Part (a) of the diagram above shows a hypothetical evolutionary history of a gene. The ancestral genome had two copies of this gene (A and B) which were paralogs. At some point, the ancestral species split into two daughter species, each of whose genomes contain two copies of the ancestral duplicated gene (A1,A2 and B1,B2). These genes are all homologous to one another but are they paralogs or orthologs? Since the duplication event that created genes A and B occurred before the speciation event that created species 1 and 2, A genes will be paralogs of B genes and 1 genes will be orthologs of 2 genes: •A1 and B1 are paralogs •A1 and B2 are paralogs. •A2 and B1 are paralogs. •A2 and B2 are paralogs. •A1 and A2 are orthologs. •B1 and B2 are orthologs This however, is a very simple case. What happens when a duplication occurs after a speciation event? In part (b) of the above diagram, the ancestral gene was duplicated only in species 2's lineage. Therefore, in (b): •A2 and B2 are orthologs of A1. •A2 and B2 are paralogs of each other. A common misconception is that paralogous genes are those homologous genes that are in the same genome while orthologous genes are those that are in different genomes.As you can see in the example above, this is absolutely not true. While it can happen that way, ortho- vs paralogy depends exclusively on the evolutionary history of the genes involved. If you do not know whether a particular homology relationship is the result of a gene duplication or a speciation event, then you cannot know if it is a case of paralogy or orthology. References 1.R.A. Jensen, Orthologs and paralogs - we need to get it right, Genome Biology, 2(8), 2001
The terms orthologue, paralogue, and homologue are often used incorrectly in scientific literature. This section defines orthologue..
According to M. J. Kobayashi and K.K. Simizu, orthologues are genes "in two different species that derive from the same ancestral gene of the common ancestor."
According to R.A. Jenson, orthologs are genes that happen after speciation, and paralogues are genes that result after duplication. Jenson also says that ortholog genes and paralog genes are both examples of homologous genes.
This website provides a more detailed explanation with illustrations:
Orthologous and Paralougous
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