Screening data for libraries created in this study (TKH001.A0101 from TKH001, and XXX001.A18276 and XXX001.A18277 from TKH009) were obtained through shallow shotgun sequencing. SNP enrichment was performed using three capture sets: the 1240k and Twist panels for population genetic analyses, and the Archaic Admixture panel for investigating archaic ancestry. All capture data presented here were aligned to the human reference genome (hg19, GRCh37), filtered for PCR duplicates, filtered for mapping quality of 25 and a minimum length of 30 base pairs. The shallow shotgun data was processed similarly, except with a mapping quality threshold of 30. Additionally, Archaic Admixture capture data were generated from 22 previously existing libraries (van de Loosdrecht et al., 2018) derived from seven Taforalt individuals (TAF09, TAF010, TAF011, TAF012, TAF13, TAF014, TAF015). We provide BAM files from these libraries, aligned to the human reference genome (hg19, GRCh37) and filtered for PCR duplicates. Merged data for each individual, processed analogously to the Takarkori data, are also included.
Additional abstract from last year:
Known as one of the most arid areas on the planet today, the Sahara Desert was, in fact, a green savannah in the Holocene, dotted by forests and water bodies that promoted human occupation and fostered pastoralism. Due to the present-day climatic conditions, ancient DNA does not preserve well in the region, resulting in limited knowledge of the Sahara’s demographic past. Here, we report the first ancient human genome-wide data from the Saharan Pastoral Neolithic. We obtained genomic data from two ca. 7000-yearold female pastoralists buried in the Takarkori rock shelter at the heart of the Tadrart Acacus massif in southwestern Libya, which was used as a burial ground by pastoral communities. We find that the majority of the Takarkori individuals’ ancestry stems from a previously unknown lineage that appears to have remained isolated for most of its existence. Both individuals are most closely related to the preceding 15,000-year-old foragers from Morocco associated with the Iberomaurusian techno-complex, whereas both Takarkori and Iberomaurusian individuals are distantly related to sub-Saharan African lineages. The quality of one of the genomes from Takarkori is sufficient to detect prospective Neandertal ancestry and we find evidence for few segments of ancestry that sum to a total comparable to that detected in the genomes of sub-Saharan Africans. Our results therefore support a model of cultural diffusion, rather than human migration, for the emergence of pastoralist subsistence in the Sahara region.
Related Articles while we wait for the actual article:
To start the discussion, here are some f3 stats, an MDS plot based on them and a qpgraph with the European side based on a simplified version of one of Kale's plus Neandertal and Africans added.
For those interested while we wait for more official sources, here are bed/bin/fam files for TKH001 and TKH009. The link will work for a month.
In the zip file I provide 2 versions: the usual without filtering, except for quality of course and those I prefer to use with trimming to remove most of ancient dna damage. I also provide a version of TKH001 with only Shotgun and Twist Capture merged so as to have as little capture bias as possible.
Super interesting stuff! The Takarkori samples seem to really help resolve the phylogeny. Looks like a big impact of ANA on West and East Africa in the qpgraph. Connected to the spread of Y-DNA E and mtDNA L3?
(02-05-2025, 04:55 AM)Lank Wrote: Super interesting stuff! The Takarkori samples seem to really help resolve the phylogeny. Looks like a big impact of ANA on West and East Africa in the qpgraph. Connected to the spread of Y-DNA E and mtDNA L3?
This is in agreement with Lipson et al (2020), as can be seen in Figure 5. It models the bulk of the ancestry in Mota (71%) and Niger-Congo peoples (69%) as having derived from the same source that produced the Aboriginal African ancestry in the Taforalt hunter-gatherers.
Figure 5:
Show Content
Spoiler
Figure 4(a) models 88% of the ancestry in Niger-Congo peoples as having derived from this source (though it excludes the Taforalt hunter-gatherers).
$rankdrop
# A tibble: 3 × 7
f4rank dof chisq p dofdiff chisqdiff p_nested
<int> <int> <dbl> <dbl> <int> <dbl> <dbl>
1 2 10 14.1 1.69e- 1 12 492. 8.91e-98
2 1 22 507. 3.14e-93 14 8016. 0
3 0 36 8523. 0 NA NA NA
$popdrop
# A tibble: 7 × 14
pat wt dof chisq p f4rank Dinka.DG Morocco_Iberomaurusian.AG Yoruba.DG feasible best dofdiff chisqdiff p_nested
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl> <dbl>
1 000 0 10 14.1 1.69e- 1 2 0.389 0.375 0.237 TRUE NA NA NA NA
2 001 1 11 73.2 3.00e-11 1 0.649 0.351 NA TRUE TRUE 0 -333. 1
3 010 1 11 406. 3.45e-80 1 3.41 NA -2.41 FALSE TRUE 0 314. 0
4 100 1 11 92.0 6.75e-15 1 NA 0.416 0.584 TRUE TRUE NA NA NA
5 011 2 12 4445. 0 0 1 NA NA TRUE NA NA NA NA
6 101 2 12 3013. 0 0 NA 1 NA TRUE NA NA NA NA
7 110 2 12 8081. 0 0 NA NA 1 TRUE NA NA NA NA
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?
(02-05-2025, 04:22 AM)crashdoc Wrote: To start the discussion, here are some f3 stats, an MDS plot based on them and a qpgraph with the European side based on a simplified version of one of Kale's plus Neandertal and Africans added.
02-05-2025, 10:46 AM (This post was last modified: 02-05-2025, 10:48 AM by masta.)
(02-05-2025, 10:23 AM)Norfern-Ostrobothnian Wrote: Takarkori does not seem to need any Natufian
I looked at it looks like Saharan HG lineage , i don't think they have much Neolithic ancestry,
they show affinity to Dinka and East african pastoral neolithic ..probably can fit as dinka + some iberomaurusian admixture..not sure tho.
(02-05-2025, 10:23 AM)Norfern-Ostrobothnian Wrote: Takarkori does not seem to need any Natufian
I looked at it looks like Saharan HG lineage , i don't think they have much Neolithic ancestry,
they show affinity to Dinka and East african pastoral neolithic ..probably can fit as dinka + some iberomaurusian admixture..not sure tho.
Both my qpAdm and qpGraph also has some West African ancestry.
I think it can be modelled in G25 once we get the coordinates for it.
02-05-2025, 01:49 PM (This post was last modified: 02-05-2025, 01:57 PM by venustas.)
(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
(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
Obviously, I didn't mean these samples literally carry the root mtDNA N lineage (they lived 7 kya, after all, not 50-60 kya). But their mtDNA N diverged from the root, just like many other N lineage, but in this case they are apparently of mostly non-Eurasian ancestry.
This is obviously not enough to say that mtDNA N originated in North Africa, but it is certainly a possibility. And not such a crazy one, when the Neanderthal admixtures in proto-Eurasians apparently dates to just around 45-50 kya.
I wonder if mtDNA M1 descends from a similar group in the Paleolithic, whether that was in North Africa or just outside in West Asia.
