Re: Dating with DNA? Problems and Current Approaches

In sci.archaeology message news:ee9mnt$sl4$1@xxxxxxxxxxxxxxxx by Doug
McDonald <mcdonald@xxxxxxxxxxxxxxxxxxx> . . . :

There are many problems with using DNA to date anything.

First is the use of STR variances.

Short tandem repeat ? used in DNA testing (Biology). Autosomal or Y
chromosome

The problem here is that
the variance is strongly influenced by population
bottlenecks. This effect appears to be up to a factor of
four. For the Y chromosome and some autosomal markers the
actual rate is well known from father-son and genealogical
studies. To get the "right" answer from these markers at
several thousand years requires assuming a factor of 4
slower rate. But this depends on unknown population
dynamics.

Yep.

This applies to anything that looks at diversity.

The archies here are complaining about the abbreviations

This problem does not arise with SNPs

SNPs = Single Nucleotide Polymorphisms, a point mutation
or single position convertant.

if you have enough of
them that all lines differ by vary many. You can just use
the average rate. But what is the rate? It's too slow to
directly measure, and worse, it is highly variable between
sites (on the DNA that is, not places on the planet.) Some
of these difference ratios can be well calibrated, some
can't. But the overall rate is exceedingly poorly known,
except possibly for human mtDNA,

mtDNA = mitochondrial DNA.

full-genome sequenced Y chromosomes. These dates fall into
the very useful 0-100kYr range. Enough mtDNA full genomes
have been sequenced (mine included, for example) that we
KNOW for certain that no +-20% quality measurement of their
origin date will ever be attainable.

Yep. But part of that is the problem of calibration.

How well autosomal pseudo-haplogroups (or point mutations in
them) will be dateable is still an open question, as it
depends on many things like how long haplogroup blocks we
can find.

There are long blocks, as we had a lecture on this
by a person who is in the human variation project,
in some spots 300,000 nt. But the rate of mutation
that is a different question.
The molecular anthropologist need to connect with
the folks analyzing the structure of the human genome
and you could have some pretty definite studies in fast
order. However one study showed that rate divergence
from chimpanzees differs with chromosomal segments.
One needs then quite a few segments to creat a
worthy picture.

The original question is whether we can used ancient
DNA to date a human. Aside from the wide confidence range
we have to consider if we have some remote site with
modest SNP rates, who is going to be confident of the
sequencing.


.

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