Kavey
A secondary goal of phylogenetic analysis is to determine the timing of ancestral sequence divergence. In RNA viruses where spontaneous mutation (i.e., divergence) is common, phylogenetic analysis can determine when separate genetic lineages arose relative to each other. This concept gave rise to the idea of a molecular clock – using the mutation rate of biomolecules to determine the time in prehistory when two or more biomolecules diverged, with the benchmark time before divergence based on fossil or archeological dates.36,37 Timing the emergence of new mutations is important in analysis of viral epidemics because it allows us to infer the pattern and order of evolutionary change, especially when correlated with historic data.
Diversity of Endophytes and Biotechnological Potential
Published in Luzia Valentina Modolo, Mary Ann Foglio, Brazilian Medicinal Plants, 2019
Daiani Cristina Savi, Chirlei Glienke
First, we use the blast tool to identify the possible fungal or bacterial genus to which the isolate belongs. For a final or more precise identification, a dataset containing all the sequences of type species of the valid fungal species belonging to the respective genus is obtained through a search on the Mycoback database (www.mycobank.org/) and for bacteria and actinomycetes using search on the List of Prokaryotic Names With Standing in Nomenclature (www.bacterio.net/). After selecting the sequences of valid species, the identification is based on an evolutionary framework using a phylogenetic approach (Figure 5.2). Phylogeny reconstructs the tree-like pattern that describes the evolutionary relationships between species with a predictive value (Pace et al., 2012), different from a similarity analysis via Blast. Many approaches to phylogenetic inference have been used and the relative merits of these methods have been an important consideration for phylogenetic analysis (Holder et al., 2008). The topology of the phylogenetic tree, as well as the order of branching events, is determined from the sequences of the analyzed region and, despite the fact some methods use distance-matrix to perform the phylogeny analysis, the most valuable methods are based on standard statistical techniques, such as maximum likelihood and Bayesian inference (Bogusz and Whelan, 2017).
Testing for genetic mutation of seasonal influenza virus
Published in Journal of Applied Statistics, 2023
Phylogeny is concerned with the evolution of groups and specifically about the lines of descent and relationships among groups. It is one of the best tools for understanding the evolution of pathogens. A phylogenetic tree is a diagram depicting a phylogeny through lines of evolutionary descent from a common ancestor. Throughout this article, the phrase ‘phylogenetic tree’ and ‘evolutionary tree’ are used interchangeably. Influenza viruses are permanently changing, undergoing genetic changes over time and monitoring these changes in the genome is fundamental to the production of vaccines on a seasonal basis. The RNA genes of influenza are made up of nucleotides. It is the composition of these nucleotides and the differences which account for the different viruses. The differences and ancestry of viruses are demonstrated through the use of a phylogenetic tree. The tree shows how different viruses are related to each other and are grouped together based on how close their corresponding nucleotides are. Specifically the phylogenetic trees of influenza viruses will usually display how similar the viruses hemagglutinin (HA) or neuraminidase (NA) genes are to one another. The tree consists of branches and branch lengths. Groups on the same branch share the same nucleotides. At a split of a branch, the length of the branch indicates how different (i.e. the number of nucleotide differences) from each other the groups are.
Integration of network pharmacology and intestinal flora to investigate the mechanism of action of Chinese herbal Cichorium intybus formula in attenuating adenine and ethambutol hydrochloride-induced hyperuricemic nephropathy in rats
Published in Pharmaceutical Biology, 2022
Na Li, Mukaram Amatjan, Pengke He, Boheng Zhang, Xianyan Mai, Qianle Jiang, Haochen Xie, Xiaoni Shao
In our study, LEfse analysis (Segata et al. 2011) was adopted to seek biomarkers with statistically significant differences (LDA score > 4). As shown in Figure 10A, the main microbial species that differed between CG and other groups were Ruminococcaceae, Ruminococcaceae_UCG_005, Ruminococcaceae_UCG_014, Clostridiales and Clostridia. The main microbial species that differed between FHG and other groups were Bacteria. The main microbial species that differed between FLG and other taxa were Allobaculum, Erysipelotrichaceae, Bifidobacteriales, Bifidobacteriaceae, Erysipelotrichales, Erysipelotrichia, Catenibacterium, Bifidobacterium, Actinobacteria, Actinobacteria. An evolutionary diagram was shown in Figure 10B to demonstrate the distribution patterns of phylogenetic relationships for species that play an important role in each group. The functional prediction results of enrichment at three different levels of the ko metabolic pathway were shown in Figures 10C–E.
Multiple genetic analyses for Chinese Hunan Han population via 46 A-STRs
Published in Annals of Human Biology, 2022
Yunying Zhang, Yating Fang, Man Chen, Ming Zhao, Hui Xu, Congying Zhao, Jiangwei Lan, Bofeng Zhu
To illustrate the genetic relationships between the Hunan Han and 13 reference populations and also to visualise genetic distances between populations, diverse parameters were utilised to present the results of phylogenetic analyses in the form of cladograms. The neighbor-joining tree shown in Figure 5(A) was built based on the DA distance matrix by using MEGA 7.0 software. The results demonstrated that all 14 populations formed roughly three major clades from top to bottom. The uppermost clade consisted of Gansu Hui and the branch extending from Yi from West China and Sichuan Tibetan, while the middle clade included three branches, namely the branch consisting of Sichuan Han and Beijing Han, the branch including Liaoning Han and Shandong Han, and the last branch of Shaanxi Han. The remaining six populations together formed the bottom clade in the figure. The Hunan Han grouped first with the branch made up of Hainan Han and Hainan Ha Hlai, and then gathered with Guangdong Han, Zhejiang Han, Hubei Tujia in sequence. Results from the unrooted tree (Figure 5(B)), constructed by PHYLIP based on allelic frequencies, turned out to be similar to the findings above, except that Sichuan Han did not form a branch with Beijing Han.