Human genomes from the Green Sahara reveal ancestral North African lineage
#46
(02-05-2025, 01:49 PM)venustas Wrote:
(02-05-2025, 09:23 AM)Lank Wrote: They apparently have a unique mtDNA N subclade derived from the root. With mostly ANA ancestry, about 23% East African, and 15% Levantine ancestry (according to the qpgraph by crashdoc). I wonder if this indicates an origin of mtDNA N in North Africa?

Not at all it is a very derived variety and the main special thing about it is it went extinct. With the low resolution of mtdna all branches of N are unique.
I looked at the mutations of this N branch it literally has more differences from Basal N either in theory or compared to ancient N samples like Oase than most modern people do. It seems for some weird reason this type of N had a higher rate of mutation. Iirc and afaik

Would the extra mutations not come from someone else's mtDNA? Has anyone checked?
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#47
(02-05-2025, 01:49 PM)venustas Wrote:
(02-05-2025, 09:23 AM)Lank Wrote: They apparently have a unique mtDNA N subclade derived from the root. With mostly ANA ancestry, about 23% East African, and 15% Levantine ancestry (according to the qpgraph by crashdoc). I wonder if this indicates an origin of mtDNA N in North Africa?

Not at all it is a very derived variety and the main special thing about it is it went extinct. With the low resolution of mtdna all branches of N are unique.
I looked at the mutations of this N branch it literally has more differences from Basal N either in theory or compared to ancient N samples like Oase than most modern people do. It seems for some weird reason this type of N had a higher rate of mutation. Iirc and afaik

Is there a link between this Green Sahara and some Yoruba ( like Yoruba-1 -2 -3  ) ?
I find such  higher rate of mutations in some Yoruba, that I can't explain anyway.
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#48
Enough speculation about the mtdna
Mitomaster_1901528

Sequence Predicted Haplogroup Total Variants Variants
MF479727.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details
MF479728.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details

This is rcrs they are very similar I will convert the top one to CRS soon to make it easier. You can do it on mitomaster.com

Also I don't have time or a high enough IQ probably or computing power of someone could find a way to fix the mtdna tree using these tools that would be great.

Running blast will be useful perhaps
https://blast.ncbi.nlm.nih.gov/Blast.cgi
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#49
(02-12-2025, 03:55 PM)venustas Wrote: Enough speculation about the mtdna
Mitomaster_1901528

Sequence Predicted Haplogroup Total Variants Variants
MF479727.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details
MF479728.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details

Pre-N with 8701G (N has 8701A) and 23 private mutations, which seems like a reasonable amount AFAICT. Oase 1 had pre-N lacking 2 mutations, so diverged before this lineage.
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#50
(02-13-2025, 04:51 AM)Megalophias Wrote:
(02-12-2025, 03:55 PM)venustas Wrote: Enough speculation about the mtdna
Mitomaster_1901528

Sequence Predicted Haplogroup Total Variants Variants
MF479727.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details
MF479728.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details

Pre-N with 8701G (N has 8701A) and 23 private mutations, which seems like a reasonable amount AFAICT. Oase 1 had pre-N lacking 2 mutations, so diverged before this lineage.
Any chance it is a back mutation?Oase is unlikely to be back mutation given its age and lack of private mutations but there is no way to prove 8701G is not a back mutation is there?
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#51
(02-13-2025, 04:51 AM)Megalophias Wrote:
(02-12-2025, 03:55 PM)venustas Wrote: Enough speculation about the mtdna
Mitomaster_1901528

Sequence Predicted Haplogroup Total Variants Variants
MF479727.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details
MF479728.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details

Pre-N with 8701G (N has 8701A) and 23 private mutations, which seems like a reasonable amount AFAICT. Oase 1 had pre-N lacking 2 mutations, so diverged before this lineage.
If it is not a back mutation perhaps it is a distant relative of N21 https://www.yfull.com/mtree/N21/ which also has  8701G
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#52
(02-13-2025, 03:45 PM)venustas Wrote:
(02-13-2025, 04:51 AM)Megalophias Wrote:
(02-12-2025, 03:55 PM)venustas Wrote: Enough speculation about the mtdna
Mitomaster_1901528

Sequence Predicted Haplogroup Total Variants Variants
MF479727.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details
MF479728.1 N (N) 38 A73G, A263G, A374G, T414G, T689C, A750G, A1438G, A2706G, A3505G, A4769G, T5814C, T6524C, C7028T, A7874G, A8389G, A8701G, A8860G, C9449T, T10020C, A11590G, C11704T, G11719A, C12705T, A14070G, G14305A, C14766T, A15236G, A15326G, T15461C, T16092C, T16172C, C16186T, C16187T, C16223T, C16234T, G16244A, A16335G, T16519C Variant Details

Pre-N with 8701G (N has 8701A) and 23 private mutations, which seems like a reasonable amount AFAICT. Oase 1 had pre-N lacking 2 mutations, so diverged before this lineage.
Any chance it is a back mutation?Oase is unlikely to be back mutation given its age and lack of private mutations but there is no way to prove 8701G is not a back mutation is there?
No, it could have back-mutated; this has happened in a couple of young branches. However, it is rare, so this is not an unstable position.

Since Oase 1 also has 8701G, it must be either the last or second last of 5 N mutations, so that fits. For N21 and Takarkori to be related, they sharing no other mutations, it would have to have back-mutated again shortly after it happened, which seems unlikely. I didn't actually realize N21 had 8701G - it might well actually be extant pre-N. Huh.
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#53
(02-05-2025, 01:49 PM)venustas Wrote:
(02-05-2025, 09:23 AM)Lank Wrote: They apparently have a unique mtDNA N subclade derived from the root. With mostly ANA ancestry, about 23% East African, and 15% Levantine ancestry (according to the qpgraph by crashdoc). I wonder if this indicates an origin of mtDNA N in North Africa?

Not at all it is a very derived variety and the main special thing about it is it went extinct. With the low resolution of mtdna all branches of N are unique.
I looked at the mutations of this N branch it literally has more differences from Basal N either in theory or compared to ancient N samples like Oase than most modern people do. It seems for some weird reason this type of N had a higher rate of mutation. Iir
Image below


Attached Files Thumbnail(s)
   
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#54
Does this mean that this "Takarkori" branch of Haplogroup N is the same as the one found in the Oase samples, and is somehow related to N21? Apologies, not super familiar with mtDNA.

Nonetheless, it is interesting that this lineage is not found in any modern human population.
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#55
(02-16-2025, 05:35 PM)alchemist223 Wrote: Does this mean that this "Takarkori" branch of Haplogroup N is the same as the one found in the Oase samples, and is somehow related to N21? Apologies, not super familiar with mtDNA.

No, Oase maternal line is missing 2 of the 5 defining N mutations, so Takarkori forms a clade with all other N against Oase (as they all share 4 out of 5 mutations).

It could possibly be related to N21, if they share a back-mutation (that is they originally had all 5 N mutations), but if so it must have happened very early, so I don't think it's likely. Otherwise, they wouldn't be related. Alternatively, they could both have independently back-mutated, or they could both be pre-N, or one of each.

If they are both pre-N (i.e. never had the 5th mutation), since they don't share any other mutations, there is no reason to think they are related. Takarkori, N21, and the rest of N would be equally sister branches.
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#56
(02-16-2025, 05:52 PM)Megalophias Wrote:
(02-16-2025, 05:35 PM)alchemist223 Wrote: Does this mean that this "Takarkori" branch of Haplogroup N is the same as the one found in the Oase samples, and is somehow related to N21? Apologies, not super familiar with mtDNA.

No, Oase maternal line is missing 2 of the 5 defining N mutations, so Takarkori forms a clade with all other N against Oase (as they all share 4 out of 5 mutations).

It could possibly be related to N21, if they share a back-mutation (that is they originally had all 5 N mutations), but if so it must have happened very early, so I don't think it's likely. Otherwise, they wouldn't be related. Alternatively, they could both have independently back-mutated, or they could both be pre-N, or one of each.

If they are both pre-N (i.e. never had the 5th mutation), since they don't share any other mutations, there is no reason to think they are related. Takarkori, N21, and the rest of N would be equally sister branches.

OK, so would it be best to say then that this lineage would be just basal Haplogroup N*?
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#57
I don't think we can really say from current data. mtDNA is tricky that way.
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#58
Published.
(04-02-2025, 03:32 PM)theplayer Wrote: Ancient DNA from the Green Sahara reveals ancestral North African lineage

https://www.nature.com/articles/s41586-025-08793-7

Abstract
Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch1. DNA rarely preserves well in this region, limiting knowledge of the Sahara’s genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals’ ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco2, associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.

What do we think?
Quote:No group shares extra affinity with Takarkori genomes compared with Taforalt, as measured by f4 statistics of the form f4(chimpanzee, X; Takarkori, Taforalt)
I blame 1240k.

Quote:With this revised model, we estimated that the Taforalt ancestry retains a comparable 60.8% (±1.8%) contribution from Natufians, with the remaining 39.2% (±1.8%) derived from Takarkori.
I don't even know who/what to blame.
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#59
(04-02-2025, 10:15 PM)kolompar Wrote: Published.
(04-02-2025, 03:32 PM)theplayer Wrote: Ancient DNA from the Green Sahara reveals ancestral North African lineage

https://www.nature.com/articles/s41586-025-08793-7

Abstract
Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch1. DNA rarely preserves well in this region, limiting knowledge of the Sahara’s genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals’ ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco2, associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.

What do we think?
Quote:No group shares extra affinity with Takarkori genomes compared with Taforalt, as measured by f4 statistics of the form f4(chimpanzee, X; Takarkori, Taforalt)
I blame 1240k.

Quote:With this revised model, we estimated that the Taforalt ancestry retains a comparable 60.8% (±1.8%) contribution from Natufians, with the remaining 39.2% (±1.8%) derived from Takarkori.
I don't even know who/what to blame.

What specifically do you take issue with these two quoted excerpts, and how to do you think the 1240k panel is leading the authors astray?
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#60
https://podcasts.apple.com/us/podcast/ev...0701973157
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