Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups

Abstract

With the rapid advancement of large-scale sequencing initiatives, the need for efficient and accurate methods for inferring orthologous and paralogous relationships has never been more critical. Hierarchical orthologous groups (HOGs) provide a powerful solution to this challenge, offering a precise, scalable framework to study gene families and their evolutionary histories across diverse species. In this review, we introduce the concept of HOGs and explore their advantages over traditional methods. Next, we highlight key applications of HOGs, including their use in representing gene families, inferring ancestral genomes, tracking gene gain and loss events, functional annotation, and phylogenetic profiling. We overview the process of constructing HOGs and discuss the challenges and limitations of HOG inference. The HOG framework provides a clear and structured approach to organizing homologous genes, making it possible to gain deeper insights into gene family and species evolution.

Keywords: Ancestral genomes; Comparative genomics; Gene function; Hierarchical orthologous groups; Orthology; Orthology benchmarking; Paralogy; Phylogenetics.