Ancient Egyptians

[GHurier]

Do you mean the massive diversification of mtDNA N and M? I have always found it peculiar how many primary branches there are of N ( around 20) and M (around 50) compared to L3 (Around 7). That is something I feel has been underexplored in popgen research regarding OoA. In a much more attenuated fashion it's sort of true for y-DNA as well, most of CT's splits occurred amongst ancestral Eurasians with just E in Africa.

The number of branch just illustrates that the expansion of humans during OoA was very very fast, a couple of millenia at most to spread N & M mtDNA in many different places from where it evolved separately.
Even now, a lot a direct subclades of M and N appear to be concentrated in limited geographical area on the "southern path".
Whereas the branch who stayed in Africa had less space to expand and produce diversity.

Something that is true for both mtDNA and Y-DNA is that you need "space" to produce diversity, without geographical expansion/migration you can't produce surviving diversity because "old" diversity is regularly replaced by newer diversity producde in situ.
That's why diversity bursts are amazing proxies for migrations/expansions.
M & N gigantic diversity burst just shows the very fast OoA expansion over the entirety of Eurasia.

Also, female lineages are showing less mobility than male lineages, a lot of them appear to be almost "established" since OoA (or post-LGM for Europe). Which probably explains why so many mt-Lineages from that time survived compared to Y-lineages, they faced less competition from nearby geographical regions, whereas Y-lineage had apparently a higher degree of mobility (inducing more competition and replacement).


To come back on what I meant :

By "fixing rate", I mean the probability with which a mutation will be conserved after occuring (many mutation are just lost with time because the concerned lineage is not propagated).
If you have no significant "natural selection" related to a given mutation, then your apparent mutation rate is roughly constent (for Y-DNA it seems to be a descent approach).
Whereas, when natural selection is significantly at play, you can have apparent boost of the mutation rate (because the "environement pressure" will favor the conservation of "positive" mutations helping the population to adapt).
This last scenario fits well with what is seen for mtDNA.

Thus, when you send a population into new harsh living conditions, the lucky ones that will receive favorable mutations will breed efficientely, whereas the others will struggle and likely fail to pass their lineage.
If there is room for significant DNA adaptation to the new living conditions, this effect will boost the apparent mutation rates even if the mutations occurs with the same probability (because some mutations will be positively selected and conserved with a higher probability when randomly occuring).
Once you starts to "maximize" your DNA adaptation to these new conditions, your fixing rate goes back to normal, and thus the "apparent number of mutation with time" is reduced.

For instance, when you compare diversity burst in the Y-tree and the mt-tree, you can get a good temporal "alignement" before N and M or after N and M (for exemple, there is good chances that Y-DNA IJ and mtDNA U lived at roughly the same epoch).
But at the time of N & M (~OoA), these two haplogroup are afected by too many mutations (which de-sinchronize the temporal alignement).
The easiest way to explain that, is by an increased fixing rate induced by natural selection (which make sense considering that humans were significantly changing of life condition) during OoA

[Kale]

What exactly do you mean by point 2., "environmental pressure"?

Natural selection.
For instance, you have a significant increase of the mtDNA fixing rate during the OoA phase.
Which somehow makes sense, as humans needed to adapt to colder environements (a role that you expect mtDNA to contribute).

Do you mean the massive diversification of mtDNA N and M? I have always found it peculiar how many primary branches there are of N ( around 20) and M (around 50) compared to L3 (Around 7). That is something I feel has been underexplored in popgen research regarding OoA. In a much more attenuated fashion it's sort of true for y-DNA as well, most of CT's splits occurred amongst ancestral Eurasians with just E in Africa.

That is an interesting point regarding body heat/cold environment adaption, that does seem like a good possible explanation M/N diversification, however the earliest branch splitting had to have occurred in Southwest Asia, I'm not really sure if climate was ever cold enough there to drive such a strong evolutionary pressure on the mtDNA in that way?

Keep in mind, mt-dna mutates very slowly, on average once every ~2000-2500 years. If M* and N* (with no extra mutations) played a role in the rapid population of Eurasia ~45kbp, then you could have M* and N* present across vast areas, ready to mutate into primary branches at their leisure. 
It's probably a similar story with mt-H. 100+ primary lineages, do we think it really expanded that rapidly? When? H13c already exists in Kotias ~7700BC. It's more likely that unmutated H* was still present at the start of the Neolithic, and that rapid expansion is what allowed so many primary branches of H.

[James100]

Bell Beaker ancestry in the Guanches:

The genomic history of the indigenous people of the Canary Islands (Serrano et al. 2023):

"considering the best-fitting model, the CIP [Guanche] ancestry can be explained as the admixture of Morocco_LN (73.3% ± 2.2%), Morocco_EN (6.9% ± 1.0%), Germany_BB (13.4% ± 1.8%) and Mota (6.4% ± 1.3%). ... Gran Canaria and Lanzarote have the highest Germany_BB contribution (16.2% ± 2.2% and 17.9% ± 3.3%, respectively)."

Supplementary information:

"Two indigenous individuals belong to the R-M269 haplogroup: one from Punta Azul (El Hierro) and one from Guayadeque (Gran Canaria). R-M269 is the most common haplogroup in Western Europe, although it is also found in North Africa in lower frequencies. When ancient individuals were further classified within R-M269, both showed derived SNPs on the branch clustering R-L11 individuals. Although the R-L11 lineage is commonly restricted to Western Europe, it was common in Early Bronze Age populations from Europe and could have reached North Africa with Bronze Age migrations from this region (as implied by the presence of Bell Beaker pottery). Analysis using pathPhynder confirmed previous results as both individuals were placed within the R-L11 branch of the R-M269 haplogroup (R1b1a2a1a)."

https://www.nature.com/articles/s41467-023-40198-w

The demography of the Canary Islands from a genetic perspective (Fregel et al. 2020):

"a European Bronze Age component [in Guanche samples] can be explained by the presence of Bell-Beaker pottery in the North African archaeological record … The presence of lineages that were frequent in Europe during the Bronze Age (H1e1a and H4a1) supports the idea of later migrations in North Africa after the Neolithic period.”

https://academic.oup.com/hmg/article/30/R1/R64/6028725

Takabuti, Thebes (660 BC - 25th/Nubian dynasty) - mtDNA H4a1:

The first reported case of the rare mitochondrial haplotype H4a1 in ancient Egypt (Drousou et al. 2020):

“Takabuti belonged to mitochondrial haplogroup H4a1. … in the archaeological record H4a1 has been reported in sixth–fourteenth century CE remains sourced from the Canary Islands, and three additional ancient DNA samples, two from Bell Beaker and Unetice contexts (2500–1575 BCE) at Quedlinburg and Eulau, both in Saxony-Anhalt, Germany, and one individual from early Bronze Age Bulgaria … Perhaps the most intriguing aspect of our findings, which is of great archaeological interest and importance, is the observation of a predominantly European haplogroup in an Egyptian individual located in Southern Egypt.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7550590/

[James100]

Correct link:

The genomic history of the indigenous people of the Canary Islands (Serrano et al. 2023):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10427657/

[James100]

Ancient H4a1 samples:




https://docs.google.com/spreadsheets/d/1...edit#gid=0

[FormosanAristocrat]

https://twitter.com/Geno_Mena/status/175...2253465773

[Kale]

Whilst not regarding the specific Ancient Egyptian samples discussed here, I do wonder, using the Ancient Egyptian samples currently available, was there a migration from Egypt to the Levant during the bronze age?

right = c('Congo_Mbuti.DG', 'Kenya_Naivasha_PastoralN', 'Levant_N', 'Anatolia_Barcin_N.SG', 'Anatolia_Boncuklu_N.SG', 'Iran_TepeAbdulHosein_N.SG', 'Iran_Wezmeh_N.SG', 'CHG.SG', 'Morocco_OUB002_Epipaleolithic.SG', 'Morocco_SKH001_MN.SG', 'Italy_GrottaContinenza_HG.SG', 'Sweden_StoraForvar_HG.SG', 'RUS_Arkhangelsk_HG.SG', 'Botai.SG', 'Andaman_100BP.SG', 'RUS_Primorsky_DevilsCave_N.SG', 'Peru_RioUncallane_1800BP.SG')
allsnps=TRUE

Jordan_AinGhazal_EBA
Israel_Pekiin_CA 0.355991 0.0613428 5.80331
Iran_HajjiFiruz_CA 0.269605 0.0365082 7.38479
Egypt_AbusirElMeleq_TIP 0.374404 0.0713389 5.24824
Tail: 0.56
Adding Natufian to the right causes no problems except to the snp count, so I left it out.

Israel_Megiddo_IBA
Israel_Pekiin_CA 0.548086 0.0923836 5.93272
Iran_HajjiFiruz_CA 0.142168 0.0518251 2.74324
Egypt_AbusirElMeleq_TIP 0.309746 0.107951 2.86933
Tail: 0.41

Israel_Hazor_MLBA
Israel_Pekiin_CA 0.372889 0.0743569 5.01485
Iran_HajjiFiruz_CA 0.518601 0.0364365 14.2330
Egypt_AbusirElMeleq_TIP 0.108511 0.0824005 1.31687
Tail: 0.25

Israel_Megiddo_MLBA (for whatever reason the tail was a hard fail in the above 3-way setup, but works fine as a mix, qpadm is a fickle mistress)
Israel_Megiddo_IBA 0.324825 0.0802663 4.04685
Israel_Hazor_MLBA 0.675175 0.0802663 8.41169
Tail: 0.23

Israel_TelShadud_MLBA
Israel_Pekiin_CA 0.441232 0.0950402 4.64259
Iran_HajjiFiruz_CA 0.408043 0.0514445 7.93170
Egypt_AbusirElMeleq_TIP 0.150725 0.106174 1.41960
Tail: 0.45

Israel_Ashkelon_LBA
Israel_Pekiin_CA 0.398622 0.0833343 4.78341
Iran_HajjiFiruz_CA 0.591018 0.0470284 12.5672
Egypt_AbusirElMeleq_TIP 0.0103603 0.0952887 0.108726
Tail: 0.52

Jordan_Baqah_LBA
Israel_Pekiin_CA 0.361628 0.0391785 9.23026
Iran_HajjiFiruz_CA 0.495606 0.0220498 22.4766
Egypt_AbusirElMeleq_TIP 0.142766 0.0427415 3.34022
Tail: 0.07

Israel_Ashkelon_IA
Israel_Pekiin_CA 0.217220 0.0724622 2.99770
Iran_HajjiFiruz_CA 0.493432 0.0419030 11.7756
Egypt_AbusirElMeleq_TIP 0.289348 0.0780089 3.70916
Tail: 0.46

Israel_Megiddo_IA
Israel_Pekiin_CA 0.273054 0.0923682 2.95615
Iran_HajjiFiruz_CA 0.490651 0.0536703 9.14193
Egypt_AbusirElMeleq_TIP 0.236295 0.102020 2.31616
Tail: 0.56

Israel_AbelBethMaacah_IA
Israel_Pekiin_CA 0.330092 0.0889799 3.70974
Iran_HajjiFiruz_CA 0.463142 0.0509514 9.08987
Egypt_AbusirElMeleq_TIP 0.206766 0.0964423 2.14394
Tail: 0.19

[Qrts]

Whilst not regarding the specific Ancient Egyptian samples discussed here, I do wonder, using the Ancient Egyptian samples currently available, was there a migration from Egypt to the Levant during the bronze age?

Hardly the case with all that we know about the social dynamics of BA Levantine communities. (strong nomadic pastoralist presence, group differentiation, higher endogamy etc.) Unless the migration took place well before ~3500 BC since that's when the oldest Levant BA-like sample pops up in Batman. 

In all likeliness the higher Natufian/PPNB is the result of a cline straddling between Jordan EBA and Alalakh MLBA (more ANF). Megiddo IBA & Jordan EBA represent the population of Palestine and Transjordan in the EBA-IBA; then the Amorites (Alalakh MLBA/Kilis MBA types) move into Palestine sometime in the MBA and replace slightly more than half of the former genepool, forming Megiddo MLBA/Hazor MLBA/Jordan LBA types. That's also most likely where the J2a (J-M92) and R1b in Megiddo came from.

[ilabv]

Whilst not regarding the specific Ancient Egyptian samples discussed here, I do wonder, using the Ancient Egyptian samples currently available, was there a migration from Egypt to the Levant during the bronze age?

right = c('Congo_Mbuti.DG', 'Kenya_Naivasha_PastoralN', 'Levant_N', 'Anatolia_Barcin_N.SG', 'Anatolia_Boncuklu_N.SG', 'Iran_TepeAbdulHosein_N.SG', 'Iran_Wezmeh_N.SG', 'CHG.SG', 'Morocco_OUB002_Epipaleolithic.SG', 'Morocco_SKH001_MN.SG', 'Italy_GrottaContinenza_HG.SG', 'Sweden_StoraForvar_HG.SG', 'RUS_Arkhangelsk_HG.SG', 'Botai.SG', 'Andaman_100BP.SG', 'RUS_Primorsky_DevilsCave_N.SG', 'Peru_RioUncallane_1800BP.SG')
allsnps=TRUE

Jordan_AinGhazal_EBA
Israel_Pekiin_CA        0.355991 0.0613428 5.80331
Iran_HajjiFiruz_CA      0.269605 0.0365082 7.38479
Egypt_AbusirElMeleq_TIP 0.374404 0.0713389 5.24824
Tail: 0.56
Adding Natufian to the right causes no problems except to the snp count, so I left it out.

Israel_Megiddo_IBA
Israel_Pekiin_CA        0.548086 0.0923836 5.93272
Iran_HajjiFiruz_CA      0.142168 0.0518251 2.74324
Egypt_AbusirElMeleq_TIP 0.309746 0.107951  2.86933
Tail: 0.41

Israel_Hazor_MLBA
Israel_Pekiin_CA        0.372889 0.0743569  5.01485
Iran_HajjiFiruz_CA      0.518601 0.0364365 14.2330
Egypt_AbusirElMeleq_TIP 0.108511 0.0824005  1.31687
Tail: 0.25

Israel_Megiddo_MLBA (for whatever reason the tail was a hard fail in the above 3-way setup, but works fine as a mix, qpadm is a fickle mistress)
Israel_Megiddo_IBA 0.324825 0.0802663 4.04685
Israel_Hazor_MLBA  0.675175 0.0802663 8.41169
Tail: 0.23

Israel_TelShadud_MLBA
Israel_Pekiin_CA        0.441232 0.0950402 4.64259
Iran_HajjiFiruz_CA      0.408043 0.0514445 7.93170
Egypt_AbusirElMeleq_TIP 0.150725 0.106174  1.41960
Tail: 0.45

Israel_Ashkelon_LBA
Israel_Pekiin_CA        0.398622  0.0833343  4.78341
Iran_HajjiFiruz_CA      0.591018  0.0470284 12.5672 
Egypt_AbusirElMeleq_TIP 0.0103603 0.0952887  0.108726
Tail: 0.52

Jordan_Baqah_LBA
Israel_Pekiin_CA        0.361628 0.0391785  9.23026
Iran_HajjiFiruz_CA      0.495606 0.0220498 22.4766
Egypt_AbusirElMeleq_TIP 0.142766 0.0427415  3.34022
Tail: 0.07

Israel_Ashkelon_IA
Israel_Pekiin_CA        0.217220 0.0724622  2.99770
Iran_HajjiFiruz_CA      0.493432 0.0419030 11.7756
Egypt_AbusirElMeleq_TIP 0.289348 0.0780089  3.70916
Tail: 0.46

Israel_Megiddo_IA
Israel_Pekiin_CA        0.273054 0.0923682 2.95615
Iran_HajjiFiruz_CA      0.490651 0.0536703 9.14193
Egypt_AbusirElMeleq_TIP 0.236295 0.102020  2.31616
Tail: 0.56

Israel_AbelBethMaacah_IA
Israel_Pekiin_CA        0.330092 0.0889799 3.70974
Iran_HajjiFiruz_CA      0.463142 0.0509514 9.08987
Egypt_AbusirElMeleq_TIP 0.206766 0.0964423 2.14394
Tail: 0.19

Yes, during the Early Bronze Age c. 3700 BC

Closest sample to this migration is I4521

Then another migration by Amorites c. 2200 BC during the 1st Intermediate Period

[Kale]

1) Hardly the case with all that we know about the social dynamics of BA Levantine communities. (strong nomadic pastoralist presence, group differentiation, higher endogamy etc.) Unless the migration took place well before ~3500 BC since that's when the oldest Levant BA-like sample pops up in Batman. 

2) In all likeliness the higher Natufian/PPNB is the result of a cline straddling between Jordan EBA and Alalakh MLBA (more ANF).

3) Megiddo IBA & Jordan EBA represent the population of Palestine and Transjordan in the EBA-IBA; then the Amorites (Alalakh MLBA/Kilis MBA types) move into Palestine sometime in the MBA and replace slightly more than half of the former genepool, forming Megiddo MLBA/Hazor MLBA/Jordan LBA types. That's also most likely where the J2a (J-M92) and R1b in Megiddo came from.

1) Batman rejects Egypt and Natufian as third sources
Mesopotamia_Batman_LCA
Israel_Pekiin_CA 0.276086 0.0548299 5.03532
Iran_HajjiFiruz_CA 0.723914 0.0548299 13.2029
Tail: 0.11

2) It doesn't appear to be Natufian/PPNB. Like I said I can put Natufian in the right and things are fine, except the snp count. If given the choice between Natufian and Egpyt, they choose Egypt. The model fails if Natufian is in the right, and Levant_N is moved to the left (to replace Egypt).
Jordan_AinGhazal_EBA
Israel_Pekiin_CA 0.336252 0.0734797 4.57612
Iran_HajjiFiruz_CA 0.297548 0.0943283 3.15439
Natufian 0.0322743 0.0905311 0.356500
Egypt_AbusirElMeleq_TIP 0.333925 0.151853 2.19901
Tail: 0.42

3) Agreed.

[Woz]

One paper that had access to a neolithic Egyptian sample described it as pretty much a straightforward Natufian pastoralist, if I remember correctly. Those Bronze Age Egyptians were just a mixture of Natufian pastoralists, Natufian-Anatolian mixed neolithic farmers (Levant PPNB/PPNC like), with a large dollop Mesopotamian on top.

It's likely that the Naqada I period in Egyptian (pre-)history just reflects an ongoing movement of people from the Fertile Crescent into Egypt in the 4th millenium BC, bringing significant amounts of ISR_C like (Ghassoulian?) ancestry into Egypt (itself a mixture of roughly 75% Levantine Neolithic and 25% Mesopotamian). Naqada II might have been a Mesopotamian horde invasion for all we know.

It's likely that Ancient Egyptians derived a major part of their ancestry (perhaps over 50%) not from the Neolithic, and certainly not from the Epipaleolithic, but from the Chalcolithic to early Bronze Age (i.e. 4th millenium BC) arrivals from the Fertile Crescent, all bringing varying but substantial amounts of Mesopotamian ancestry into the country. If that's correct, then so much for the "indigenousness" of Ancient Egypt.

[James100]

Do you think the ancient Egyptian samples will ever be published?

Quite frankly what the f**k is going on.

[Kale]

I know this is achronological, but I thought it was interesting...
right = c('Congo_Mbuti.DG', 'Kenya_Naivasha_PastoralN', 'Levant_N', 'Anatolia_Barcin_N.SG', 'Anatolia_Boncuklu_N.SG', 'Iran_TepeAbdulHosein_N.SG', 'Iran_Wezmeh_N.SG', 'CHG.SG', 'Morocco_OUB002_Epipaleolithic.SG', 'Italy_GrottaContinenza_HG.SG', 'Sweden_StoraForvar_HG.SG', 'RUS_Arkhangelsk_HG.SG', 'Botai.SG', 'Andaman_100BP.SG', 'RUS_Primorsky_DevilsCave_N.SG', 'Peru_RioUncallane_1800BP.SG')
allsnps=TRUE

Morocco_SKH001_MN.SG
Egypt_AbusirElMeleq_TIP 1.43513 0.371019 3.86807
Jordan_AinGhazal_EBA -0.822839 0.369308 -2.22805
Morocco_KTG_EN.SG 0.329685 0.0870374 3.78785
Morocco_IAM_EN.SG 0.0580262 0.0276025 2.10221
Tail: 0.64

Morocco_SKH002_MN.SG
Egypt_AbusirElMeleq_TIP 1.46803 0.412393 3.55979
Jordan_AinGhazal_EBA -0.765034 0.389156 -1.96588
Morocco_KTG_EN.SG 0.127951 0.0899497 1.42247
Morocco_IAM_EN.SG 0.169053 0.0276662 6.11046
Tail: 0.32

The paper that published the SKH samples was called "Northwest African Neolithic initiated by migrants from Iberia and Levant"
First chronologically is IAM (local), then KTG (Iberia), then ergo SKH is Levant (+the previous 2 waves).
If they came from the Levant, they passed through Egypt, so could this be a hint of what Egypt looked like 4500BC or so?
Abusir minus Jordan_EBA? Or rather Abusir = Egypt (~4500BC) + Jordan_EBA?

Egypt_AbusirElMeleq_TIP
Morocco_SKH001_MN.SG 0.744731 0.207946 3.58136
Morocco_KTG005_EN.SG -0.276062 0.114293 -2.41538
Jordan_AinGhazal_EBA 0.531331 0.109996 4.83044
Tail: 0.54

[Woz]

Around 4500 BC there were still surprisingly few farming communities in Egypt (compared to even Europe, to say nothing of the Near East). The region was probably dominated by pastoralists. The Green Sahara was drying and those pastoralists could've been a fairly diverse bunch drawn to the river from all over: Natufian at the core, but with all sorts of N African and SSA admixtures. Just my guess.

[TanTin]

There are several Egyptian samples:

2472 JK2888 JK2888 1573 tooth 2017 ScheunemannNatureCommunications2017 Direct: IntCal20 1997 43 151 calBCE - 23 calCE (2050±24 BP, MAMS-23575) .. Egypt_Ptolemaic_contam

2473 JK2134 JK2134 1605 .. 2017 ScheunemannNatureCommunications2017 Direct: IntCal20 2609 72 787-546 calBCE (2522±24 BP, MAMS-23047) .. Egypt_ThirdIntermediatePeriod Abusir-el Meleq Egypt

2474 JK2911 JK2911 1609 .. 2017 ScheunemannNatureCommunications2017 Direct: IntCal20 2602 70 779-544 calBCE (2513±24 BP, MAMS-23617) .. Egypt_ThirdIntermediatePeriod Abusir-el Meleq Egypt


- the first one could be somehow related to greek- macedonians as it is from Ptolemaic time. But the other 2 are most likely Egyptians.

Therefore we have some data for the ancient Egyptians.