Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.

The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomic systems have been designed to describe tree-like evolution and consequently struggle to accommodate network-like evolutionary patterns. In this perspective, I consolidate and clarify terminology for describing organisms whose evolutionary history has not been strictly tree-like. I introduce two complementary concepts: epaktovars, groups (≥2) of organisms exhibiting convergent phenotypes through independent acquisition of similar functions, whether via horizontal gene transfer (HGT) or independent evolution of analogous solutions, and xenotypes, organisms that share homologous genes acquired through HGT, regardless of whether these shared genes produce similar or different phenotypes. The epaktovar concept mirrors the previously established concept of epaktologs (independent assembly of similar protein domain architectures), while xenotypes extends the concept of xenologs (horizontally transferred homologous genes) to the genome level. Recent research on homoplastic patterns in pangenome evolution enhances our understanding of these phenomena. These concepts also have important applications in synthetic biology and de-extinction efforts, where genetically modified organisms and reconstructed extinct species can be understood as xenotypes and epaktovars of their genetic donors, providing a framework for classifying organisms whose genetic composition has been shaped by human intervention rather than natural evolutionary processes. These terms collectively provide a framework for describing both phenotypic convergence arising through any evolutionary mechanism and shared genetic material resulting specifically from gene transfer across diverse lineages.