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Of Terms in Bi­ol­ogy: Or­tholog

by Elio

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The terms or­tholog and par­a­log have wide ac­cep­tance. Yet, we find that they are used in nu­anced ways by dif­ferent peo­ple. Sure enough, here is some of what the In­ter­net comes up with:

  • or­tholog: a gene from a dis­parate species, so sim­i­lar in ge­netic se­quence that it is as­sumed to have ori­ginated from a sin­gle gene in a com­mon an­ces­tral species.
     
  • or­tholog: ei­ther of two or more ho­mol­o­gous gene se­quences found in dif­fer­ent species.
     
  • or­thol­o­gous: ex­hibit­ing or­thol­ogy; hav­ing been sep­a­rated by a spe­ci­a­tion event.
     
  • or­thologs: ho­mol­o­gous genes that re­sult from spe­ci­a­tion events (as op­posed to par­alogs, which re­sult from du­pli­ca­tion and sub­se­quent di­ver­gence in a lin­eage).
     
  • or­thol­o­gous: groups of genes or pro­teins from dif­fer­ent or­gan­isms that have the same func­tion are said to be or­thol­o­gous.
     
  • or­thol­o­gous: genes in dif­fer­ent species are or­thol­o­gous when their phy­logeny is iden­ti­cal to the phy­logeny of the species.

We deleted the ones that seemed like du­pli­ca­tions (par­alogs?). We find the first one most to our lik­ing. Which do you think is most use­ful?

 

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Jonathan Badger
17 years ago

Well, "groups of genes or pro­teins from dif­fer­ent or­gan­isms that have the same func­tion are said to be or­thol­o­gous" is the way most bioin­for­mati­cists use the term, even though most evo­lu­tion­ary bi­ol­o­gists are hor­ri­fied by it.
I'm not sure it is an is­sue of "use­ful­ness"; both the evo­lu­tion­ary and bioin­for­mat­ics mean­ings are use­ful — but as the evo­lu­tion­ary bi­ol­o­gists had the term first, I sup­pose their mean­ing of traits/genes sep­a­rated by a spe­ci­a­tion event has pri­or­ity, and the bioin­for­mat­i­cans should in­vent a new term.

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Matt Hudson
17 years ago

I agree with Jonathan Bad­ger that to most bioin­for­mat­ics types "or­thol­o­gous" is syn­ony­mous with "shared func­tion" as well as "shared lin­eage". How­ever I think the two are both im­plied by the evo­lu­tion­ary de­f­i­n­i­tion, since "func­tion" here is in the broad sense of bio­chem­istry and struc­ture, not the nar­row sense of fit­ness in a par­tic­u­lar or­gan­ism. Thus, if du­pli­ca­tion and sub­func­tion­al­iza­tion has oc­curred, the gene is no longer a strict or­tholog in ei­ther sense.
It is cer­tainly im­plicit to most bioin­for­mat­ics peo­ple that or­thol­ogy im­plies com­mon an­ces­try. Home­o­plasy would never be con­fused with or­thol­ogy.

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Rhea Miller
17 years ago

lol. Way to point out one of the hard­est parts of grad­u­ate school. While learn­ing NEW information....where do you get it?!?!? when do you trust it?!?!? how do you know that you are get­ting the best an­swer?!?!?!
...what a co­nun­drum.

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