Characterizing and Transforming DAGs within the I-LCA Framework

Abstract: We explore the connections between clusters and least common ancestors (LCAs) in directed acyclic graphs (DAGs), focusing on DAGs with unique LCAs for specific subsets of their leaves. These DAGs are important in modeling phylogenetic networks that account for reticulate processes or horizontal gene transfer. Phylogenetic DAGs inferred from genomic data are often complex, obscuring evolutionary insights, especially when vertices lack support as LCAs for any subset of taxa. To address this, we focus on $I$-lca-relevant DAGs, where each vertex serves as the unique LCA for a subset $A$ of leaves of specific size $|A|\in I$. We characterize DAGs with the so-called $I$-lca-property and establish their close relationship to pre-$I$-ary and $I$-ary set systems. Moreover, we build upon recently established results that use a simple operator $\ominus$, enabling the transformation of arbitrary DAGs into $I$-lca-relevant DAGs. This process reduces unnecessary complexity while preserving the key structural properties of the original DAG. The set $C_G$ consists of all clusters in a DAG $G$, where clusters correspond to the descendant leaves of vertices. While in some cases $C_H = C_G$ when transforming $G$ into an $I$-lca-relevant DAG $H$, it often happens that certain clusters in $C_G$ do not appear as clusters in $H$. To understand this phenomenon in detail, we characterize the subset of clusters in $C_G$ that remain in $H$ for DAGs $G$ with the $I$-lca-property. Furthermore, we show that the set $W$ of vertices required to transform $G$ into $H = G \ominus W$ is uniquely determined for such DAGs. This, in turn, allows us to show that the transformed DAG $H$ is always a tree or a galled-tree whenever $C_G$ represents the clustering system of a tree or galled-tree and $G$ has the $I$-lca-property. In the latter case $C_H = C_G$ always holds.