Orthology and sequence identity/similarity

Question

[Dunois]

Say we have two sequences X1 and X2 that are orthologs to one another. A third sequence X3 gets found that happens to be orthologous to both X1 and X2.

Now the species X3 comes from is phylogenetically closer to the species X2 comes from than that of X1. However, X3 is more identical to X1 than it is to X2.

Does this mean that X3 is more (?) orthologous to X1 than it is to X2? If homology is a binary yes/no thing (two sequences are either homologs or they are not), then wouldn't orthology--by virtue of being a subset--also be a binary yes/no thing?

Why would it be the case that a sequence from a species that is evolutionarily closer is less identical* than one from a species that is (evolutionarily) farther away? I thought that orthologous sequences are similar, and the smaller the evolutionary distance between them, the more identical they should be.

In general, what is the right way to interpret sequence similarity/identity in the context of sequence orthology?

* - or similar, if we are looking at the similarity score.

Answer 1

[Mensur Dlakic]

There is no more or less orthologous, so this is also a binary term. By definition, orthologs perform the same function in different species, meaning that they can be linked by common ancestor through the evolution of species.

Orthology is defined by common function, not by sequence identity. However, all genes in two or three species don't necessarily evolve at the same rate with respect to their evolutionary distances. Separately, it is possible that an ortholog with higher sequence similarity between more distantly related species is not an ortholog, but a horizontally transferred gene. If there are several other genes in close proximity to yours that follow the same pattern (being more similar in sequence than expected by evolutionary distance), that would make a horizontal transfer a more likely scenario.