A form of homology in which two or more genes within the same genome are related by a gene-duplication event and have since diverged in sequence and possibly in function.

Principle

When a gene duplicates within a lineage, the redundant copy is freed from the original selective constraints and may accumulate substitutions, regulatory changes, or structural modifications that produce new or partitioned functions while retaining a recognisable ancestral relationship.

Demonstration

In vertebrates, the alpha- and beta-globin gene clusters are paralogs: they originated by successive duplications of an ancestral globin gene and diverged to produce multiple haemoglobin subunits with distinct expression patterns.

Misapplication

Labeling genes from different species that share a single-copy ancestral gene (orthologs) as paralogs, or attributing similarity produced by horizontal transfer or convergence to paralogy.

Consequence

Recognition of paralogy explains within-genome gene family expansion, functional redundancy, neofunctionalization or subfunctionalization, and complicates orthology inference across species.

Reversal

Orthology — genes related by speciation events without an intervening duplication, preserving one-to-one relationships across lineages.

Boundary

Applies only to genes related by duplication within a lineage’s genomic history; excludes homologous relationships created by speciation (orthologs) or by horizontal transfer (xenologs). Uncertainty arises when duplication timing relative to speciation is ambiguous (in-paralogs vs out-paralogs).

Semantic Tension

Tension with 'orthology' (both are homology types) and with usages that loosely call any similar paralogous domain a paralog without establishing duplication history; also competes with lay use of 'paralog' to mean simply 'similar gene'.

Synthesis

Paralogy designates homologous genes that arose through duplication within a genome; identifying paralogs reveals gene-family dynamics and potential novel functions, but requires careful phylogenetic timing to distinguish from orthology and other sources of similarity.