Quantitative Taxonomy, or the 2% difference

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From: Bryan J. Maloney (jacobus@sonata.cc.purdue.edu)
Date: Fri 29 Apr 1994 - 13:32:47 EEST

Well, I think I can dispell the argument regarding the use of simple quantitative DNA sequence homology comparison as the primary criterion of taxonomic classification. Let us accept that "a chimpanzee" has a "98% sequence homology" with "a human". Note the quotes. This is because, as anyone who has done a good deal of sequencing (like me) can tell you, the "human DNA sequence" is about as unitary a body as the UN General Assembly. There is quite a bit of variation, not all of it phenotypically visible. However, there is plenty of empirical evidence to support the supposition that, all DNA sequence polymorphisms aside, humans are all still humans.

But humans aren't chimpanzees (except for certain administrators and editors) and chimpanzees aren't humans (regardless of cute 1960's spy comedy/parody TV shows). Inasmuch as we understand biology, we look to the "genetic code" for a reason why. Ultimately, the basic "type" of organism something turns out to be is determined by genetic coding, but it's a great deal more complicated than simple quantitative analysis would make things appear. For example:

UL33, a protein that may be necessary for packaging Herpes Simplex II DNA into the capsid, can be mutated in the laboratory. A single amino-acid mutation has been constructed that has a completely inactive UL33 protein. Thus, we have two radically different sorts of organisms, if classified by how they infect and propagate, but their DNA difference is no more than a SINGLE nucleoside out of hundreds of thousands. There are more dramatic examples, and examples that are less esoteric, but none leap to mind right now. My point is that a very tiny quantitative "difference" in genetic code can result in a dramatic qualitative difference in the outcome. However, it is also documented that the DNA sequence of the cytochrome C gene can differ from individual to individual, but the protein itself is identical
(due to degeneracy of the genetic code).

Now, what has this to do with chimpanzees and humans?

The point I am trying to make is that genetic homology is probably an inadequate criterion to use as a means of classification on its own. It can be probably used to clarify some finer points, but I wouldn't swear by it.

Another way of looking at this: A male human shares greater sequence homology over his entire genome with a male chimpanzee than does a male human share with a female human or a male chimp with a female chimp. Does this make male chimpanzees more closely biologically related to male humans than female humans are related to male humans?

(For the astute: Yes, I am talking about the XX/XY chromosome pairs. I
consider it an excellent way to illustrate the absurdity of quantitative genetic taxonomy as a primary method.)

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