orthologues

Orthologues are genes in different species that originated from a single gene in the last common ancestor as a result of speciation. They are typically expected to retain the same or similar function across species, though functional divergence can occur over evolutionary time.

Orthology is contrasted with paralogy, where paralogous genes arise by gene duplication within a species. Because duplications can precede or follow speciation, relationships between genes can be one-to-one, one-to-many, or many-to-many. Whole-genome duplications and horizontal gene transfer can further complicate orthology assignments.

Orthology is widely used for predicting gene function in newly sequenced organisms; by assuming conserved function in orthologs, researchers transfer annotation between species. However, orthologs are not guaranteed to have identical roles; neofunctionalization and subfunctionalization can alter function after duplication or speciation. Functional inference should consider additional evidence.

Identification methods include phylogenetic reconstruction to distinguish speciation events from duplications, and synteny or conserved gene neighborhoods. Heuristic approaches such as reciprocal best BLAST hits provide quick, low-resolution candidates, while dedicated tools (for example OrthoFinder, OrthoMCL, eggNOG) compare multiple genomes to produce orthology relationships. Limitations include incomplete genomes, rapidly evolving genes, and lineage-specific losses.