Fig. 1: HOGs explicitly model gene lineage, thus ancestral gene contents.
From: EdgeHOG: a method for fine-grained ancestral gene order inference at large scale
Left: the species tree displays the evolutionary relationships between four extant species (S1, S2, S3 and S4). Its internal nodes are proxies for ancestors (A1,2, A1,2,3 and A1,2,3,4). The central gene tree illustrates an example of inferred evolutionary history for a gene family (coined X) present in all species. The HOG object of the family X can be computed from the reconciled gene tree of X as in EggNOG or using fast graph-based methods as in OMA. Once pyHAM processes the HOG of family X, the graph on the right is created: each node corresponds to an extant or ancestral gene and each edge links a descendant gene to its parent gene in its most direct ancestor. When paralogues are connected to the same parental gene, it models an event of gene duplication (happening here between ancestor A1,2,3,4 and descendant A1,2,3). The collection of gene nodes of all HOGs’ graphs at a given ancestral level eventually serves as proxies for its ancestral gene content.
