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| Abstract : Perpustakaan Tuanku Bainun |
| The objective of the study was to develop a supermatrix framework by incorporating the unique evolutionary signals of each gene that can improve phylogenetic inferences. The aim was to address the issue of the supermatrix approach, which potentially disregards individual gene properties. The study involved two main experiments: i) Experiment 1 focused on the effect of evolutionary signals across housekeeping genes on phylogeny inference using Chlorellaceae species. ii) Experiment 2 involved the development of a bioinformatics framework using the supermatrix approach. The framework incorporates unique properties of each gene in phylogenetic tree construction, such as sequence heterogeneity, sequence informative sites, taxonomic conflicts at the kingdom level, and tree distance between the gene tree and species tree. The genes were concatenated, based on their similar gene properties, into a supermatrix for phylogeny inference. Generated phylogenetic tree was compared with tree-of-life, which was used as a benchmark dataset, to validate the usability of the supermatrix framework. Our findings revealed that each individual housekeeping gene has different evolutionary signals, and ignoring these signals would affect the inferred phylogeny. The developed bioinformatics framework demonstrated an improvement in the accuracy of the inferred phylogenetic trees compared to the conventional tree inference approach based on Robinson-Foulds tree distance and Shimodaira Hasegawa test. This framework also corroborates with previous studies, which suggest that incorporating more genes in the supermatrix approach can enhance phylogenetic inference. Analysing individual gene properties by considering the unique evolutionary signals in gene concatenation through the supermatrix approach could improve phylogenetic inferences. The improvement of using the supermatrix approach could enhance the understanding of the evolutionary relationships between species, which further could be applied in various fields such as biodiversity conservation, medicine and healthcare. |
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