Paralogy

Paralogy describes a relationship between genes that originated from duplication within a single genome. Paralogous genes are homologous genes that arose by duplication events and then diverged within the lineage. This is distinct from orthology, where the homologous genes are related by speciation events (one gene in each species).

Gene duplication creates paralogs and provides raw material for evolutionary novelty. Duplications can occur via unequal crossing over, replication errors, retroposition, or whole-genome duplication. After duplication, duplicates may acquire new functions (neofunctionalization), partition the ancestral function (subfunctionalization), or one copy may become nonfunctional as a pseudogene. Some paralogs are highly similar and retain redundancy; others diverge substantially.

Examples of gene families with paralogs include the globin genes (alpha and beta globins and other lineage-specific duplications), the Hox gene clusters in vertebrates, and the olfactory receptor gene family. Paralogs within a genome may reside on different chromosomes or within the same region, and their relationships are inferred through sequence similarity, phylogenetic analysis, and genomic context.

Distinguishing paralogs from orthologs is central in comparative genomics. Paralogs are identified through gene trees and synteny analysis; in-paralogs are duplications after a speciation event, while out-paralogs predate the speciation. Understanding paralogy aids in functional annotation and understanding the evolution of gene families.