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gihanga.rwanda
10-21-2020, 07:37 PM
A preprint on the genetic landscape of the Middle East was just posted. Almarri et al. 2020 includes samples from 137 individuals at 30x whole genome coverage, as well as a few ancient samples including the Natufians, Antolia-N, and Iranian-N. My only regret is that they didn't include Dzudzuana or Taforalt.

https://www.biorxiv.org/content/10.1101/2020.10.18.342816v1

https://i0.wp.com/www.gnxp.com/WordPress/wp-content/uploads/2020/10/mideast1.jpg?w=780&ssl=1


The Middle East is an important region to understand human evolution and migrations, but is underrepresented in genetic studies. We generated and analysed 137 high-coverage physically-phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations, but find Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. A divergence in population size within the region starts before the Neolithic, when Levantines expanded while Arabians maintained small populations that could have derived ancestry from local epipaleolithic hunter-gatherers. All populations suffered a bottleneck overlapping the archaeologically-documented 4.2 kiloyear aridification of the area, while regional migrations increased genetic structure, and may have contributed to the spread of the Semitic languages. We identify new variants that show evidence of selection, some dating from the onset of the desert climate in the region. Our results thus provide detailed insights into the genomic and selective histories of the Middle East.

Razib Khan has already made a post (https://www.gnxp.com/WordPress/2020/10/20/the-genetic-history-of-the-middle-east-into-arabia/) on his blog and Lazaridis has some interesting commentary on his Twitter (https://twitter.com/iosif_lazaridis?ref_src=twsrc%5Egoogle%7Ctwcamp%5E serp%7Ctwgr%5Eauthor).

gihanga.rwanda
10-21-2020, 07:53 PM
The study also attempted to date the arrival of Iranian ancestry in the Middle East. Razib seems to be a bit skeptical of the admixture dates, but I don't think they're very far fetched. The admixture date for the Levant seems sound and the admixture date for East Africa seems to correspond with the arrival of Semitic languages in the Ethiopian highlands vis-a-vie South Arabia. Someone can correct me if I am wrong, but Iranian ancestry is either absent or low in groups like the Somali and the ancient pastoralists from Kenya/Tanzania (see Kenya_Pastoralists_IA), but present at higher frequencies in the highlands among groups like the Amhara and Tigrinya. As for Egypt, wouldn't these results suggest that Egyptians experienced some gene-flow from the Levent during the historic era, possibly mediated by Semitic settlers who are attested in the historical and archeological record. @Agamemnon

The midpoint estimate of Iranian admixture into Egypt is around 1780 BC, which would place it at the end of the Middle Kingdom (2050 to 1710 BC). The admixture model in the supplements gives this for Egyptians: 45% Levant_N, 32% Iran_N, 8% EHG (Eastern European Hunter-Gatherer), and 15% Mota (African).


We explored whether this ancestry penetrated both the Levant and Arabia at the same time, and found that admixture dates mostly followed a North to South cline, with the oldest admixture occurring in the Levant region between 3,900 and 5,600 ya (Table S3), followed by admixture in Egypt (2,900-4,700 ya), East Africa (2,200-3,300) and Arabia (2,000-3,800). These times overlap with the dates for the Bronze Age origin and spread of Semitic languages in the Middle East and East Africa estimated from lexical data (Kitchen et al., 2009; Figure S8).This population potentially introduced the Y-chromosome haplogroup J1 into the region (Chiaroni et al., 2010; Lazaridis et al., 2016). The majority of the J1 haplogroup chromosomes in our dataset coalesce around ~5.6 [95% CI, 4.8-6.5] kya, agreeing with a potential Bronze Age expansion; however, we do find rarer earlier diverged lineages coalescing ~17 kya (Figure S9). The haplogroup common in Natufians, E1b1b, is also frequent in our dataset, with most lineages coalescing ~8.3 [7-9.7] kya, though we also find a rare deeply divergent Y-chromosome which coalesces 39 kya (Figure S9).

Helves
10-21-2020, 08:27 PM
The study also attempted to date the arrival of Iranian ancestry in the Middle East. Razib seems to be a bit skeptical of the admixture dates, but I don't think they're very far fetched. The admixture date for the Levant seems sound and the admixture date for East Africa seems to correspond with the arrival of Semitic languages in the Ethiopian highlands vis-a-vie South Arabia. Someone can correct me if I am wrong, but Iranian ancestry is either absent or low in groups like the Somali and the ancient pastoralists from Kenya/Tanzania (see Kenya_Pastoralists_IA), but present at higher frequencies in the highlands among groups like the Amhara and Tigrinya. As for Egypt, wouldn't these results suggest that Egyptians experienced some gene-flow from the Levent during the historic era, possibly mediated by Semitic settlers who are attested in the historical and archeological record. @Agamemnon

The midpoint estimate of Iranian admixture into Egypt is around 1780 BC, which would place it at the end of the Middle Kingdom (2050 to 1710 BC). The admixture model in the supplements gives this for Egyptians: 45% Levant_N, 32% Iran_N, 8% EHG (Eastern European Hunter-Gatherer), and 15% Mota (African).
Actually the timeframe for the Levant is not accurate. Iran_N admixture shows up already in CA samples from Peqi’in Cave, Israel dated to around 6200 yBP so one questions the dating for the other regions aswell.

gihanga.rwanda
10-21-2020, 08:32 PM
Actually the timeframe for the Levant is not accurate. Iran_N admixture shows up already in CA samples from Peqi’in Cave, Israel dated to around 6200 yBP so one questions the dating for the other regions aswell.

I totally forgot about the people from the Peqi’in Cave. You're right, I remember them being ~15-20 Iranian Chalcolithic, but then again perhaps the later admixture dates is picking up on increased Iranian ancestry in the Levant since the culture at Peqi’in Cave?

drobbah
10-21-2020, 08:53 PM
The study also attempted to date the arrival of Iranian ancestry in the Middle East. Razib seems to be a bit skeptical of the admixture dates, but I don't think they're very far fetched. The admixture date for the Levant seems sound and the admixture date for East Africa seems to correspond with the arrival of Semitic languages in the Ethiopian highlands vis-a-vie South Arabia. Someone can correct me if I am wrong, but Iranian ancestry is either absent or low in groups like the Somali and the ancient pastoralists from Kenya/Tanzania (see Kenya_Pastoralists_IA), but present at higher frequencies in the highlands among groups like the Amhara and Tigrinya. As for Egypt, wouldn't these results suggest that Egyptians experienced some gene-flow from the Levent during the historic era, possibly mediated by Semitic settlers who are attested in the historical and archeological record. @Agamemnon

The midpoint estimate of Iranian admixture into Egypt is around 1780 BC, which would place it at the end of the Middle Kingdom (2050 to 1710 BC). The admixture model in the supplements gives this for Egyptians: 45% Levant_N, 32% Iran_N, 8% EHG (Eastern European Hunter-Gatherer), and 15% Mota (African).
Both the South Cushitic pastoralists especially the early ones and modern Somalis have Iranian ancestry:

With Proto-Natufian & ANA (Simulated)

PNs

https://i.imgur.com/jqHaiVz.jpg



Somalis
https://i.imgur.com/Tl9QSxQ.jpg




Without Proto-Natufian/ANA


PNs

https://i.imgur.com/NSc98gp.jpg


Somalis
https://i.imgur.com/zZseB85.png

gihanga.rwanda
10-21-2020, 08:59 PM
Both the South Cushitic pastoralists especially the early ones and modern Somalis have Iranian ancestry:

With Proto-Natufian & ANA (Simulated)

PNs

https://i.imgur.com/jqHaiVz.jpg



Somalis
https://i.imgur.com/Tl9QSxQ.jpg




Without Proto-Natufian/ANA


PNs

https://i.imgur.com/NSc98gp.jpg


Somalis
https://i.imgur.com/zZseB85.png



Thanks for the correction! The supplemental docs mentioned that the Somali have some Iranian admixture but I didn’t realize that it extended to these early pastoralists as well. This definitely makes me second guess some of these admixture dates.

pmokeefe
10-21-2020, 09:11 PM
There's an existing thread for this paper here:
https://anthrogenica.com/showthread.php?21992-The-Genomic-History-of-the-Middle-East

gihanga.rwanda
10-21-2020, 09:21 PM
There's an existing thread for this paper here:
https://anthrogenica.com/showthread.php?21992-The-Genomic-History-of-the-Middle-East

And here I thought I’d beaten the rate race. Moderators - could someone delete or archive this thread since there already appears to be an active thread on the same subject?

TheIncredibleHulk
10-22-2020, 12:04 AM
Both the South Cushitic pastoralists especially the early ones and modern Somalis have Iranian ancestry:

With Proto-Natufian & ANA (Simulated)

PNs

https://i.imgur.com/jqHaiVz.jpg



Somalis
https://i.imgur.com/Tl9QSxQ.jpg




Without Proto-Natufian/ANA


PNs

https://i.imgur.com/NSc98gp.jpg


Somalis
https://i.imgur.com/zZseB85.png



Hmm, what are the Sudanese represent here?

pmokeefe
10-22-2020, 01:03 AM
And here I thought I’d beaten the rate race. Moderators - could someone delete or archive this thread since there already appears to be an active thread on the same subject?

No worries mate, alas I've done that myself.
Now what I do is search for the title along with "site:anthrogenica.com" in the search bar. If someone has already posted the article it usually shows up.