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From: "Steven Bird" <>
Subject: [DNA] Cruciani 2007 dating method and the demic diffusion model ofE3b and J2
Date: Mon, 19 Mar 2007 07:13:55 -0400
In-Reply-To: <951608.66345.qm@web81104.mail.mud.yahoo.com>


There may be a serious scientific controversy brewing concerning the demic
diffusion model, if Cruciani's conclusions concerning TMRCA are correct.
Semino and others have assumed widely that the expansion of E3b and J into
Europe was the signature genetic event of the Neolithic demic diffusion
model. Since 85% of Europe's E3b's are E-V13, then obviously V-13 ought to
represent that diffusion generally. The same can be said for J-M12.

Unless there is a serious flaw to Cruciani's approach to dating the
subclade's coalescence, there is no way that E-V13 or J-M12 can be part of
the Neolithic expansion into Europe. Their expansion occurred during the
EBA at the earliest. This does not even account for the possibility of an
in situ population expansion of these subclades PRIOR to the expansion to
the rest of Europe, which would seem to be a likely scenario to me. This
last scenario would delay the entry into Europe even further.

Here are the key findings concerning the age of V-13 and J-12 in Europe from
Cruciani 2007:

"E-V13 chromosomes sampled in western Asia and their
coalescence estimate detect a likely Paleolithic exit out of Africa of E-M78
chromosomes devoid of the V13 mutation, which later occurred somewhere in
the Near
East/Anatolia. The refinement of location for the source area of such
movements and
associated chronologies here attained may be relevant to controversies on
the spread of
cultures (and languages) between Africa and Asia in the corresponding
timeframes
(Bellwood 2004; Ehret, Keita and Newman 2004, and references therein).
As to a western Asia-Europe connection, our data suggest that western Asians
carrying E-V13 may have reached the Balkans anytime after 17.0 ky ago, but
expanded
into Europe not earlier than 5.3 ky ago."

"We used tetranucleotide microsatellite data in order to obtain a
coalescence estimate for the J-M12 haplogroup in Europe. By taking into
consideration two different demographic expansion models (see
methods), we obtained TMRCA estimates very close to those of E-V13, i.e. 4.1
ky
(95% C.I. 2.8-5.4 ky) and 4.7 ky (95% C.I. 3.3-6.4 ky), respectively. Thus,
the
congruence between frequency distributions, shape of the networks, pair-wise
haplotypic
differences and coalescent estimates point to a single evolutionary event at
the basis of
the distribution of haplogroups E-V13 and J-M12 within Europe, a finding
never
appreciated before."

The main difficulty for demic diffusion will arise from the dating
methodology used by Cruciani:

"To estimate the time to the most recent common ancestor (TMRCA) of
haplogroups we used the seven tetranucleotide loci and applied the average
square
distance (ASD) method (Goldstein et al. 1995), where the ancestral haplotype
was
assumed to be the haplotype carrying the most frequent allele at each
microsatellite
locus. We employed a microsatellite evolutionarily effective mutation rate
(Zhivotovsky
et al. 2004). However, since the loci used here and those used by
Zhivotovsky et al.
(2004) do not overlap completely, we calculated the microsatellite mutation
rate as
follows: we obtained the mean and standard deviation of the father-to-son
mutation rates
reported by Gusmao et al. (2005) for the same loci here used, and reduced
them by a
factor 3.6 [i.e. the discrepancy between the rate estimate obtained from
population data
and that obtained from father-to-son transmissions (Zhivotovsky et al.
2004)]. This
resulted in an evolutionarily effective rate = 7.9 x 10-4 (SD = 5.7 x 10-4
), a figure that
was also used in recalculating the E-M215 coalescence age (data from
Cruciani et al.
2004). Recently, Zhivotovsky, Underhill and Feldman (2006), showed that
reduced loss
of diversity in an expanding population brings the evolutionarily effective
rate closer to
the germ-line rate than in constant-size populations. Thus, in the case of
expanding
populations, we used a correction of the 7.9 x 10-4 value, that was
calculated as follows.
With reference to figure 2 in Zhivotovsky, Underhill and Feldman (2006), the
values of
accumulated variance in 200-300 generations for the scenarios of i) a single
rate for
exponential population growth and ii) growth with four distinct consecutive
rates, were
compared with the amount accumulated in constant size populations. This
resulted in
evolutionarily effective mutation rates decreased of factors 2.4 and 2.8,
respectively
(instead of 3.6), i.e. 11.9 x 10-4 (SD = 8.5 x 10-4) and 10.2 x 10-4 (SD =
7.3 x 10-4),
which were applied to haplogroups E-V13 and J-M12 found in Europe. C.I.s for
the
ASD (and TMRCA) were obtained as follows: mutations on the microsatellite
genealogy
were simulated using a Poisson process, in which the total number of
mutational events
was calculated based on branch length and assuming that mutations at each
microsatellite were gamma-distributed with mean and standard deviation
calculated as
above. Each mutation increased or decreased allele length by one step (each
with
probability 0.5). ASD was then evaluated for the simulated data and the
whole process
repeated 1000 times, to quote the central 95% of values. This method
represents a
refinement of that by Thomas et al. (1998) and Scozzari et al. (2001), as it
also takes into
account heterogeneity of mutation rates across loci. An independent dating
method (
statistics; Forster et al. 1996; Saillard et al. 2000) was also used to
assay how robust the
time obtained is to choice of method.

Both dating procedures rely on the appropriate choice of a haplotype to be
considered ancestral, which remains an uncontrolled source of uncertainty.
We observe
that the &#8722;based ages are slightly younger than the ASD-based ones
(fig. 1). The
difference is significant only for the root of the entire haplogroup, this
being attributable
to the relevant departure from a star-like structure because of repeated
founder effects
(Saillard et al. 2000). Only values obtained from ASD are quoted in the
text."

I would greatly appreciate any comments concerning any potential issues or
problems with Cruciani's approach to establishing the TMRCA date range.


Steve




>
>E-V13 is derived from a population (M78) that was a part of the Neolithic
>and possibly Paleolithic (Oppenheimer) expansion into Europe.
>
> Gary
>
>Steven Bird <> wrote:
> Not so fast. The population boom of E-V13 (Balkans) is not old enough to
>be
>part of the Neolithic expansion, according to the new Cruciani paper. It is
>early Bronze age. This is a major problem to be overcome by proponents of
>the Demic Diffusion model for E3b1a2 and J-M12.
>
>M-78 might of course be Neolithic, but the migration route would be
>different; not directly from the Balkans.
>
>Steve
>
>
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