Homology/similarity/identity: proper usage.

Joe Felsenstein joe at evolution.u.washington.edu
Sat Feb 2 15:23:45 EST 1991

In article <11223 at uhccux.uhcc.Hawaii.Edu> ronald at uhunix1.uhcc.Hawaii.Edu (Ronald A. Amundson) writes:
> The
>problem is that the criteria by which the common source is identified
>is different in the molecular and "macroscopic" inferences of
>homology.  I can think of two differences -- forgive my ignorance if
>I've got facts wrong.
>1)  Good macroscopic evolutionary inferences of homology are based on
>"shared derived" characteristics.  The nests of other sets of traits
>disallow certain similarities to count as homologies.  Mere similarity
>alone can never be used to judge two traits as homologous.  (Unless
>I'm wrong) the "mere similarity" (i.e. molecular identity or
>similarity, in the absence of evidence provided by other hierarchies
>of traits) of molecular sequences is used as a sufficient criterion
>for the term "homology" in molecular genetics.

>Ron Amundson
>Dept. of Philosophy
>University of Hawaii at Hilo
>Hilo, HI  96720-4091
>ronald at uhunix.bitnet

As far as I can see "homology" as used by morphological systematists
is the same thing.  Many studies of morphology don't actually base
themselves on characters where ancestral and derived states can be
predetermined.  Instead they toss the data into a computer, get a tree
by (say) Wagner parsimony, and use an outgroup criterion to root the tree,
and in the process determine after the fact which states are ancestral and
where the synapomorphies are.  That's the same thing molecular evolutionists

They will often use more than one sequence and judge "homology" by where
the sequence fits in on a phylogeny of the sequences, where they might
use (say) Wagner parsimony with outgroup-rooting.  If this is done, then I see
no real difference between the two processes.

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
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