The genomic history of southeastern Europe-Mathiesen et al

[IronSide]

The source of Eurasian ancestry in Toubou and Ethiopians is likely separate since the Eurasian ancestry in Luxmanada is specifically described as lacking ancestry from Farmers from Anatolia (So EEF/Sardinian like groups).
Is there any evidence of Natufian like ancestry in LBK? The ultimate source of haplogroup T could be somewhere near the Levant.

Any Natufian like ancestry in Neolithic Europe is from their origin in Anatolia, 34% of Anatolian farmers ancestry is Levant Neolithic like, that would mean 22% Natufian. Most Natufian signals in Southern Europe is from this source.

 

[holderlin]

Any Natufian like ancestry in Neolithic Europe is from their origin in Anatolia, 34% of Anatolian farmers ancestry is Levant Neolithic like, that would mean 22% Natufian. Most Natufian signals in Southern Europe is from this source.

Was just going to post this. Shows up in admixture and formal stats.

 

[Govan]

Tubus have Berber admixture , this explain their mtdna H , possible ydna T1 and genetic affinity to Iberian/Sardinian farmers. It's mostly those in Chad neighbouring Chadics have higher Rv88 , those in Libya much less, more E1b1b. In the Sahel , populations are so mixed to each other that both Chadics and non-Chadics show Rv88. However Eurasian ancestry is all seperate thing together it generally appears significantly only in pastoralists groups ( Toubu , Fulanis , Bagaras) while most Chadic-speakers with maximum R1b are compact sendatary populations.

 

[Angela]

Any Natufian like ancestry in Neolithic Europe is from their origin in Anatolia, 34% of Anatolian farmers ancestry is Levant Neolithic like, that would mean 22% Natufian. Most Natufian signals in Southern Europe is from this source.

So we've been saying here since the paper came out, but you'll never convince some people. Some of it may also have been part of later migrations. Mycenaeans had about 5% additional Levant Neolithic I think. Other groups may have had more.

 

[IronSide]

So we've been saying here since the paper came out, but you'll never convince some people. Some of it may also have been part of later migrations. Mycenaeans had about 5% additional Levant Neolithic I think. Other groups may have had more.

Everyone in West Eurasia received admixture from the four (WHG, EHG, Natufian, IranNeo), everyone received Natufian, and everyone received WHG and EHG, even in the Middle East, geneflow has always been bidirectional, this reduced the genetic differentiation overtime.

You can see Fst values decrease over time in each region for all four most differentiated Holocene populations, its interesting that in the Eurasian Steppe and the Levant, relatedness to EHG and Natufians decreased in favor of the other components.

 

[Alpenjager]

The source of Eurasian ancestry in Toubou and Ethiopians is likely separate since the Eurasian ancestry in Luxmanada is specifically described as lacking ancestry from Farmers from Anatolia (So EEF/Sardinian like groups).

Is there any evidence of Natufian like ancestry in LBK? The ultimate source of haplogroup T could be somewhere near the Levant.

The unique T found in the ancient Levant is T1(xT1a) = T1b. This is found in PPNB not in Mesolithic Levant together with an increased EEF influx into the Levant populations not previously found in Mesolithic Natufians. So it is believed that this T1b branch came from further North. Eastern Black sea or Aegean sea. T1b is not found in Ancient remains from Europe, only T1a, so this Neolithic lineage in PPNB is not ancestral to those found in Europe.

 

[Ygorcs]

Tubus have Berber admixture , this explain their mtdna H , possible ydna T1 and genetic affinity to Iberian/Sardinian farmers. It's mostly those in Chad neighbouring Chadics have higher Rv88 , those in Libya much less, more E1b1b. In the Sahel , populations are so mixed to each other that both Chadics and non-Chadics show Rv88. However Eurasian ancestry is all seperate thing together it generally appears significantly only in pastoralists groups ( Toubu , Fulanis , Bagaras) while most Chadic-speakers with maximum R1b are compact sendatary populations.

If that "Berber admixture" has really closer genetic affinities to Iberian and Sardinian farmers, then they definitely also mixed with the European or maybe (I think this is less probable) Northern Near Eastern (Northwest Anatolian?) immigrants.

The native Berbers were certainly much older than the later big mixing between Anatolian_Neolithic and Levant_Neolithic that would've made their Near Eastern ancestors more related to Sardinians, since they have some minor but important Ancient Subsaharan African ancestry, their autosomal and Y-DNA makeup "smells" much more of Neolithic Levant (then without much EEF-like admixture), and since Proto-Berber is very divergent in relation to Semitic and probably was already evolving in North Africa by the mid to late Neolithic, possibly even earlier than 4,000-4,500 BC.

I find it much more likely that the Proto-Berbers themselves were totally Levant_Neolithic plus some Subsaharan African already dwelling in North Africa, and then they mixed a lot with European_Neolithic newcomers, while some groups (present-day Chadic speakers, especially the nomad pastoralists) migrated further and/or developed through relative isolation their own genetic makeup and distinctive linguistic identity (maybe they were the ones who mixed with the "other", probably earlier Near Easterners in North Africa, the Chadic speakers - I say "earlier" because Chadic is much more divergent and glottochronologically much older than others in comparison with the Afro-Asiatic languages near the Levant).

 

[Promenade]

The unique T found in the ancient Levant is T1(xT1a) = T1b. This is found in PPNB not in Mesolithic Levant together with an increased EEF influx into the Levant populations not previously found in Mesolithic Natufians. So it is believed that this T1b branch came from further North. Eastern Black sea or Aegean sea. T1b is not found in Ancient remains from Europe, only T1a, so this Neolithic lineage in PPNB is not ancestral to those found in Europe.

Thanks for the info guys, any idea how Natufian ancestry entered East Africa relatively recently without introducing any EEF or CHG ancestry as well?

 

[Angela]

The Ewan Calloway paper of 2015 had to be corrected. The "European farmer like ancestry" did not spread throughout Africa.
This is about the original uncorrected paper. It's fine except for when they talk about expansion, and when they talk about Neanderthal in Africans.

Bottom line, it moved into the Horn of Africa 9,000 years ago, before there was large scale mingling with more Iran Neo people in the ancient Near East.

See:
https://www.nature.com/news/first-ancient-african-genome-reveals-vast-eurasian-migration-1.18531

That wasn't the last such migration, however.

Hodgson et al:2014
"Early Back to Africa Migration into the Horn of Africa"
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004393

We're talking of waves of migration.

"Populations in the Horn of Africa (HOA: Ethiopia, Eritrea, Djibouti, and Somalia) have substantial non-African ancestry [11]–[15]. The most recent genomic studies estimate 30–50% non-African ancestry in the Cushitic and Semitic speaking populations of the HOA resulting primarily from admixture around 3 ka [16], [17]. This timeframe corresponds to the estimated time of origin of the Ethiosemitic languages [18] and there are some carved inscriptions in South Arabian scripts associated with temple ruins and ritual items in South Arabian styles dated to the early first millennium BCE in the north Ethiopian highlands [19]–[23]. These linguistic and archaeological connections have been cited in the recent population genomic studies to support a hypothesis of high levels of non-African migration into the HOA around 3 ka.However, more recent archaeological research shows that non-African influences in the HOA were limited and transient. Of the early first millennium BCE inscriptions in non-African scripts complete enough to identify a language, only a small proportion are written in a non-African (South Arabian) language - the majority are written in indigenous proto-Ge'ez [24]. In the HOA, architecture with non-African (primarily South Arabian) elements is entirely monumental or ritual [25] and ritual items with exclusively non-African elements are rare [26]. There are few to no indications of non-African material culture in everyday objects: the ceramics and lithics found outside of the ritual context are almost entirely indigenous with clear local precedents [24], [25], [27]. While earlier scholarship conceived of a South Arabian origin D'MT polity with sovereignty over much of the northern HOA, it is now clear that this polity, if it ever existed at all as an integrated state [24], was geographically restricted to the regions around Yeha and Aksum in what is now the Tigray region of Ethiopia [25]. Artifacts with non-African features are effectively absent in the material culture (ritual or otherwise) of contemporaneous populations in the Eritrean highlands on the Asmara plateau (the “Ancient Ona”) [25], [28], [29]. Prior to the first millennium BC, the archaeology of the HOA is less well studied, but what is available shows no substantial non-African material culture beyond trade relations [25]. Taken all together, the archaeological data could be consistent with limited non-African (primarily South Arabian) migration into the north Ethiopian highlands at the outset of the first millennium BCE, but cannot support large-scale population movements from any foreign population.
Archaeological data indicate trade between the HOA and Arabia by at least 8 ka [30], [31] and genetic analyses of mitochondrial and Y chromosome data suggest much earlier migrations into the HOA. Mitochondrial data are suggestive of as many as three waves of prehistoric non-African migration into the HOA. First, HOA populations carry several unique M1 lineages of the otherwise South and East Asian mitochondrial haplogroup M [13], [32]–[34]. Many of these HOA M1 lineages have deep roots, diverging from M1 representatives elsewhere 20–30 ka [34]–[36]. Second, representatives of N1a and N2a in the HOA diverged from their most closely related haplotypes in the Middle East and the Caucasus 15–20 ka [37]. Third, in the Eurasian mitochondrial HV1 and R0a lineages there are several sub-haplogroups (HV1a3, HV1b1, R0a2b, R0a2g) that are found in both the HOA and the Arabian Peninsula. Within these shared sub-haplogroup lineages, the HOA and Arabian haplotypes are distinct, suggesting that the migration that brought these lineages into the HOA happened soon after the sub-haplogroups began to diversify at 6–10 ka [38], [39].
Y chromosome data are also suggestive of at least two episodes of non-African migration into the HOA prior to 3 ka. First, HOA populations carry E-M78 Y chromosomes at high frequencies [40], [41]. E-M78 originated in northeastern Africa around 19 ka with a descendant lineage (E-V32) unique to the HOA that arrived by at least 6 ka [41]. Because northern African populations in this timeframe are inferred to have substantial non-African ancestry [42], [43], the expansion south of E-M78 could have introduced non-African ancestry into the HOA prior to 6 ka. Second, some HOA populations carry moderate to high frequencies of T-M70 (previously K2-M70) Y chromosomes [44]–[46]. The T haplogroup originated in the area of the Levant approximately 21 ka and the T-M70 sub-haplogroup was present in northeast Africa by at least 14 ka, possibly arriving in the HOA as early as 5 ka [44], [45], [47]."

 

[AdeoF]

If that "Berber admixture" has really closer genetic affinities to Iberian and Sardinian farmers, then they definitely also mixed with the European or maybe (I think this is less probable) Northern Near Eastern (Northwest Anatolian?) immigrants.

The native Berbers were certainly much older than the later big mixing between Anatolian_Neolithic and Levant_Neolithic that would've made their Near Eastern ancestors more related to Sardinians, since they have some minor but important Ancient Subsaharan African ancestry, their autosomal and Y-DNA makeup "smells" much more of Neolithic Levant (then without much EEF-like admixture), and since Proto-Berber is very divergent in relation to Semitic and probably was already evolving in North Africa by the mid to late Neolithic, possibly even earlier than 4,000-4,500 BC.

I find it much more likely that the Proto-Berbers themselves were totally Levant_Neolithic plus some Subsaharan African already dwelling in North Africa, and then they mixed a lot with European_Neolithic newcomers, while some groups (present-day Chadic speakers, especially the nomad pastoralists) migrated further and/or developed through relative isolation their own genetic makeup and distinctive linguistic identity (maybe they were the ones who mixed with the "other", probably earlier Near Easterners in North Africa, the Chadic speakers - I say "earlier" because Chadic is much more divergent and glottochronologically much older than others in comparison with the Afro-Asiatic languages near the Levant).

I really do understand that even in my admixture it makes sense and shows that

 

[Promenade]

Bottom line, it moved into the Horn of Africa 9,000 years ago, before there was large scale mingling with more Iran Neo people in the ancient Near East.

If this were true it means that a west Eurasian like people existed somewhere in the Horn of Africa or further north relatively isolated for millennia before they spread out since the Ethiopian hunter gatherer from around 2500bc lacked any west Eurasian ancestry as do all the other ancient east africans. Autosomally it does not even appear until around 1200bc with Luxmanda in Tanzania, so a large group (mind you Luxmanda was modeled as over 1/3rd Natufian) of people harboring Natufian ancestry must have spread across east Africa some time between 2500 and 1200bc, very likely introducing Pastorilism and Chushitic languages.

 

[Alpenjager]

If this were true it means that a west Eurasian like people existed somewhere in the Horn of Africa or further north relatively isolated for millennia before they spread out since the Ethiopian hunter gatherer from around 2500bc lacked any west Eurasian ancestry as do all the other ancient east africans. Autosomally it does not even appear until around 1200bc with Luxmanda in Tanzania, so a large group (mind you Luxmanda was modeled as over 1/3rd Natufian) of people harboring Natufian ancestry must have spread across east Africa some time between 2500 and 1200bc, very likely introducing Pastorilism and Chushitic languages.

As we know T-M184 is the most widespread Eurasian lineage in East Africa, I will give you some details. T1a1a2 in Northern Somalis belonging to Dirs and Garhajis (perhaps also other Isaaq Tribes) belongs to a T1a1a2 subclade most probably coming from Arabian Peninsula Red Sea coast. But this lineage doesn't seems to match those found further south and west in Africa. So there should be at least two different T-M184 waves into East Africa If not more. This mean, that there should be different Eurasian autosomal influxes.

 

[Angela]

We were discussing the Balkan Bronze age samples and the Iron Age one as well on the thread about the Varna "King".

Based on the pca, Eastara posted the following, which looks correct to me.

"As far as I can see Varna are the red outlined orange squares and probably only Varna outlier, who has more Yamnaya [compared to the other Varna samples] falls over the Tuscans. In fact the Balkan Bronze age (blue filled red circles) is all over the Tuscans.''

(As one of our posters pointed out, the coverage of the Varna "King" is poorer than that of Varna outlier, so we don't know if the "King" might have had more "steppe", but imo it's more likely he didn't, as most of it seems to arrive in the Bronze Age. Perhaps, as well, there is some ambiguity in the dating and the Varna Outlier should be dated later.)



This is from a poster on another forum who sees Vucedol as close to modern North Italians, but doesn't see Balkan Bronze Age as close to modern Tuscans.

"Using the Global25 data, I relabelled the samples with the more precise culture labels from Mathieson's paper and then placed them on a Neighbour Joining Tree with local populations: https://imgur.com/a/tm6ce

Results: A few of the Croatian Vucedol and EMBA / LBA samples sit with North Italians (Bergamo) while most Balkans_BA from Bulgaria sit either with early Neolithic or in a "no man's land" between Sardinians and North Italians. https://imgur.com/a/tm6ce

(Certainly no where near enough WHG rich Middle Neolithic ancestry to sit too near to the Basques.) One Bulgarian sample (I2165) is probably by chance sitting fairly near recent Bulgarians, Serbs, Romanians.

We'd probably reasonably expect the Croatians of this time to tend to be North Italian like (it's not too far from Bergamo to Croatia and closer than to Bulgaria?), until they get more admixture from whatever expanding genetic wave links Baltic BA / Balts / Slavs / Hungarians.

Judging from the position of the Bulgaria_IA, the Bronze Age Bulgarians would need more Mycenaean/Anatolia_BA-like ancestry to get to there, and then more of the Balt-Slav / Baltic BA type ancestry to get to present day position."


So, what to make of it? Just a difference because of different methodology? Even just in terms of PCAs, I think Northern Italians are quite a bit "north" of Vucedol, and closer to Balkan Bronze Age, and Balkan Bronze Age is indeed pretty close to Tuscans. The Balkan Iron Age sample is pretty close to Mycenaeans, which are close to Southern Italians/Sicilians. The Balkan one looks more "western" but equally "south".

Of course, this doesn't mean all of Northern Italy never changed since that era. There could have been meanderings back and forth. Interesting none the less.

 

[Ownstyler]

When you keep using terms like "more northern" or "more western" are you referring to the typical genetic profiles of northern and western Europe today, one specific point in time, or whatever time the sample comes from? I think it would be more useful to use specific populations like WHG, Scandinavians, Minoans, etc.

 

[bicicleur 2]

We were discussing the Balkan Bronze age samples and the Iron Age one as well on the thread about the Varna "King".

Based on the pca, Eastara posted the following, which looks correct to me.

"As far as I can see Varna are the red outlined orange squares and probably only Varna outlier, who has more Yamnaya [compared to the other Varna samples] falls over the Tuscans. In fact the Balkan Bronze age (blue filled red circles) is all over the Tuscans.''

(As one of our posters pointed out, the coverage of the Varna "King" is poorer than that of Varna outlier, so we don't know if the "King" might have had more "steppe", but imo it's more likely he didn't, as most of it seems to arrive in the Bronze Age. Perhaps, as well, there is some ambiguity in the dating and the Varna Outlier should be dated later.)



This is from a poster on another forum who sees Vucedol as close to modern North Italians, but doesn't see Balkan Bronze Age as close to modern Tuscans.

"Using the Global25 data, I relabelled the samples with the more precise culture labels from Mathieson's paper and then placed them on a Neighbour Joining Tree with local populations: https://imgur.com/a/tm6ce

Results: A few of the Croatian Vucedol and EMBA / LBA samples sit with North Italians (Bergamo) while most Balkans_BA from Bulgaria sit either with early Neolithic or in a "no man's land" between Sardinians and North Italians. https://imgur.com/a/tm6ce

(Certainly no where near enough WHG rich Middle Neolithic ancestry to sit too near to the Basques.) One Bulgarian sample (I2165) is probably by chance sitting fairly near recent Bulgarians, Serbs, Romanians.

We'd probably reasonably expect the Croatians of this time to tend to be North Italian like (it's not too far from Bergamo to Croatia and closer than to Bulgaria?), until they get more admixture from whatever expanding genetic wave links Baltic BA / Balts / Slavs / Hungarians.

Judging from the position of the Bulgaria_IA, the Bronze Age Bulgarians would need more Mycenaean/Anatolia_BA-like ancestry to get to there, and then more of the Balt-Slav / Baltic BA type ancestry to get to present day position."


So, what to make of it? Just a difference because of different methodology? Even just in terms of PCAs, I think Northern Italians are quite a bit "north" of Vucedol, and closer to Balkan Bronze Age, and Balkan Bronze Age is indeed pretty close to Tuscans. The Balkan Iron Age sample is pretty close to Mycenaeans, which are close to Southern Italians/Sicilians. The Balkan one looks more "western" but equally "south".

Of course, this doesn't mean all of Northern Italy never changed since that era. There could have been meanderings back and forth. Interesting none the less.

IMO there were multiple incursions from the steppe into the Balkans, and even more into the Carpathian Basin, but not many yet by the time of the 'Varna king'
Vucedol is one of them, and I believe some of it ended up into northern Italy as well
the Carpathian Basin was a transit room between the steppe and northern Europe and northern Italy as well
it was probably Unetice who first controlled the whole amber trade route from the Baltic till the Carpathian Basin where others took over toward the Aegean
they were traders who tried to get hold of the trade routes by force, in the same tradition as the Bell Beaker people

 

[zanipolo]

The unique T found in the ancient Levant is T1(xT1a) = T1b. This is found in PPNB not in Mesolithic Levant together with an increased EEF influx into the Levant populations not previously found in Mesolithic Natufians. So it is believed that this T1b branch came from further North. Eastern Black sea or Aegean sea. T1b is not found in Ancient remains from Europe, only T1a, so this Neolithic lineage in PPNB is not ancestral to those found in Europe.

what can be T1b ? as xT1a = T1a1, T1a2 and T1a3

 

[Angela]

When you keep using terms like "more northern" or "more western" are you referring to the typical genetic profiles of northern and western Europe today, one specific point in time, or whatever time the sample comes from? I think it would be more useful to use specific populations like WHG, Scandinavians, Minoans, etc.

I was referring to the PCA directly below my comment.

 

[Angela]

IMO there were multiple incursions from the steppe into the Balkans, and even more into the Carpathian Basin, but not many yet by the time of the 'Varna king'
Vucedol is one of them, and I believe some of it ended up into northern Italy as well
the Carpathian Basin was a transit room between the steppe and northern Europe and northern Italy as well
it was probably Unetice who first controlled the whole amber trade route from the Baltic till the Carpathian Basin where others took over toward the Aegean
they were traders who tried to get hold of the trade routes by force, in the same tradition as the Bell Beaker people

Yes, I think that's right. Depending on the analysis, into Tuscany as well.

 

[davef]

We were discussing the Balkan Bronze age samples and the Iron Age one as well on the thread about the Varna "King".

Based on the pca, Eastara posted the following, which looks correct to me.

"As far as I can see Varna are the red outlined orange squares and probably only Varna outlier, who has more Yamnaya [compared to the other Varna samples] falls over the Tuscans. In fact the Balkan Bronze age (blue filled red circles) is all over the Tuscans.''

(As one of our posters pointed out, the coverage of the Varna "King" is poorer than that of Varna outlier, so we don't know if the "King" might have had more "steppe", but imo it's more likely he didn't, as most of it seems to arrive in the Bronze Age. Perhaps, as well, there is some ambiguity in the dating and the Varna Outlier should be dated later.)



This is from a poster on another forum who sees Vucedol as close to modern North Italians, but doesn't see Balkan Bronze Age as close to modern Tuscans.

"Using the Global25 data, I relabelled the samples with the more precise culture labels from Mathieson's paper and then placed them on a Neighbour Joining Tree with local populations: https://imgur.com/a/tm6ce

Results: A few of the Croatian Vucedol and EMBA / LBA samples sit with North Italians (Bergamo) while most Balkans_BA from Bulgaria sit either with early Neolithic or in a "no man's land" between Sardinians and North Italians. https://imgur.com/a/tm6ce

(Certainly no where near enough WHG rich Middle Neolithic ancestry to sit too near to the Basques.) One Bulgarian sample (I2165) is probably by chance sitting fairly near recent Bulgarians, Serbs, Romanians.

We'd probably reasonably expect the Croatians of this time to tend to be North Italian like (it's not too far from Bergamo to Croatia and closer than to Bulgaria?), until they get more admixture from whatever expanding genetic wave links Baltic BA / Balts / Slavs / Hungarians.

Judging from the position of the Bulgaria_IA, the Bronze Age Bulgarians would need more Mycenaean/Anatolia_BA-like ancestry to get to there, and then more of the Balt-Slav / Baltic BA type ancestry to get to present day position."


So, what to make of it? Just a difference because of different methodology? Even just in terms of PCAs, I think Northern Italians are quite a bit "north" of Vucedol, and closer to Balkan Bronze Age, and Balkan Bronze Age is indeed pretty close to Tuscans. The Balkan Iron Age sample is pretty close to Mycenaeans, which are close to Southern Italians/Sicilians. The Balkan one looks more "western" but equally "south".

Of course, this doesn't mean all of Northern Italy never changed since that era. There could have been meanderings back and forth. Interesting none the less.

Where did you get that map from? It wasn't in the paper. It doesn't look like the lazaridis pca, I guess it's because only one sample was used from each population.

 

[bicicleur 2]

can anyone tell me where this sample comes from :
Ukraine Copper Age 2890–2696 R1b1a1a2a2b-BY3293
https://genetiker.wordpress.com/y-snp-calls-for-i5884/

I5884

I can't find it