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Ase
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I don't really know how to conclude with the DNA Tribes stuff. I don't know if the data they had to work with would be enough to suggest that the Amarnas were closest related to Great Lakes Africans. But considering that Egyptian demographics ranged based on where an Egyptian lived and when they were born, is it possible the DNA tribes material could be accurate if we're discussing more local/regional groups of AE? If you feel that on the other hand, there is not enough information DNA tribes reviewed to suggest the African connection of the Amarnas, please explain that too.
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the lioness,
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The DNA Tribes article used its raw data from an earlier Discovery Channel-financed, Egyptian-led study from 2010 by Albert Zink et al. that was published in the Journal of the American Medical Association (JAMA). It was this JAMA study's researchers that actually extracted the DNA from the mummies. The DNA Tribes authors just analysed the raw data, which had been made publicly available for independent analysis:

DNA Tribes used their own method called Match Liklihood (MLI)
South Africa scored highest, Great Lakes had a similar score and West Africa noticeably lower but third place and much higher than North Africa

You can't disregard the South African score and just look at the Great Lakes because the way they scored the Great Lakes is the same methodology as how they scored South Africa and the other regions

The root question is the accuracy of the raw Albert Zink Data

Also like Abusir being only half the picture, maternal mitochondrial DNA,
the Amarna were tested for nuclear DNA

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Forty2Tribes
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The raw data is substantiated by the relationships. The MLI scores might be boosted by the exclusive Twa and Khoi markers. The Tribes score for Ramses iii demonstrates that these markers have the same genetic pattern as they do in modern Africans.The same genetic pattern in the sense that their Tribes score is stronger in the Horn so more diversity equates to more inclusion.
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Swenet
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quote:
Originally posted by the lioness,:
The root question is the accuracy of the raw Albert Zink Darta

 -

quote:
Originally posted by Fourty2Tribes:
The raw data is substantiated by the relationships. The MLI scores might be boosted by the exclusive Twa and Khoi markers. The Tribes score for Ramses iii demonstrates that these markers have the same genetic pattern as they do in modern Africans.

Thanks.  -
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Ase
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On that whole accuracy bit, people have been claiming that the STR(?) tested are too few or did I get that acronym mixed up? And about the raw data being substantiated by relationships, can this be explained in more detail?
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the lioness,
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quote:
Originally posted by Fourty2Tribes:
The raw data is substantiated by the relationships. The MLI scores might be boosted by the exclusive Twa and Khoi markers. The Tribes score for Ramses iii demonstrates that these markers have the same genetic pattern as they do in modern Africans.The same genetic pattern in the sense that their Tribes score is stronger in the Horn so more diversity equates to more inclusion.

The topic is Amarna not the Ramses line
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Swenet
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quote:
Originally posted by Oshun:
On that whole accuracy bit, people have been claiming that the STR(?) tested are too few or did I get that acronym mixed up? And about the raw data being substantiated by relationships, can this be explained in more detail?

There may be surprises ahead in that department. Surprises as in: we don't know how well Amarna 8 STR results would scale to genome-wide Amarna results. It may not scale perfectly (I don't think it will, at all and I've said why in many different threads). But at the same time, Eurasians never have MLI scores like the Amarnas, even when you only analyse Eurasians with 8 STRs. So this indicates that there is something African there that isn't going to go away when you sequence more Amarna markers. If that were true then random Eurasians would have all sorts of Great Lakes/South African results with 8 STRs, which is simply not the case.

Here are some valid concerns, as far as I'm concerned:
  • Are the Amarna MLI scores typical of some ancient North African aDNA also consisting of 8 STRs? Maybe the reason why SSA regions score highest right now is because the ancient North African populations that would have better scores are extinct.
  • Related to the previous point: do modern North African pooled regions have lower MLIs with Amarnas because they're admixed with lower MLI score-having Eurasians? Egypt and Sudan are pooled in the Levantine DNA Tribes region.
  • Related to the previous point: would it make a difference in terms of MLI scores if populations were compared individually as opposed to pooled regions? According to the 4 alleles used by DNA consultants, some modern Egyptians don't underperform and have some of the highest frequencies of Amarna alleles. But we don't know how these modern Egyptian samples perform in DNA tribes, because these Egyptian samples are pooled in the "Levantine" DNA Tribes region.
  • To what extent did Hawass et al fill in blanks in the allele table? Contamination is a bogus explanation as 42tribes said. The reason it's bogus because the alleles are structured like a family, which is something you can't get with contamination or errors. But it's still possible that they filled in the blanks of data they didn't have, by looking at the other Amarna family members and filling in allele values based on their expectations of who is related to who. I don't think they did a lot of that, but I think it's a valid concern someone might have. In one article they said they didn't publish all their results for fear that detractors would look for weaknesses in their genetic data.

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xyyman
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You got it right. Using our eyeball you can see differences in "races" easily. Take TH01 AND TPOX as an example.

Africans and Chinese/Native Americans have similar repeats compared to Europeans. But Chinese and Europeans are similar compared to Africans(TPOX). Then when you take CSF1PO Europeans and Africans are similar but not Chinese or Apaches. So with using only your eye balls and using only THREE STRs we already see racial or geographic differences. You only need 3 STRs. 8 is more than enough. The Abusir will give similar results. Bet on it! But this was not performed for the Abusirs.

STRs are recombined as "blocks" of genes that is why STRs are used and NOT random SNPs(as with the Abusir paper) is used to determine "race" by INTERNATIONAL law enforcement agency. SNPs cannot!!!

And these CODIS STRs are taken over the ENTIRE human genome on many chromosomes unlike the SNPs for the Abusir which was taken only from ONE chromosome(#19) if IIRC.

quote:
Originally posted by Oshun:
On that whole accuracy bit, people have been claiming that the STR(?) tested are too few or did I get that acronym mixed up? And about the raw data being substantiated by relationships, can this be explained in more detail?

quote:
Originally posted by xyyman:
[q] @Lioness..

“All humans are related” and have commonality. Native Americans “genes” were found in the Amarnas……….DNAConsultants.

The utility of short tandem repeat loci beyond human identification: Implications for development of new DNA typing systems(1999)

Notice THO1 repeats are very similar in Africans(AFRAMS) and Native American. That does not mean the Amarnas are Native American

 -


Quote by DNAConsultants
“Like most of the other genes in the family, it is Central African in ancient origin, but unlike the other markers it has a sparse distribution outside Africa with a worldwide average frequency of 4%. Still, Africans and African-influenced populations (1 in about 10) are about twice or three times as likely to have it as non-Africans”. [/q]



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Forty2Tribes
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quote:
Originally posted by the lioness,:
The topic is Amarna not the Ramses line

The Topic is DNA Tribes. Ramses had a DNATribes test that included not just MLI scores but a Tribes score as well.

quote:
Originally posted by Oshun:
On that whole accuracy bit, people have been claiming that the STR(?) tested are too few or did I get that acronym mixed up? And about the raw data being substantiated by relationships, can this be explained in more detail?

The raw data produced these relationships
 -

It was also similar to Ramses iii's markers so you have that relationship too.

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Ase
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quote:
Originally posted by Fourty2Tribes:
quote:
Originally posted by the lioness,:
The topic is Amarna not the Ramses line

The Topic is DNA Tribes. Ramses had a DNATribes test that included not just MLI scores but a Tribes score as well.

...And his results were similar to the Amarnas?


quote:
Originally posted by the lioness,:
quote:
Originally posted by Fourty2Tribes:
The raw data is substantiated by the relationships. The MLI scores might be boosted by the exclusive Twa and Khoi markers. The Tribes score for Ramses iii demonstrates that these markers have the same genetic pattern as they do in modern Africans.The same genetic pattern in the sense that their Tribes score is stronger in the Horn so more diversity equates to more inclusion.

The topic is Amarna not the Ramses line
Well it's about how DNA Tribes whether or not it's feasible/sensible for people to use their results to determine population affinity.
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Swenet
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quote:
Originally posted by xyyman:
Africans and Chinese/Native Americans have similar repeats compared to Europeans. But Chinese and Europeans are similar compared to Africans(TPOX). Then when you take CSF1PO Europeans and Africans are similar but not Chinese or Apaches. So with using only your eye balls and using only THREE STRs we already see racial or geographic differences. You only need 3 STRs. 8 is more than enough. The Abusir will give similar results. Bet on it! But this was not performed for the Abusirs.

Gramps, weren't you investigating Abusir affinities with low amount of markers? What happened?
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the lioness,
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quote:
Originally posted by Oshun:
Well it's about how DNA Tribes whether or not it's feasible/sensible for people to use their results to determine population affinity.

The way science works is you publish test results and other scientists can test the same specimen and see if they get the same results. This requires standardized methodology and peer review.
Dna Tribes "MLI" ( Match Likelihood) score is their own brand of proprietary methodology and at the end of some of their digest articles they sell testing.
That is why you don't see scientific journal articles don't cite DNA Tribes as a reference.
It doesn't mean they are wrong it means their articles might be suggestive but they are a private testing company selling products so they are not a reference as credible as a scientific journal article.
For the same reason DNA Tribes cannot be relied on as a credible reference to the DNA of Ramses III.
Additionally DNA Tribes did not conduct the testing on the actual mummy samples themselves. It's not primary research.

If you want a credible reference look below to Rameses III as tested by the Zahi Hawass team including Albert Zink

______________________________________________________

BMJ. 2012 Dec 14;345:e8268. doi: 10.1136/bmj.e8268.
Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study.

Hawass Z1, Ismail S, Selim A, Saleem SN, Fathalla D, Wasef S, Gad AZ, Saad R, Fares S, Amer H, Gostner P, Gad YZ, Pusch CM, Zink AR.

‘Our analysis showed that Ramesses III and unknown man E shared the same paternal lineage and had identical alleles at autosomal markers, strongly suggesting that they were father and son. However, based on the genetic testing, any differentiation among the several sons of Ramesses III was not possible.


‘Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a.

_____________________________


 -
African spatial distribution of haplogroup E3a-M2. Rosa et al. (2007)

wikipedia

The discovery of two SNPs (V38 and V100) by Trombetta et al. (2011) significantly redefined the E-V38 phylogenetic tree. This led the authors to suggest that E-V38 may have originated in East Africa. V38 joins the West African-affiliated E-M2 and the northern East African-affiliated E-M329 with an earlier common ancestor who, like E-P2, may have also originated in East Africa.[2]. The downstreams SNP E-M180 possibly originated on the moist south-central Saharan savannah/grassland of northern Africa between 14,000-10,000 years BP[3].[4][5][6] According to Wood et al. (2005) and Rosa et al. (2007), such population movements changed the pre-existing population Y chromosomal diversity in Central, Southern and southern East Africa, replacing the previous haplogroups frequencies in these areas with the now dominant E1b1a1 lineages. Traces of earlier inhabitants, however, can be observed today in these regions via the presence of the Y DNA haplogroups A1a, A1b, A2, A3, and B-M60 that are common in certain populations, such as the Mbuti and Khoisan.

__________________________________________

some believe Ramses group might have been E3b not E3a
but can't prove that at this point

What are you up to, trying to battle some white supremacists on some other forum?

Key; analysis by Hawass team:
"we determined the Y chromosomal haplogroup E1b1a"

_______________________

DNA Tribes MLI scores
South Africa ( bantu not incl. Khosian ) 326.94
African Great Lakes 323.76
Tropical West African 142.84
Sahelian 39.14

^^ take with a few grains of salt

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Forty2Tribes
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quote:
Originally posted by Oshun:
...And his results were similar to the Amarnas?

His was, but his son's seemed to be a little different. Makes me wonder about his kid's mom and how long American ancestry lingered in North Africa. http://dnatribes.com/dnatribes-digest-2013-02-01.pdf

Notice Ramses and his son have scores in parentheses. Those are Tribes scores. They substantiate the credibility of the results because they are so inflated.

STR test are extremely objective and literal. They are the best at determining what you are they are not good at determining what else you are. The MLI scores reflect this. The Armana family and Ramses iii had exclusive markers in Khoi and Batwa so any location that had a combination of those markers was going to have the best scores. The test basically sees them as Pygmy-Bushmen Et al.

The Tribes score deals with the Et al and it substantiates the MLI scores because its inflated. This shows that these genes are still in rotation. That means that the low MLI scores are caused by the algorithm having less STRs not because the STRS are extinct or undicerning. I wondered about this until I compared Ramses iii's Tribes score(the one in parentheses) to my own.

The Tribes Score sorta works backwards in comparison to the MLI score. Its higher in areas where you have the least mismatches instead of the strongest matches. My MLI score is much higher in Tropical West Africa at more than 600 thousand compared to just 2K in the horn however my Tribes score is higher in the Horn at 31 compared to 26 in Tropical West Africa. Ramses iii had a Tribes score of 93 in the Horn and 84 in the great lakes region where the higher MLI scores were higher.

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the lioness,
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 -  -
_______Amenhotep III ______________________________________Tutankhamun_

 -

why the big difference in the MLI's ?

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the lioness,
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quote:
Originally posted by Fourty2Tribes:
quote:
Originally posted by Oshun:
...And his results were similar to the Amarnas?

His was, but his son's seemed to be a little different. Makes me wonder about his kid's mom and how long American ancestry lingered in North Africa. http://dnatribes.com/dnatribes-digest-2013-02-01.pdf

Notice Ramses and his son have scores in parentheses. Those are Tribes scores. They substantiate the credibility of the results because they are so inflated.

STR test are extremely objective and literal. They are the best at determining what you are they are not good at determining what else you are. The MLI scores reflect this. The Armana family and Ramses iii had exclusive markers in Khoi and Batwa so any location that had a combination of those markers was going to have the best scores. The test basically sees them as Pygmy-Bushmen Et al.

The Tribes score deals with the Et al and it substantiates the MLI scores because its inflated. This shows that these genes are still in rotation. That means that the low MLI scores are caused by the algorithm having less STRs not because the STRS are extinct or undicerning. I wondered about this until I compared Ramses iii's Tribes score(the one in parentheses) to my own.

The Tribes Score sorta works backwards in comparison to the MLI score. Its higher in areas where you have the least mismatches instead of the strongest matches. My MLI score is much higher in Tropical West Africa at more than 600 thousand compared to just 2K in the horn however my Tribes score is higher in the Horn at 31 compared to 26 in Tropical West Africa. Ramses iii had a Tribes score of 93 in the Horn and 84 in the great lakes region where the higher MLI scores were higher.

"Tribes score"

that is a private company's undisclosed unique methodology.
That cannot be used as scientific data reference
As far as DNA testing companies go African ancestry .com has the largest database of African lineages

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xyyman
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?? Not sure what you are asking. What is low markers?

quote:
Originally posted by Swenet:
quote:
Originally posted by xyyman:
Africans and Chinese/Native Americans have similar repeats compared to Europeans. But Chinese and Europeans are similar compared to Africans(TPOX). Then when you take CSF1PO Europeans and Africans are similar but not Chinese or Apaches. So with using only your eye balls and using only THREE STRs we already see racial or geographic differences. You only need 3 STRs. 8 is more than enough. The Abusir will give similar results. Bet on it! But this was not performed for the Abusirs.

Gramps, weren't you investigating Abusir affinities with low amount of markers? What happened?


--------------------
Without data you are just another person with an opinion - Deming

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quote:
Originally posted by the lioness,:
 -  -
_______Amenhotep III ______________________________________Tutankhamun_

 -

why the big difference in the MLI's ? [/QB]

Recombination in one inbred generation. Tut has two copies of D18s51=19

Consultants profiled it.
https://dnaconsultants.com/king-tut-gene/
quote:
Like most of the other genes in the family, it is Central African in ancient origin, but unlike the other markers it has a sparse distribution outside Africa with a worldwide average frequency of 4%.
Tukuler researched it through http://spsmart.cesga.es/ and found that its Mbuti and pan-Africa.


quote:
Originally posted by the lioness,:
"Tribes score"

that is a private company's undisclosed unique methodology.
That cannot be used as scientific data reference
As far as DNA testing companies go African ancestry .com has the largest database of African lineages

Their method is disclosed and reviewed.
https://patents.google.com/patent/US8285486B2/en

They also have a relatively large database which is why their journals were used as mainstream sources. The Armana test black balled them. This was their wikipedia page before the censorship campaign. https://isogg.org/wiki/DNA_Tribes
Every instance where they were cited was removed (except the ones they missed).


One day African Ancestry will be my ancestry test dismount to back check them all. Saving the best for last [Wink] .

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the lioness,
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Swenet
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quote:
Originally posted by xyyman:
?? Not sure what you are asking. What is low markers?

quote:
Originally posted by Swenet:
quote:
Originally posted by xyyman:
Africans and Chinese/Native Americans have similar repeats compared to Europeans. But Chinese and Europeans are similar compared to Africans(TPOX). Then when you take CSF1PO Europeans and Africans are similar but not Chinese or Apaches. So with using only your eye balls and using only THREE STRs we already see racial or geographic differences. You only need 3 STRs. 8 is more than enough. The Abusir will give similar results. Bet on it! But this was not performed for the Abusirs.

Gramps, weren't you investigating Abusir affinities with low amount of markers? What happened?

You were talking about checking the Abusir sample's affinities using 8 STRs to see what would happen. I'm surprised no one has done this yet (or something equivalent).
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Ase
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So if you can't use it to get an idea of how much SSA they had...what do you use this for?
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xyyman
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Young man I know you are sharper than your buddy ^, I speculated that pop STRs can be pulled from the bam files SNP for the Abusir. Elmaestro volunteered to pull those STRs. 2 weeks later he came back and said it cannot be done. He tried. He suggested the researchers removed those relevant SNPs so it canNOT be done. Keep up.

I am now speculating that MOMI2 and GPS can be used. Maybe other software.....

quote:
Originally posted by Swenet:
quote:
Originally posted by xyyman:
?? Not sure what you are asking. What is low markers?

quote:
Originally posted by Swenet:
quote:
Originally posted by xyyman:
Africans and Chinese/Native Americans have similar repeats compared to Europeans. But Chinese and Europeans are similar compared to Africans(TPOX). Then when you take CSF1PO Europeans and Africans are similar but not Chinese or Apaches. So with using only your eye balls and using only THREE STRs we already see racial or geographic differences. You only need 3 STRs. 8 is more than enough. The Abusir will give similar results. Bet on it! But this was not performed for the Abusirs.

Gramps, weren't you investigating Abusir affinities with low amount of markers? What happened?

You were talking about checking the Abusir sample's affinities using 8 STRs to see what would happen. I'm surprised no one has done this yet (or something equivalent).


--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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You are such a ditz! It is not about "how much" , it is about which geographic modern population they belong to. SMH.

quote:
Originally posted by Oshun:
So if you can't use it to get an idea of how much SSA they had...what do you use this for?



--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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Good info forty2tribes....on the patented method.

------
As far as DNA testing companies go African ancestry .com has the largest database of African lineages
Their method is disclosed and reviewed.
https://patents.google.com/patent/US8285486B2/en

They also have a relativel

--------------------
Without data you are just another person with an opinion - Deming

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Swenet
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quote:
Originally posted by xyyman:
Young man I know you are sharper than your buddy ^, I speculated that pop STRs can be pulled from the bam files SNP for the Abusir. Elmaestro volunteered to pull those STRs. 2 weeks later he came back and said it cannot be done. He tried. He suggested the researchers removed those relevant SNPs so it canNOT be done. Keep up.

Not sure what you mean with "they removed it". But there is no reason why you shouldn't be able to use equivalent markers if genotype information is incomplete. There are many panel sets of STRs, CODIS and non CODIS. Tishkoff et al 2009 used 800+ STR markers plus indels.

quote:
We genotyped a panel of 1327 polymorphic markers, consisting of 848 microsatellites, 476
indels (insertions/deletions), and three SNPs (single-nucleotide polymorphisms), in 2432
Africans from 113 geographically diverse populations (fig. S1), 98 African Americans, and 21
Yemenites (table S1).

Possibly some polymorphic SNPs with the same discrimination power will also be equivalent for our intents and purposes. One day I will look into it myself because I refuse to believe this is all there is to say about it. Maybe you're not creative enough to work around the problem, so you gave up.
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xyyman
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It is not about "creativity". It is being able to use the tools. These tools are NOT Windows based. I said so before. It has been over 15 years since I have done any serious programming. I don't have the time to learn to use Ubuntu and Unix etc.

I prefer CODIS STRs because it is a subset of what is internationally used. Agreed there may be others like Tishkoff's but I never looked into it. ElMaestro? Ahem! You are up! Thoughts?!


sides - JAMA/HAWASS used 8 from CODIS for the Amarnas which DNATribes used and published their report. DNAConsultants used the same set.

--------------------
Without data you are just another person with an opinion - Deming

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Swenet
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No worries. I'll look into it. Too big of an opportunity.
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the lioness,
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quote:
Originally posted by Oshun:
So if you can't use it to get an idea of how much SSA they had...what do you use this for?

DNA Tribes MLI scores are not percentages, no you can't use it

As for Rameses III you can say his paternal haplogroup was determined by the Zawi Hawass team to be E1b1a aka E-M2 and the result was published in the British Medical Journal.
And E1b1a is the predominant subclade in Western Africa, Central Africa, Southern Africa and the African Great Lakes,
That means the ancestry from his father is African but mother unknown.

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Ase
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quote:
Originally posted by xyyman:
You are such a ditz! It is not about "how much" , it is about which geographic modern population they belong to. SMH.

 -

Wow it is not that serious. Please feel free to come back to my thread when you've cooled down and don't do this kinda thing. Thanks.

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Elmaestro
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ayo xyyman, Don't do that... I didn't say they were "removed" man. Chances are they either weren't mapped or covered when sequencing...
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