Paralogy means close similarity of nonallelic chromosomal segments or DNA sequences within a species, indicative of a close evolutionary relationship which may or may not have predated speciation. For example, the two different human a-globin genes (see Figure 7.11) are paralogous. Different degrees of paralogy can be identified in a DNA sequence family with more than two members. For example, although all 38 human HOX genes are clearly related and so to some extent can be considered as paralogs, there is an especially close structural and functional relationship between specific genes in the four clusters. As a result, in the HOX gene family, the term paralogous is customarily confined to sets of particularly related genes (see below and Figure 14.5).

Orthology means close similarity of chromosomal segments or DNA sequences between species. For example, the major human sex-determining gene is SRY and its ortholog in mouse is the Sry gene. In gene families with closely related members in a species, it may be difficult to recognize true orthologs between species.

Homology was initially used to describe the relationship of allelic chromosomal segments. Since then it has been widely used in a loose sense to signify any type of relatedness indicative of a common evolutionary origin, whether within or between species.