PDA

View Full Version : Genetic History of the Near East (Iron & Classical Ages) - Haber at al. 2020



bicicleur
28-05-20, 22:02
The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world’s great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4

kingjohn
28-05-20, 22:48
ID Period Sex (genetic) Y Haplogroup MT Haplogroup

( e-v65 individual from hellenistic beirut
E-v65 is a branch of e-m78 which is today
Found in north west africa , spain )

SFI-56 Iron Age II female - U1a1a
SFI-55 Iron Age II male J H2a
SFI-43 Iron Age III female - T2c1+146
SFI-50 Iron Age III female - U1a
SFI-36 Iron Age III female - R0a1a
SFI-42 Iron Age III male J1-M267 H2a
SFI-45 Iron Age III male J-M304 T2a1b1
SFI-34 Iron Age III male J1-M267 T1a2
SFI-35 Iron Age III male I2a1b-M436 R0a1a
SFI-39 Iron Age III male H2-P96 I1b
SFI-44 Iron Age III male J1a2a1a2-P58 T2c1+146
SFI-47 Iron Age III male G2a2a1a2-L91 W6
SFI-20 Hellenistic female - H41
SFI-5 Hellenistic male Q1b-M346 K1a5a
SFI-12 Hellenistic male E1b1b1a1a2-V65 H14a
SFI-24 Early Roman female - H8b
SFI-33 Early Roman female - T1
SFI-11 Early Roman male G2a2b-L30 N1b1
SFI-15 Early Roman male G2a2b1a2-M3302 I1c1

Angela
29-05-20, 03:54
This is a fascinating paper which purports to answer questions I (and a lot of people) have had about how much admixture occurred in the Levant during the period after 1000 BC.

Well, this is quite some finding:

"
We found that the Lebanese Iron Age population can be modeled as a mixture of the local Bronze Age population (63%–88%) and a population related to ancient Anatolians or ancient South-Eastern Europeans (12%–37%) (Table 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#tbl2) and Figure 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig2)B). We replicated these results by running DyStruct
44 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib44)
with 166,693 transversions present in set 1 and showed that a Steppe-like ancestry, typically found in Europeans, appears in the Near East starting from the Iron Age II (Figure 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig2)D). A potential source of this exogenous ancestry could be the Sea Peoples, a seafaring group of people with a disputed origin who attacked the Eastern Mediterranean and Egypt after the Bronze Age (1200–900 BCE). One of our successful models for admixture involved an ancestry source related to the Ashkelon (a city situated ∼170 miles south of the Beirut sites) Iron Age I population, which was previously identified as possibly descending from Sea-Peoples-related admixture.
18 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib18)
In addition, according to ancient Egyptian texts and archaeology, the Sea Peoples conquered the Levant but failed to conquer the Egyptians. Therefore, we tested whether the Eurasian gene flow to Lebanon during the Iron Age had also reached ancient Egypt by quantifying the Steppe ancestry in both regions at that time and found f4(Sidon_BA, Beirut_IAII; Steppe_EMBA, Chimp) is significantly negative (Z score = −4.13), but f4(Sidon_BA, Egypt_prePtolemaic; Steppe_EMBA, Chimp) has a value not significantly different from zero (Z score = 0.317), suggesting that either ancient Egypt did not receive the Eurasian gene flow that the Levant received during the Iron Age or that the Eurasian ancestry was replaced in Egypt as in Ashkelon, where in contrast to the Beirut_IAII, the European-related ancestry was no longer significant in the Ashkelon Iron Age II population.
18 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib18)
Additional Iron Age samples from the Levant coast and Egypt could reveal whether the Iron Age admixture had a north to south cline as a result of the location of the source populations or from differences in the scale of the successful migrations to the north or south of the Levant during this period."

So, the area around Beirut definitely shows signs of admixture with Southeastern European/Anatolian sources. As we've discussed often I have always tended to believe that many of the Sea Peoples came from Southern Italy or Sardinia.

See our discussion of the Sidon paper:
https://www.biorxiv.org/content/biorxiv/early/2017/05/26/142448.full.pdf

See our discussion of the Philistines of Ashkelon paper
https://www.eupedia.com/forum/threads/38852-Philistine-DNA!?highlight=Philistines

What I said then I'd say now:

"Everything I know of the Sea Peoples indicates that they were "groups" of people, not necessarily from one place. Plus, as they moved south and east they would change genetically.

One of those samples looks extremely Sardinian to me, and they have been connected to the Sea Peoples. Others could have come from southern Italy. Others could have been from the Aegean. I honestly don't know if at that period there's was a whole bunch of difference between these people.

The really intriguing bit is the yDna "L".

Is it the Druze who have "L"? What kind?

I'll really read the paper in depth later and compare to my books on the Sea Peoples."

Angela
29-05-20, 04:05
I don't know why they didn't include Sardinians as we have samples, or ancient Sicilian samples.



Beirut_IA
Sidon_BA
Anatolia_MLBA
4.44 × 10−01
0.63
0.37
0.06


Beirut_IA
Sidon_BA
Ashkelon_IAI
4.29 × 10−01
0.69
0.31
0.05


Beirut_IA
Sidon_BA
Anatolia_EBA
3.38 × 10−01
0.80
0.20
0.03


Beirut_IA
Sidon_BA
Mycenaean
2.17 × 10−01
0.77
0.23
0.04


Beirut_IA
Sidon_BA
Minoan_Odigitria
1.32 × 10−01
0.80
0.20
0.04


Beirut_HER
Beirut_IA
Butkara_H
4.93 × 10−01
0.92
0.08
0.01


Beirut_HER
Beirut_IA
Aligrama2_IA
4.46 × 10−01
0.93
0.07
0.01


Beirut_HER
Beirut_IA
Indus_Periphery
3.88 × 10−01
0.93
0.07
0.01


Beirut_HER
Beirut_IA
Swat_H
3.24 × 10−01
0.92
0.08
0.01


Beirut_HER
Beirut_IA
SPGT_IA
2.65 × 10−01
0.93
0.07
0.01



As to any migration from to the Levant during the Hellenistic and Early Roman periods, Hellenistic period perhaps from people brought from Central Asia and the Indus region by Alexander's generals when they took over the near east, but I'm at a loss to explain it for early Roman period.

Angela
29-05-20, 04:14
Well, I should have read further...

"We found that the Hellenistic and early Roman population can be modeled as a mixture of the local population, Beirut_IA (88%–94%), and a Central/South Asian population (6%–12%) (Tables 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#tbl2) and S8 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1) and Figure 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig2)C). We then analyzed haplotype segments shared between the ancient Lebanese and modern populations in set 2 by using ChromoPainter44 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib44)
on 2.5 million imputed SNPs and found that two Hellenistic individuals (SFI-5 and SFI-12) and one early Roman individual (SFI-11) had excess haplotype sharing with Central and South Asians (Figures 2 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig2)E and S9 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)), thus confirming the qpAdm results. The relationship of ancient Lebanon with Central and South Asia also manifests in the presence of haplogroup L1a1-M27 among the modern Lebanese Y chromosome lineages (Figure S10 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

The following requires deeper thought:

"We next tested the genetic changes between the Hellenistic/early Roman period and the late Roman period (Qed_LRoman) and found little genetic differences from the f4-statistics (Figure S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)), which is notable because during this period there was significant population movement between the Near East and Europe, as identified from the genomes of ancient Near Easterners found in Rome at that time.16 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib16)
When we model Qed_LRoman as a mixture of the Hellenestic/early Roman period population and another ancient population, we find successful models involving ancient Anatolians and South-Eastern Europeans (Table S9 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). However, because this ancestry was already present in Lebanon starting from the Iron Age, its excess in Qed_LRoman could be from population structure, especially because the Qed_LRoman samples were from a remote mountainous region, whereas the Hellenistic/early Roman samples were from the coast, and in addition, we found that the admixture models were not significant when Beirut_IA was used as the source of the local ancestry, showing that Qed_LRoman derived all of its ancestry from preceding local populations (Table S9 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

Whether they're correct about this or not, the people used to define some of the samples from late Imperial Rome have, perhaps, a significant portion of "Italianate"/Greek like like ancestry.

Angela
29-05-20, 04:20
"From the late Roman period to the medieval period, we detect an increase in African ancestry (Figure S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)B), but that increase remains slightly below statistical significance (Z score = −2.4) and accounts for ∼2.9% of Lebanon_Medieval’s ancestry when ancient East Africans are used in the admixture model (Table S10 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). The final genetic change observed in Lebanon occurred after the Crusaders’ period but, as we showed previously,4 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib4)
was not related to the Crusaders themselves. We found4 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib4)
an increase in ancestry related to populations from the Caucasus and Turks in the modern Lebanese population after the medieval period (Figure S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)C and Table S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). Using admixture-induced linkage disequilibrium (LD) decay,47 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib47)
,48 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib48)
we show that admixture occurred around 1640–1740 CE when Lebanon was under Ottoman rule (Figure S12 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). The LD-decay test also detects significant admixture that occurred during the Hellenistic period, which is consistent with our more direct inferences from the ancient individuals analyzed here (Figure S12 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

Much better way of measuring the "African" ancestry in the Levant than using Somalis, for goodness sakes, as happens in the other paper.

I wasn't aware, I must say, that the Caucasus influence increased that much during Ottoman rule.

"Finally, we fit all the ancient and modern Lebanese data into an admixture graph model showing their relationship with other ancient populations by using data in set 2. The graph supports the results reported here, showing substantial genetic continuity in Lebanon since the Bronze Age interrupted by three significant admixture events during the Iron Age, Hellenistic period, and Ottoman period, each contributing 3%–11% of non-local ancestry to the admixed population (Figures 3 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig3) and S13 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

I'll look at the Supplement tomorrow, but this was excellent.

Angela
29-05-20, 04:45
I couldn't resist this last PCA. Fascinating. You can see the Lebanese move progressively north from Sidon, and then pulled toward the Caucasus probably during the Ottoman Era if they're correct.

So, the Lebanese, and perhaps by implication the Jews, were already different in the Iron Age from the Bronze Age samples from Sidon. That might "lower" the amount of actual European, as in, acquired in Europe, ancestry in Jews.

I wonder if the same thing happened to the Druze.

In fact, it would be nice if someone did the same analysis for them. Look how close they are to Turkish Jews, who have quite a bit of Sephardic, as in Sepharads from Spain and Portugal.

Is it possible I was on to something in saying some of the "European" admixture in Ashkenazim occurred in the Levant itself?

I know one thing: if someone wants to model Levantine ancestry in Europe they have to take all of this into consideration. Could "some" of what is picked up as "Levantine" in Europe actually be Southeastern European?

https://i.imgur.com/D8PDx6p.png

Angela
29-05-20, 05:04
Anyone know if these G2a2 lineages are found in Italy or Greece? They come from samples from Beirut in the Early Roman period.
G2a2b-L30
G2a2b1a2-M3302

This one is from the Iron Age.
G2a2a1a2-L91


I wish so many population geneticist didn't totally ignore yDna.

Angela
29-05-20, 05:16
AH HA!

The Sardinians did occur to them, as well as modern Italian populations.


https://i.imgur.com/3wtOAag.png


Should have checked Sicily too. It might be up to the Crete level.


They should have also looked at modeling Sidon plus ancient Sardinian and Sicilian samples, but this is important too.

real expert
29-05-20, 05:19
"From the late Roman period to the medieval period, we detect an increase in African ancestry (Figure S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)B), but that increase remains slightly below statistical significance (Z score = −2.4) and accounts for ∼2.9% of Lebanon_Medieval’s ancestry when ancient East Africans are used in the admixture model (Table S10 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). The final genetic change observed in Lebanon occurred after the Crusaders’ period but, as we showed previously,4 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib4)
was not related to the Crusaders themselves. We found4 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib4)
an increase in ancestry related to populations from the Caucasus and Turks in the modern Lebanese population after the medieval period (Figure S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)C and Table S11 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). Using admixture-induced linkage disequilibrium (LD) decay,47 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib47)
,48 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#bib48)
we show that admixture occurred around 1640–1740 CE when Lebanon was under Ottoman rule (Figure S12 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1)). The LD-decay test also detects significant admixture that occurred during the Hellenistic period, which is consistent with our more direct inferences from the ancient individuals analyzed here (Figure S12 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

Much better way of measuring the "African" ancestry in the Levant than using Somalis, for goodness sakes, as happens in the other paper.

I wasn't aware, I must say, that the Caucasus influence increased that much during Ottoman rule.

"Finally, we fit all the ancient and modern Lebanese data into an admixture graph model showing their relationship with other ancient populations by using data in set 2. The graph supports the results reported here, showing substantial genetic continuity in Lebanon since the Bronze Age interrupted by three significant admixture events during the Iron Age, Hellenistic period, and Ottoman period, each contributing 3%–11% of non-local ancestry to the admixed population (Figures 3 (https://www.cell.com/ajhg/fulltext/S0002-9297(20)30155-5?fbclid=IwAR0fSA962IFxVPeS98djTJ2QbYuvUqJ8GtAbsWQ nkKPU1UcrEv1-_8j8lt4#fig3) and S13 (https://www.cell.com/cms/10.1016/j.ajhg.2020.05.008/attachment/34f491ed-18c3-42f4-a183-658345512cde/mmc1))."

I'll look at the Supplement tomorrow, but this was excellent.





Thanks a lot for this post. By African ancestry do they mean SSA only or was North African ancestry included too? In the Egyptian paper, it was also suggested that the SSA admixture in Egyptians increased in Roman times. What do you think? Are the Romans responsible for the increase in Sub-Saharan African gene flow into the Levant or rather the Arab slave trade?

Palermo Trapani
29-05-20, 06:15
Thanks a lot for this post. By African ancestry do they mean SSA only or was North African ancestry included too? In the Egyptian paper, it was also suggested that the SSA admixture in Egyptians increased in Roman times. What do you think? Are the Romans responsible for the increase in Sub-Saharan African gene flow into the Levant or rather the Arab slave trade?


Real expert: The paper I think you are referring to is the one linked below Schuemann et al 2016 and the paper documented increase SSA in Egypt Post Roman empire days. So I think the wording of this paper might not have been as clear as the one linked below but I think they are saying the same thing, increased since Roman times through medieval period

https://www.nature.com/articles/ncomms15694

real expert
29-05-20, 08:14
Real expert: The paper I think you are referring to is the one linked below Schuemann et al 2016 and the paper documented increase SSA in Egypt Post Roman empire days. So I think the wording of this paper might not have been as clear as the one linked below but I think they are saying the same thing, increased since Roman times through medieval period

https://www.nature.com/articles/ncomms15694


Yep, they were referring to SSA admixture.

real expert
29-05-20, 08:16
Did I understand this correctly? Is this Bronze Age Southern Levant paper suggesting that the East African gene flow entered into the Levant after the Bronze Age by using the East African ( to be more precise Somali) admixture in present-day Levantine people ????? Can someone explain? It's also odd that they model Tuscans as around 40% Middle Eastern and 60%European. A bit strange.


https://www.cell.com/cell/fulltext/S0092-8674(20)30487-6

Angela
29-05-20, 14:09
Thanks a lot for this post. By African ancestry do they mean SSA only or was North African ancestry included too? In the Egyptian paper, it was also suggested that the SSA admixture in Egyptians increased in Roman times. What do you think? Are the Romans responsible for the increase in Sub-Saharan African gene flow into the Levant or rather the Arab slave trade?


It's SSA. They're using an ancient East African sample. It has nothing to do with North Africa.

What this paper specifically says is below. That means the period of Arab Expansion and thus the Arab slave trade.
"From the late Roman period to the medieval period,

real expert
29-05-20, 15:56
It's SSA. They're using an ancient East African sample. It has nothing to do with North Africa.

What this paper specifically says is below. That means the period of Arab Expansion and thus the Arab slave trade.
"From the late Roman period to the medieval period,







Yes, I found that out too. However, the ancient East African samples that are used to determine the SSA admixture were also around 40-50% Western Eurasian. What I don't understand is why that other study about Bronze Age Southern Levant concludes that the East African gene flow entered into the Levant after the Bronze Age by using the East African ( to be more precise Somali) admixture in present-day Levantine people. What do you think Angela? It's also odd that they model Tuscans as half Middle Eastern.




For the LINADMIX analysis of present-day populations, we used a background dataset of 1,663 present-day and ancient individuals from 239 populations genotyped by using SNP arrays and focused our analysis on 14 Jewish and Levantine present-day populations, along with modern English, Tuscan, and Moroccan populations that were used as controls. We used LINADMIX to model each of the 17 present-day populations as an admixture of four sources: (1) Megiddo_MLBA (the largest group) as a representative of the Middle-to-Late Bronze Age component; (2) Iran_ChL as a representative of the Zagros and the Caucasus; (3) Present-day Somalis as representatives of an Eastern African source (in the absence of genetic data on ancient populations from the region); and (4) Europe_LNBA as a representative of ancient Europeans from the Late Neolithic and Bronze Age (Methods S1I; Table S4; Figure S4). We also applied PHCP to these 17 present-day populations (Methods S1G; Table S4; Figure S4). Comparison of PHCP and LINADMIX shows that they agree well with respect to the Somali and Europe_LNBA component, and therefore also for the combined contribution of Iran_ChL and Megiddo_MLBA (Methods S1G; Figure S4). However, they deviate regarding the respective contributions of Iran_ChL and Megiddo_MLBA (Figure S4), likely because of the fact that the Megiddo_MLBA and Iran_ChL are already very similar populations (Table S3). To only consider results that are robust and shared by LINADMIX and PHCP, we have combined Megiddo_MLBA and Iran_ChL to a single source population representing the Middle East for our main results (Figure 5). We further verified these conclusions, as well as the robustness of the estimations, by using a different representative for the Bronze Age Levantine groups as a source (Tables S4 and S5; Methods S1J) and using perturbations to the ADMIXTURE parameters (Table S4; Methods S1K). Combined, these results suggest that modern populations related to the Levant are consistent with having a substantial ancestry component from the Bronze Age Southern Levant and the Chalcolithic Zagros. Nonetheless, other potential ancestry sources are possible, and more ancient samples might enable a refined picture (Table S4).







The results show that since the Bronze Age, an additional East-African-related component was added to the region (on average ∼10.6%, excluding Ethiopian Jews who harbor ∼80% East African component), as well as a European-related component (on average ∼8.7%, excluding Ashkenazi Jews who harbor a ∼41% European-related component). The East-African-related component is highest in Ethiopian Jews and North Africans (Moroccans and Egyptians). It exists in all Arabic-speaking populations (apart from the Druze). The European-related component is highest in the European control populations (English and Tuscan), as well as in Ashkenazi and Moroccan Jews, both having a history in Europe (Atzmon et al., 2010, Carmi et al., 2014, Schroeter, 2008). This component is present, although in smaller amount, in all other populations except for Bedouin B and Ethiopian Jews. As expected, the English and Tuscan populations have a very low Middle-Eastern-related component. Whereas LINADMIX and PHCP have high uncertainty in estimating the relative contributions of Megiddo_MLBA and Iran_ChL, the results and simulations nevertheless suggest that additional Zagros-related ancestry has penetrated the region since the Bronze Age (Methods S1I). Except for the populations with the highest Zagros-related component, PHCP estimates lower magnitudes of this component (Figure S4A), and therefore detection by PHCP of a Zagros-related ancestry is likely an indication for the presence of this component. Indeed, examining the results of LINADMIX and PHCP on all four source populations (Figure S4), we observe a relatively large Zagros-related component in many Arabic-speaking groups, suggesting that gene flow from populations related to those of the Zagros and Caucasus (although not necessarily from these specific regions) continued even after the Iron Age (Methods S1I).
Altogether, the patterns of the present-day populations reflect demographic processes that occurred after the Bronze Age and are plausibly related to processes known from the historical literature (Methods S1I). These include an Eastern-African-related component that is present in Arabic-speaking groups but is lower in non-Ethiopian Jewish groups, as well as Zagros-related contribution to Levantine populations, which is highest in the northernmost population examined, suggesting a contribution of populations related to the Zagros even after the Bronze and Iron Ages.











Estimating the ancestry proportions in present-day Middle Eastern populations with substantial sub-Saharan African admixture (as well as multiple sources of admixture from different parts of the Mediterranean), is difficult. We addressed the problem by developing two statistical techniques and then testing the robustness of our inference on the basis of a comparison between these methods, simulations, and perturbations of the input (see STAR Methods; Methods S1F–S1K). We examined 14 present-day populations that are historically or geographically linked to the Southern Levant and tested the contributions of East Africa, Europe, and the Middle East (combining Southern Levant Bronze Age populations and Zagros-related Chalcolithic ones) to their ancestry. We found that both Arabic-speaking and Jewish populations are compatible with having more than 50% Middle-Eastern-related ancestry. This does not mean that any these present-day groups bear direct ancestry from people who lived in the Middle-to-Late Bronze Age Levant or in Chalcolithic Zagros; rather, it indicates that they have ancestries from populations whose ancient proxy can be related to the Middle East. The Zagros- or Caucasian-related ancestry flow into the region apparently continued after the Bronze Age. We also see an Eastern-African-related ancestry entering the region after the Bronze Age with an approximate south-to-north gradient. In addition, we observe a European-related ancestry with the opposite gradient (north-to-south). Given the difficulties in separating the ancestry components arriving from the Southern Levant and the Zagros, an important direction for future work will be to reconstruct in high resolution the ancestry trajectories of each present-day group, and to understand how people from the Southern Levant Bronze Age mixed with other people in later periods in the context of processes known from the rich archaeological and historical records of the last three millennia.



https://www.cell.com/cell/fulltext/S0092-8674(20)30487-6

Angela
29-05-20, 16:21
^^Let's keep the discussion of that paper on the thread for that paper. Otherwise, we'll muddy things up.

In this paper they're using variously Kenya Early Neolithic, Kenya Iron Age, Tanzania PN, and YRI.

https://i.imgur.com/66cTg52.png

I think Somalis would have more recent Arab ancestry as well. The proportions I don't know. I've always believed that the gene flow from the Near East into East Africa was continuous, and, of course, there was gene flow in the other direction as well, almost all of it female during the period of the Arab slave trade to the best of my recollection, perhaps because they took fewer men, or the men weren't allowed to mate.

ashraff
29-05-20, 16:31
Hi, how could this E-V65 haplogroup get into Hellenistic Beirut?
What historical event could fit into it?

real expert
29-05-20, 17:25
^^Let's keep the discussion of that paper on the thread for that paper. Otherwise, we'll muddy things up.

In this paper they're using variously Kenya Early Neolithic, Kenya Iron Age, Tanzania PN, and YRI.

Ok. Somalis unlike the Ethio-Semites from Eritrea and Norhern Ethiopia didn't receive significant additional Arab/Semitic admixture, though. However, I will move this specific question to you to the other thread.
https://i.imgur.com/66cTg52.png

I think Somalis would have more recent Arab ancestry as well. The proportions I don't know. I've always believed that the gene flow from the Near East into East Africa was continuous, and, of course, there was gene flow in the other direction as well, almost all of it female during the period of the Arab slave trade to the best of my recollection, perhaps because they took fewer men, or the men weren't allowed to mate.

Ok. As far as I know Somalis unlike the Ethio-Semitic people from Eritrea or Northern Ethiopia didn't receive much of additional Arab/Semitic admixture. However, I will move this specific question to the other thread that I didn't notice.

Angela
29-05-20, 18:26
Ok. As far as I know Somalis unlike the Ethio-Semitic people from Eritrea or Northern Ethiopia didn't receive much of additional Arab/Semitic admixture. However, I will move this specific question to the other thread that I didn't notice.

Do you have a source for that, real expert?

It's a topic which interests me.

If you do, perhaps you can post it in the appropriate thread.

I'm going to be discussing the "Tuscan" issue as well.

Maciamo
29-05-20, 18:31
I took the liberty of changing a bit the thread title so that it's easier to find as there are many similar papers on the ancient Levant.

Maciamo
29-05-20, 18:43
The PCA shows that:

- Bronze Age and Iron Age Sidon fitted within the Egyptian & Bedouin cluster.

- In contrast, Iron Age Beirut was much closer to Palestinian & Jordanian cluster. So there were major genetic differences between two Lebanese cities only 40 km apart!

- Medieval and Modern Lebanese fit either within the Palestinian + Jordanian cluster, or are shifted toward Turkish Jews (presumably the Turkish-Caucasian component that came with the Ottoman occupation).


As for the presumed origin of the Sea Peoples, based on the mixture proportions in the paper the best matches are Anatolians (37%) and Mycenaeans (23%). Western Anatolia seems like a reasonable candidate. I wrote back in 2009 in my R1b history that "the Indo-Europeans from the Black Sea shores are excellent candidates for being the mysterious Sea Peoples". I always thought there might have been a connection between the fall of Troy and the subsequent Bronze Age collapse. It's just a personal hypothesis of course, but considering the animosity between the Trojans/Luwians (https://en.wikipedia.org/wiki/Luwians) of NW Anatolia and the Mycenaean Greeks, I can well imagine how Trojan survivors mobilised support of their Luwian cousins to seek revenge on the Greeks, and while they were at it also rampage across the Hittite Kingdom (including the northern Levant) to their immediate east.

Maciamo
29-05-20, 19:03
Here is the haplogroup table from the paper.

https://www.eupedia.com/forum/attachment.php?attachmentid=12119

That confirms that I2a1b-M436 was already in the Levant by the Iron Age. The question is who brought it?

No R1a or R1b, but that's surely because of the small sample size as there is no doubt that the Indo-Iranians (Mitanni) had already brought them to the region. On the other hand the Mitanni Kingdom covered mostly the area of modern Kurdistan, not Lebanon.

Maciamo
29-05-20, 19:11
This mixture table shows that Medieval Lebanese had acquired 2-3% of East African DNA, while Modern Lebanese have an additional 7 to 17% Caucasian.

https://www.eupedia.com/forum/attachment.php?attachmentid=12120

ashraff
29-05-20, 19:14
Hello Maciamo,
What is your opinion on the E-V65 sample in Beirut Hellenic period?
Thanks in advance!

kingjohn
31-05-20, 09:46
Hello Maciamo,
What is your opinion on the E-V65 sample in Beirut Hellenic period?
Thanks in advance!
That is a great question ashraf
I am not sure even maciamo have answere
For it....
Most of e1b1b1 in lebanon are indeed e-m78 derived clades mainly e- v22:thinking:
There are also some e-m123 but mainly in the inland part much much less in costal lebanon ..
To find e-v65 is much less expected this clade is more north west african iberian..( even present in basque groups: araba, western bizkaia ):smile:
https://forwhattheywereweare.files.wordpress.com/2012/03/yhaplogroup_basque.jpg
source: https://academic.oup.com/mbe/article/29/9/2211/1077096

p.s
But maybe e-v65 has a levant branch there are some Palestinians who carry it....
https://www.yfull.com/tree/E-BY8823/

Maciamo
31-05-20, 11:19
Hello Maciamo,
What is your opinion on the E-V65 sample in Beirut Hellenic period?
Thanks in advance!

E-V65 is a North African lineage found from Egypt to Morocco. It is also found in Palestine, Lebanon, Greece, southern Italy, Sicily and Sardinia. Considering that the Levant was under Egyptian rule for nearly 500 years during the New Kingdom period (1550-1069 BCE), then that the Levant and Egypt remained a few more centuries on and off in the same political entity under Assyrian then Persian rule before Alexander's conquest, it is not that surprising that Egyptian lineages should have settled in Lebanon by then.

Regio X
01-06-20, 00:13
Anyone know if these G2a2 lineages are found in Italy or Greece? They come from samples from Beirut in the Early Roman period.
G2a2b-L30
G2a2b1a2-M3302

This one is from the Iron Age.
G2a2a1a2-L91


I wish so many population geneticist didn't totally ignore yDna.G2a2b-L30 is very old (TMRCA of 14400 ybp). It's the most common nowadays in Europe (especially the subclade G2a2b2a1-L140.
G2a2a1a2-L91, Ötzi's, is also very old (TMRCA of 10400 ybp). As you know, it's more common in Sardinia, Corsica etc., but it's also found in Middle East.
G2a2b1a2-M3302 (5800 ybp), under G-M406, is found in Russia, Armenia and Italy (Crotone and Cagliari) according to YFull (https://yfull.com/tree/G-M3302), and also in other European countries according to FTDNA Public Tree (https://www.familytreedna.com/public/y-dna-haplotree/G;name=G-M3302). G-M406 is present in places such Greece and South Italy, yes, but it's more concentrated in Turkey. According to Maciamo's map, there would be hotspots in what seems Dagestan and also in Levant. I don't know exactly when it arrived in Levant, but it was likely in Iron Age. No Gs from BA were found yet neither before that.

https://cache.eupedia.com/images/content/Haplogroup-G2a-M406.png

ashraff
01-06-20, 02:56
E-V65 is a North African lineage found from Egypt to Morocco. It is also found in Palestine, Lebanon, Greece, southern Italy, Sicily and Sardinia. Considering that the Levant was under Egyptian rule for nearly 500 years during the New Kingdom period (1550-1069 BCE), then that the Levant and Egypt remained a few more centuries on and off in the same political entity under Assyrian then Persian rule before Alexander's conquest, it is not that surprising that Egyptian lineages should have settled in Lebanon by then.

Thank you for the answer, but don't you think it could be moved in either way via Mediterranean such as being transported by the Phoenicians in the times of Carthage? Is it possible?, if no, then why?

real expert
02-06-20, 00:10
There is an Egyptian sample from a mother with her son from 500 BC in the Haber paper.


The study suggests that the son of the Egyptian woman had a father who himself was Egyptian-Lebanese.

"Thus, these results suggest that SFI-43 was an Egyptian woman and SFI-44 was her son from a man who himself had both Egyptian and Lebanese ancestries. The structure of this family in
Lebanon highlights population movements and the heterogeneous society that existed at that time, but additional sampling is needed if we are to understand whether this cross-cultural mixing was common or whether our samples were exceptional."

The genetic makeup of this Egyptian woman appears to be similar to those of the Abusir mummies. Surely we can't draw definite conclusions about the ethnicity of the ancient Egyptians from the Old or Middle Kingdom, especially in Upper Egypt from these samples alone.


https://i.imgur.com/4PrI0ie.png

However, for now, it doesn't look good for the Afrocentrists and their Black Egypt myth who btw are much more present and get more support from the media, the film industry, and even universities to promote their openly anti-rational ideas. Something Nordicists can only dream of.

Jovialis
02-06-20, 01:54
Very fascinating paper, I leave for a couple days, and I almost missed these intriguing discoveries.

Goes to show, that because of so much mixing over time, using modern populations in DNA tests can be misleading.

Jovialis
02-06-20, 02:17
https://i.imgur.com/TDyhZbP.png

I would bet in addition to the Anatolian/Caucasian ancestry from the Early Bronze Age, tests like MTA are also picking up this South-Eastern European-like admixture that entered Anatolia in the Iron and Classical ages. Though I don't think I have a direct connection with those people, there is just shared overlapping source ancestry.

Maciamo
04-06-20, 18:01
Thank you for the answer, but don't you think it could be moved in either way via Mediterranean such as being transported by the Phoenicians in the times of Carthage? Is it possible?, if no, then why?

If E-V65 was present in Lebanon during the Phoenician period then it could obviously have been among the lineages that settled in Carthage. But E-V65 is most common in Libya, which wasn't Phoenician, and is also found in Egypt and Morocco, which also weren't colonised by the Phoenicians.

Angela
04-06-20, 20:12
There is an Egyptian sample from a mother with her son from 500 BC in the Haber paper.


The study suggests that the son of the Egyptian woman had a father who himself was Egyptian-Lebanese.

"Thus, these results suggest that SFI-43 was an Egyptian woman and SFI-44 was her son from a man who himself had both Egyptian and Lebanese ancestries. The structure of this family in
Lebanon highlights population movements and the heterogeneous society that existed at that time, but additional sampling is needed if we are to understand whether this cross-cultural mixing was common or whether our samples were exceptional."

The genetic makeup of this Egyptian woman appears to be similar to those of the Abusir mummies. Surely we can't draw definite conclusions about the ethnicity of the ancient Egyptians from the Old or Middle Kingdom, especially in Upper Egypt from these samples alone.


https://i.imgur.com/4PrI0ie.png

However, for now, it doesn't look good for the Afrocentrists and their Black Egypt myth who btw are much more present and get more support from the media, the film industry, and even universities to promote their openly anti-rational ideas. Something Nordicists can only dream of.


Aw...I feel so bad for them.

Anyone who is surprised that some Egyptians might show up in the Levant Bronze Age or even Iron Age, and some admixed people, perhaps, from the Zagros, hasn't done very much reading in the history and archaeology of the Near East. It was, to repeat myself, a very "cosmopolitan" place, a crossroads of the world. Equally, it's well known that there was a period when Egypt was ruled by people from closer to the south, and so they undoutedly carried some more SSA. It depends on the period and how many people came.

It reminds me of the discussions of the remains analyzed in the Antonio et al paper. How on earth could people not expect that people from all over the known world wouldn't show up in the remains. In Late Antiquity, as just one example, you get the remains of people obviously on pilgrimage or something from the north, while in the Imperial Era some will come as merchants or travelers from all over the Mediterranean. Some would have settled, some not. A lot of the dna would get washed out if they did stay. It all depends on the numbers of the incomers.

Once you get into more sophisticated civilizations population genetics gets much more complex. It's not like looking at a bunch of clearly defined Anatolian Neolithic people moving into areas where groups of clearly different Mesolithic hunter gatherers are living.

ashraff
06-06-20, 21:53
That is a great question ashraf
I am not sure even maciamo have answere
For it....
Most of e1b1b1 in lebanon are indeed e-m78 derived clades mainly e- v22:thinking:
There are also some e-m123 but mainly in the inland part much much less in costal lebanon ..
To find e-v65 is much less expected this clade is more north west african iberian..( even present in basque groups: araba, western bizkaia ):smile:


Thank you kingjohn for your answer, I have just seen it :rolleyes2:,
Your expectation is right, the V65 has interesting Variety in Iberia, based on latest results in either in FTDNA or Yfull in General. I have seen most of the Branches under Z1231>V65 seems like to be radiated out of North Spain 4000-5000 years ago as pr Yfull ages.
Unfortunately V65 is not studied well in studies, because all the samples studied in peer reviewed papers focus only on those samples found in North Africa where they belong to a recent branch under V65 i.e E-V1174 aged 1500 years .this is why everyone says it is found only in North Africa, of course there must be ancient branches in North Africa such as PF2159, but it is either non-tested or extinct.
I hope in future, the picture gets more and more clearer!

ashraff
06-06-20, 22:00
If E-V65 was present in Lebanon during the Phoenician period then it could obviously have been among the lineages that settled in Carthage. But E-V65 is most common in Libya, which wasn't Phoenician, and is also found in Egypt and Morocco, which also weren't colonised by the Phoenicians.

Thanks for your answer, Yes, but the branches under E-V65 in Sardinia, Italy and Iberia are higher in Ages than those in North Africa, it exceeds 3000-4000 years, while in North Africa, 99% of the results belong to only one branch under E-V65 aged 1500 years, which indicates a Pan-mediterranian spread of E-V65 branch. I wish E-V65 is studied well in the future!