Can Fst values tell us something about the source of migration from unknown periods ?

[IronSide]

Fst is a measure of population differentiation due to genetic structure, tells you how similar or different two populations are, most of you know it I assume.

These results are from the supplementary tables in Lazaridis et al(2016) "genetic structure of the world's first farmers"

Levant:

	WHG	EHG	Anatolia_N	Levant_N	Natufian	CHG	Iran_N
Levant BA	0.099	0.084	0.019	0.014	0.062	0.057	0.047
Saudi	0.095	0.081	0.026	0.030	0.076	0.056	0.053
Bedouin A	0.089	0.073	0.023	0.026	0.073	0.050	0.045
Syrian	0.085	0.069	0.022	0.028	0.077	0.046	0.042
Yemeni Jew	0.099	0.085	0.029	0.029	0.073	0.060	0.056
Lebanese	0.085	0.068	0.019	0.025	0.075	0.046	0.042
Palestinian	0.089	0.073	0.022	0.027	0.076	0.050	0.046

So it's clear that modern Levantines have more affinity to European hunter-gatherers and CHG compared to the Levant EBA samples from Jordan, Saudi and Yemeni Jews don't seem to have been affected though.

And so it's safe to say some population with higher CHG than Levant BA admixed to the Levant, increased affinity to WHG and EHG may correlate with CHG ancestry since it contains them, notice how Anatolia_N and Levant_N ancestry decreased.

What could be the source of this ancestry?

Iran:

	WHG	EHG	Anatolia_N	Levant_N	Natufian	CHG	Iran_N
Iran Chalcolithic	0.099	0.078	0.027	0.035	0.090	0.037	0.021
Iranian	0.087	0.063	0.027	0.037	0.089	0.038	0.029

Similarly to the Levant, Iranians have more affinity to European hunter-gatherers than the Iranian Chalcolithic, and Iran_N ancestry decreased, the rest stayed the same.

Caucasus & Anatolia:

	WHG	EHG	Anatolia_N	Levant_N	Natufian	CHG	Iran_N
Armenia MLBA	0.082	0.055	0.023	0.034	0.089	0.033	0.036
Armenia	0.088	0.070	0.021	0.031	0.085	0.040	0.040
Georgia	0.091	0.070	0.027	0.039	0.094	0.033	0.041
Turkey	0.081	0.061	0.021	0.032	0.085	0.041	0.040

Armenians have less affinity to European hunter-gatherers than Armenia MLBA samples, and slightly higher ancestry from the Levant, Iran_N and CHG ancestry decreased.

Georgians have less ancestry from the Levant than Armenians and Armenia MLBA, less Anatolia_N, but a higher affinity to CHG,

Turkey has higher levels of affinity to European hunter-gatherers than Armenians and Georgians and similar to MLBA Armenia, and slightly more Levant affinity compared to Middle Bronze Age Armenia.

Europe:

	WHG	EHG	Anatolia_N	Levant_N	Natufian	CHG	Iran_N
Europe LNBA	0.056	0.040	0.025	0.040	0.091	0.050	0.054
Europe MNChl	0.061	0.075	0.012	0.030	0.088	0.071	0.070
Finnish	0.058	0.043	0.036	0.052	0.100	0.058	0.063
German	0.057	0.048	0.025	0.042	0.092	0.052	0.058
Italian North	0.069	0.059	0.016	0.032	0.087	0.051	0.055
English	0.060	0.048	0.026	0.042	0.094	0.053	0.058
Greek	0.073	0.060	0.016	0.031	0.084	0.049	0.050
Spanish	0.062	0.57	0.18	0.34	0.087	0.054	0.058
Russian	0.57	0.41	0.34	0.49	0.099	0.054	0.058

In Europe, general affinity to WHG and EHG seem to have reached maximum levels in the Bronze Age, only to decrease afterward, Finns and Russians still have similar levels to the Bronze Age, North Europeans have more affinity to hunter-gatherers than south Europeans, who have more Anatolian farmer ancestry.

compared to the Middle Neolithic, CHG and EHG affinity increased throughout Europe, due to the Indo European migrations, but they don't correlate, CHG in southern Europeans have similar levels to Northerners but lower levels of EHG affinity, suggesting a secondary source of CHG than the IE migrations.

 

[Ygorcs]

Very interesting! This experiment also seems to me to confirm that there was a relatively high impact of "northern" (with more WHG and especially EHG affinity) migrations - and not just CHG-heavy ones from the Caucasus/Anatolia - into the Levant and probably Mesopotamia, possibly mainly with incursions of Indo-Iranians, Greeks and later Turks. If you compare that region with the much more isolated Arabian Peninsula, the growth of affinity towards WHG/EHG was much more pronounced together with CHG. Most of it must've come from West Asia (Anatolia, South Caucasus and North Iran), but I'd guess some of that came with other documented conquests/migrations.

Besides, about the Arabians (Saudis and Yemeni Jews), I find it surprising that they basically distanced themselves from all populations or remained virtually stable in relation to Levant_BA. So what other admixture introgressed into their gene pool to account for a more or less even differentiation from all those ancient population structures? Or are we to assume that the genetic structure in Arabia was already quite distinct from the Levant in the Bronze Age, and so what we may be seeing is that there was a pre-Semitic expansion indigenous population that was absorbed and changed their makeup, distancing them from Levant_N, Natufian and Anatolia_N, and concomitantly later migrations to the Levant didn't impact Arabia much if at all?

 

[Angela]

Very interesting! This experiment also seems to me to confirm that there was a relatively high impact of "northern" (with more WHG and especially EHG affinity) migrations - and not just CHG-heavy ones from the Caucasus/Anatolia - into the Levant and probably Mesopotamia, possibly mainly with incursions of Indo-Iranians, Greeks and later Turks. If you compare that region with the much more isolated Arabian Peninsula, the growth of affinity towards WHG/EHG was much more pronounced together with CHG. Most of it must've come from West Asia (Anatolia, South Caucasus and North Iran), but I'd guess some of that came with other documented conquests/migrations.

Besides, about the Arabians (Saudis and Yemeni Jews), I find it surprising that they basically distanced themselves from all populations or remained virtually stable in relation to Levant_BA. So what other admixture introgressed into their gene pool to account for a more or less even differentiation from all those ancient population structures? Or are we to assume that the genetic structure in Arabia was already quite distinct from the Levant in the Bronze Age, and so what we may be seeing is that there was a pre-Semitic expansion indigenous population that was absorbed and changed their makeup, distancing them from Levant_N, Natufian and Anatolia_N, and concomitantly later migrations to the Levant didn't impact Arabia much if at all?

Perhaps the difference is that Iran Chl/CHG just didn't impact Arabia as much? Also, I've been struck that the SSA haplogroups in Arabia are predominately mtDna. There's been, I think, a steady drip of what we could call more "southern" ancestry to balance whatever ancestry came from the north. Just a thought.

 

[IronSide]

Very interesting! This experiment also seems to me to confirm that there was a relatively high impact of "northern" (with more WHG and especially EHG affinity) migrations - and not just CHG-heavy ones from the Caucasus/Anatolia - into the Levant and probably Mesopotamia, possibly mainly with incursions of Indo-Iranians, Greeks and later Turks. If you compare that region with the much more isolated Arabian Peninsula, the growth of affinity towards WHG/EHG was much more pronounced together with CHG. Most of it must've come from West Asia (Anatolia, South Caucasus and North Iran), but I'd guess some of that came with other documented conquests/migrations.

Besides, about the Arabians (Saudis and Yemeni Jews), I find it surprising that they basically distanced themselves from all populations or remained virtually stable in relation to Levant_BA. So what other admixture introgressed into their gene pool to account for a more or less even differentiation from all those ancient population structures? Or are we to assume that the genetic structure in Arabia was already quite distinct from the Levant in the Bronze Age, and so what we may be seeing is that there was a pre-Semitic expansion indigenous population that was absorbed and changed their makeup, distancing them from Levant_N, Natufian and Anatolia_N, and concomitantly later migrations to the Levant didn't impact Arabia much if at all?

I believe the earliest population in Arabia was similar to the West Eurasian ancestry in Horn Africans minus say 90% of the African ancestry, the extremely differentiated Bedouin B (highest Southwest Asian) would probably fit this model.

This population would have probably spoken some Afro-Asiatic language, a dialect of Cushitic maybe, and later Semitic pastoralists from the north brought CHG ancestry.

In most ADMIXTURE runs, the components that peaks in Arabians and Horn Africans seem to be the same in Natufians but with less Anatolia Neolithic, I don't know how to explain this.

 

[Ygorcs]

Perhaps the difference is that Iran Chl/CHG just didn't impact Arabia as much? Also, I've been struck that the SSA haplogroups in Arabia are predominately mtDna. There's been, I think, a steady drip of what we could call more "southern" ancestry to balance whatever ancestry came from the north. Just a thought.

Good observation. I also thought that something more African or even Subsaharan African would've distant enough from any of those Eurasian structures to pull Arabians (Saudis and Yemeni Jews) apart from virtually all of them at the same time, and if that was coupled by a lesser impact of HG/Iran_Chalc that would also help explain their mostly stagnant (i.e. continuously more distant) affinity with Anatolian_Neo, EHG and WHG, too.

 

[Ygorcs]

I believe the earliest population in Arabia was similar to the West Eurasian ancestry in Horn Africans minus say 90% of the African ancestry, the extremely differentiated Bedouin B (highest Southwest Asian) would probably fit this model.

This population would have probably spoken some Afro-Asiatic language, a dialect of Cushitic maybe, and later Semitic pastoralists from the north brought CHG ancestry.

In most ADMIXTURE runs, the components that peaks in Arabians and Horn Africans seem to be the same in Natufians but with less Anatolia Neolithic, I don't know how to explain this.

I'd bet on that too: a Cushitic or Cushitic-related indigenous population, much more Natufian and less CHG than Bronze Age Levant. But the fact they share less Anatolia_Neolithic than Natufians is really a puzzle. Maybe they came partly from a more southern Natufian population or even an originally North African Natufian-like population (we know such a population already existed in North Africa even 15,000 years ago) with less shared (or perhaps more diluted) ancestry with Anatolian farmers.

 

[IronSide]

The Sub-Saharan influence in Arabia is exaggerated:

	Yoruba	Mbuti	Ju_hoan_North
Levant BA	0.147	0.201	0.216
Saudi	0.135	0.192	0.209
Bedouin A	0.118	0.176	0.193
Syrian	0.126	0.183	0.201
Yemeni Jew	0.136	0.193	0.209
Lebanese	0.129	0.186	0.203
Palestinian	0.126	0.184	0.201

It's definitely not the reason they seem the most distant, SSA ancestry in higher in Lebanese, Syrians, Palestinians, and Negev Bedouins, it's even exaggerated for them, for example, WHG still shares more with them than the amount Yoruba or Mbuti shares, and we usually think WHG is non-existant in the Levant and Arabia.

 

[Angela]

The Sub-Saharan influence in Arabia is exaggerated:

	Yoruba	Mbuti	Ju_hoan_North
Levant BA	0.147	0.201	0.216
Saudi	0.135	0.192	0.209
Bedouin A	0.118	0.176	0.193
Syrian	0.126	0.183	0.201
Yemeni Jew	0.136	0.193	0.209
Lebanese	0.129	0.186	0.203
Palestinian	0.126	0.184	0.201

It's definitely not the reason they seem the most distant, SSA ancestry in higher in Lebanese, Syrians, Palestinians, and Negev Bedouins, it's even exaggerated for them, for example, WHG still shares more with them than the amount Yoruba or Mbuti shares, and we usually think WHG is non-existant in the Levant and Arabia.

Perhaps using an East African population would be more helpful? It was my understanding that's where most of it comes from, through women from there.

 

[IronSide]

Perhaps using an East African population would be more helpful? It was my understanding that's where most of it comes from, through women from there.

East Africans would indeed share more ancestry with Arabians than West Africans, first I didn't find East African populations in supplementary table 4, and second that affinity is caused by West Eurasian migrations from Arabia.

But that wasn't my point. The premise that they're distant is due to African gene flow is false, because it didn't affect Levantines who have more.

 

[Angela]

East Africans would indeed share more ancestry with Arabians than West Africans, first I didn't find East African populations in supplementary table 4, and second that affinity is caused by West Eurasian migrations from Arabia.

But that wasn't my point. The premise that they're distant is due to African gene flow is false, because it didn't affect Levantines who have more.

West Eurasian gene flow from Arabia into Africa is not responsible for all of the affinity. There's the substantial amount of African mtdna to consider. I think the gene flow went both ways. I don't keep files of every paper, and my memory can certainly be faulty, but I thought Arabia had more of it than the Levant?

I also vaguely recall some analysis of Yemeni dna which postulates quite a bit of relatively recent gene flow.

 

[IronSide]

This is the link to the whole table: https://www.biorxiv.org/highwire/filestream/16360/field_highwire_adjunct_files/3/059311-4.xlsx

In it, you'll find Pairwise Fst of West Eurasian populations who score >=90% West Eurasian at K=3, in addition to some ancient West Eurasian populations, and also a group of East Asian, African, American and Oceanic populations for comparison.

Fst is below and its standard error is above the diagonal.
Values above 0.02, 0.04, and 0.06 are highlighted in color.

We computed squared allele frequency differentiation between all pairs of ancient West Eurasians (Methods; Fig. 3; Extended Data Fig. 3), and found that the populations at the four corners of the quadrangle had differentiation of FST=0.08-0.15, comparable to the value of 0.09-0.13 seen between present-day West Eurasians and East Asians (Han) (Supplementary Data Table 3). In contrast, by the Bronze Age, genetic differentiation between pairs of West Eurasian populations had reached its present-day low levels (Fig. 3): today, FST is ≤0.025 for 95% of the pairs of West Eurasian populations and ≤0.046 for all pairs. These results point to a demographic process that established high differentiation across West Eurasia and then reduced this differentiation over time.

Quoting David Reich from his book:

Today, the peoples of West Eurasia—the vast region spanning Europe, the Near East, and much of central Asia—are genetically highly similar. The physical similarity of West Eurasian populations was recognized in the eighteenth century by scholars who classified the people of West Eurasia as “Caucasoids” to differentiate them from East Asian “Mongoloids,” sub-Saharan African “Negroids,” and “Australoids” of Australia and New Guinea. In the 2000s, whole-genome data emerged as a more powerful way to cluster present-day human populations than physical features.

The whole-genome data at first seem to validate some of the old categories. The most common way to measure the genetic similarity between two populations is by taking the square of the difference in mutation frequencies between them, and then averaging across thousands of independent mutations across the genome to get a precisely determined number. Measured in this way, populations within West Eurasia are typically around seven times more similar to one another than West Eurasians are to East Asians. When frequencies of mutations are plotted on a map, West Eurasia appears homogeneous, from the Atlantic façade of Europe to the steppes of central Asia. There is a sharp gradient of change in central Asia before another region of homogeneity is reached in East Asia.

I say good luck convincing many of the ethnicities in that list that they're similar.

 

[Ygorcs]

The Sub-Saharan influence in Arabia is exaggerated:

	Yoruba	Mbuti	Ju_hoan_North
Levant BA	0.147	0.201	0.216
Saudi	0.135	0.192	0.209
Bedouin A	0.118	0.176	0.193
Syrian	0.126	0.183	0.201
Yemeni Jew	0.136	0.193	0.209
Lebanese	0.129	0.186	0.203
Palestinian	0.126	0.184	0.201

It's definitely not the reason they seem the most distant, SSA ancestry in higher in Lebanese, Syrians, Palestinians, and Negev Bedouins, it's even exaggerated for them, for example, WHG still shares more with them than the amount Yoruba or Mbuti shares, and we usually think WHG is non-existant in the Levant and Arabia.

Okay, I think that's convincing though I think using an East African would've been better (maybe one of the least West Eurasian-admixed sources, mainly south of Kenya, would help). So, what is your main hypothesis for that uniform distancing from virtually all those ancient populations, especially in comparison with the situation of Levant_BA? Do you think the indigenous Pre-Semitic Arabians, those Cushitic-related West Eurasians, had themselves already much less affinity with those populations than the Levantine populations, even though they were also Afro-Asiatic and - I presume - shared a lot of common ancestry with Natufians? Or do you think they were not particularly Natufian-like nor very close to other Levantine/Mesopotamian populations?

 

[IronSide]

Okay, I think that's convincing though I think using an East African would've been better (maybe one of the least West Eurasian-admixed sources, mainly south of Kenya, would help). So, what is your main hypothesis for that uniform distancing from virtually all those ancient populations, especially in comparison with the situation of Levant_BA? Do you think the indigenous Pre-Semitic Arabians, those Cushitic-related West Eurasians, had themselves already much less affinity with those populations than the Levantine populations, even though they were also Afro-Asiatic and - I presume - shared a lot of common ancestry with Natufians? Or do you think they were not particularly Natufian-like nor very close to other Levantine/Mesopotamian populations?

I don't know Ygorcs, in relation to Levant BA it seems they're only different on Anatolia_N, but didn't get any closer to Natufians or CHG, does that mean geneflow outside this group ? maybe, and maybe its East African, if it was that we would expect uniform distancing from all groups and not just Anatolian farmers, right?

 

[Ygorcs]

I don't know Ygorcs, in relation to Levant BA it seems they're only different on Anatolia_N, but didn't get any closer to Natufians or CHG, does that mean geneflow outside this group ? maybe, and maybe its East African, if it was that we would expect uniform distancing from all groups and not just Anatolian farmers, right?

I don't know, maybe I'm misinterpreting things, because as I have understood they got at least a bit more distant from all ancient farmer populations they are compared to: Anatolia_N, Iran_N and even more so Levant_N. They also were pulled significantly apart from Natufian. But it's interesting they became closer to WHG, EHG and CHG, what IMO can be most probably associated with the incoming of Semitic peoples heavy on CHG and, via that, with a bit more affinity to EHG/WHG.

[TABLE="class: cms_table"]
[TR]
[TD]WHG
[/TD]
[TD]EHG[/TD]
[TD]Anatolia_N[/TD]
[TD]Levant_N[/TD]
[TD]Natufian[/TD]
[TD]CHG[/TD]
[TD]Iran_N[/TD]
[/TR]
[/TABLE]
[TABLE="class: cms_table"]
[TR]
[TD]Levant BA
[/TD]
[TD]0.099[/TD]
[TD]0.084[/TD]
[TD]0.019[/TD]
[TD]0.014[/TD]
[TD]0.062[/TD]
[TD]0.057[/TD]
[TD]0.047
[/TD]
[/TR]
[TR]
[TD]Saudi
[/TD]
[TD]0.095
[/TD]
[TD]0.081[/TD]
[TD]0.026[/TD]
[TD]0.030[/TD]
[TD]0.076[/TD]
[TD]0.056[/TD]
[TD]0.053
[/TD]
[/TR]
[/TABLE]