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Jean M
11-02-2013, 01:14 PM
http://tobias-lib.uni-tuebingen.de/volltexte/2013/6993/

Dissertation by Rabab Khairat Ibrahim Abd Elhay


In the current study, DNA samples from eight Egyptian mummies were obtained and tested for the first time using the NGS technology. They were radiocarbon dated and placed within a time period between the Third Intermediate and the Graeco-Roman times (806 BC–124 AD). Initial characterization experiments using different established protocols for DNA extraction and polymerase chain reaction (PCR) and NGS showed variabilities in the retrievability and amplifiablitiy of the extracted DNA from the various Egyptian mummy samples. This can be due to the differences in the preservation status of the mummies or to the technical handling through the NGS multistep protocol. The inadequate storage environment within the mummy collection was the inducer of a bacterial bloom in the Egyptian mummy samples. This could be inferred from the reversal of the Eukaryota/Bacteria ratio in different samples taken from the same mummy after a lapse of time interval of 1.5-2.0 years.

We found that increasing the DNA concentration for NGS had a positive effect on the quality of the NGS library and the subsequent sequencing. As a result of a series of optimization experiments, the complete human mitochondrial genome of one mummy was recovered with an average coverage of 190 folds using the unique mapped reads. Using the identified mitochondrial SNPs of this mummy, haplogroup I2 was defined with a quality score of 97.7%. In addition, we address some of the SNPs that might be associated with certain human disease.

This is the first study of Egyptian mummies using Next Generation Sequencing.

Anglecynn
11-02-2013, 01:22 PM
That seems unusual.

Jean M
11-02-2013, 02:02 PM
This is quite a late mummy - 402-385 BC, which is after the Greek takeover. The details are now in my online North African aDNA table. http://www.ancestraljourneys.org/nafricaadna.shtml

Jean M
11-02-2013, 02:15 PM
That seems unusual.

Quick lift from Wikipedia:

Haplogroup I is found at very low frequencies (generally < 3%) throughout Europe, West Asia and South Asia. Quote from Fernandes 2012:


Haplogroup I, which is by far the most frequent clade within N1, dates to ∼25 ka ago and is overall most frequent in Europe, but the facts that it has a frequency peak in the Gulf region and that its highest diversity values are in the Gulf, Anatolia, and southeast Europe suggest that its origin is most likely in the Near East and/or Arabia.

Anglecynn
11-02-2013, 02:31 PM
Quick lift from Wikipedia:

Haplogroup I is found at very low frequencies (generally < 3%) throughout Europe, West Asia and South Asia. Quote from Fernandes 2012:

Ahh that makes sense then.

ADW_1981
11-02-2013, 02:35 PM
http://tobias-lib.uni-tuebingen.de/volltexte/2013/6993/

Dissertation by Rabab Khairat Ibrahim Abd Elhay



This is the first study of Egyptian mummies using Next Generation Sequencing.

My dad is I2 and it seems very Atlantic European, but also found at low frequency throughout the Caucasus. Perhaps this signals human trafficking at a very early date between Europe and Egypt? Not sure....

Jean M
11-02-2013, 02:48 PM
My dad is I2 and it seems very Atlantic European..

We have a bit of a problem with I2 in that it is one of the rarer haplogroups and so we might need to do a lot more testing of ancient DNA before we pick it up in Europe. I would guess that it arrived in Europe with the early farmers from the Near East. So far we have mtDNA I appearing in Spain with farmers 4090-3960 BC, and I1 also in Spain a bit later.

ADW_1981
11-02-2013, 08:38 PM
We have a bit of a problem with I2 in that it is one of the rarer haplogroups and so we might need to do a lot more testing of ancient DNA before we pick it up in Europe. I would guess that it arrived in Europe with the early farmers from the Near East. So far we have mtDNA I appearing in Spain with farmers 4090-3960 BC, and I1 also in Spain a bit later.

Possibly, but I2 is a pretty specific designation, and would not necessarily represent all of I. I have not seen I2 turn up in Spain, but I suppose it could. I have seen it in Greece and Georgia though...

I just ran through the mutations, thanks to your website and saw only 2 differences between my father's sequence and the mummy. While we are on the topic of mtDNA, Jean, you might want to take a look at the Icelandic, pre-Christian mtdna I. There are similar sequences there as well, some of which are I2. I noticed your site doesn't have that aDNA data there.

Jean M
11-02-2013, 09:07 PM
Icelandic, pre-Christian mtdna I.

What paper was that?

ADW_1981
11-02-2013, 11:56 PM
What paper was that?

Here you go

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000343

Jean M
11-05-2013, 04:53 PM
Just found an article on the basis of the dissertation: Rabab Khairat et al., First insights into the metagenome of Egyptian mummies using next-generation sequencing, Journal of Applied Genetics, August 2013, Volume 54, Issue 3, pp 309-325. http://link.springer.com/article/10.1007/s13353-013-0145-1

Salkin
12-04-2014, 01:31 PM
My mtFullSequence at FTDNA came back yesterday and confirmed 23andMe's assignment of I2. I wonder how exactly I'm related to that mummy. :) The mtDNA I project will probably come along and assign me to a further subclade at some point.

I've asked for a report on my FASTA file by Dr. Ann Turner. It'll be interesting to see how that plays out.

I don't have any matches closer than a GD of 2, which I gather likely puts the common ancestor a long way back. Full spectrum (all three regions) matches seem to mostly be in the British Isles, though there's a Norwegian and a German. I suppose commonality might even be from IE speakers before they split.

Also, it appears my mtDNA actually does say GATTACA in one place. ;)

ADW_1981
12-04-2014, 06:46 PM
My mtFullSequence at FTDNA came back yesterday and confirmed 23andMe's assignment of I2. I wonder how exactly I'm related to that mummy. :) The mtDNA I project will probably come along and assign me to a further subclade at some point.

I've asked for a report on my FASTA file by Dr. Ann Turner. It'll be interesting to see how that plays out.

I don't have any matches closer than a GD of 2, which I gather likely puts the common ancestor a long way back. Full spectrum (all three regions) matches seem to mostly be in the British Isles, though there's a Norwegian and a German. I suppose commonality might even be from IE speakers before they split.

Also, it appears my mtDNA actually does say GATTACA in one place. ;)

My dad is two steps from the Egyptian at FGS, what is the FTDNA kit# or surname on yours? Curious how far you are from him. I'm fairly close to a bunch of Norwegians, don't recall Swedes were in there.

Salkin
12-04-2014, 07:11 PM
My dad is two steps from the Egyptian at FGS, what is the FTDNA kit# or surname on yours? Curious how far you are from him. I'm fairly close to a bunch of Norwegians, don't recall Swedes were in there.

FTDNA kit 367588, surname Karlsson. Sounds like an interesting comparison to make, do let me know if you find anything.

Salkin
12-04-2014, 07:38 PM
Word from the project admin:


Reviewing your results, I see that your most distinctive mutations are T8119C and G8557A. You are one of seven project members with one or both of these markers, and all of you belong to a new subclade of I2 that has not yet been officially identified. I anticipate that this subclade will be added to the next update of the mtDNA tree. I don't know when this update will take place, but I hope it will be sometime in 2015.

ADW_1981
12-04-2014, 09:53 PM
FTDNA kit 367588, surname Karlsson. Sounds like an interesting comparison to make, do let me know if you find anything.

I guess your kit is more than the maximum steps away... I do see some Norwegians and at least 1 Swede from a quick scan of the results. No such Karlsson anywhere.

Salkin
12-05-2014, 01:51 PM
I guess your kit is more than the maximum steps away... I do see some Norwegians and at least 1 Swede from a quick scan of the results. No such Karlsson anywhere.

Sorry, I goofed a bit (probably too little caffeine). Karlsson is my surname, but that's likely not what's showing in the project's listing - it lists my maternal grandmother whose surname was Olsfelt. But presumably you checked for the kit number also.

CuChulain
11-22-2015, 03:34 PM
Im a Swede I2 I have an additional mutation 12136. Anyone else have this?

Bdeed
03-18-2017, 06:19 PM
Also, I2 with no matches on ftdna, all a mystery!

GMan71
05-27-2017, 01:16 PM
Also, I2 with no matches on ftdna, all a mystery!

My daughters (hence my wife's) have just come in and is I2 and no matches in FTDNA either.