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From: "Sandy Paterson" <>
Subject: Re: [R-M222] Coyne and Golden project families
Date: Wed, 9 Dec 2009 20:46:08 -0000
References: <mailman.10427.1260379516.2036.dna-r1b1c7@rootsweb.com><001401ca7907$bc00a010$aa00a8c0@Sisko>
In-Reply-To: <001401ca7907$bc00a010$aa00a8c0@Sisko>


No, we cannot test the DNA of the original male.

But we can make a reasoned guess at his haplotype. We can observe the modal
of the M222+ population. In the knowledge that M222+ is very young (some 60
generations), we can work out (no college education required) that it won't
be too far from the observed modal. We can (and have) done simulations that
test the frequency with which a given set of marker values produce an
observed modal different to the starting haplotypes due to mutation over 60
generations.

@
More specifically, there is a flaw in logic. In order for the exact 67-67
matches with the modal
haplotype to be meaningless (or less meaningful), you would have to assume
or propose that the markers
for the modal haplotype have not mutated at all since the original male
(almost infinitely small
probablility) or that they have experienced a long series of mutations and
reverse mutations that
coincidentally reverted to the original (modal) haplotype (also infinitely
improbable). In order to
argue that the off-modal matches are more significant indicaters of
relatedness (to one another) than the
"on-modal" matches are (to one another), you would have to argue that the
laws genetics and probability
somehow apply differently to the modal than to any other haplotype. This
isn't tenable.
@


Plain rubbish.

You simply have to observe that either way (meaning either no mutations or
mutations that have reversed), there is no evidence that any mutations have
been passed down from a common ancestor.

@
In order to argue that the off-modal matches are more significant indicaters
of relatedness (to one another) than the
"on-modal" matches are (to one another), you would have to argue that the
laws genetics and probability
somehow apply differently to the modal than to any other haplotype. This
isn't tenable
@

This goes beyond plain rubbish.

If there is no evidence of mutations having been passed down, there is no
evidence. That's that. Laws of probability? Laws of Genetics? No. Just plain
logic. The absence of evidence is just that. An absence of evidence.

If, on the other hand there is evidence that mutations MAY have been passed
down (the evidence being off-modal matches), then there exists a non-zero
probability that the mutations may have occurred in a common ancestor.

@
I have searched for "expert opinion" about this discussion with little
success. It seems most references
are too basic to address this, or too advanced to bother discussing it. I
would certainly hope there is
someone monitoring this thread who could fill that information void
authoritatively. I'd sure like to
know if I'm completely off base with my understanding of things.
@

I give you my authoritative opinion that you are way off base. If you want a
second opinion, contact me tomorrow and I'll give you a second opinion with
the greatest of pleasure.


Sandy




-----Original Message-----
From:
[mailto:] On Behalf Of Gregory Brown
Sent: 09 December 2009 19:42
To:
Subject: Re: [R-M222] Coyne and Golden project families

Hi Sandy,

R.C.'s reply touched on some of the points I would have made in response, so
I won't repeat them (thanks
R.C.). R.C.'s comments about the significance of the "modal haplotype" are
another way of stating what I
tried to say initially...the modal may be portrayed as an estimate of the
original male ancestor, but it
is simply a derivation from the living descendants who have been tested...we
cannot (in most cases!)
actually test the "original male".

More specifically, there is a flaw in logic. In order for the exact 67-67
matches with the modal
haplotype to be meaningless (or less meaningful), you would have to assume
or propose that the markers
for the modal haplotype have not mutated at all since the original male
(almost infinitely small
probablility) or that they have experienced a long series of mutations and
reverse mutations that
coincidentally reverted to the original (modal) haplotype (also infinitely
improbable). In order to
argue that the off-modal matches are more significant indicaters of
relatedness (to one another) than the
"on-modal" matches are (to one another), you would have to argue that the
laws genetics and probability
somehow apply differently to the modal than to any other haplotype. This
isn't tenable.

Comments R.C. made about the nature of the evolution of populations ("if one
of his descendants, who
somehow out-propagated his brothers and/or cousins, was the first with a
value of 25") is also right on
the money and certainly not tangential. The distribution of variations of
these markers among living
descendants would certainly be a result of this process, thus the calculated
modal is an artifical
construct derived from the end result of generations and generations of
mutations and "differential
fecundity" (for lack of a better term). That more people in the tested
sample are "close to the modal"
is not surprising, since the modal is derived from this sample!

A large number of on-modal matches simply means that, by reasons of sample
bias or by the natural process
of the evolution of the population, that the sample is composed of more
people who have more closely
shared ancestry than not...and it is their fault that the calculated modal
is what it is!! :-) The off
modal matches probably represent sub-groups who may be more closely related
to on another than they are
to the modal-matchers, because 1) their group is under represented in the
sample or 2) their ancestors
produce fewer descendants.

There's nothing magical about STR haplotypes!

I have searched for "expert opinion" about this discussion with little
success. It seems most references
are too basic to address this, or too advanced to bother discussing it. I
would certainly hope there is
someone monitoring this thread who could fill that information void
authoritatively. I'd sure like to
know if I'm completely off base with my understanding of things.

Greg




>
> Message: 2
> Date: Wed, 9 Dec 2009 10:44:29 -0000
> From: "Sandy Paterson" <>
> Subject: Re: [R-M222] Coyne and Golden project families
> To: <>
> Message-ID: <000401ca78bc$95f38630$c1da9290$@com>
> Content-Type: text/plain;charset="us-ascii"
>
> Aha!
>
> @
> The bottom line: 1) Within the limitations of probability,
> the likelyhood of
> relatedness between two
> individuals within a haplogroup is characterized by the
> genetic distance
> between the haplotypes of the
> two individuals, regardless of how close they are, or are not, to some
> calculated modal value.
> @
>
>
> OK, let's examine the evidence.
>
> Let us pretend that we know beyond doubt that the M222+ modal
> is exactly as
> estimated, ie that the entire population of M222+ is
> descended from one man
> with the haplotype
>
> 13,25,14,11,11,....
>
> Let us assume further that the age of M222+ is indeed 60
> generations (1800
> years).
>
> On the one hand, we compare Mackenzie 26917 (who matches the
> M222+ modal
> 67/67) to Coyne N49082 (who matches M222 66/67). They are a
> gd of 1 from
> each other.
> On the other hand, we compare Paterson 118913 (yours truly,
> 60/67 with M222)
> and Lamont 94014 (59/67 with M222). They too are a gd of 1
> from each other.
>
> According to your statement above, in the absence of any further
> information, the likelihood of Mackenzie being related to
> Coyne is exactly
> the same as the likelihood of Paterson being related to Lamont.
>
> Well, let's compare Mackenzie with Coyne. Coyne has DYS576 =
> 17 compared
> with the modal value of 18. That's the only difference. On
> the face of it
> therefore, it could be argued (as you seem to do) that they
> are closely
> related. However, there is no evidence whatsoever of any
> common mutations
> from the M222+ modal. That is a big problem because that's
> the only way to
> logically conclude probable kinship.
>
> Now compare Paterson with Lamont. Paterson has (compared to
> Lamont and the
> M222+ modal):
>
> PatersonLamontM222
>
> DYS439131312
> DYS449313130
> DYS570181817
> CDYa393938
> DYS481262625
> DYS446151513
> DYS487141413
>
> So Paterson and Lamont match on all 7 of the markers where Paterson is
> off-modal. The evidence of common mutations is both obvious
> and compelling.
> Lamont has one additional mutation, but that doesn't detract from the
> strength of the reasoning.
>
> I think your use of the phrase "..some calculated modal
> value" is the clue
> to where (I believe) you are going wrong. It suggests that in
> your opinion,
> a modal is some meaningless set of numbers that have no relevance to
> probability of kinship. Whilst I agree that it is impossible
> to be sure of
> the haplotypes of the founder male (and simulations of 67
> marker haplotypes
> using Monte Carlo seldom deliver all 67 of the starting
> haplotypes as the
> end modal), I'd suggest that modal value are indeed the best
> estimate in
> statistical terms of the founder haplotype.
>
> So. There is no evidence whatsoever of Mackenzie and Coyne
> having shared any
> mutations, whereas there is clear and compelling evidence
> that Paterson and
> Lamont have indeed shared mutations. It is remotely possible,
> I suppose,
> that all seven of the shared mutations came about
> independently (so called
> parallel mutations) but as you have pointed out, it's a question of
> probability.
>
> There is no doubt in my mind as to where the balance of
> probability lies.
>
> I look forward to your reply.
>
>
> Sandy
>
>
> Message: 5
> Date: Wed, 9 Dec 2009 11:38:01 -0500
> From: "R. C. Mac Donald" <>
> Subject: [R-M222] modal=ancestral?
> To: "dna-r1b1c7" <>
> Message-ID: <>
> Content-Type: text/plain;charset="iso-8859-1"
>


> Sandy,
>
> I don't mean to derail the discussion with tangential
> questions, but you said something that I believe needs
> clarification. You proposed for the sake of argument:
> "Let us pretend that we know beyond doubt that the M222+modal
> is exactly as estimated, ie that the entire population of
> M222+ is descended from one man with the haplotype 13,25,14,11,11...."
>
> I don't know if anyone is arguing for this position, but it
> appears to me to involve a mistake about the significance of
> modal haplotypes.
>
> Knowing what the M222+ modal is only tells us what are the
> most common STR values for each marker among those of us with
> a specific SNP mutation, not what those values were for the
> first man who had the mutation. The modal will slowly but
> steadily change over generations but the values for the first
> M222+ man can't.
>
> Now, should we assume that his haplotype was
> 13,25,14,11,11... because those are the prevalent values now,
> or even because (if we could know this) they have been and
> will the prevalent values among all M222+ men from the first
> to the end of time? Then what about those of us (about 7% of
> M222+ the last time I checked) who have 13,24,14,11,11...?
> It could be we descended from someone who had a reverse
> mutation, but it's also possible and, I think, more likely
> that the first M222+ man had the R1b1 modal value of 24 and
> one of his descendants, who somehow out-propagated his
> brothers and/or cousins, was the first with a value of 25.
>
> Or is there something I'm overlooking? I can't claim
> expertise in any field relevant to this question; I hope, by
> the way, that this doesn't devalue my saying that I agree
> with your point about the greater significance of off-modal matches.
>
> R.C.
>


R1b1c7 Research and Links:

http://clanmaclochlainn.com/R1b1c7/
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