Pinhasi et al-Ancient dna recovery

[Angela]

Thanks to Dienekes for the link:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129102

"Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone"

The technical aspects are beyond me, but basically they can recover dna from remains in hotter and wetter climates.

" These results suggest that it may be possible to obtain endogenous DNA from part C also for samples with relatively low amounts of endogenous DNA from hot environments, although extreme caution will be necessary in the interpretation of the results obtained from such samples."


I hava a feeling very few will exercise extreme caution.

Apparently the have a sample from Jordan 10,000 years ago and one from just around the time of the departure to Europe. It should be very interesting.

 

[Fire Haired14]

Apparently the DNA files are available online and Felix already has plans to analysis them.

Do ctrl+F "AG037"
http://www.y-str.org/p/ancient-dna.html

 

[Maleth]

Very interesting and much needed, lets hope the technology keeps on growing at a fast pace. Exciting times

 

[Fire Haired14]

Updates on analysis are being posted on this ANthrogencia thread. ADMIXTURE results for Neolithic Near Easterns are being posted already!!

 

[Fire Haired14]

8,400 year old Female from Turkey. Her genome is of low coverage. Her results are consistent with what we heard about other Neolithic Anatolian.

Dodecade K12b. See the Post

12 ancestral populations 166770 total SNPs
67 flipped SNPs
0 heterozygous SNPs
0 no-calls
166356 absent SNPs
0.002482 genotype rate
mode genomewide

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Gedrosia
0.00% Siberian
20.76% Northwest_African
0.00% Southeast_Asian
65.30% Atlantic_Med
0.00% North_European
0.00% South_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% East_Asian
13.94% Caucasus 0.00% Sub_Saharan

Dodecade K7b. See Post

0.00% South_Asian 0.00% West_Asian
0.00% Siberian
0.00% African
51.93% Southern
48.06% Atlantic_Baltic 0.00% East_Asian

MDLP K27. See the Post.

0.00% Nilotic-Omotic
0.00% Ancestral-South-Indi
0.00% North-European-Balti
0.00% Uralic
0.00% Australo-Melanesian
0.00% East-Siberean
0.00% Ancestral-Yayoi
41.12% Caucasian-Near-Easte
0.00% Tibeto-Burman
0.00% Austronesian
0.00% Central-African-Pygm
0.00% Central-African-Hunt
0.00% Nilo-Saharian
3.64% North-African
0.00% Gedrosia-Caucasian
0.00% Cushitic
0.00% Congo-Pygmean
0.01% Bushmen
0.00% South-Meso-Amerindia
55.24% South-West-European
0.00% North-Amerindian
0.00% Arabic
0.00% North-Circumpolar
0.00% Kalash
0.00% Papuan-Australian
0.00% Baltic-Finnic
0.00% Bantu

MDLP K14. See the Post.

0,00 ANE0,00 ANI
14,76 ASI
33,48 Caucasian
0,00 Mesolithic
51,75 Neolithic
0,00 East-Asian
0,00 Subsaharian
0,00 Near-East
0,00 Pygmy
0,00 Amerindian
0,00 Papuan
0,00 Siberian 0,00 Altaic

Eurogenes AMI K8. See the Post.

8 ancestral populations 101647 total SNPs
0 flipped SNPs
0 heterozygous SNPs
0 no-calls
101332 absent SNPs
0.003099 genotype rate
mode genomewide

0.00% Amerindian
0.00% Siberian
18.44% Euro_HG
0.00% Oceanian
0.01% Sub-Saharan
4.73% Southeast_Asian
76.82% LBK 0.00% South-Central_Asian

 

[Fire Haired14]

I put her results in a spreadsheet along with Stuttgart's. Davidski got ANE K8 results for her, I also put them in the spreadsheet.

BAR100(8400YBP Western Antolia) is the Red dot. She's just South of EEF.

 

[LeBrok]

Thanks, very interesting. So no Gedriosia but some Caucasus in 12b, but not a lot. I had a hunch that Gedrosia was more to the east.

In K8 it says 18.44% Euro_HG. Does this equals to WHG roughly? It might mean that first contact with WHG was actually in Anatolia, as some of us suspected. Unless this person is from back migration from Balkans to Anatolia.

We need the one 10,000 y old from Syria to confirm. This BAR100 looks so Neolithic Balkan like that it could be a back migration at that point.

 

[LeBrok]

I put her results in a spreadsheet along with Stuttgart's. Davidski got ANE K8 results for her, I also put them in the spreadsheet.

BAR100(8400YBP Western Antolia) is the Red dot. She's just South of EEF.

Can you point to it with an arrow or a letter. I can't find it with my eyes. Sorry.

Edit: I found her. She looks less WHG than EEF farmers. It might be true than that mixing mixing of ENF and WHG happened in Anatolia. Interesting question is what Y-hg were WHG in Anatolia? C, F or even I2?
I have a feeling that I'm rushing to much into unknown...

 

[Angela]

Thanks for doing this, Fire Haired.

Is this the link? I don't see a PCA.
https://docs.google.com/spreadsheets/d/1rTFReasuRyyWY169OhCjoW9bvVByu-Lrb50Xqu76Pak/edit?pli=1#gid=0

I don't want to rain on anyone's parade but I don't think this can be relied upon. The results seem to be all over the place, don't they? I mean, if you go by Dodecad K-7b she's almost identical to Stuttgart...about a four percent difference, which would mean there was almost no admixture in Europe. (Lazardis did say it might only be a few percent difference.) Yet there's a big difference in K-12b results.

So, as far as I'm concerned, this doesn't settle much of anything.

Does anyone have a map showing where the sample was found?

For comparison, this is the map from Haak et al for the Neolithic spread into Europe (Renfrew used to think that the Indo-European languages moved into Europe with the farmers.).


It's basically the same as Paschou et al:
http://www.pnas.org/content/111/25/9211.abstract

 

[Fire Haired14]

She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.

Here's a spreadsheets with her and Stuttgarts ADMIXTURE results. According to ANE K8 Stuttgart is around 90% Neolithic Antolian and 10% WHG. But, BAR100 is of very low coverage, and so her results may not be realistic. I'm can't wait for the 10,000YBP Syrian. If it's of good coverage we might see Off the Charts levels of Basal Eurasian.

https://docs.google.com/spreadsheets/d/1rTFReasuRyyWY169OhCjoW9bvVByu-Lrb50Xqu76Pak/edit#gid=0

 

[Fire Haired14]

There's also a Late Neolithic Female from Turkmenistan that will be analysed. That'll be very interested, and probably ANE-rich.

 

[Angela]

She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.

Here's a spreadsheets with her and Stuttgarts ADMIXTURE results. According to ANE K8 Stuttgart is around 90% Neolithic Antolian and 10% WHG. But, BAR100 is of very low coverage, and so her results may not be realistic. I'm can't wait for the 10,000YBP Syrian. If it's of good coverage we might see Off the Charts levels of Basal Eurasian.

https://docs.google.com/spreadsheets/d/1rTFReasuRyyWY169OhCjoW9bvVByu-Lrb50Xqu76Pak/edit#gid=0

Well, that's right on the proposed route according to Paschou et al and Haak...from the juncture of southeast Anatolia/Northern Levant all along the coast, some peeling off for Cyprus maybe, others hitting the Greek islands and mainland Greece, and then bifurcating from there.

 

[LeBrok]

She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.

This might as well be true, screwing the results. However her WHG/Near Eastern from K8 run makes sense. She is closer to epicenter of farmer's homeland, therefore have more Near Eastern than Stuttgart does. K12b makes sense if we imagine that she is from different and later wave of migration than Stuttgart. Her tribe first went south to (Egypt?)picking some N-W African hunter-gatherer admixture and later migrated north to Anatolia. At time when most of Caucasus admixture left Anatolia for some reason. Or part of her genome containing more Caucasus is missing.

 

[Fire Haired14]

Davidski keeps updating his post. In "Identity by Decent" he was able to use more SNPs than in ADMIXTURE. The results are consistent with ADMIXTURE. She's closest to South Europeans: Tuscan, Sardinian, Basque, and Spanish_Murcia. This and ADMIXTURE confirm to me she's ancestral to EEF. Most South Europeans today are probably 50%+ Neolithic Anatolian, and all other Europeans should be just under 30% at the least.

https://docs.google.com/spreadsheet...exi9FdyS7zVzSdZpDBPQTcRak/edit#gid=1507216515

 

[LeBrok]

Davidski keeps updating his post. In "Identity by Decent" he was able to use more SNPs than in ADMIXTURE. The results are consistent with ADMIXTURE. She's closest to South Europeans: Tuscan, Sardinian, Basque, and Spanish_Murcia. This and ADMIXTURE confirm to me she's ancestral to EEF. Most South Europeans today are probably 50%+ Neolithic Anatolian, and all other Europeans should be just under 30% at the least.

https://docs.google.com/spreadsheet...exi9FdyS7zVzSdZpDBPQTcRak/edit#gid=1507216515

Probably not ancestral, but containing the same or most ancestry (ancestral genes) as EEF folks.

 

[Maciamo]

This is almost as interesting as the 101 genomes from Allentoft et al. study. The Dodecad K12b is the one that particularly got my attention.

If the data is reliable, then it would appear that Near Eastern Neolithic farmers brought most of the Atlantic_Med admixture to Europe. This is important because it means that this admixture, which peaks in the Basques and Sardinians (70-75%), is therefore not native to Europe.

In the same way, those Neolithic farmers carried 21% of Northwest_African admixture. Modern Maghrebans have 35-45% of Northwest_African and 20-25% of Atlantic_Med admixture, and all of it could ultimately have been inherited from Anatolian or Levantine Neolithic farmers (some of it via the Phoenicians and Arabs).

Genetic drift could explain why some genes, which now make up the Atlantic_Med admixture, ended up being present at higher frequencies in Southwest Europe, while another set of genes from Neolithic farmers survived at much higher frequencies in Northwest Africa. From a modern standpoint it could look like the two have different origins, but it may just be one big family whose genes got divided early between two continents then evolved separately for thousands of years.

 

[arvistro]

I hope one day they standartize those things. I have a feeling what is EEF and ENF and what not changes from study to study...
Making it difficult to compare.

 

[bicicleur 2]

I agree, we need some standard here.
And a simple number telling what coverage there is.

 

[Maleth]

I hope one day they standartize those things. I have a feeling what is EEF and ENF and what not changes from study to study...
Making it difficult to compare.

Totally agree with you. Samples are far too small to be able to have a good idea and population set ups and densities to be able to claim if someone was a farmer or a hunter gatherer, besides we still need to decipher other ancient dna from North Africa, middle east and southern Europe to be able to come close to any kind of accuracy and get the big picture..

 

[Fire Haired14]

This is almost as interesting as the 101 genomes from Allentoft et al. study. The Dodecad K12b is the one that particularly got my attention.

If the data is reliable, then it would appear that Near Eastern Neolithic farmers brought most of the Atlantic_Med admixture to Europe. This is important because it means that this admixture, which peaks in the Basques and Sardinians (70-75%), is therefore not native to Europe.

In the same way, those Neolithic farmers carried 21% of Northwest_African admixture. Modern Maghrebans have 35-45% of Northwest_African and 20-25% of Atlantic_Med admixture, and all of it could ultimately have been inherited from Anatolian or Levantine Neolithic farmers (some of it via the Phoenicians and Arabs).

Genetic drift could explain why some genes, which now make up the Atlantic_Med admixture, ended up being present at higher frequencies in Southwest Europe, while another set of genes from Neolithic farmers survived at much higher frequencies in Northwest Africa. From a modern standpoint it could look like the two have different origins, but it may just be one big family whose genes got divided early between two continents then evolved separately for thousands of years.

I think the NorthWest African score was noise. This Neolithic Anatolian is of very low coverage. All her results make sense except the NorthWest African score. It could be real, I don't know. In all the other tests she doesn't score any African. So, it could be like you said she didn't have NW African ancestry, NW Africans have decent from her people and African ancestry.