Orthologie

Orthology is a concept in comparative genomics that describes genes in different species that originated from a single gene in the last common ancestor and diverged through speciation events. Orthologous genes, or orthologs, are often assumed to retain the same or similar function across species, making them particularly informative for functional annotation and evolutionary studies. However, orthologs can diverge in function over time, though generally to a lesser extent than paralogs.

Paralogous genes arise by duplication within a genome. Duplications can produce gene family members that evolve new or partitioned functions. When duplications occur on a large scale, such as whole-genome duplications, the resulting paralogs are sometimes referred to as ohnologs. Distinguishing orthologs from paralogs is a central challenge in comparative genomics, because paralogs can confound functional inference if misidentified as orthologs.

Identification of orthologs relies on both phylogenetic and sequence-based approaches. Common methods include reciprocal best-hit analyses in pairwise sequence comparisons, and more sophisticated phylogenetic tree–species-tree reconciliation. Clustering approaches and databases, such as OrthoMCL, OrthoDB, and eggNOG, integrate information across multiple species to infer orthology relationships. These methods are imperfect and can be affected by gene loss, hidden paralogy, horizontal gene transfer, and incomplete lineage sorting.

Applications of orthology include transferring functional annotation between species, reconstructing ancestral gene repertoires, and informing evolutionary and biomedical studies. Orthology remains a central concept in genomics, guiding the interpretation of gene function across the tree of life.