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Archiver > GENEALOGY-DNA > 2008-11 > 1227902766


From: "David Faux" <>
Subject: Re: [DNA] TRMCA for R1b1
Date: Fri, 28 Nov 2008 12:06:06 -0800
References: <cc9.42b05535.3661a19b@aol.com>
In-Reply-To: <cc9.42b05535.3661a19b@aol.com>


I agree with what you are saying Alan, and there is a bit more.

When the paper was in first draft, the year given for the age of R1 was
30,000 years. Somehow by the final draft someone (I don't know how many of
the authors) had decided upon another date. Well that is inspiring.
Generally in a paper of this nature the first and last authors are those who
will have the final say. I know there was disagreement, I have spoken to
one or more of the authors.

How people can accept Karafet's dating as almost sacrosanct when she admits
that she is very hesitant about using the C/T proposed date for calibration,
is way beyond me. Also folks chronically forget about confidence
intervals. It is much more settling to just accept the number in the middle
of it all, like the red dot as the "most likely estimate" in the ABDNA
biogeographical test - but anyone with a stats 101 under their belt won't
accept a single study's date with a novel dating procedure when the
author(s) are not terribly confident and the confidence bands are very wide.

Anyway, it is clear that people "want" to accpet Karafet's number in the
final draft as a calibration point and then go from there. It is not
possible to do that. It is out and out wrong since you are calibrating on a
date that was calibrated on a date on which the primary author has little
confidence. This reaches into the absurd category.

I have said it once and I will say it again, nothing except seeing a
securely dated skeletal sample (such as those from the Corded Ware culture
in Germany) will convince me of the age of U152. When they bring forward a
sample that is 6500 years BP + or - 500 years at least we will know that the
mutation had occured before that time. Why would anyone accept anything
that is riddled with assumptions built upon assumptions - I guess my
experience and training has ensured that I see the world from a different
angle than most of the posters here (present company excepted).

David K. Faux.


On 11/28/08, <> wrote:
>
> What no one, apart from a couple of contributors, seems to want to discuss
> is the basis on which Kararfat's datings have been established it states
> quite
> clearly in the supplementary data that the age of MRCA-CT is assumed to be
> 70,000 years and it would seem that all dates have been estimated relative
> to
> that.
> On Page 2 of the main text states when talking about the method used to
> estimate the relative ages of internal nodes, - To estimate the age of
> the nodes,
> we partitioned the time interval between the most recent common ancestor
> (MRCA) of all lineages in branches C through T (denoted MRCA-CT) and the
> present
> into two subintervals: one extending from the MRCA-CT to the internal node
> whose age is estimated, and a second extending from the internal node to
> the
> present. The number of mutations in each subinterval follows a binomal
> distribution with parameter p i equal to the relative length of the
> subinterval. The
> relative length of the subinterval is multiplied by the assumed age of the
> MRCA-CT to obtain the age in years of the internal node.
> On Page 7 of the main text it states - To provide estimates of the age of
> the nodes, we chose to fix the time to the most common ancestor of CT
> (defined
> by P9.1, M168 and M294) at 70 thousand years ago (Kya), which is consistent
> with previous estimates from genetic and archaeological data, and is the
> chronological approximation given in Jobling et al. for the first major
> human
> out-of-africa dispersals. We estimate the times for intermediate nodes by
> using
> linear interpolation. The age estimates in years should be viewed
> with caution
> because we do not know if the calibration date chosen above is accurate.
>
> This fact has been mentioned by a couple of correspondents in the present
> flow but it seems to be being ignored. I made a post about it when Karafat
> was
> published but again it seemed to be ignored.
> The argument about when R1b1 may have arose seems to have two distinct
> opposing views, that of David Faux who argues that the archaeological
> record
> should be taken into account when trying to estimate ages and that of
> Ken Nordvedt
> who argue that mathematics alone will be sufficient. I am neither
> archaeologist nor mathematician, some of what I have quoted form Karafat
> here makes no
> sense to me at all and I have not read much about statistics
> and mathematics.
> I have read over the last nearly sixty years many articles and books on
> the
> subject of the prehistory of Britain and its archaeology from various well
> known and not so well known practitioners and I have seen views change one
> way
> or the other over the years.
> Karafat has used a date on which all his other estimates are based, that
> date as he admits himself is based on previous estimates from the work of
> others
> including himself and the archaeological record. It is interesting to note
> from the table 2 given in the main text that between his work of 2002 and
> 2008
> there has been a huge revision of the ages of the 11 major clades mostly
> upward based on presumably the same starting date. It should also be noted
> that
> Karafat himself put a caveat on the accuracy of his datings because the
> accuracy of the calibration date is unknown.
> What does all this mean? To me it means we have to wait and see, we do not
> know what future developments will bring. Whatever estimates people give to
> the
> relatives ages of the clades are just that estimates not facts but
> estimates
> and estimates will change as new data comes to light.
> Should we rely totally on the archaeological record, no, history has shown
> that ideas about mass migrations, ancient ethnic cleansings have
> changed over
> the years from civilisation and agriculture spreading from Europe to
> the Near
> East to that which we now believe to be correct that it spread from
> the Near
> East to Europe. The fields of geology and palaeontology have changed from
> believing the world began as the Bible stated some 5000 years ago to the
> belief
> now that it is billions of years old. Should we rely on the mathematical
> answer, again no, Mathematics is only as good as the data supplied and as
> yet we
> do not have totally accurate data. Karafat seems to have relied on some
> knowledge form both fields and that is probably how we should be treating
> this
> now. No one is totally correct and all ideas and view points should be
> accepted
> without prejudice.
>
> Alan M
>
>


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