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From:
Subject: Re: [DNA] Male Line Specific Y-STR Average Mutation Rates
Date: Sat, 15 Jan 2005 10:16:58 EST


In a message dated 01/13/05 9:06:39 PM Pacific Standard Time,
writes:

> What if every male line has a different deck of cards. Each deck would
> have the same total number of cards as in a standard deck. But some
> decks would have four more hearts and less other suits and some with six
> more hearts in it and less other suits. And another male line has a deck
> with four less hearts in it, etc. and another male line has a deck with
> six less hearts in it, etc. Same number of total cards but a different
> amount of hearts (potential mutations that can occur for the simulation
> game you suggested) at random using your game. It is still a random
> process within the specific male line, but since each male line has a
> different deck of cards, one male with a deck with more hearts
> (potential mutations in his games), and another with less hears
> (potential mutations in his games), the number of hearts obtained
> typically would not be the same for each game comparing a game played
> with one standardized deck and other games played with different heart
> amount containing decks.
>
> Does that help you see what I am trying to say. Not all male lines are
> playing from the same deck. Humor intended. :-)

Oh, I know what you've been saying all along, but I think that's an admirably
clear way of stating the difference between the two models. It conveys the
mystery and the element of chance better than the shoe size analogy. Your shoe
size is not mysterious, but -- did your hand come from a regular deck or a
stacked deck? How can we possibly tell? Only by dealing many hands, and since the
absolute rate is so low, we may have to hang around a long time to observe any
mutations at all. It's more like dealing from decks with a thousand cards
each, where only one to six of them are hearts. You can pay a little extra and
draw more than 12 cards, but most hands are not going to have any hearts at all.
When a heart comes along, it makes an abrupt change in your calculations --
all of a sudden you go from a mutation rate of zero to a mutation rate of one
divided by the number of hands that were dealt.

I don't (and I can't) say that you're wrong about each male line having its
own intrinsic mutation rate, its own deck of cards. What I wanted to say is
that dealing hands from a regular deck can *also* give you quite a wide range of
results, purely by chance, and that when we're dealing with rare events, it
takes a lot of data to reach a conclusion, probably more data than any one male
line can provide.

We are just barely getting into the range of data where we can start to
assert that different Y-STRs have different mutation rates. Dupuy's 2004 study made
a big contribution to that -- more than half of the results. No one ever said
they were all identical, just that we had no firm basis for claiming they
were different when the observed rate could change so quickly from one study to
another. It's instructive to look at the YHRD data that Jim Elliott
consolidated onto one page. It shows how all the rates are based on a rather small number
of mutations, and a single mutation can make a big blip when calculating the
average in individual studies (URL ends with html).

http://freepages.genealogy.rootsweb.com/~gallgaedhil/YHRD_mutation_rates.html

There were even quite a few studies where DYS392 and DYS393 didn't mutate at
all. But we knew it must have mutated sometime, since there are different
alleles (see the histograms at Ybase).

http://ybase.org/statistics.asp

Now suppose that each male line does have its own intrinsic mutation rate.
What could account for it? It could be something structural -- a particular
sequence is more stable or more accident prone. I think we may be seeing this in
DYS388 -- it seems relatively stable when it's in the vicinity of 12 repeats
(one of the shortest STRs), but more variable when it's in the region of 15-17
(in Haplogroup J). Some studies are starting to list mutation rates subdivided
by haplogroup, and I think that might be worth including as one of the fields
in your log.

It could be something functional, but this I find harder to imagine. If there
is a Y-linked gene that influences the efficiency of
copying/proof-reading/repairing DNA, then half of the world is denied access to this tool. No fair! Of
course, the Y has been sequenced so recently that there are newly discovered
genes with no known function, but I would expect most of them to be connected
with male-specific duties like making sperm, not general housekeeping tasks
like DNA duplication.

None of this negates the value of your log. Collecting data into one place is
very helpful, as it helps people gain a broader perspective on what can
happen in DNA projects. And if some population geneticist wants to find cases with
a high or low mutation rate for further study, it will be a handy starting
point. As I said before, we should flag cases that deviate from "expected" values
and keep an eye on them. There could be interesting discoveries lurking
within them, even if it turns out that there is not a distinctive mutation rate for
every single male line. I do think that genetic genealogists are an untapped
resource!

Ann Turner - GENEALOGY-DNA List Administrator
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