Richard Owen, an English biologist who lived from 1804 to 1892, introduced the term homology, stating that it is "the same organ in different animals under every variety of form and function."
Today, we use the term homology is used to characterize biological species that share a common evolutionary ancestory.
Note that homology is a binary qualitative measure - either two sequences are homologous or not. Homology cannot be quantified. Thus, it is incorrect to claim that "two sequences are 55% homologous" - we use percent identity or similarity to quote numbers, which we will talk about in the next lesson.
There are two subclasses of homology - orthologous and paralogous.
Paralogous is when gene duplication occurs, but both copies descend side-by-side during the history of the organism (para = in parallel). This phenomenon occurs within the species. For example, human alpha-1 globin is paralogous to alpha-2 globin because they resulted from a gene duplication that arose from a single organism. Paralogous genes are assumed to carry common functions.
When speciation occurs, and a gene is inherited in both species, these sequences are said to be orthologous (ortho = exact). For example, the human and rat myoglobins are orthologous - the sequence that codes for this protein comes from a common ancestral gene.
In simplified terms, orthology is the homology between species, while parology is the homology within species. If you see the figure below from Jensen et al., the ancestral gene has two copies of a particular gene (A and B). Relative to the ancestral genome, this is considered paralogs since they are within its own species.
However, once speciation occurs, two copies of genes A and B are created. Since the duplication of A and B genes occurred before speciation, A and B genes are still considered paralogs. However, genes A1 and A2 are orthologs, as are B1 and B2.
In the second case, gene duplication occurs after speciation. Thus, A2 and B2 are orthologs of A1, while A2 and B2 are paralogs of each other.
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