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This broad definition encompasses all the working definitions proposed so far in the literature.

Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.

Convergence usually implies a notion of adaptation.

Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.

Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.

The term is sometimes also used for anatomical structures.

The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).

The converse of pro-orthologous.

This term is usually contrasted to apomorphy.

Used for structures in distantly related taxa.

The genes have diverged before a speciation event.

Used for structures in closely related taxa.

Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.

The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.

These genes may come out as paralogs in a single-genome analysis.

This may include examples of orthology, paralogy and xenology.

This phenomenon is usually due to gene conversion process.

Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.

On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.