Dienekes' analysis of ancient autosomal DNA

Discussions concerning Autosomal DNA.

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PostPosted: Mon Jul 02, 2012 9:10 pm
Academic publications have begun to publish autosomal DNA data of ancient European remains, but their analysis and conclusions are hopelessly stunted by comparisons with data from the 1000 Genomes project, which notoriously neglected to sample any modern humans between the Netherlands and China.

Dienekes has stepped into the breach by applying his own K7b and K12b admixture calculators to ancient autosomal DNA data:

http://dienekes.blogspot.com/2012/07/br ... on-of.html

Especially look at his chart entitled Ancient European DNA (K12b). It shows the principal autosomal components (in terms of modern populations) of the ancient Europeans tested:

Oetzi, the North Italy farmer: 58% Atlantic_Med, 22% Caucasus, 8% Southwest_Asian, 6% Northwest_African
Gok4, the South Swede farmer: 81% Atlantic_Med, 9% Southwest_Asian, 6% North_European, 4% Caucasus
Ajv52, Gotland hunter-gatherer: 78% North_European, 13% Atlantic_Med, 4% Sub_Saharan
Ajv70, Gotland hunter-gatherer: 76% North_European, 21% Atlantic_Med, 5% South_Asian
Bra, Northwest Spain hunter-gatherer: 45% Atlantic_Med, 42% North_European, 10% East_African

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PostPosted: Mon Jul 02, 2012 10:12 pm
lgmayka wrote:Academic publications have begun to publish autosomal DNA data of ancient European remains, but their analysis and conclusions are hopelessly stunted by comparisons with data from the 1000 Genomes project, which notoriously neglected to sample any modern humans between the Netherlands and China.

Dienekes has stepped into the breach by applying his own K7b and K12b admixture calculators to ancient autosomal DNA data:

http://dienekes.blogspot.com/2012/07/br ... on-of.html

Especially look at his chart entitled Ancient European DNA (K12b). It shows the principal autosomal components (in terms of modern populations) of the ancient Europeans tested:

Oetzi, the North Italy farmer: 58% Atlantic_Med, 22% Caucasus, 8% Southwest_Asian, 6% Northwest_African
Gok4, the South Swede farmer: 81% Atlantic_Med, 9% Southwest_Asian, 6% North_European, 4% Caucasus
Ajv52, Gotland hunter-gatherer: 78% North_European, 13% Atlantic_Med, 4% Sub_Saharan
Ajv70, Gotland hunter-gatherer: 76% North_European, 21% Atlantic_Med, 5% South_Asian
Bra, Northwest Spain hunter-gatherer: 45% Atlantic_Med, 42% North_European, 10% East_African


Yea that is serious problem with the 100) genomes Project. Did any of these hunter gatherers make it to Kazakhstan via the steepe corridor and have they been tested for ydna?
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PostPosted: Tue Jul 03, 2012 1:09 am
The East African admixture is most probably linked with the same ancient movement that brought E1b1b1a1b to Spain 7000 years ago.
Ancient DNA suggests the leading role played by men in the Neolithic dissemination. Lacan et al.
http://www.pnas.org/content/108/45/18255

The hunter-gatherer types had a continuum from Iberia to Finland before the agricultural waves occupied Southern Europe. We can think that haplogroup I and R1a were mesolithic haplogroups in Europe associated with the Northern_European component and U5 mtDNA while the other haplogroups arrived with the agricultural and livestocks movements.
Y DNA - Barcelos - Minho - Portugal. Colonial Brazil
MtDNA - Ilha Terceira, Azores, Portugal
Brazilian Portuguese Founding People
http://www.familytreedna.com/public/m365/
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PostPosted: Tue Jul 03, 2012 4:24 pm
RCO wrote:The East African admixture is most probably linked with the same ancient movement that brought E1b1b1a1b to Spain 7000 years ago.
Ancient DNA suggests the leading role played by men in the Neolithic dissemination. Lacan et al.
http://www.pnas.org/content/108/45/18255

The hunter-gatherer types had a continuum from Iberia to Finland before the agricultural waves occupied Southern Europe. We can think that haplogroup I and R1a were mesolithic haplogroups in Europe associated with the Northern_European component and U5 mtDNA while the other haplogroups arrived with the agricultural and livestocks movements.


Isn't R1a too recent? What about N1c? And mtdnas U2e/U4?
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PostPosted: Tue Jul 03, 2012 6:32 pm
newtoboard wrote:
RCO wrote:Isn't R1a too recent? What about N1c? And mtdnas U2e/U4?

N1c is more recent in Europe than R1a.
Our ancestors lived in Siberia then.
Y-DNA: N1с1d*; P188-; M178+; P298+; P21-; P67-; P119-; L248+(23andMe); L248-(FamilyTreeDNA); L550+; L1025+
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PostPosted: Tue Jul 03, 2012 7:02 pm
newtoboard wrote:Isn't R1a too recent? What about N1c?

Both R1a1a1 and N1c1 are too recent, but their predecessors (R1a*, N1*) could have been present in Europe prior to the Neolithic, along with other ancient orphaned remnants that barely survive in Europe today (C*, F, Q1a3*).
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PostPosted: Tue Jul 03, 2012 10:38 pm
Here I agree with Regueiro, 2012
High levels of Paleolithic Y-chromosome lineages characterize Serbia:

"The estimated range expansion (14.0±3.3 KYA) (Supplementary
Table 3), associated mean variance (0.384) and high haplotype diver-
sity (0.9905±0.0178) (Table 1) also evident in the phylogenetic net-
work (Supplementary Fig. 1C) among Serbian R1a1a-M198 carriers,
are consistent with previous studies (Peričić et al., 2005; Semino
et al., 2000; Wells et al., 2001) that suggest the common ancestor
for all R1a1a-M198 individuals in the Balkans existed in Paleolithic
times. The R1a1a7 defining marker, M458, exhibits a Central and
Eastern European compartmentalization within the R1a haplogroup
(Underhill et al., 2010). While R1a1a7-M458 displays high diversity
among Slavic and Finno-Ugric peoples (coalescent time ~11 KYA),
R1a1a*(xM458) has the most diversity among Indo-Aryan and
Dravidian speakers (coalescent time in India ~14 KYA) (Underhill
et al., 2010). Analysis of both chromosomes in Serbia revealed higher
R1a1a7-M458 diversity than R1a1a*(xM458) and yielded coalescent
times at ~14 KYA (mean variances ~0.448) and 11 KYA (mean vari-
ance 0.306), respectively. Therefore, this high diversity and estimated
age of microsatellite variation in Serbia, might be in flated by the
aforementioned superimposed migrations involving R1a individuals
that penetrated Europe thus placing the R1a haplogroup more recent
in time, duringthe early Holocene (Klyosov, 2009), rather than repre-
senting a deeper Paleolithic signal in Europe (Peričić et al., 2005;
Semino et al., 2000)".

http://pt.scribd.com/doc/82200261/Maria ... ize-Serbia

I think the structure and the stratification of R1a1a in Eastern Europe is a case of a very slow and gradual process of colonization and speciation of different R1a SNPs irradiating and growing from equidistant points already established in Eastern Europe and Scandinavia for a long time and not a fast front of an advancing surfing wave like R1b in Western Europe. That would be the reason why the ancient Northern_European component was more preserved in that region (Northeastern Europe) in opposition to Iberia and France, for example.
Y DNA - Barcelos - Minho - Portugal. Colonial Brazil
MtDNA - Ilha Terceira, Azores, Portugal
Brazilian Portuguese Founding People
http://www.familytreedna.com/public/m365/
http://www.familytreedna.com/public/Brasil/
http://j1bm365.blogspot.com.br/

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PostPosted: Sun Jul 08, 2012 7:04 pm
It seems then that the North European autosomal component from K12b is a signal at least to some degree of ancestry from ancient Mesolithic European hunter-gatherers. What do others think about this?

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PostPosted: Wed Jul 11, 2012 7:54 pm
My estimations of the cluster membership for those Neolithic and Mesolithic samples are significantly different from Dienekes' results

North-European-Mesolithic Neolitic-Mediterranean Rest (unclassified) Caucasian
OETZI 0.00% 83.01% 6.12% 10.87%
STE7 0.00% 40.26% 59.73% 0.00%
IRE8 51.64% 48.36% 0.00% 0.00%
GOK4 0.00% 69.77% 30.23% 0.00%
AJV70 33.01% 24.29% 15.89% 26.81%
AJV50 70.81% 0.00% 29.19% 0.00%
BRA1 69.27% 30.72% 0.00% 0.00%
BRA2 90.36% 4.12% 0.00% 5.52%

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PostPosted: Thu Jul 12, 2012 2:47 pm
Vadim Verenich wrote:My estimations of the cluster membership for those Neolithic and Mesolithic samples are significantly different from Dienekes' results

North-European-Mesolithic Neolitic-Mediterranean Rest (unclassified) Caucasian
OETZI 0.00% 83.01% 6.12% 10.87%
STE7 0.00% 40.26% 59.73% 0.00%
IRE8 51.64% 48.36% 0.00% 0.00%
GOK4 0.00% 69.77% 30.23% 0.00%
AJV70 33.01% 24.29% 15.89% 26.81%
AJV50 70.81% 0.00% 29.19% 0.00%
BRA1 69.27% 30.72% 0.00% 0.00%
BRA2 90.36% 4.12% 0.00% 5.52%


How does that work? Is there any way to tell which analysis is more accurate?
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