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Phylogenetic approaches to evolutionary relationships in level of intra-species and inter-secies

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농업생명과학대학 농생명공학부
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서울대학교 대학원
학위논문 (석사)-- 서울대학교 대학원 : 농업생명과학대학 농생명공학부, 2018. 8. 김희발.
Molecular phylogenetics exploits sequence information to understand relationships among organisms and reveal the history of their evolution. It is an essential analysis method in comparative genomics and can be used not only to build a classification system for organisms but also to track the evolutionary pathway of each gene and the overall evolutionary history of a genome. The dN/dS ratio is a widely used parameter to understand the evolution of accelerated gene sequences. This ratio compares the rate of non-synonymous substitutions (dN), which are base substitutions that cause changes in coding proteins, and the rate of synonymous substitutions (dS), which are base substitutions that do not alter coding proteins. These values are used to reveal genetic flow between phylogenetically-related species and to estimate the rate of evolution of orthologous genes among species.

In this thesis, I use phylogenetic approaches to examine evolutionary relationships in two very different groups of organisms. In the first study, mitochondrial genome sequences from 148 baleen whales were analyzed to trace the spatio-temporal dynamics of endangered fin whales ( Balaenoptera physalus ) within the baleen whale (Mysticeti) lineage. I constructed a precise phylogenetic tree using three methods, namely the Bayesian coalescent approach, Bayesian inference, and maximum likelihood method and confirmed that there is a significant correlation between evolution and geographical location. The analyses were also used to predict the most recent common female ancestor, the timing of each differentiation, and the rate of evolution of the species. In addition, environmental events during each period of differentiation are suggested as evidence of the accuracy of the tree.

In the second study, I first constructed a whole genome sequence of the new Lactobacillus plantarum strain GB-LP1 through de novo assembly and then compared it to the genomes of previous Lactobacillus plantarum strains to understand the genetic evolutionary basis of differences in useful lactic acid bacteria. I also identified the functional elements and potential risk of genes in the new Lactobacillus plantarum GB-LP1. The results confirmed which genes underwent GB-LP1-specific evolutionary acceleration, supporting the hypothesis that evolution in the Lactobacillus plantarum species group resulted in functional differences related to the inhibition of toxin expression and production of antimicrobial substances.
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