Degree
Doctor of Philosophy (PhD)
Department
Biological Sciences
Document Type
Dissertation
Abstract
In situ diversification shapes species diversity in large, topographically complex islands. However, our understanding of in situ diversification is limited by inefficient, complicated software requiring significant bioinformatics skills and, in many taxa, an unresolved taxonomy. In my dissertation, I combined the development of high-performance, user-friendly software with integrative morphological and molecular approaches to understand how a large, topographically complex island, such as Sulawesi, generates species diversity. I developed SEGUL, a high-performance, cross-platform phylogenomic software featuring efficient solutions for common phylogenomic tasks, such as alignment summary and manipulation. My approach laid a foundation for scalable genomic software to advance genomic research and aid teaching, where access to computing resources is limited. Using a combination of large-scale sampling across Sulawesi and an integrative approach combining mitochondrial genes, nuclear exons, ultra-conserved elements (UCEs), and morphological studies of external and skull features, I determined species boundaries within the Bunomys division, the largest group of murine rodents in Sulawesi, Indonesia. I tested whether Sulawesi’s known Areas of Endemism (AoEs), mountain isolation, or a combination of factors promoted diversification of the group. My phylogenetic analyses yielded several novel results, including the underestimation of species diversity in the Bunomys division, the paraphyly of the genus Taeromys, and greater genetic divergence among montane species than in lowland taxa. A complex interplay of paleo-islands and mountain formation may have promoted the diversification of the group in Sulawesi. Support for Sulawesi’s AoE paradigm was mixed. Morphological data indicated that divergent populations within the genus Frateromys found in the molecular studies represent distinct species, and I describe one of these as a new taxon. Overall, my dissertation highlights the significance of fieldwork, integrative empirical studies, and innovative technological solutions in unraveling the complexities of biodiversity.
Date
5-15-2025
Recommended Citation
Handika, Heru, "In Situ Diversification of Insular Rodents: from Efficient Software to Integrative Empirical Approaches" (2025). LSU Doctoral Dissertations. 6799.
https://repository.lsu.edu/gradschool_dissertations/6799
Committee Chair
Esselstyn, Jacob A.
Included in
Biodiversity Commons, Bioinformatics Commons, Computational Biology Commons, Evolution Commons, Genomics Commons, Integrative Biology Commons, Molecular Genetics Commons