Comparison of The Accuracy of Phylogenetic Tree Construction Methods Using DNA Sequences of Small Ruminants
Project no. 23553 · Status: Kapanmış (Yayın bekleniyor) · 2021
Summary
<p>Small ruminant husbandry contributes to meeting the protein demand and contributes to the economy in our country through the production of important products. Therefore, knowing the productivity capabilities of small ruminants is important in terms of herd continuity and profitability of the enterprise. For this purpose, the phylogenetic tree method, which allows decision-making about whether animals in small ruminant flocks are raised for milk, meat, or both milk and meat, can be utilized. Phylogenetic analyses are methods that help us understand biological diversity by examining the evolutionary relationships and histories of organisms. Phylogenetic trees are constructed using data from DNA markers or DNA sequence information, which are common throughout the animal's entire genome and allow us to analyze the genome for genetic diversity.</p><p>In this study, phylogenetic trees were constructed using the DNA sequences of protein kinase family members to understand the genetic factors affecting performance traits in small ruminants, and the accuracies of these trees were compared. In the study, phylogenetic trees were constructed using the Neighbor Joining and Bootstrap methods with data obtained from DNA sequences of protein kinase family members taken from the NCBI (National Center for Biotechnology Information) database. The accuracy of the constructed phylogenetic trees was tested using the Maximum Parsimony and Maximum Likelihood methods and different distance calculation algorithms, including Tajima-Nei, Jukes Cantor, and p-distance. According to these results, in small ruminants with low sample size and few nucleotide changes, the Tajima-Nei method was found to be reliable in determining genetic relationships when used in conjunction with the Maximum Parsimony assumption, such as in the AMPK gene sequence datasets. Additionally, it was revealed that phylogenetic trees could contribute to the development of strategies for breeding programs by revealing the genetic determinants of performance traits in small ruminants, utilizing similarity and dissimilarity information.</p>