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Placing ancient DNA sequences into reference phylogenies

By pf2431

Dec. 22, 2020


Rui Martiniano, Bianca de Sanctis, Pille Hallast, Richard Durbin,
December 20, 2020
A very important publication which inserts in the haplogroup tree all the ancient DNA samples, we find the samples of Ifri n’Amr (IAM4, IAM5 and IAM7):

IAM4 and IAM7 are E-L19* (positive for L19, negative for PF2431 and M81)
IAM5 is PF2535* (positive for PF2535 and negative for M81)

Here is an excerpt from the article:

"Three Moroccan Early Neolithic samples carry E1b1b1b1-M310.1 lineages [17], with the lineage of sample IAM.5 further refined to E1b1b1b1a1∼-PF2535 with a single supporting marker. In our analysis, they were placed ancestrally to present-day Mozabite and Saharawi North African lineages (Figure 5B), which is in agreement with the finding from autosomal analyzes that these samples comprised an endemic Maghrebi element still retained in present-day North African populations "

Here M310.1 is equivalent to L19.
Of the 84 snps equivalent to M81, only one was found positive in the old IAM5 dna. It should be remembered that 30,933 snps were found to be positive while each human being has between 3,000 and 5,000 positive snps. Of these 30,933 snps, nearly 28,000 are false positives, it was suspected that PF2535 was the same.
All of the AMIs if related to each other, one would be inclined to think that this small group as a whole had identical results and that they were all L19*. I remind you that all the samples from the Tafoghalt site are all E-M78*, similarly for those from Raqefet Cave (Natufian) which are all E-Z830*. I am quoting what IAM study author R. Fregel said about IAM5 and which goes in this direction:

"IAM.5 only showed one derived SNP, while the remaining were ancestral. We used this evidence to propose that the lineage present in IAM was ancestral to modern E-M81. And it makes sense, IAM samples are around 7,000 years old, while coalescence age for E-M81 is much younger.
Regarding the use of low-coverage data, you have to be careful when analyzing the data. We always classify the mutations taking into account if they can be related to DNA damage (C to T, G to A). The derived SNP in 557 can't be produced by cytosine deamination, so we considered it. Are the mutations that make no sense attributable to DNA damage?"

Which explains why this sample in the article is defined L19*.

In conclusion: What should be remembered is that the majority of the North African population belongs to the L19 (PF2431+M81) sub-haplogroup which was discovered in its ancestral state in skeletons discovered in North Africa and dated at carbon 14 of approximately 7000 years old. It is therefore endogenous to North Africa and has two branches PF2431 and PF2535. It is hoped that other known ancient sites will be studied to gain more information on its history and migrations.


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