DEVELOPMENT OF A BIOINFORMATIC ANALYSIS PACKAGE TO TEST GLOBAL PHYLOGEOGRAPHIC RELATIONSHIPS OF SPECIES BY USING GEOTAGGED DNA SEQUENCES FROM GENBANK

Date

2024-1-25

Author

Aktaş, Caner

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In this thesis, I introduce “PhyloGeoTagging”, a novel R package and Shiny web application specifically designed to enhance phylogeographic research from a bioinformatics perspective. This package eases key challenges in phylogeographic studies using GenBank sequences, such as selecting, downloading, processing, filtering, and analyzing. It can handle and analyze complete datasets from GenBank searches, offering versatile data filtering options before and after downloading sequences. PhyloGeoTagging enables the elimination of the present problem of lacking geographical coordinate information in GenBank by utilizing Nominatim API for geocoding. The package automates key bioinformatic approaches, including clustering homologous sequences and sequence alignment, as well as conducting advanced phylogeographic analyses, such as haplotype detection and the construction of haplotype networks, genetic barrier analysis, Isolation by Distance, Analysis of Molecular Variance, and investigations of diversity and differentiation parameters. Additionally, two new genetic richness measures, Weighted Haplotype Richness and Cross-Country Weighted Haplotype Endemism, are introduced by me, specifically designed to deal with large and complex datasets. The practical application and effectiveness of this package are demonstrated by using specific case studies and examples, such as the entire organelle DNA data available from GenBank for the family Fagaceae, and the genera Salvia and Apis. The user-friendly interface of this package, equipped with dynamic maps and infographics, makes complex datasets more accessible and interpretable, supporting both research and educational purposes. By integrating advanced computational tools with phylogeographic research, PhyloGeoTagging enriches our understanding of global biodiversity patterns and provides a foundation for future discoveries in the realm of phylogeography.

Subject Keywords

Phylogeographic Analysis Tools, Automated Phylogeography, GenBank, Geocoding, Shiny Web Application

URI

https://hdl.handle.net/11511/108725

Collections

Graduate School of Natural and Applied Sciences, Thesis