The genomic history of the Middle East.(Final paper)

[real expert]

Highlights
• Middle Easterners do not have ancestry from an early out-of-Africa expansion

• Basal Eurasian and African ancestry in Arabians deplete their Neanderthal ancestry
• Populations experienced bottlenecks overlapping aridification events
• Identification of recent single and polygenic signals of selection in Arabia

Summary

The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 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 found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15–20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.

We next tested whether we can model our populations as deriving ancestry from one of the sampled regional Bronze Age populations and found that the Middle Bronze Age population from Sidon (Sidon_BA) could be a source of ancestry for some modern Levantine and Arabian populations (Tables S3 and S4). Our phylogenetic modeling suggests that modern Levantines could have directly derived their ancestry from a Sidon_BA-related population; however, Arabians require additional ancestry from a Natufian-related population (Figures 3 and S3).

https://www.cell.com/cell/fulltext/S0092-8674(21)00839-4

 

[kingjohn]

Thanks
In addition to the local ancestry from Epipaleolithic/Neolithic people, we found an ancestry related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange component in Figure 1B; Table 1). Previous studies showed that this ancestry was not present in the Levant during the Neolithic period but appeared in the Bronze Age where ∼50% of the local ancestry was replaced by a population carrying ancient Iran-related ancestry (Lazaridis et al., 2016). 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 3,300 and 5,900 ya (Table S2), followed by admixture in Arabia (2,000–3,500 ya) and East Africa (2,100–3,300 ya). 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 2). 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 did find rarer earlier diverged lineages coalescing ∼17 kya (Figure S2). 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 found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).

:cool-v:

 

[real expert]

Thanks
In addition to the local ancestry from Epipaleolithic/Neolithic people, we found an ancestry related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange component in Figure 1B; Table 1). Previous studies showed that this ancestry was not present in the Levant during the Neolithic period but appeared in the Bronze Age where ∼50% of the local ancestry was replaced by a population carrying ancient Iran-related ancestry (Lazaridis et al., 2016). 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 3,300 and 5,900 ya (Table S2), followed by admixture in Arabia (2,000–3,500 ya) and East Africa (2,100–3,300 ya). 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 2). 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 did find rarer earlier diverged lineages coalescing ∼17 kya (Figure S2). 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 found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).


:cool-v:

Do you think the Semitic language originated in Mesopotamia and came with the J carriers to the Levant?

 

[kingjohn]

Do you think the Semitic language originated in Mesopotamia and came with the J carriers to the Levant?

Dont know
I think the way they tie y haplogroup j to iranian
Ancestery who came from north to south could be logic
But to tie the iranian ancestery with semtic language looks like a strach to me

 

[Leopoldo Leone]

The suggestion that Semitic languages came with J from Iran is as moronic as the suggestion that Albanians and the Albanian language come from north africa because of haplo E.
They got the linguistic bit utterly wrong, an example of what happens when one tries to link genetics too much with culture/language.

 

[bicicleur 2]

Basal Eurasian is an OOA branch, and it split into 2 branches :
one contributing to the Levant
another contributing to Ganj Dareh

 

[Jovialis]

Great find,

Strangely the study seems to link the wrong page for public data. Nevertheless, I found it here: https://www.ebi.ac.uk/ena/browser/view/PRJEB28504?show=reads

Unfortunately, they are not in BAM format.

 

[kingjohn]

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 found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).

maybe they are speaking about this branch :there are some rare cases of e-m215 positive but e-m35 negetive ( almost all individuals who are e-m215+ are also e-m35+)
and there is this branch e-m215> e-v16


https://www.yfull.com/tree/E-V16/



https://i.imgur.com/wd5LWRV.png

 

[Angela]

The pre-print was discussed here at some length; I don't think the paper has changed in the interim.
The Genomic History of the Middle East (eupedia.com)

As for J ydna carriers bringing Semitic with them when they went south I don't know.

We'll see whether Agamemnon is as wrong about this as he was about the Etruscans.

 

[Riverman]

Good to see
Basal Eurasian -> Levant HG -> Natufian/Levant N

I think this paper supports the Levantine-Arabian home of Basal Eurasian somewhat. Not conclusive, but indicative:

Since EmiratiA and SaudiA have less than 3% of African ancestry (Table 1), the depletion of Neanderthal ancestry in Arabia cannot be explained by the African ancestry alone.Lazaridis et al., 2016
proposed that a basal Eurasian population, with low-to-no Neanderthal ancestry, had contributed different proportions to ancient and modern Eurasians, reaching ∼50% in Neolithic Iranians and Natufians. Since Arabians have an excess of Natufian-like ancestry compared to elsewhere in the Middle East, we found they also carry an excess of basal Eurasian ancestry that will reduce their Neanderthal ancestry.

n addition to differences in EHG and African ancestries, we observed an excess of Natufian ancestry in Arabia compared with the Levant (Figures 1B and 1E). When we substituted Levant_N with Natufians as source of ancestry in the Middle East, we found that Arabians could be successfully modeled (Table 1), whereas none of the present-day Levantines could be modeled as such.

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 did find rarer earlier diverged lineages coalescing ∼17 kya (Figure S2). 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 found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).

Fig 2:
https://www.cell.com/cell/fulltext/S0092-8674(21)00839-4#figs2

To me this suggests that E1b1b either was born in the Near East or moved there no later than 25.000 years ago, which would be in line with my suggestion from earlier posts that Natufians should be largely derived from local Levantine foragers.

Our results do not support a complete replacement of the Arabian populations by Levantine farmers. In addition, our models suggest that Arabians could have derived their ancestry from Natufian-like local hunter-gatherer populations instead of Levantine Farmers. The identification of lithic assemblages in Northern Arabia, some of which appear similar to ones made by Levantine farmers (Crassard and Drechsler, 2013a
), in addition to the movement of animal domesticates between the Levant and Arabia, have been suggested to occur either due to population movements or through cultural diffusion (Guagnin et al., 2017; Petraglia et al., 2020). Our results suggest the latter scenario and/or limited migration from the Levant.

https://www.cell.com/cell/fulltext/S0092-8674(21)00839-4

 

[Hawk]

The suggestion that Semitic languages came with J from Iran is as moronic as the suggestion that Albanians and the Albanian language come from north africa because of haplo E.
They got the linguistic bit utterly wrong, an example of what happens when one tries to link genetics too much with culture/language.

You should carefully read the statement, it's not far-fetched to think Semitic languages spread with Y-DNA J1, as per Afro-Asiatic language, linguistic methodology is very accurate on predicting North-East Africa to Levant spread during Mesolithic/Neolithic times. Somewhere during the Bronze Age maybe some Y-DNA J1 Iranian-Caucasian goat herders after adopting Pre Proto-Semitic language from some E-M35 group, either in Levant or Mesopotamia then time after became more dominant.

 

[Leopoldo Leone]

You should carefully read the statement, it's not far-fetched to think Semitic languages spread with Y-DNA J1, as per Afro-Asiatic language, linguistic methodology is very accurate on predicting North-East Africa to Levant spread during Mesolithic/Neolithic times. Somewhere during the Bronze Age maybe some Y-DNA J1 Iranian-Caucasian goat herders after adopting Pre Proto-Semitic language from some E-M35 group, either in Levant or Mesopotamia then time after became more dominant.

I wrote "it came from Iran" not that the spead of semitic tongues is strongly linked with J1 haplo, which is likely, but as you've written it seems likelier that who brought J1 into the Levant and Arabia adopted a previous language.

 

[Hawk]

To me this suggests that E1b1b either was born in the Near East or moved there no later than 25.000 years ago, which would be in line with my suggestion from earlier posts that Natufians should be largely derived from local Levantine foragers.

As for Natufian E-M35, yes they were probably Levantine foragers, Ramonian let's say. As for our E-M78 ancestor, we were the Mushabians probably, bringing the Afro-Asiatic tongue, ANA autosomal and the flint microlith technology. :wink:

 

[kingjohn]

As for Natufian E-M35, yes they were probably Levantine foragers, Ramonian let's say. As for our E-M78 ancestor, we were the Mushabians probably, bringing the Afro-Asiatic tongue, ANA autosomal and the flint microlith technology. :wink:

only ancient dna from kebaran culture
https://en.wikipedia.org/wiki/Kebaran_culture
who will show e-z830 could prove it
maybe e-z830 arrived in natufian period from sinai

 

[bicicleur 2]

As for Natufian E-M35, yes they were probably Levantine foragers, Ramonian let's say. As for our E-M78 ancestor, we were the Mushabians probably, bringing the Afro-Asiatic tongue, ANA autosomal and the flint microlith technology. :wink:

flint microlith technology came from India, it probably arrived in the Middle East along with Basal Eurasian

 

[bicicleur 2]

it would have been much more interesting if Anatolian farmers also appeared in the picture
whatever model, it is either with Levant N or with Anatolian N, never with both

 

[Hawk]

flint microlith technology came from India, it probably arrived in the Middle East along with Basal Eurasian

I have already discussed and shared the paper with you. The oldest human planned mining was in Paleolithic Egypt not in Israel, not in India or Anatolia. So the trajectory of influences is clear.

 

[Riverman]

I have already discussed and shared the paper with you. The oldest human planned mining was in Paleolithic Egypt not in Israel, not in India or Anatolia. So the trajectory of influences is clear.

But you don't know it for the haplogroup E1b1b, because it looks like being in the Near East since at least 25.000 years BP. I'm not saying I know it for sure, but there are several possible alternatives.

 

[Angela]

To quote a well known comment about mistakes often made in discussions about genetic influences, "sometimes a pot is just a pot".

 

[bicicleur 2]

I have already discussed and shared the paper with you. The oldest human planned mining was in Paleolithic Egypt not in Israel, not in India or Anatolia. So the trajectory of influences is clear.

what has mining to do with geometric microliths ?