Re: Human/chimp similarity measures
Wed, 6 Oct 1999 06:43:17 EDT

In a message dated 9/27/99 5:15:07 PM !!!First Boot!!!,

Stephen Jones responded to my recent post, outlining his objections.
Stephen covered several different techniques for assessing degree
of similarity of genomes across species.

Stephen cited King and Wilson (1975) as a relevant authority, and
in the quoted material there was discussed these techniques:

Immune reactions
Protein sequences
Annealing techniques

The first three techniques are based upon small-scale
sampling, which Stephen cites as a difficulty. DNA
hybridization, though, is based upon large-scale sampling,
involving much longer stretches of DNA than are referenced by
any of the other techniques. DNA hybridization provides a
comparison without reference to whether the sequence being
analyzed is composed of coding regions, non-coding regions,
or a mixture of the two.

WRE>The number of genes/loci comes from genomic
WRE>sequencing studies. Stephen is invited to explain why anyone
WRE>would expect the number of loci found via genomic sequencing
WRE>to alter our opinion of the confidence with which to hold the
WRE>DNA hybridization result.

SJ>I already said "why". "If humans have The have *twice* as many
SJ>genes (140,000) as previously thought (60,000-80,000)" and
SJ>"unless of course chimps turn out to have twice as many genes
SJ>as first thought too", then the statement that `humans share
SJ>98% of their genes with chimps' will be wrong. Humans and
SJ>chimps might share 98% of their *known* genes, but that does
SJ>not necessarily mean that they share 98% of their total genes.

That's why I clarified my response to address the similarity of
DNA, not genes.

SJ>The problem with the assumption that humans share 98% of their
SJ>genes was that: a) it was based on only a limited number of
SJ>proteins and fragments of DNA; b) those fragments of human DNA
SJ>that did not closely match that of chimps were discarded; and
SJ>c) as King and Wilson pointed out, their study only compared
SJ>structural genes. There might be major differences in
SJ>regulatory genes:

A genetic distance found by DNA hybridization is not subject to
the same criticisms as the small-scale smapling methods that
Stephen argues against above.

I'll restore the remainder of my discussion of DNA
hybridization as a measure of genetic similarity.

Of course, skeptics can point to the position of Dr. Marks on
the original DNA hybridization work. See
<>. But
even Marks' table would not increase the difference more than
another 1.7 percent or so. Marks criticizes the claim that
DNA hybridization is capable of resolving the three-way split
between humans, chimpanzees, and gorillas. Marks does not
appear to argue that there are huge differences between humans
and chimpanzees. I would welcome correction on my
characterization of Marks' stance from anyone who has the
relevant papers.

Even the anti-evolutionary page at
<> manages to
recognize and discuss the differences in approach.

A basic description of DNA hybridization can be found at

Another link:

I find it interesting that the small-scale and large-scale
genetic similarity measures all lead to such nicely congruent

Wesley >>

***** It is also interesting that divergence time estimates based on DNA data
and the model of local molecular clocks provide times largely congruent with
the times inferred from the fossil record.

For example in:

Mol Phylogenet Evol 1998 Jun;9(3):585-98

Toward a phylogenetic classification of Primates based on DNA evidence
complemented by fossil evidence.

Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell
G, Groves CP
Department of Anatomy and Cell Biology, Wayne State University School of
Medicine, Detroit, Michigan, 48201, USA.

A highly resolved primate cladogram based on DNA evidence is congruent with
extant and fossil osteological evidence. A provisional primate classification
based on this cladogram and the time scale provided by fossils and the model
of local molecular clocks has all named taxa represent clades and assigns the
same taxonomic rank to those clades of roughly equivalent age.