10th U6+ Consortium of African Universities International Conference

Darwin’s Tree of Life has long served as the dominant framework for explaining biological diversity. It depicts all organisms as descending from a single common ancestor through a branching pattern of descent with modification. Historically, it has provided a coherent conceptual foundation, but recent advances in molecular biology, and genomics has challenged its universality and explanatory adequacy. This paper critically evaluates whether the Tree of Life remains a valid representation of biological history or whether it has been fundamentally undermined by emerging empirical evidence. It is based on a review and synthesis of published literature, drawing on recent findings from evolutionary biology, molecular genetics, comparative genomics, and phylogenomics to assess the strengths and limitations of the traditional Tree of Life model and alternative frameworks. Recent developments in DNA sequencing and phylogenomic analyses have revealed extensive genetic complexity that is inconsistent with a strictly tree-like evolutionary model. Processes such as horizontal gene transfer, hybridization, and conflicting molecular phylogenies suggest that evolutionary relationships are often reticulate rather than hierarchical. Developments unraveled recently also indicate that substantial genomic components do not conform to vertical descent, thereby challenging the assumption of universal common ancestry. This paper, therefore, highlights the dependency graph model as an alternative framework, that explains nested biological patterns and genetic overlap through shared functional modules rather than linear descent. In conclusion, accumulating molecular evidence suggests that the traditional Tree of Life is no longer sufficient, and that network-based models provide a more accurate representation of evolutionary relationships in the genomic era.