GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2006-12 > 1166873219


From: "John McEwan" <>
Subject: Re: [DNA] Eye color, lactose intollerance, height,and many other traits...
Date: Sun, 24 Dec 2006 00:26:59 +1300
In-Reply-To: <BAY103-DAV145A745C0D5E37BFF20C38C8CC0@phx.gbl>


Dear Richard

All base pairs are not "essential" otherwise you would not see
significant insertions and deletions that differ between people. Some of
these variants may affect minimally, slightly, or a lot the fitness of
an individual, but this may only be relevant under certain
circumstances.

What I said was that there are large scale features of the genome which
would not remain the way they are, given the random nature of mutation,
if they had no function. This suggests that there has to be a selective
force to maintain them. These large scale features affect the 99% of the
genome that does not code for protein. Having a function and being
essential for an individual to leave viable offspring are different
things.

To use a car analogy, a car may have 5 or 6 things that may not work
very well or may even be broken, but they still have a function and they
may not be essential for the car to get me from point a to point b. For
instance one of the brakes may not be well adjusted or a light may only
work on dip, or a tire may be worn. To take another example the horn may
not work, and this may not affect things for years, until it needs to be
used, and its absence then may then result in a crash.

The purging mechanism for deleting superfluous nucleotides is called
deletion and its "observed" rate is approximately 1E-9/bp/generation.
This is about 10 fold lower than the SNP mutation rate. Its true rate
may be higher, but not observed, because of non viable offspring. This
may sound very low, but it is sufficient to get rid of a lot of DNA
pretty quickly (on geological time scales) if it had no function.

Yes a few base pairs are lost at the ends of telomeres each generation
when somatic cells replicate, and if they get too short the cells become
non viable. However, they are rebuilt during meiosis (i.e. the formation
of sex cells). Cancer cells often have "learnt" to evade this process as
well.

I am not an expert, but I may have spent a little more time learning
about some aspects. You certainly are not speaking out of turn at all,
this list exists to inform and discuss things related to DNA genealogy.
The question about whether the results provide information about the
phenotype (i.e. what you observe) of an individual is a key question
that most new members have concerns about. All I am saying is I don't
think there is a significant issue, but people need a better
appreciation than simply saying its "junk DNA" and has no function. As
more and more variants are examined and sequence obtained, this argument
becomes less sustainable. Sequencing of the whole mitochondrial genome
meant DNA genealogy has now officially gone past that point.

Normally, I don't respond but in this case/thread Sasson made a rather
challenging statement that I felt required a response.

Cheers

John McEwan


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