Phylogenetic Classification and Alternative Representations of Biological Relationships: A Systematic Literature Review of Tree, Network, and Dependency Graph Models

Advances in phylogenetics and molecular biology have demonstrated that biological relationships cannot always be adequately represented by a single model, particularly when evolutionary data reveal genealogical discordance, horizontal gene transfer, hybridization, recombination, and other reticulate processes. These conditions require critical evaluation of the functions, limitations, and evidential foundations of various representations of biological relationships. This study aims to compare the Tree of Life (TOL), phylogenetic networks, and the Dependency Graph of Life (DGL) through a systematic literature review approach by examining their representational targets, inferential functions, evidence characteristics, and respective evidential positions. The synthesis indicates that the development of these three approaches is more appropriately understood as an expansion of representational space rather than a linear replacement of one paradigm by another. The TOL primarily represents the branching history of lineages, phylogenetic networks accommodate genealogical conflicts and reticulate evolutionary processes, whereas the DGL provides a representation based on modularity and dependency relationships, although its empirical support remains comparatively limited within the reviewed literature. Gene tree–species tree discordance does not automatically invalidate tree-based models, as some incongruences can be addressed through genealogical reconciliation approaches. Therefore, researchers should guide the selection of biological representations by research questions, the nature of available evidence, and the relationships to be inferred, rather than by model complexity alone. This principle of interpretive caution also carries social implications when biological variation and classification are applied to humans, as scientific classifications do not inherently provide a basis for establishing hierarchies of value, rights, or social status among groups. Within this context, this study contributes to Sustainable Development Goal 10 (Reduced Inequalities), particularly Target 10.3, by emphasizing the importance of interpreting biological knowledge in ways that prevent its misuse in legitimizing discrimination and that support equal opportunities and fair treatment among human populations.