In Situ Diversification of Insular Rodents: from Efficient Software to Integrative Empirical Approaches

Abstract

In situ diversification is pivotal in shaping 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. My software development project resulted in 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 in teaching where access to computing resources is lacking. 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 the species boundaries within the Bunomys division, the largest group of murine rodents in Sulawesi, Indonesia. I tested whether Sulawesi’s known areas of endemism, mountain isolation, or a combination of various 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, tectonic plates, and mountain formation may have promoted the diversification of the group in Sulawesi. Support for Sulawesi’s Areas of Endemism paradigm was mixed. Morphological data indicated that divergent populations within the genus Frateromys found in the molecular studies represent a distinct species. Overall, my dissertation highlights the significance of fieldwork, integrative empirical studies, and innovative technological applications in unraveling the complexities of biodiversity.