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From: "Anatole Klyosov" <>
Subject: Re: [DNA] R-U152 and R-L21 on the European Continent
Date: Tue, 8 Dec 2009 22:37:31 -0500
References: <mailman.6234.1260309884.2086.genealogy-dna@rootsweb.com>


From: "Alister John Marsh" <>

>I suspect that STR mutations have relatively similar mutation behaviour now
>to millions of years ago.
>But that does not mean that STRs mutate randomly, with each mutation event
>having 50% chance of being a mutation up or down.

Dear John,

Frankly, I do not have a slightest desire to convince anyone in power of
science and,
concurrently, in its weakness at any given moment of time. Science is never
perfect,
because it is conducted by people. It is never complete, finished, done.

If I see that I cannot convince, I easily give up with my attempts to
convince, and just
refer to mine and other's studies. It does not help, though, because people
who are in
doubt do not like to read. Why bother, right? It is so comfortable to be in
doubt, since
you are not responsible for an answer, either way. It is so easy and
comfortable to sit
on a fence watching the game down there.

Back to your specific comment. No, it does not mean that the mutations
always go randomly.
However, they do not have to. I would not like to flash with my own studies,
far less to claim
that they are necessarily complete and free of flaws. However, I have
analyzed specifically
non-randomness (asymmetry) of mutations in haplotypes, from m=0.5 (complete
randomness)
to m=1 (complete one-sidedness), and developed an approach to handle those
cases with
any "m" value. The theory and practical examples are published in the last
issue of J. Genet.
Geneal. Hence, non-randomness is not a problem whatsoever in calculations of
TMRCA's.

>As we keep saying, if we can recover good Y-DNA from well dated
>archaeological sites, it would give some good data to verify the
>reliability
>of statistical analysis of mutations.

Again, you should read the literature. There are good examples already of
what you are
"keep saying". Let me give you just a few. I have published in June of 2008
that TMRCA
of German R1a1 haplotypes is 4700 years (with a certain margin of error). A
few months
later Haak at all published on excavated R1a1 in Germany with dating of 4600
ybp.
I have published a series of works on R1a1 on the Russian Plain with TMRCA
of 4750 ybp,
and their migrations to the East with arriving to Ural Mountains at about
4000 ybp and moving
down to India at about 3600 ybp. Recently Keyser et al have published on
excavated R1a1
in South Siberia, just East of Ural, with dating between 3800 and 3400 ybp.
Indian
"Indo-European" R1a1 haplotypes have the TMRCA of 4050 ybp, in a good line
with the above.
I have published data on Native American haplotypes with the TMRCA of 16,000
ybp, which is
in a good line with archaeological data, and gave a number of references to
the data in the last issue
of JGG. According to my published data on the Jewish and Arabic haplotypes,
the Jews
and the Arabs split (in J1 group) 4,000 ybp(plus-minus a margin of error,
all in the publication),
which is in a good line with independent estimates.

The list goes on and on. According to calculations of haplotypes, a "young"
Scandinavian R1a1 branch
has the TMRCA of 1500 ybp, in the middle of the 1st millennium AD, and their
ancestral haplotypes
show a good match with those from the Russian Plain and with a set of
Central Asia haplotypes.
Ask David F., and he would gladly confirm that archaeological and other data
confirm an arrival
of the Asians (or, more carefully, people from the East) to Scandinavia in
the middle of the 1st millennium.

The thing with the skeptics is that they do not read and they do not listen.
When they read, e.g., the above,
they keep saying "this is not enough". Nothing is enough for them. Never.
Because it is so comfortable
to be a skeptic.

Regards,

Anatole Klyosov

>>>>>>>
Folks who work with mutations in haplotypes keep working and analyzing new
and new data.
And they come again and again to the conclusion that STR mutations have the
same frequency
now and thousands and millions years ago. There is not a single proven fact
or an observation
which would show otherwise. Recently a paper was published (Sun, J.X.,
Millikin, J.C.,
Patterson, N., Reich, D.E. 2009. Microsatellites are molecular clocks that
supports accurate
inferences about history. Mol. Biol. Evol. 26, 1017-1027) which showed that
mutations are
ticking with a constant rate for the last two million years at least.
<<<<<<<

I suspect that STR mutations have relatively similar mutation behaviour now
to millions of years ago.

But that does not mean that STRs mutate randomly, with each mutation event
having 50% chance of being a mutation up or down. It could be that for some
STRs, there is a favoured "sweet spot" which mutations tend to hover around.
DYS439 is moderately fast mutating, but seems to predominantly hover around
a narrow range of values.

Uniform mutation behaviour does not mean that some STR values are not
favoured for long term survival over others. It does not mean that an
allele value which has appeared benign for hundreds, thousands, or millions
of years may not be fatal or highly favoured in an extraordinary population
stress event which causes a "bottle neck".

You have confidence in statistical analysis of mutations. However, when the
haplogroup aging by variance of variance method was discussed some time ago,
it emerged that some doing the analysis selectively culled the data,
removing closely related haplotypes, and removing "outliers" which seemed
exceptions to the preconceived rules of mutation. Further, some selectively
culled the markers to use in calculations based on various factors including
mutation rates. Using either slow or fast mutating markers in calculations
enabled differing results to be obtained which varied by a factor of 50
fold.

I am not a mathematical expert. But it just seems to me that some
assumptions are underpinning results from statistical analysis which have
not been fully tested, because they are hard to test with available data.

As we keep saying, if we can recover good Y-DNA from well dated
archaeological sites, it would give some good data to verify the reliability
of statistical analysis of mutations.

To a significant degree, the statistical analysis lobby group have changed
my views on ages of haplogroups, particularly younger subclades, but I would
feel more comfortable with further corroborating evidence for estimates
involving longer time spans.

Some genealogists are happy to accept a birth certificate as
incontrovertible evidence of parenthood. Other genealogists like to
corroborate evidence by evidence from more than one source. I make no
apology for leanings towards the conservative group who seek more than one
piece of evidence.

When I became involved in genetic genealogy, I proved that two well
documented lines, regarded for 400 years as descending from two brothers, in
fact have male lines from different haplogroups.

Anatole, your confidence in the statistical analysis may be well placed. You
may be right. I am just one of those painful people who is sitting on the
barbed wire fence until more evidence is available. With advances in DNA
science, it is likely we will have good archaeological DNA evidence before
long. I hope!

John.





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