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Wednesday, October 14, 2020

A new model for the genomic formation of First American ancestors in Asia (Ning et al. 2020 preprint)


Over at bioRxiv at this LINK. The main topic of the preprint is largely outside the scope of this blog. However, the manuscript includes a detailed discussion about how to get the most out of the qpAdm mixture modeling program. I've used qpAdm regularly over the years, and I plan to use it more often in the future, so I'll be looking very carefully at the qpAdm methodology that Ning et al. are recommending. Here's the preprint abstract:

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia.

Ning et al., The genomic formation of First American ancestors in East and Northeast Asia, bioRxiv, posted October 12, 2020, doi: https://doi.org/10.1101/2020.10.12.336628

See also...

Ancient ancestry proportions in present-day Europeans

Major updates to ADMIXTOOLS

Yamnaya-related ancestry proportions in present-day Poles

268 comments:

1 – 200 of 268   Newer›   Newest»
Anthony Hanken said...

Does anyone know what the terminal SNP for M54A is? The study says its using ISOGG 2016 nomenclature in which case "N1b1" is (L731, L733).

In the supplemtary this seems to be contradicted with its calls being N1b1 F1052: G-> T (2), M2256: G-> A (2), L391: G-> C (2), M2117: G-> A (2), F1753: T-> G (1)
This looks like N-Tat in Yfull.

Sofia Aurora said...

Wonderful article!

There is also anorher BIG one about East Asia coming:

https://www.biorxiv.org/content/10.1101/2020.06.03.131995v1

Pavel Flegontov said...

Hello David! Thanks for sharing my work! I'd like to highlight some aspects of the study that are buried in the supplements, but are nevertheless important. I hope the community will find them useful.

First, when qpWave was introduced back in 2012 (Reich et al. 2012), it was a very simple test for the number of gene flows (in any direction) between a set of outgroups ("right" populations) and another set of populations ("ingroups" or "left" populations). When qpAdm was introduced in 2015, it was clearly stated in the supplements of Haak et al. 2015, Mathieson et al. 2015 and Lazaridis et al. 2016 that the method works under the following assumptions (see Fig. S24 in my paper): 1) there are no gene flows from the target group or source proxies into the outgroups; 2) there are no gene flows from the outgroups into the proxy sources (after their divergence with the true sources); 3) outgroups are not cladal with proxy sources.

While assumption 1 is usually taken care of by choosing outgroups much deeper in time than the source proxies, assumption 2 was ignored in all papers published after 2016. Both assumptions (1 and 2) are nearly impossible to control in the "proximal" setup used, e.g., by Narasimhan et al. 2019, when both ingroups and outgroups are close it time and space. Assumption 2 is actually impossible control, if we single out a certain subset of targets from a wider set of ingroups.

Imagine there was a gene flow from outgroups into B, but for some reason (e.g. a later 14C date) we picked A as a target. A simple qpWave test would reject the cladality of A and B, and that prompts us to test more complex models for A. There is a good chance we would find non-rejected qpAdm models for A with plausible admixture proportions, but those models are wrong! To take care of this serious problem, I suggest to test all plausible sources as targets too (see SI p. 5).

Second, we showed on simulated data that ranking alternative qpGraph models by the worst residual (Z-score) is less reliable than ranking by model likelihood. Comparing qpGraph models is tricky, and it is very hard to find one best model even for a moderate number of groups. We introduced some new methods to put model comparison on a firm statistical footing and to search the graph space automatically (see SI sections 12 and 13).

Third, we showed on simulated data that removal of rare variants from analysis skews many f4-statistics away from 0 and dramatically increases the false positive rate of admixture tests based on qpAdm or qpGraph. The second problem as we showed exacerbates the first one (see SI p. 24).

There is a general problem discussed in SI section 13 that f4-statistics calculated on whole-genome shotgun data and those calculated on the 1240K panel are often not well correlated (Figs. S52, S53). This issue was noticed by Bergstrom et al. 2020 (the HGDP shotgun paper), but was not discussed a lot. Statistics including three African groups or two African groups+an archaic group are severely affected (Fig. S53B), and the same effects are reproduced by rare variant depletion (Fig. S53E). Since f-statistics are affected, all downstream analyses like qpAdm and qpGraph are affected too. I believe that the issues we noticed on simulated and real data are the same.

Fourth, biased gene conversion (Pouyet et al. 2018, Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences, eLife) is potentially another confounding factor that could lead to false positive signals of gene flow. To take care of biased gene conversion, only GC and AT sites should be considered. This issue is discussed in SI section 13.

Pavel Flegontov said...

In my view, there are multiple problems with the standard archaeogenetic toolkit composed of PCA, ADMIXTURE, f-statistics, qpAdm, and qpGraph. The basic methods and especially popular protocols like qpAdm with "rotating" outgroups and "proximal" qpAdm modelling were not tested well on simulated data. The most popular set of sites (1240K) is likely not optimal for inferring demographic history due to its complex ascertainment scheme (many HumanOrigins panels + an Illumina panel), the paucity of rare variants and its susceptibility to gene conversion (in fact, the HumanOrigins panel lacks G<->C and A<->T sites altogether). And we've not explored the effects of recurrent mutations (Amos 2020 R. Soc. Open Sci.) and biased gene conversion (Pouyet et al. 2018 eLife) on f-statistics and the derived methods.

My suggestion at the moment is to check most important results on both 1240K and shotgun data, and to be mindful of qpAdm assumptions.

Michalis Moriopoulos said...

@Dr. Flegontov

Thank you for your illuminating posts, sir. I've really enjoyed reading your work and hope to see more in the near future. What do you think of this paper's revision of Kolyma1 and its relation to Saqqaq/Paleo-Eskimos/Neo-Eskimos/etc.? Did it surprise you? That's as big a reversal as the USR1 finding, in my opinion.

Also, would you mind clearing something up for me? Myself and some others at Anthrogenica are fairly sure that there was a mix-up between two samples in the Paleo-Eskimo preprint. I believe this was corrected in the final paper but it appeared in preprint form again later down the road in another [possibly Reichlab] paper, so I'd like clarification:

It seems like there was a mix-up of the samples I7760 and I7781, right? The latter was labelled Ust Belaya Neolithic despite having ancestry (e.g., steppe) that a sample of that age could not possibly have. The sample I7760 on the other hand was originally labelled medieval despite looking like a Neolithic sample. It seems pretty obvious they were mixed-up somewhere along the way. Just making sure we've got it straight.

I do remember there was a geographic error at one point in the original preprint concerning Ust Belaya (the Baikal HGs). I suppose it doesn't help that there are at least two sites called Ust Belaya in Asia: one along Angara in Baikalia and one in Chukotka-Kamchatka. It must be difficult to keep all of these samples straight sometimes!

Davidski said...

I haven't had a chance to properly look at the Ning et al. supp info yet. When I do, I'll try to apply the authors' recommendations to some ancient European models. That should be interesting.

But that might take a while, like a week or so.

Pavel Flegontov said...

@Davidski It would be very interesting to take a look at your results on ancient Europeans. I'm now doing similar work on published shotgun data.

pnuadha said...

@daviski

You usually dont post DNA studies on Asia. Did you just find this article interesting or does it help to uncover the relation of ANE towards Ancient Europeans.

side note: I did not know that ANE went all the way up to the artic ocean in Northern Siberia, as evidenced by Yana. It seems that ANE dominated ancient Siberia.

Davidski said...

@pnuadha

I shared it because of the discussion about qpAdm in the supp info, but yeah, the ANE thing is interesting, and I'll be getting into that in more detail soon.

old europe said...



@pnuadha

I think IIRC that it's Yana being at least partially ancestral to ANE which is a younger genetic cluster than Ancient North Siberians

Rob said...

It might benefit the article to elaborate on its broader implications so it’s more generalisable for prehistorians

Tigran said...

Is there anything that indicates everything in between Eastern Europe and Yana RHS was ANE and not something ENA related?

Guy said...

Hum... You know, this paper can almost be read as an retraction. Cheers,
Guy

gamerz_J said...

@Sofia Aurora

Do you know when that paper is supposed to be published?

gamerz_J said...

Interesting paper, a minor point that stood out to me is the presence of most likely ANE admixture in NE China. Apparently it's there in some samples but not in others.

Also, would it be correct to assume that in this paper ANE seem less ENA-shifted than the previous one about Salkhit and Denisovan ancestry in East Asians?

Tigran said...

How has the ENA shift changed? Also does anybody believe that paper that argued the French were 20-25% East Eurasian?

A said...

@ Davidski

Back in 2018 you wrote:

“One of the most remarkable discoveries in the recent Narasimhan et al. 2018 preprint has to be the presence of what are essentially Eastern European migrant populations within the Inner Asian Mountain Corridor (IAMC) during the Middle to Late Bronze Age (MLBA). … Narasimhan et al. labeled these groups as belonging to the "forest/steppe MLBA" complex (for instance, see the main figure from the preprint here). This is indeed what they are in terms of their genetic structure, but certainly not geography, because the IAMC is well south of the steppe. … Strikingly, most of these people cluster with Bronze Age Eastern Europeans, and even some Bronze Age Central Europeans. … Two of the MLBA IAMC individuals are from Kashkarchi in the Ferghana Valley, in what is now Uzbekistan, and basically on the doorstep of the Indian subcontinent. (…) the MLBA IAMC groups are rich in Y-haplogroup R1a-M417, and in particular its R1a-Z93 subclade, which is today an especially frequent marker in Indo-European-speaking South Asians. (…) Clearly, many populations in South Asia, particularly those speaking Indo-European languages, derive the bulk of their steppe-related ancestry from the peoples of the MLBA IAMC.”

https://eurogenes.blogspot.com/2018/04/on-doorstep-of-india.html

Is this still correct? Narasimhan et al. 2019 gives the impression that Indo-Europeans were already significantly admixed by the time they reached 'the doorstep of India'.

Davidski said...

@A

What I said is still correct.

I don't know why Narasimhan et al. seemingly included the IAMC, and especially the Fergana Valley, as part of the steppe.

This is South Central Asia, and it's well south of the Eurasian steppe. Take a look at any decent map.

You would have to get in touch with the lead authors of Narasimhan et al. and ask them what their thinking was behind their decision.

Davidski said...

@Tigran

Also does anybody believe that paper that argued the French were 20-25% East Eurasian?

I don't think many people ever did.

These sorts of distal models show that the French are partly East Asian-related, not actually part East Asian.

A said...

Thanks.

Sofia Aurora said...

It will appear propably in the first months of 2021

mary said...

@Tigran
Which paper is this?

Vladimir said...

FTDNA clarified Y haplogroups from the article https://www.nature.com/articles/s41467-018-06024-4#MOESM1
Goran Rundfeldt’s R&D group at Family Tree DNA reanalyzed the Y DNA samples from this paper and has been kind enough to provide a summary of the results. Michael Sager has utilized them to branch the Y DNA tree – in a dozen places.


https://dna-explained.com/2020/10/16/longobards-ancient-dna-from-pannonia-and-italy-what-does-their-dna-tell-us-are-you-related/

gamerz_J said...

@Davidski

"These sorts of distal models show that the French are partly East Asian-related, not actually part East Asian."

Well, wouldn't that translate to substantial East Eurasian admixture over the last 20k years or so? I don't think that there is such an amount in French given that nor ANE nor any other of their ancestral populations seemed to have had this, but I am trying to understand how that number would come up.

Are they comparing them to Kostenki?

ejmohr said...

But do we have any idea about mitochondrial haplotype X which is most common in eastern NA and parts of Europe but not NE Asia. There's the mystery I'd like to see solved.

Tigran said...

@ejmohr

That is interesting. You would expect there to be U in the American gene pool not X.

And Id like to see UP data to settle whether the paternal lineages of ANE came from a SE Asian or Tianyuan like population.

A said...

@Davidski

"You would have to get in touch with the lead authors of Narasimhan et al. and ask them what their thinking was behind their decision."

Hasn't any one else asked them?

Samuel Andrews said...

@All,

Off topic. The name for 'Steppe people' needs to be updated.

Does anyone have a new name to give "Steppe people" aka "Yamnaya." Both names are what have been used up to 2020 but they are inaccurate in key ways.

Steppe sends the false message they were people of the entire Eurasian Steppe which they were not. It also gives the false message they were Steppe nomads in the same sense which historical Sycthians and Turks were.

Yamnaya is inaccurate because they weren't all from Yamnaya. And because the Yamnaya genetic profile predates the Yamnaya cultue.

I'm looking for a name which doesn't have the word 'people' at the end it. Kurgan sounds like a good base for a new name. But Kurgish and Kurgianian don't make sense.

There's no name for them which is as goof for example as the name 'Anatolian Farmers.'

Copper Axe said...

@Samuel Andrews
Western Steppe Herders perhaps? That is the term I tend to use.

Tigran said...

@Samuel Andrews

Aren't they often called Western Steppe Herders (WSH)?

Tigran said...

Also what is everybody's opinion on whether Basal Eurasian is a real thing or not?

Samuel Andrews said...

Western Steppe Herder is accurate but too long. It works for DNA papers.

I should have been specific. I'm specifically looking for a name which is one word and is easy to remember. A name which as simple as English, Spanish, French, etc.

I don't think anyone has a name like that for them. I'm looking for a new name based on a river, city, lake, or Latin version of an English descriptive.

I'm making Youtube series on population History of Europe. Steppe-anything, WHG, EHG, etc do not roll off the tongue well.

Michalis Moriopoulos said...

Western Steppe [Herders] works just fine for me. So does Pontic-Caspian Steppe [Herders].

Eneolithic Western Steppe (Progress-like), EBA Western Steppe (Yamnaya-like), MLBA Western Steppe (Sintashta-like).

Vladimir said...

I find this position in the paper interesting:

The Genomic History of the Middle East

«In addition to the local ancestry from Epipaleolithic/Neolithic people, we find an ancestry
related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange
component in Figure 1C; Table S1). Previous studies showed that this ancestry was not
present in the Levant during the Neolithic period, but appears in the Bronze Age where
~50% of the local ancestry was replaced by a population carrying ancient Iran-related
ancestry (Lazaridis et al., 2016). We explored whether this ancestry penetrated both the
Levant and Arabia at the same time, and found that admixture dates mostly followed a North
to South cline, with the oldest admixture occurring in the Levant region between 3,900 and
5,600 ya (Table S3), followed by admixture in Egypt (2,900-4,700 ya), East Africa (2,200-
3,300) and Arabia (2,000-3,800). These times overlap with the dates for the Bronze Age
origin and spread of Semitic languages in the Middle East and East Africa estimated from
lexical data (Kitchen et al., 2009; Figure S8).
This population potentially introduced the Y chromosome haplogroup J1 into the region (Chiaroni et al., 2010; Lazaridis et al., 2016). The majority of the J1 haplogroup chromosomes in our dataset coalesce around ~5.6 [95% CI,
4.8-6.5] kya, agreeing with a potential Bronze Age expansion; however, we do find rarer
earlier diverged lineages coalescing ~17 kya (Figure S9)»

Together with the fact that J1 is found both in the North of Russia and in Khvalynsk, and finally the standard of CHG is also J, it is suspected that it was some extinct subclades of J1 that introduced CHG to the steppe


Gabriel said...

@Samuel Andrews

I don’t think it’ll be that easy to find a simple word without the word “people” in it. I would consider “Kurgan people”, but it has the word “people” in it, so I don’t think you’ll like it. Maybe “Kurgan herders” or “Kurgan pastoralists”? I don’t think they’re much better myself, but maybe they’ll work...

@Tigran

Try to browse /pol/ a little bit less. ANE weren’t the super East Asian people you think they were either. Not all ANE people were like Yana.

Helgenes50 said...

@ Samuel Andrews

What is or will be the name of your Youtube Channel ?

Ryan said...

@Tigran - "How has the ENA shift changed? Also does anybody believe that paper that argued the French were 20-25% East Eurasian?"

If "West Eurasian" and "East Eurasian" are the product of incomplete mixing of two distinct, deeper sets of lineages that would make sense. I believe David's deeper treemix runs showed hints of that albeit in the opposite direction? We just lack samples of that those deeper lineages.

I think it's really interesting that West Eurasian mtDNA variation is nested within East Eurasian mtDNA variation, but for Y-DNA it's the reverse. Seems like the West/East Eurasian split was complex.

@David - Thanks for posting this. I know it's sort of out of your wheelhouse but I think understanding the origins of non-European groups helps us understand the deeper origins of West Eurasians.

Norfern-Ostrobothnian said...

Ponto-Caspian Equestrian?

Samuel Andrews said...

@Helgenes50,

Here is a link to my Youtube channel. You can subscribe and hit the bell so you get a notification when I start posting videos in December. (I'm probably going to change the name because Population genetics doesn't mean what I thought it did).

https://www.youtube.com/channel/UCoL-O5egSxkfvkCGGE0vN1Q?view_as=subscriber

My first videos will be a series on the Population history of Europe which is going to be about 20 videos long. Each video will be around 10 minutes.

I think the series will be really good. I'm going to explain it in a way which sounds like a storybook not a scientific paper. Whenever, you put any information into a narrative form you see connections and details you didn't notice when you looked in raw numbers and stats.

It is going to be interesting.

Samuel Andrews said...

By the way, when I change the name of my channel, the channel's address won't change. You'll stay subscribed after the name change.

andrew said...

"https://en.wikipedia.org/wiki/Proto-Semitic_language"

Paleo-Ukrainians?

Bob Floy said...

@sam

Just subbed, looking forward to your videos.

Ebizur said...

Ryan wrote,

"I think it's really interesting that West Eurasian mtDNA variation is nested within East Eurasian mtDNA variation, but for Y-DNA it's the reverse."

Why do you say so? Are you perhaps considering only subclades of O-M175 (or NO-M214) as "East Eurasian Y-DNA"?

Ric Hern said...

@ Tigran

I think we should look at the Early Neanderthal Y-DNA and MtDNA first before making theories about what Basal Eurasians could have been....Later Neanderthal all had Modern Human Y-DNA and MtDNA...If Early Neanderthals turn out the same then serious questions comes to light.

TLT said...

Ric Hern, there is early Neanderthal DNA from Iberia. Those had parental markers that clustered with Denisovans in a different clade from late Neanderthals and modern Humans as far as I recall. On the other hand, their autosomal DNA was grouped with the later Neanderthals in different clade from modern Humans.

Carlos Aramayo said...

@Davidski

What do you think of this new study?

https://tinyurl.com/y3w48swt

"Bronze Age pastoralists in what is now southern Russia apparently covered shorter distances than previously thought. It is believed that the Indo-European languages may have originated from this region, and these findings raise new questions about how technical and agricultural innovations spread to Europe. An international research team, with the participation of the University of Basel, has published a paper on this topic. During the Bronze Age (ca. 3900 - 1000 BCE), herders and their families moved across the slopes of the Caucasus and the steppes to the north, taking their sheep, goats and cattle with them. It is believed that the Indo-Germanic groups, who brought the Indo-European languages and technical innovations such as wagons, domestic horses and metal weapons to Europe, may have originated from this region."

Ryan said...

@Ebizur - "Why do you say so? Are you perhaps considering only subclades of O-M175 (or NO-M214) as "East Eurasian Y-DNA"?"

We're dancing close to breaking one of David's rules here (sorry David), but I'm suggesting everything under Y-DNA K2 as "East Eurasian" and that F(xK2) is "West Eurasian." C and DE who knows.

@David - Do you have any interest in revisiting this post now that we have better samples from the region? I thought it was a really good one. https://eurogenes.blogspot.com/2016/07/layers-of-ancient-north-eurasian.html

Also interesting that this paper links Indo-European with Uralic, Yukaghir and Eskaleut as a clade.

Copper Axe said...

@Carlos Amayo

That Eureka article really misrepresents the finding of the research article in my opinion.

Also they apparently didn't get the memo from Wang's paper that the Indo-Europeans did not migrate out of the Caucasus...

Bonus points for the usage of Indo-Germanic lol

Gabriel said...

@Copper Axe

They’re German speakers, it’s not surprising they said “Indo-Germanic”, even if it’s a little weird regarding English usage.

Davidski said...

@Carlos

I haven't read it. Might read it one day. But it sort of sounds like they're denying the migrations from the steppe, which is really dumb at this stage.

And I don't know why so many people keep saying that the Indo-Europeans came from the Caucasus. That's really weird and nonsensical.

Carlos Aramayo said...

@Davidski and Copper Axe

Yes, it sounds weird to try to deny steppe migrations through this study. Anyway the full paper can be found free here:

https://tinyurl.com/y28lzwqt

Gabriel said...

@Davidski

Maybe they are one of the remaining immobilists who want to deny steppe migrations and think a European origin of the Indo-Europeans is Eurocentric and oppressive, basically biased academics... or is that too much?

Sofia Aurora said...

Guys we might want to move a bit southwestern because there is a new preprint on the block:


https://www.biorxiv.org/content/10.1101/2020.10.18.342816v1

.

Sofia Aurora said...

Oh! Lads you might want to check out the below article:

https://papers.ssrn.com/sol3/Papers.cfm?abstract_id=3661949

It also deals with a ghost pre-Colombian Americanoid GHOST population that binds together with the current post!

Rob said...

I think they mean, in terms of “day to day”, the migration paths of pastoralists were fairly well defined and local. Between highland / lowland & summer/ winter pastures
Of course, they must have undertaken longer distant treks in certain key episodes. We have to evaluate why this occurred and how they were facilitated

Vladimir said...

I read the entire paper. There are no statements that refute the migration theory. This work clarifies some details that were known before it. For example, it is claimed that already at the Eneolithic sites of Progress2 and Vonuchka, people ate the meat of domesticated animals, in particular sheep and goats. An interesting point is that the sheep from Progress2 were not local, but imported or driven from the more Northern arid region of the Caspian steppes. From which we can assume that the Progress2 people could also have come from the more Northern regions of the Northern Caspian or Lower Volga region. It is also noted that people of the early phase of the Maikop culture ate the same food, and at later stages the nutrition of people in the Caucasus region and the steppe region began to differ. From which we can conclude that these were different populations. The main conclusion seems to be that the Bronze age population of this territory was not nomadic. It follows that the nomadic way of life over long distances is probably already an invention of the Scythian time.

Palacista said...

Slopes of the Caucasus.

Davidski said...

@Vladimir

Can you quote the relevant parts about Progress-2 and Vonyuchka?

Vladimir said...

"The dataset for Progress comprised six sheep/goat bones with δ13C values between -20.7 and -15.4 ‰ (avg. -19.1 ± 1.9 ‰) and δ15N values between 5.7 and 10.0 ‰ (avg. 7.7 ± 1.7 ‰)."
"The sheep BZNK 640/1 from PROG2 is another possible example for such interregional connections. Its δ13C value of -15.4 ‰ implies substantial contributions of C4 plants, which, according to the data presented by [17], did not occur in the piedmont area, but north of it, i.e., in the drier Caspian steppe. Therefore, the result points to a non-local origin of this animal also."
"The highest δ15N value–BZNK 640/1, the same sheep from PROG2 as discussed above–complements the apparently exotic δ13C value and underlines the possible non-local origin of the animal."

Unfortunately, they didn't date this bone. The Appendix says that the "bronze age" was probably determined by the archaeological context

Ric Hern said...

As far as I understand it they said that they are waiting for Older Neanderthal Y-DNA to see if it will confirm their observations. So let's see what the future holds.

Is it not strange at all that they propose a possible admixture event which occured between 370 000 and 100 000 years ago and that the oldest evidence of Morphological Modern Humans in Eurasia only pop up in the Middle East around 100 000 years ago, basically at the very end of their proposed admixture date ?

Ric Hern said...

@ TLT

Came across the Apidima Cave Skull found in Greece. Apparently a Homo Sapiens dated to around 200 000 plus years ago. This certainly could point to the admixture event between 370 000 and 100 000 ybp. described in that paper. Then again we should consider how far Anatomically Modern Humans could have been spread at such an early date or even start wondering where they could also have originated.

epoch said...

"The first burial mounds between the Caucasus, the Caspian Sea, and the lower Don and Volga Rivers date to the Eneolithic of the late 5th millennium BCE [41]. Some of these graves contained bones of domesticated animals, whereas most bone artifacts represent wild species [20, 18]. Despite the evidence for domesticated animals, it is still unclear whether the communities who erected the earliest mounds in the southern Russian steppe represent the first pastoralists or late hunter-gatherers [42, 43]."

andrew said...

@ejmohr

"But do we have any idea about mitochondrial haplotype X which is most common in eastern NA and parts of Europe but not NE Asia. There's the mystery I'd like to see solved."

mtDNA X very likely took a Northern route from the Near East (where mtDNA X haplogroup diversity is greatest) to NE Asia prior to the LGM (ca. 20,000 years ago).

The founding population of Northern Native Americans (as the paper calls them) made up of pre-LGM Northeast Asians (30% or so) and East Asians (70% of so) was confined to a refugium with an effective population size in the low 100s of people or so, and contained a population with some of these pre-LGM NE Asian mtDNA X folks. So, by virtue of this founder effect, mtDNA X became common in Northern Native Americans where the founders expanded rapidly for 14,000 years or so.

But the LGM killed off everyone else in Northern Eurasia, because it was too cold for sustained habitation (even now NE Asia is so marginal in climate for humans that the population density is extremely low). This left the only other reservoirs of mtDNA X people in the world in European refugia and West Asia and Southeast Asia.

When Northern Asia was repopulated post-LGM because it became marginally tolerable to live there again climate-wise, the source for the replacement population didn't have anyone with mtDNA X in it, or at least, the percentage of the source of the replacement population that was non-mtDNA X was so large that mtDNA X became extreme rare in Northeast Asia. No subsequent mtDNA X rich population migrated to the region anew post-LGM.

andrew said...

@SofiaAurora

Very subtle.

"The genomic histories of Indigenous groups in the Americas have been recently enriched by modern and ancient data, but the dataset on continental Central America is still meagre. Here, we report ten ancient pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama, on the Isthmian land-bridge connecting North and South America. Our analysis reveals extensive sub-structure in the geographic area with pre-colonial Panamanians clustering separately.

On a continental scale, the Isthmian populations are distinguished by a previously unknown Indigenous component in the Americas. This component derives from the admixture of different early Indigenous groups that originated from the same northern North American source in the late Pleistocene. The earlier population(s) moved further south, leaving differential footprints in South America, while another group remained restricted to the Isthmo-Colombian area, expanded locally during the early Holocene and left genomic traces up to now."

Rob said...

@ epoch
Very interesting
Although occasional feasts and offerings had domesticated animals in earlier periods, I think it would point to Yamnaya people being the first true pastoralists. This adaptational advantage would explain why one specific clan (Z2103) marginalised other steppe groups are a time of changing ecology between 32-2700 BC.

Vladimir said...

LBC 63.4 Accepted: 17.06.2018
NEW DATA ON THE CHRONOLOGY AND DEVELOPMENT OF CATTLE BREADING DURING THE ENEOLITHIC AND EARLY BRONZE AGE IN THE SOUTHERN URAL REGION 1
Nina L. Morgunova
Orenburg State Pedagogical University, Orenburg, Russian Federation
Natalia V. Roslyakova
Samara State University of Social Sciences and Education, Samara, Russian Federation
Marianna A. Kulkova
Herzen State Pedagogical University, Saint Petersburg, Russian Federation
Abstract. Introduction. The article considers the features of cattle breeding and consumption of meat products in the Eneolithic cultures (the Samara culture) and the Early Bronze Age cultures (the Repin stage of the Pit Grave culture) on the territory of the Southern Urals (the Samara Trans-Volga region). The paper specifies the chronology of these cultures on the base of radiocarbon dating. The main site for the study was Turganik settlement located in the Southern Ural region (Orenburg region). Methods. More than 800 m2 of the settlement area was excavated. There were six paleosoil layers. Four upper layers were empty, without artifacts. The sixth layer contained Eneolithic finds. The fifth layer contained finds of the Early Bronze Age. The archaeozoological collection was analyzed in accordance with the methodological scheme developed by E.E. Antipina. For radiocarbon dating collagen was treated from bone samples on the base of the standard procedure and radiocarbon activity was measured by Quantulus 1220 low background scintillation counter. Analysis and Results. As a result 32 radiocarbon dates were obtained on animal bones and on organics from pottery of different types from different cultural layers of Turganik settlement. The Eneolithic complex includes ceramics, flint and bone tools. The paper specifies the finds of developed and later stages of the Samara culture. The artifacts of the second stage of the Samara culture were dated to 4900-4500 cal BC. The artifacts of the later stage belong to the period o\ of 4300-3800 cal BC. We suggest that from the Early Eneolithic local people practiced cattle breeding without o agriculture. Hunting played a secondary role and fishing was poorly developed. Beef was the main food in the people's diet during the Eneolithic period. The Early Bronze Age assemblage includes ceramics of the Repin stage of the Pit Grave culture, stone macro-tools, flint arrowheads, items made of bones and copper, slags and ¡5 scarps of copper ore. The technological analysis supported that ceramics belong to the Pit Grave culture. The layer age is from 3800 to 3300 cal BC. During the Repin stage the role of sheep breeding was increased and ^ consumption of sheep meat prevailed in comparison with the Eneolithic period. This is an evidence of the ^ transition to the nomadic form of stock breeding.

https://cyberleninka.ru/article/n/novye-dannye-o-hronologii-i-razvitii-skotovodstva-v-eneolite-i-rannem-bronzovom-veke-yuzhnogo-priuralya

Rob said...

New on Neolithic lower Don

https://www.sciencedirect.com/science/article/abs/pii/S1040618219300126

Abstract
The multilayer settlement Rakushechny Yar situated in the lower Don River (Rostov region, Russia) is one of the oldest early Neolithic sites in this region, dated to the 7th and 6th millennia BC. Recent investigations have shown a particular importance of this site in the study of the spread of the Near Eastern “Neolithic package” and the neolithisation of Eastern Europe. Long-term study has provided unique evidence of lives of ancient communities. New 14C dates contribute to refining the chronology of the recently excavated to dating the development of cultural traditions more precisely. The excellent preservation state of organic materials led to uncovering a rich assemblage of faunal and fish remains, household constructions, hunting and fishing tools, as well as pottery. The subsistence strategies and the life cycle of these communities were reconstructed through multiple proxies, which describe a particular system of resource management determined by specific economic, environmental and cultural conditions. Rich fish remains, shell middens, site location, specific toolkit with restricted categories, and incomplete context of tool production testify all that it was a specialized site for aquatic resource procurement. Faunal remains indicated the use of resources from other ecological niches as well. Finds of bones of domesticated animals in the same Early Neolithic layers may suggest even a more complicated organization of this ancient community and may indicate the northern limit of the Neolithic package distribution.

Rob said...

Take home points from main text

* Although usually thought to begin 7th mill BC, it is still difficult to date due to ''inhomogeneity of bulk samples, insufficient control over sample
taphonomy, and perhaps 14C reservoir effects in charred food remains
on pottery. In general, these factors should tend to produce misleadingly
old dates.''

* A future study will produce more data, however curentl new dates from freshly excavated material ''it is clear that all samples date to an interval spanning no more than a few decades, centered around c.5600 cal BC''

* Economy - mostly fish, molluscs, hunted deer. Also domestic cattle & sheep - subject of ongoing investigation (? aDNA)

* Pottery - ''pottery similar to Rakushechny Yar tradition is known to the west in Northern Pontic area (site Puhach I) and to the east – within Northern Caspian complexes. Single fragments with a complicated geometrical design typical for Lower Volga cultural area
(see in e.g. Vybornov, 2008) were found in Rakushechny Yar site.''

* Near Eastern influences ?
''The Lower Don area might have been included even in a wider cultural network. Relations between the steppe areas of Eastern Europe, from the Black Sea to the Azov Sea, with Armenia and Central Anatolia could also be evidenced by finds of obsidian that originated from deposits located in the latter regions..''


Samuel Andrews said...

@Ancient Roman DNA,

I'm starting to realize the paper, Antino 2019, was really miss leading. And their conclusions are completely wrong.

The Imperial Roman samples are probably all slaves. Not just some, but basically all of them were slaves.

One cemetary is in Pontus, a trade center, and the paper even mentions they're probably slaves. Two other cemeteries are associated with villas. Villas is where most slaves worked in ancient Rome. Yeah, I think they were slaves as well.

Their DNA supports the idea they were slaves. Because basically none of Imperial Roman samples have any Italian ancestry. Almost all have significant European ancestry but it comes from Greece. Greek-Near Eastern mixed slaves, which is interesting and brings up questions about Greek kingdoms in Near East.

It is absurd that Antonio 2019, concludes the re-appearance of Italian ancestry in Late Roman, Early medieval samples is due to immigration from other parts of Europe. Which is very unrealistic.

But I guess, it is typical that genetic experts don't know how to interpret ancient DNA data in a realistic way. They don't understand the concept their DNA samples might not represent the whole population of a time period especially for a society as complex as ancient Rome.

Gabriel said...

@Samuel Andrews

Do you agree they still contributed ancestry to Italians though, or that the Near Eastern ancestry is from a different source?

Simon_W said...

It would be outlandish to assume that descendants of slaves, especially of liberated slaves, left no impact whatsoever on the Italian gene pool. But slaves were not the only Near Easterners in ancient Italy, hence I assume something more complex.

mzp1 said...

Both the above archeological studies seem to point to animal domestication predating farming in the region. Isn't it about time Historians update their theories?

Samuel Andrews said...

@Gabriel,

Yeah the Near Easter admix in modern Italy is from Roman era. The debate over when Italians got Near East admix is over. Davidski predicted this.

The Imperial Samples (Slaves) though aren't like a perfect match. Near East admix is so minor outside of Southern Italy that it is hard to model it. You can model it as coming from Syria, Iraq, Anatolia doesn't matter.

Roman Historians should be paying attention to this DNA. Because, it could mean Near Eastern slaves had offspring with Italians. Or were they immigrants not slaves? There's lots of historical questions.

Michalis Moriopoulos said...

@Samuel Andrews

I feel like I've had this conversation too many times already, but I could not disagree with you more on Rome. It is possible that some of the people in the Roman study were slaves, but all of them? Come on. That's like saying all the non-Norse plotting samples in the Viking study were slaves. Some of them surely were, but all of them? There's no evidence for that at all. We already saw outliers in the Republic era. East Med immigration was already happening then.

And there isn't a single West Med sample in the Imperial set. Not even one. There are plenty of Norse samples in the Viking study, by contrast. It is therefore very likely that by the Imperial era, many if not most Central Italian Latins had an East Med genetic profile, especially considering how Central and Southern Italians plot today. How did this happen? Possibly through strong assimilation of Greek/Near Eastern type people during the Republic/Hellenistic era, probably involving Magna Graecia.

If we took your tack, it would be tantamount to saying that Central and Southern Italians are descendants of Greek-Near Eastern slaves. That's not believable, if you ask me.

Samuel Andrews said...
This comment has been removed by the author.
Samuel Andrews said...

This would suggest.....

South Dutch and Flemish are the "real" Dutch/Franks even though they are the least Germanic. They are the Franks who admixed with Roman Gauls.

Northern Dutch are descendants of Frisians assimilated by Dutch in the Middle Ages. Germanic but not Frankish.

Samuel Andrews said...
This comment has been removed by the author.
Michalis Moriopoulos said...

I should also say I could believe the East Med was a more cosmpolitan profile in Central Italy, and that people from rural areas better preserved the original West Med Latin profile, which then bounced back later on when the cities fell into ruin. Sure, maybe. It's also possible that Northern Italian ancestry piggybacked south with Germanic incursion into Central Italy, swinging Central Italians back toward the mainstream European cline that way.

Either way, there's no way it's just slaves. That sounds like a Nordicist fantasy from another era.

Rob said...

@ mzp
There’s nothing strange about those studies, although I’d like to see some isotopic data to back Morgunova et al’s claims
It’s long been know that local groups incorporated animals into their fisher-hunter economy whilst agriculture was limited
By 5500 BC “”farmers”” (agropastoralists) had reached the carpathian basin, so animals were brought east by local HGs

Samuel Andrews said...

@Michalis,

Most of them in my opinion are mixtures between Greeks and various Near East populations almost all from Syria and Anatolia.

The only way I can think such a mixture could happen, is in the Greek kingdoms in the Near East which were created by Alexander's conquests in circa 323bc. Selecudia.

I can't see it being a legacy of Magna Gracia.

Rob said...

LBK in western Ukraine by 5500 BC

A said...

@Samuel Andrews

Juvenal described it in 118 AD. Rome becoming 'Greek', but those 'Greeks' actually being mostly 'Syrian' rather than 'real Greeks'.

https://sourcebooks.fordham.edu/ancient/juvenal3.asp

Michalis Moriopoulos said...

@A

There is almost certainly "real Greek" ancestry (if you mean Mycenaean-like) in the Roman samples, so Juvenal's bigotry is a moot point. Ironically, both Near Easterners and Greeks are the very kinds of people responsible for Latins like Juvenal having a civilization in the first place, which might not have been obvious to him but should be obvious to those simpletons today who echo his anti-Oriental sentiments.

Anyway, East Med takeover of Central Italy MIGHT have been mostly a cosmopolitan phenomenon (I reserve judgment on that), but I completely dismiss the idea that all of those East Med samples (half the set) were slaves. Some of them surely were, but most or all of them? No, that's not a realistic explanation. Mass immigration of FREE Greek-Near Eastern type people into cosmopolitan Italy makes more sense to me, especially if they were citizens of the Roman Empire. This process was probably par for the course in Magna Graecia during the Hellenistic era, and the same mixed Mycenaean-Near Eastern profile which took root in Southern Italy (which is typical of today's Southern Italians, Western Jews, and Greek Islanders like myself) made its way to Central Italy, too, where it became a real demographic force.

A said...

@ Michalis

"Ironically, both Near Easterners and Greeks are the very kinds of people responsible for Latins like Juvenal having a civilization in the first place, which might not have been obvious to him but should be obvious to those simpletons today who echo his anti-Oriental sentiments."

Ironically that's a bigoted statement.

Ironically, the Ancient Greeks were also bigoted.

"anti-Oriental sentiments"

Ironically you expressed an anti-Latin sentiment.

Samuel Andrews said...

@Michalis,

It is strange there is no one example of a pure Greek person in the Imperial samples. All of the samples with Greek ancestry, also have Near Eastern ancestry, and only few have Italian ancestry.

So, it looks like they came from a population who already had mixed Greek, Near Eastern ancestry before they came to Italy.

Magna Gracia doesn't fit the bill. Greek kingdoms in Near East do fit the bill.

gamerz_J said...

@Michalis Moriopoulos

"Ironically, both Near Easterners and Greeks are the very kinds of people responsible for Latins like Juvenal having a civilization in the first place, which might not have been obvious to him but should be obvious to those simpletons today who echo his anti-Oriental sentiments."

I don't want to derail the thread, but Indo-Europeans (broadly speaking) and Greeks to me seem to be more relevant to Roman civilization than Near Easterners from the Levant.

gamerz_J said...

In case anyone interested, I came across 2 papers that came out recently:

1) A paper on the Levant (Tell Atchana specifically) , where the most striking result to me seems to be the presence of one Central Asian outlier in 2nd millenium BS north Levant. I wonder if that sort of Central Asian ancestry is to be found in present-day inhabitants of the region or not. If anyone knows, feedback would be welcome https://www.biorxiv.org/content/10.1101/2020.10.23.351882v1

2) A paper on sub-structure in Mongolian populations, apparently driven by differential West Eurasian admixture.
https://www.tandfonline.com/doi/abs/10.1080/03014460.2020.1837952

Michalis Moriopoulos said...

@A

What a completely impotent response. If you actually think that the civilization of Rome could have developed into what it was without influences from further east, you're deluded. That's not anti-Latin sentiment; that's just history. Look up Orientalizing period. Learn where the Latins got their alphabet, and where the Etruscans got theirs, and where the Greeks got theirs. Going even further back in time, familiarize yourself with the J-rich proto-urban expansion of CHG and/or Iran Neo-like ancestry throughout West Asia, into Egypt, and into Greece. A nice pic from David to help you out:

https://1.bp.blogspot.com/-lkEU071GEU0/W1vRz0Kb_hI/AAAAAAAAHBE/MC7-df8hKLYuaLRXVNntHgu7EUCWjoaAACLcBGAs/w1200-h630-p-k-no-nu/ChL-BA_Eurasia_Eurogenes.png

So you might want to familiarize yourself with what irony actually means, if the Greek origins of the concept don't bother you too much. Keep your chin up, Juvenal!

@Samuel Andrews

I always appreciate your posts. I think you argue in good faith and in interest of the truth, even if I find some of what you say disagreeable. Anyway, these are my thoughts on the Greek problem:

How the Greeks genetically diversified after the Bronze Age is a perennial question on Anthrogenica and is of course extremely interesting to me personally as a Greek islander. I'm eagerly awaiting a nice ancient DNA time transect of the Greek world. Some stuff is easy: Pontic Greeks, Cappadocian Greeks-- these aren't mysterious. Cypriots are pretty easy to explain, too. But once you go further west, it's not so easy to tell what happened. I think the incorporation of historical Near Eastern ancestry into the circum-Aegean Greek gene pool might have started as early as the Iron Age, but perhaps limited to certain areas. For instance, some of the islands might have had a stronger Phoenician (Levant IA-like) or even Anatolia MLBA-like presence early on, while other parts of Greece and Western Anatolia (like the Ionian samples at Empuries) might have remained completely Mycenaean-like for some time to come. By the Hellenistic period, I do expect a more pervasive distribution of Near Eastern ancestry throughout much of the Greek world (both in Balkan Greece and elsewhere), but not necessarily at the same level or all of the same type. All modern Balkan Greeks have Anatolia MLBA ancestry (that persists in Northern Greeks despite Slavic dilution) while southern Greeks (Maniots, Aegean islanders) show Levant ancestry as well. So it's complicated.

I agree there's definitely the possibility of direct immigration of Syrian Greeks from places like Antioch straight to Rome, but it's also possible Magna Graecia was already full of people like what you see in the Roman study due to strong Hellenistic era migration into its territories before the Imperial era. Or maybe it's a bit of both. There are many possibilities, but those are my current thoughts on the matter. There was obviously a strong amount of Near Eastern gene flow into Southern Italy and Greece at some point in history, so it's about trying to pin down when and how this happened. The Roman samples make a Hellenistic era admixture event a parsimonious possibility, but it might only be part of the story.

Carlos Aramayo said...

@gamerz_J

The first paper you mention is a saga of a previous one claiming the case of a woman (the Lady of the well) which features Central Asian ancestry possibly connected to Indo-Aryan outliers in Northern Levant with male R1a haplogroup. This new paper adds three individuals with possible Central Asian ancestry but not confirmed by aDNA studies:

"...Indeed, dental morphology of the Well Lady shows shoveling of I2, a feature which is passed down genetically and is shared by three other individuals – 42.10.130, buried in the Royal Precinct, ALA012, buried in the extramural cemetery, and ALA139, buried in the Area 4 cemetery – as well as ALA030 (the accident victim found in Area 3), ALA132, and ALA133 (both buried in the Area 4 cemetery), although the trait is less pronounced in these latter three individuals. Of these six individuals, only ALA030 has thus far yielded sufficient aDNA preservation, and this individual is not a genetic outlier among the Alalakh population. It is possible, therefore, that the former three individuals, which show pronounced I2 shoveling, may also be genetic outliers, similar to the Well Lady..." (page 50).

Full paper at:

https://tinyurl.com/y6j7vx63

Copper Axe said...

"Northern Dutch are descendants of Frisians assimilated by Dutch in the Middle Ages. Germanic but not Frankish."

This has always been known. To begin with the entire northeastern half of the Netherlands was, and still is Saxon to this day.

In the west, the people of Holland (the region) still regularly identified as Frisians until the 11th century AD.

Carlos Aramayo said...

@gamerz_J

Regarding your question if Central Asian ancestry is to be found in present-day inhabitants of the Levant, I found that some people with R1a-YP5484* (formed 3700ybp) live today in Palestine, Southern Levant (not Northern Levant as it is Alalakh), and that´s a branch of R1a-Z94 through R1a-L657. You can find this info scrolling down the page in:

https://www.yfull.com/tree/R1a/

And maybe we can find more branches there.

On the other hand, Wikipedia says that Underhill (2009) found R1a recent branches mostly as follows: 1/121 in Omanis, 2/150 in Iranians, 1/164 in the United Arab Emirates, and 3/612 in Turkey. Although none of them in Northern Levant proper, except if we consider the Southern region of Turkey where Alalakh is found.

Joey said...

@Carlos Aramayo

Possible Steppe Maykop connection? They had derived EDAR. Did they test the Well Lady for EDAR?

Carlos Aramayo said...

@Joey

The Well Lady (ALA019) belongs to mtDNA haplogroup H2a3. The info belongs to Skourtanioti et al (2020). I do not see any connection with Maykop.

Vladimir said...

@ Carlos Aramayo
"Regarding your question if Central Asian ancestry is to be found in present-day inhabitants of the Levant, I found that some people with R1a-YP5484* (formed 3700ybp) live today in Palestine, Southern Levant (not Northern Levant as it is Alalakh), and that´s a branch of R1a-Z94 through R1a-L657. You can find this info scrolling down the page in:"


Actually, YP5484* is R1a-Z2122. This may be the Babino that went to the East, where it passed along the Eastern coast of the Caspian sea and then through Iran and became the Mittani culture in Northern Mesopotamia.

Or maybe Sintashta. More than 20 settlements are currently open in Sintashta, but paleogenetic analysis was taken only from the Kamennyi Ambar 5 settlement. However, studies of other settlements may have included other Z94 subclades, since these settlements could be formed according to the generic principle.

Archi said...

@Vladimir

"This may be the Babino that went to the East, where it passed along the Eastern coast of the Caspian sea and then through Iran and became the Mittani culture in Northern Mesopotamia."

These are generally anti-archeological fantasies.

epoch said...

@Copper Axe

Geographic names, e.g. the use of "-muiden" instead of "-monden" in place names such as Diksmuiden en St. Anna ter Muiden, suggest Frisian was spoken along the coast well into Flanders.

Vladimir said...

Rob
"There’s nothing strange about those studies, although I’d like to see some isotopic data to back Morgunova et al’s claims"

Morgunova's work has radiocarbon dates:
horse 1: 4769-4556 BCE; horse 2: 4517-4361 BCE.
Cow 1: 4681-4466 BCE. cow 2: 4221-3810 BCE.
Goat 1: 4898-4694 BCE.
There are a lot of samples, I took the oldest ones.

Alternatively, cows, goats and pigs were introduced to The black sea steppes through the Balkan agricultural archaeological cultures. Sheep through the Caucasus. The horse is domesticated directly in the black Sea-Caspian steppes.

Carlos Aramayo said...

@Vladimir

Yes, R1a-YP5484* is in the branch of R1a-Z2124 and R1a-Z2122. It is not in R1a-L657 as I told. And there's a possibility that it belongs to Mitanni ancestry as you say, even though it is now in Palestine, Southern Levant, not in Northern Levant as Mitanni was.

Rob said...

@ Vladimir

“ Morgunova's work has radiocarbon dates”

Yes I can see that. They make sense; we see domesticates in northeast Balkans by 5800 BC, Ukraine by ~ 5500 and Volga-Ural steppe by 4800 BC

But isotopic analysis are different things to C14 dates.
So, when they write “We suggest that from the Early Eneolithic local people practiced cattle breeding without agriculture. Hunting played a secondary role and fishing was poorly developed.”
they need to demonstrate this from human samples, not by counting cow bones on your hand

Ric Hern said...

To sustain cattle on grass only you usually need mineral supplements. Some protein and specifically phosphates. We needed very little supplements when our Cattle grazed in a mix of bushveld and grassy areas. The trees fruits and seeds provided a lot of those nutrients needed. Usually just a salt lick...

So I personally think that Cattle most probably spread to the East along the Forest Steppe rather than the open grassy plains...

Gabriel said...

Central Dutch cluster between North Dutch and South Dutch, suggesting they have Celtic admixture. Would this come from a South Dutch-like population or are the Central Dutch the closest to early Franks?

Garvan said...

Gabriel said...”Central Dutch cluster between North Dutch and South Dutch, suggesting they have Celtic admixture”

I think the common ancestry between Dutch and Atlantic Celts predates the Iron age, so keep this in mind when considering Celtic admixture in Dutch.

ejmohr said...

@Andrew
I don't disagree with your hypothesis but I find the story of mtDNA X to be very sketchy in the sense that the closest X to NE Asia today is, if memory serves, in the Altai region which is a long way from NE Asia.

It's totally possible that the bitter cold last LGM wiped out everyone with X in NE Asia and that a small founder population survived in Beringia. After the LGM they would have had to move south through the ice-free corridor in Alberta. My expectation would be that we would then find mtDNA X most commonly in Western NA and it would be less common in the east. For reasons that aren't yet clear, it seems that X in native Americans is most common in the east rather than the west. It's also surprising that mtDNA X didn't leave a trace in NE Asia. Even if most people were wiped out by the LGM you'd expect a smidgeon of X in the NE Asia area. I guess what we really need is a lot more ancient DNA from both Europe and Asia and NA.

Samuel Andrews said...

@Gaberial,

Lest we forget, for 500 years, modern Western Germany and Netherlands were originally territories of the kingdom of France ("Franks") for 500 years. That could be where their French-like ancestry comes from, and why Northern Netherlands (Friesland) and Lower Saxony (Saxons) lack it.

Ryan said...

@Gabriel - There's probably multiple layers of Celtic admixture in every current West Germanic speaking population. There are Celtic place names as far east as Poland after all.

JuanRivera said...

Adding on his comment, I think that the spread of cattle (and ovicaprines) to the open steppe and the North Caspian semideserts (such as the Ryn desert) could have been facilitated by gallery forests along the rivers and large enough streams.

Matt said...

What do you guys think of the theory that the Tollensee "Battlefield" was a massacre of merchants - https://www.theaustralian.com.au/world/the-times/oldest-battle-was-massacre-of-merchants/news-story/0c58fbd8a18f9b73b8f253fec71f3970 ?

@Sam, one thing about suggesting that the Roman Imperial samples were mostly slaves, that doesn't really make sense to me, is that we know that the north of the Roman Empire was also a source of slaves for Rome; Brits, Germani, Gauls. Like, that's what the documentary evidence says about slave sources, right? If these were sites of predominantly distant born slaves, why would we see only these "East Med" sourced slaves? It doesn't seem that plausible.

Samuel Andrews said...

I'll say this. I don't think the Imperial Roman samples represent old inhabitants of Italy.

I say this because, almost none of them seem to have Italian ancestry.

I don't see it as likely, they were the product of 100s of years of migration from Greece and Near East into Italy. If they were they would have significant Italian ancestry.

They seem to not at all be the descendants of earlier Latins and Etruscans of Central Italy.

Maybe, I am putting too much faith in the ability of G25 to differentiate Iron age East Balkan from Italian. Or maybe, I'm putting too much faith in Iron age Etrucans, Latins representing Iron age Italy. But, with the currents samples we have it seems Imperial Roman samples were brand new arrivals in Italy.

Archi said...

@Matt

1400 dead merchants? What kind of caravan is this? How many tens of thousands of people were there? Such gigantic caravans are even harder to believe than the army. And what could such gigantic caravans carry?

Gabriel said...

@Garvan

Yes I agree, but it’s possible that Iron Age Celtic migrations shifted the Netherlands further south, but they probably retain some Nordwestblock ancestry if they are admixed with Central Dutch Celts.

@Samuel Andrews

So you think Belgian-like Franks admixed with Scandinavian-like Frisians to create Central Dutch? What do you think happened to Central Dutch Franks? Just asking.

@Ryan

I don’t think there is a lot of Celtic ancestry in Northern Germany and the Northern Netherlands, they seem more Danish-like.

Matt said...

Sam, I suspect we'll see further sampling in the intermediary period which will resolve the questions you raise (though I have no specific news / knowledge), and that will be the better way to resolve this since there could be quite a few complex multi wave patterns here that make it obscure. Not knocking you trying to look into this with what we have now of course.

Archi, yes I think that's a reasonable comment; the argument that seems to be made is that the presence of high value goods and presence of women makes a battlefield implausible. I'm not sure about the idea of a caravan going to set up a market though; there could be other possibilities, like a wealthy community fleeing an invasive force. Another question is how much a foreign merchant community is consistent with isotope evidence (showing locals if I recall correctly)...

A said...

Egyptian DNA bombshell:

'Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship' (Gad et al. 2020)

“An investigative study was carried out on the familial relationships of a number of late 18th dynasty mummies (ca. 1550–1295 B.C.), including that of Tutankhamen. The study was based on the analysis of the autosomal and Y-chromosome STR markers in addition to mitochondrial hypervariable region 1 sequences. A 4- generation pedigree of Tutankhamun’s immediate lineage and the identity of his ancestors were established. The Royal male lineage was the Y-chromosome haplogroup R1b that was passed from the grandparent [Amenhotep III] to the father [KV55, Akhenaten] to the grandchild [Tutankhamen]. The maternal lineage, the mitochondrial haplogroup K, extended from the great-grandmother [Thuya] to the grandmother [KV35 Elder lady, Queen Tiye] to the yet historically-unidentified mother [KV35 Younger lady] to Tutankhamen.”

https://academic.oup.com/hmg/advance-article-abstract/doi/10.1093/hmg/ddaa223/5924364?redirectedFrom=PDF

(Published online 15th Oct 2020)

Joey said...

@Carlos

So what is the "Central Asian" ancestry theyre talking about then? Steppe Maykop is the only pop in the area and timeframe with confirmed derived EDAR, along with "Central Asian" ancestry. It's not that far fetched, regardless of her uniparentals.

Archi said...

@Joey

Steppe Maikop has nothing at all to do with it. It is not there.

@Matt

The isotopes show that they came from different places, and by no means that they were local all.

@A

According to Y-STR, the definition in our time is about nothing.

Ric Hern said...

@ A

Thanks. Very interesting. R1b. Wonder if it is R1b V88 or maybe from Hittite or Mycenaean influence ?

Arch Hades said...

haven't been keeping up as much the last few years but do the Imperial Romans have "Natufian" ancestry? If so this is clearly not Greek ancestry. It comes from the Levant. J2 rich CHG ancestry on the other hand was part of the Greek genetic profile from the get go. And it's possible IMO that the classical Greeks were more CHG rich than the Mycenaens.

Another thing is, is there confirmation of their 'status'? I mean in imperial Rome we even had a few Northern European genetic outliers too, no? We're these low status too? Anyway we know Carthage ruled Southern Italy before the first Punic war, and Phoenicians earlier colonized Sicily too. That's a good start on where to grasp where these East Mediterranean Greco-Levantines came from.

epoch said...

@Samuel Andrews

The Netherlands weren't part of a French kingdom. Rather, there were 4 or 5 Frankish kingdoms, sometimes, but mostly not, unified under one Merovingian kingo. The larger parts of the Netherlands and Belgium were part of Austrasia rather than Neustria. After the unification of the Frankish kingdom under Charlemagne the kingdome broke into three parts, where the Netherlands and Belgium minus the County of Flanders were part of the Middle Kingdom, later becoming the Duchy of Lorraine.

Most of the times the Country of Flanders was part of Austrasia, later of the East-Frankish kingdom and France, where it was part of the Peerage of France. This only ended in de 15th century. Yet there seem to be no notable difference between Flanders and the rest of Belgium.

epoch said...

Belgian linguist Gysselink claims there is no Celtic hydronym in Belgium or the Southern Netherlands. There are some sound shifts that look like Celtic - e.g kw -> p in -apa names descending from akwa - but which are unknown in any Celtic language.

This led to the suggestion of the Northwest block theory. However, by the time Caesar came to the area he already claimed there were some Germanic tribes that crossed the Rhine. Oddly enough Tacitus mentions the Nervians claimed Germanic descent.

Also, the Franks completely replaced the population of the Rhine area, the Southern Netherlands and the Kempen in Belgium, noted by the fact that no settlement continuity has been found that crosses the year 300. This fits the description of Roman authors of the time.

A said...

@ Archi

"According to Y-STR, the definition in our time is about nothing."

What does that mean?

epoch said...

"Most of the times the Country of Flanders was part of Austrasia, later of the East-Frankish kingdom and France, where it was part of the Peerage of France."

That should have been West Frankish kingdom.

Rob said...

I fail to see what’s so interesting about Egyptian pharaohs

Gabriel said...

@Epoch

What would be the reason why Belgians and South Dutch are so southern, in your opinion?

Romulus said...

Will be interesting if Tut has any autosomal from Europe and if there is relation to Ramses 2

capra internetensis said...

@A

Isn't that just the Tutankhamun R1b STR result from 10 years ago?

Samuel Andrews said...

@epoch,

Austrasia and Neutrasia were the two parts of early France. Not separate kingdoms. Correct? Or were they only loosely connected?

I suspect French-like ancestry in Germans in large part comes from the time when Austrasia (Western Germany) was apart of France. When France was a Germanic-Romance kingdom.

Michalis Moriopoulos said...

On Tut, it's probably V88. Not really that surprising or even exciting. What is exciting is the prospect of autosomal ancestry. That's what we desperately need from Egypt, and lots of it.

@Arch Hades

It's not purely Mycenaean-like ancestry, no, but nobody is saying that it was. These Greeks would be more like modern Greek islanders. How do you get from Mycenaean-like to Greek islander-like? By absorbing a lot of Anatolian MLBA-like and Levant IA-like ancestry, that's how. When, where, and how did that happen exactly? Your guess is as good as mine. Could be multiple waves of ancestry over time. Early Anatolian gene flow into parts of Greece is possible, as is Phoenician gene flow. Maybe even a Cypriot "back-migration" into the Aegean took place. Or maybe Hellenized Near Eastern people came into Magna Graecia and Greece itself en masse after Alexander's conquests. Nobody knows the details yet. That's all part of the fun and mystery of the East Med. But the process clearly happened in Central Italy by the time of the Roman Empire.

Samuel Andrews said...

@Arch Hades,

The Near Eastern ancestry in Imperial Rome is from Levant and Central/Eastern Anatolia.

The Levant source looks like it is mainly from pops resembling modern Lebanon, Syrian. So, yes they had lots of Natufian ancestry.

The Anatolian ancestry is not the same as the Anatolian ancestry in Myceneans and Minoans. It is mainly from Eastern Anatolia, while Myceneans' Anatolian came from Western Anatolia. It is differentiated by more Mesoptamia/ancient Iran ancetry.

Their European ancestry is mainly from East Balkans/Greece. Which makes their origins complicated. As you would expect their European ancestry to be from Italy/SW Europe.

Samuel Andrews said...

@Arch Hades,

There's only one North European individual in Roman samples. He was German, belonged to subclade of R1b U106 which was main lineage in Lombards. No information of burial, nothing really to talk about.

R31: Late Antiquity, 400-500 AD, Germanic.

In the Imperial samples there's only two fully European individuals, neither are Italian.

R37: Iberian.
R116: Gallic.

In late Antiquity, there's a rebound of Italian ancestry which resembles modern Northern Italians. 8 fully Euro individuals, 4 cluster in North Italy. Overall, in late Antiquity there's an increase of Euro ancestry in all samples which resembles modern North Italians. In imperial samples, their Euro ancestry was of East balkan origin.

Romulus said...

@Rob

The Pyramids were built at the same time the Bell Beaker Culture was beginning to spread around Europe. I think the Pharaohs were far more interesting than Europe at this time. Europe was relatively quite primitive.

Rob said...

@ Romulus
Yes fair enough
Although, firstly, Im partial to barbarians
And as Michalis said, some GW data from the population would be great

Joey said...

@Archi

The EDAR had to come from somewhere. Same source for both Steppe Maykop and these from Central Asia would make sense since theres no mention of East Asian affinity.

Davidski said...

@Joey

Are you talking about this or a related sample?

https://eurogenes.blogspot.com/2020/05/an-early-mitanni.html

If so, there's no need to posit a Steppe Maykop connection since there's already a Central Asian one.

People in Central Asia at the time were similar to Steppe Maykop, but not directly related to Steppe Maykop.

Arch Hades said...

The Near Eastern ancestry in Imperial Rome is from Levant and Central/Eastern Anatolia.

How do we know it's just not from a place like Sicily or something?

How do you get from Mycenaean-like to Greek islander-like? By absorbing a lot of Anatolian MLBA-like and Levant IA-like ancestry, that's how.

True, but I have some mega doubts ancient Island Greeks who lived on an island like Cyprus were ever Mycenean like genetically. They were probably always more genetically eastern shifted from the get go.

Samuel Andrews said...

Ancient Dog DNA.
https://phys.org/news/2020-10-ancient-dog-dna-canine-diversity.html

It says all modern European dog breeds come from one Neolithic farmer breed best represented by DNA from a Funnel beaker Dog in Sweden.

Jorge Escalante said...

Derived EDAR is present in the Motala hunter gatherers from Scandinavia. David Reich proposed that it has a west Eurasian origin.

Wise dragon said...

@Michalis Moriopoulos,

"On Tut, it's probably V88. Not really that surprising or even exciting. What is exciting is the prospect of autosomal ancestry. That's what we desperately need from Egypt, and lots of it."

Well, it’s pretty surprising since one would expect Tut who is a member of the native Egyptian dynasty to have the typical hp E1b1b. Anyway, I do think Tut will be proven to be R1b-M269. A Swiss company reconstructs King Tut's DNA profile from Discovery Channel documentary, 9 years ago. The results showed that King Tut belonged to the haplogroup R1b1a2. However, this finding was dismissed as rather speculative. Some geneticists questioned whether Gad's samples were contaminated. I agree with you, it's very exciting that there will be an upcoming paper which will reveal the autosomal DNA from Egyptian royals. Egypt has a fascinating history.

Samuel Andrews said...

@Arch Hades,
"How do we know it's just not from a place like Sicily or something?"

Because Sicily is in Western Europe. The default position is ancient pops there didn't have Syrian, Lebance, Anatolian, Greek ancestry.

Sicily was Greek territory from 800-200 BC. Which opens the door to East med admix.

But Greeks didn't have a direct relationships with the Near East until Alaexander the Great's conquests in 323bc.

So, how would Greek/Near Eastern hyprids, like we see in Imperial Rome, come into existence in 323bc.

Norfern-Ostrobothnian said...

Punic ancestry maybe?

claravallensis said...

ASH067 from Ashkelon dated to 1200-1000 BC was also at least R1b-M269, wouldn't be indeed surprising if Tut was also M269

Gabriel said...

@Wise dragon
@priscus

Only if Tut was a descendant of Hyksos, and it’s difficult already, since the Hyksos should have steppe or Kura Araxes influence or R1b-M269 in general, and their arrival in Egypt predates these samples.

Archi said...

@@

https://science.sciencemag.org/content/370/6516/579

https://i.ibb.co/bWfmGsh/Early-East-West-Eurasians-plus-Denisovans.png
https://i.ibb.co/M6pS37d/an-Qp-model-Salkhit.png
https://i.ibb.co/D9f75tP/PCA-Central-Eurasian.png
https://i.ibb.co/gdHVkBc/Eurasia-location-map-names.jpg
https://upload.wikimedia.org/wikipedia/commons/5/5b/Y-Haplogroup_Paleolithic_Migrations.png

Samuel Andrews said...

@norfern,

Good point. Punic could be a source. One Iron age Italy sample is 75% Levanti-ish, must be from Phoecians. One of the Etruscans is 50% Northwest Africans, must also be from Phoecias (carthage).

I'm a bit too opinionated on this.

It is important to get more ancient DNA from Rome/Central Italy, from 500 bc to 0ad. Cuz, there's no clear answer where this Greek, Near Eastern admixture came from.

Michealis thinks it came into Rome in 500bc to 0ad. I tend to think they were fresh of the boat from Greek kingdoms in Asia.

Samuel Andrews said...

The thing where I said they were slaves. I don't know Roman history enough to make that claim.

But the next Roman DNA study, needs to identify which burial is of slaves and which is not.

Samuel Andrews said...

If 18th dynasty comes out as R1b M269>Z2103 which it probably will.

You know, historians will do their best to cover up that the 18th dynasty of Pharohs had European Y DNA.

They'll say R1b Z2103 is Near Eastern with no mention it was a recent Bronze age arrival into the Near East from Eastern Europe.

They'll say it comes from "Eurasian Steppe nomads" instead of Eastern Europe, where R1b M269 and its ancestors had deep roots going back 10,000 years.

A microscopic section of overall ancestry in R1b M269 carriers in Near East is European, but the lineage does come from Europe.

If a Medieval European dynasty turned out to be Y DNA J2a which is entirely possible, you know historians would be all about calling their lineage Near Eastern.

Arch Hades said...

@Samuel

Sicily had already been colonized by Phoenicians well over 1,000 years before those Imperial samples. The Phoenicians came from the Levant so there's your Levantine admixture right there. And of course we know about the Greek colonies in Sicily.

Romulus said...

Blogger Samuel Andrews said...
Ancient Dog DNA.
https://phys.org/news/2020-10-ancient-dog-dna-canine-diversity.html

It says all modern European dog breeds come from one Neolithic farmer breed best represented by DNA from a Funnel beaker Dog in Sweden.

October 29, 2020 at 11:46 AM


Wow! great to finally have some insight into your maternal ancestry, very cool find.

Sofia Aurora said...

THE PAPER IS AVAILABLE NOW!!!

https://science.sciencemag.org/content/370/6516/579

Samuel Andrews said...

@Romulus,

That's a very clever way to call me a son of bitch. Lol.

Davidski said...

@Archi

Where did you get this?

https://i.ibb.co/gdHVkBc/Eurasia-location-map-names.jpg

Urki said...

@Michalis

I highly appreciate your comments, which are usually well informed, sensible and polite. I have sometimes heard that northern Greeks are recent "greeksised" slavs. May it be that before that they were "slavised Greeks"? (during 6th and 7th centuries AD).

Samuel Andrews said...

@Arch Hades,

Fair enough, but how extensive was Phoecian settlement in Sicily?

Michalis Moriopoulos said...

@Arch Hades. Samuel

Phoenician/Punic settlement in Sicily, Sardinia, and Iberia is a given. We already have ancient DNA confirming that. But Phoenician colonization is not a very satisfying way to explain the presence of Levantine ancestry in Greece or mainland Southern Italy, since these weren't really known to be Phoenician colonies. But who knows-- maybe Levantines did make an impact there. This issue can be easily solved with sufficiently dense Iron Age sampling of Southern Italy and the Greek isles. Right now we've got nothing to go on so establishing an upper bound on Near East gene flow into these areas is impossible.

Later (Byzantine-era) migrations can't be ruled out either. But based on the Imperial Roman samples, it's parsimonious to assume the modern East Med profile was pervasive in parts of Southern Europe in the centuries following Alexander's conquests (coinciding with Rome becoming an Empire). So mass Hellenistic migration of Syriac and Anatolian Greeks into the Greco-Roman world remains the most convincing explanation for now to me.

@Urki

Mainland Greeks can be sufficiently modelled with Mycenaean, Slavic, and Anatolian MLBA populations. They definitely have a lot of Northern European-style Slavic ancestry. The controversial point is how much of their Mycenaean-like ancestry is actually ancient Greek and how much of it is just pre-Slavic Balkan ancestry potentially absorbed by the Slavs before they got to Greece. That's going to be interesting to explore. I am partial to the idea (my own bias maybe) that the Slavs moved fast and didn't mix much with locals before they got to Greece. But I could be wrong. I do not believe Fallmerayer's theory of complete replacement, but I can't confidently rule out the notion that some of the Mycenaean signal in Greeks isn't actually from Thracian/Illyrian/Dacian-mixed Slavs.

Also, Aegean Greeks have Slavic ancestry, too. Just nowhere near as much as mainlanders.

CrM said...

I was looking at the Steppe Maykop outliers and noticed that while 2 out of 3 are a simple mix of Caucasus Maykop and Steppe Maykop, one among them has a more complex autosomal profile. The sample is roughly speaking half Caucasus Maykop, but his Steppe ancestry seems like a mix of Steppe Maykop and Steppe_EBA, but what's also interesting is that it has EEF ancestry that might have come in one batch along with Steppe_EBA?

Target: RUS_Steppe_Maykop_o:IV3002
Distance: 2.4229% / 0.02422853
51.2 RUS_Maykop_Novosvobodnaya
28.6 RUS_Steppe_Maykop
11.8 Yamnaya_RUS_Samara
8.4 UKR_N_o
0.0 Levant_PPNB
0.0 TUR_Tepecik_Ciftlik_N
0.0 POL_Globular_Amphora
0.0 AUT_LBK_N
0.0 WHG

Target: RUS_Steppe_Maykop_o:IV3002
Distance: 2.4809% / 0.02480867
51.8 RUS_Maykop_Novosvobodnaya
28.4 RUS_Steppe_Maykop
11.8 Yamnaya_RUS_Samara
8.0 AUT_LBK_N
0.0 Levant_PPNB
0.0 TUR_Tepecik_Ciftlik_N
0.0 POL_Globular_Amphora
0.0 WHG

Target: RUS_Steppe_Maykop_o:IV3002
Distance: 2.2618% / 0.02261797
41.0 RUS_Maykop_Novosvobodnaya:I6272
26.4 RUS_Steppe_Maykop
14.2 Yamnaya_RUS_Samara
11.6 RUS_Maykop_Novosvobodnaya:I6268
6.8 UKR_N_o
0.0 RUS_Maykop_Novosvobodnaya
0.0 Levant_PPNB
0.0 TUR_Tepecik_Ciftlik_N
0.0 POL_Globular_Amphora
0.0 AUT_LBK_N
0.0 WHG
0.0 RUS_Maykop_Novosvobodnaya:I6266
0.0 RUS_Maykop_Novosvobodnaya:I6267

Subtracting the Caucasus Maykop ancestry leaves us with a sample that has a closeness to the new Bronze Age sample from Romania.

Distance to: SM3
0.05728283 ROU_BA
0.06086078 KAZ_Maitan_MLBA_Alakul_o
0.06129073 RUS_Sintashta_MLBA_o2
0.06174611 RUS_Potapovka_MLBA_o
0.06252486 KAZ_Kyzlbulak_MLBA2
0.06844081 Yamnaya_RUS_Caucasus
0.07020318 Sarmatian_RUS_Caucasus
0.07056566 MNG_Afanasievo_1
0.07284102 Yamnaya_RUS_Kalmykia
0.07333004 Yamnaya_UKR
0.07456983 RUS_Lola
0.07491096 Sarmatian_RUS_Pokrovka
0.07508173 KAZ_Zevakinskiy_MLBA
0.07535781 RUS_Kubano-Tersk
0.07537173 Sarmatian_RUS_Caspian_steppe
0.07549419 KAZ_Dali_MLBA
0.07600221 Yamnaya_KAZ_Karagash
0.07621879 Sarmatian_KAZ
0.07627202 RUS_Catacomb
0.07787096 Sarmatian_RUS_Urals
0.07809612 RUS_Poltavka
0.07838662 Yamnaya_RUS_Samara
0.07883794 RUS_Afanasievo
0.07923943 RUS_Progress_En
0.07943004 KAZ_Chanchar2_LBA

ambron said...

Michalis, when it comes to islands, especially Crete seems to have a lot of Slavic origin:

https://onlinelibrary.wiley.com/doi/full/10.1111/ahg.12328

pricinfix said...

Hi everyone,
I was interested in determining tmrca of Yamnaya and Afanasievo. What is the tmrca of Yamnaya and Afanasievo? I read that
1. Yamnaya belonged to R1b-L51 lineage
2. Afanasievo belonged to R1b-Z2103 lineage

Can we say that tmrca was ~5500 BC (https://www.yfull.com/tree/r-l23/)?

Vladimir said...

@Samuel Andrews
«If 18th dynasty comes out as R1b M269>Z2103 which it probably will.

You know, historians will do their best to cover up that the 18th dynasty of Pharohs had European Y DNA.

They'll say R1b Z2103 is Near Eastern with no mention it was a recent Bronze age arrival into the Near East from Eastern Europe.»

This would be logical if we assume that the Tutankhamun dynasty survived from the time of the Hyksos. Taking into account the self-names of Armenians "haiki" and the dominant haplogroup Z2103 among Armenians. In this case, everything logically coincides that the Hyksos are a dynasty of shepherds, that they introduced the Egyptians to chariots, that the appearance of domesticated horses in Asia minor occurred after 2000BCE, that the Trialeti culture was at this time, the displacement of Catacomb tribes from the steppe also at this time.

Davidski said...

@pricinfix

1. Yamnaya belonged to R1b-L51 lineage
2. Afanasievo belonged to R1b-Z2103 lineage


Not true.

Both Afanasievo and Yamnaya samples mostly belong to Z2103.

One Afanasievo sample probably belongs to L51.

Foxvillager said...

Let me give a try of Greek genetics with my own bias!!!

Pontic Greeks=Half Colchians(Kartvelian) and half BA Anatolian.Genoplot and G25 models Pontic Greeks as half Georgians half Cappadocian Greeks.They are between Caucasus and east med.

Cappadocian Greeks=Mostly BA Anatolian with adittional steppe admixture(prolly from Phrygians or Galatians).Kayiseri Turks are not that different if you delete their east asian/siberian admxiture.In general they require a good chunk of Steppe DNA.

Cypriots=Mostly BA Anatolian as well but some individuals shift to the Levant while others shift to East Med(Greek islands etc).Cyprus in general was a BA kingdom with the name Alashiya but later Phoenicians and Mycaeneans colonized it.Some Cypriots are indeed closer to Northern Levantines but i think it depends to individual.I have seen Cypriot kits who are more close to Greek islands rather to Levant.

Greek islanders=I have modeled Greek islanders inclunding Cretans many times and they prefer BA Anatolian refrences instead the Emporio2 from Catalonia sample witch is a classical Greek refrence from Phocea.Their autosomal is mostly BA Αnatolian and then it has a good bulk of ancient Greek plus Levant BA/IA with a good portion of Slavic.Crete is indeed more Slavic than the other islands like Dodecannese who are also more west asian admixed.To mention that Slavic admixture in these islands is prolly a more recent phenomenon,because these islands used to be a hideway during Ottoman times for mainland Greeks.

Mainland Greece.I have explained many times that some parts of mainland Greece are not so slavic like other provinces/areas that can be.Yes Greek Macedonia and Thrace(Thracian Greeks) are the most Slavic of all.Even by ydna some lineages are 100% Slavic markers.Epirus is similar to south Albanians,it contains also a great community of Aromanian Vlachs.Most of the toponyms there are of Slavic and Vlach origins.Thessaly is the place witch one of the biggest Vlach communities in Balkans.Most people identify themselves as Vlach.Genetically they are more southern genetically than Greek Macedonia.Central Greece is also a place where Arvanites,Vlachs have settled.The area is not very sampled but some kits i have seen they are between Greek Thessaly and Peloponnese.Attica was also a place where Arvanites had settled.Most people from these lands have Albanian origins and some of them even today speaking the Arvanite Dialect.Peloponnesus is also very Slavic admixed and most kits and samples i have seen from there are shifting quite northernEven Maniots and some Laconians who are the most isolated Greeks from tis province are also quite northern genetically compared to Cretans or Greek islanders.Only the samples from G25 are not so northern shifted and that's why many Greeks from anthroforas complain that they do not represent them xD.David had mention many times about the Peloponnesian samples from G25 i am not going to discus it more.But as Michalis mantion even mainland Greeks require some BA Anatolian admixture in their modeling.I think that Greece had become something like Rome Imperial at some time.What we saw in the Roman paper have actually become pretty much in many parts of the Empire and not just in the Italic peninsula.Also repopulations from anatolia or the Levant during Byzantium Empire with christianicized folks arriving in Greek mainland.Well,ofc i am not avoiding the fact that during LBA/IA Greeks mixed with Anatolians during the colonization period thus they become more west asian admixed...but the Emporio samples do not show something like this.The samples are actually very Mycanean like but if i remember well one of it,it contains some limited Levantine admixture..but not something crazy.I think this west asian migration took place prolly during Roman and Byzantine periods but who knows it might took place much earlier.The only thing to found it out is papers-studies from Greece.

Foxvillager said...

@ Copper Axe

Well,these things are well known xD.What we don't know its why modern Northern Dutch and Northern Germans and also some Danish people are more southern genetically than Scandinavians.Most people can't answer this question :DDD.Do you really believe there was a La Tene like or any Roman migration to these lands and its people during antiquity?I bet there wasn't.But for some mysterious reason they are more southern than Swedes and Norwaygians.Also more southern than Nordic BA/IA if i am not mistaken.

A said...

R1b-V88 originated in the Balkans and has been found in the Varna culture, c.4500 BC. If it turns out the 18th dynasty was R1b-V88 then there's a genetic link between the Varna culture and the Egyptian pharaohs..

pricinfix said...

@Davidski
You are right; I also checked. What I found from my search was that the following lineages that were different in Yamnaya and Afanasievo (according to Sergey Malyshev/Kolgeh):

1. Yamnaya samples belonging to R-Y20993.
2. Afanasievo samples belonging to R-L945.

So, the tmrca seems to be between 5500 BC - 4500 BC. Am I wrong? If it is more recent, what do you think is the correct date?

ambron said...

David, what do you think about this L1029 sample from La Tene in Bohemia, the most similar to the Scandinavians in terms of the whole genome? For example, Michał recognizes L1029 as a characteristic marker of Slavic migration from Pripyat to Central Europe. I think that L1029 cannot be both in Central Europe before the Slavic migration and remain a marker of Slavic migration to Central Europe.

Gabriel said...

@Bessarion

Probably just higher TRB ancestry. Some Nordic BA samples show a southern shift, so that may be it.

Davidski said...

@ambron

Let's wait for the paper.

Davidski said...

@pricinfix

So, the tmrca seems to be between 5500 BC - 4500 BC. Am I wrong? If it is more recent, what do you think is the correct date?

Perhaps, but it's very difficult to be that precise with these things.

Anyway, even if true, of course this doesn't mean that Afanasievo split from Yamnaya at that time.

The reason that these populations have different subclades is because of rapid founder effects.

Foxvillager said...

@ Gabriel


I have ended up with the same conclusion.And Danes,taking serious G25 they are between Nordics and NorthSea Germanics.Their genes have to do with province-region.Danes(the tribe) come prolly from modern Sweden,while the Danish lands(modern Denmark) was inhabit by Northsea Germanic people(Angels,Jutes etc who were prolly less TRB admixed.Also the west germanic speakers have come in contact with other mysterious culture,that we sadly lack DNA.Northwest Block and Jastford.They might have been BB pockets,and their autosomal might have been in some way more southern than Nordic IA.But i am just guessing here!!!

Joey said...

@Davidski

I guess I wasnt clear enough, I didnt mean that they were connected to Steppe Maykop, just that both got their derived EDAR from a similar source pop in Central Asia. Steppe Maykop was just the only derived EDAR I could think of in the area.

Richard Rocca said...

@Davidski said...One Afanasievo sample probably belongs to L51.

Several of us have looked at it and there is no doubt that the SHT001 sample from Afanasievo is L51+ P310+ P311+ (3112-2918 BCE).

epoch said...

@All

"Northwest Block" isn't a culture, it's a proposed branch of the Indo-European language family. If forced to choose the Hilversum culture might be associated and the Elp culture but do take in mind that this is all just theory, and likely always will be. We actually have DNA from one of the aforementioned cultures: The U 106 from Tuithoorn is from the Hogekarspel culture, considered a local variety of the Elp culture.

Samuel Andrews said...

@pricinfix,

It seems you are trying to get confirmation Afanasievo dates all the way back 5000 BC for some reason.

Afansievo and Yamanya are identical genetically. Their common ancestor was almost definitely the Repin culture which existed from 3500-4000 BC.

Both Yamnaya and Afanasievo belonged to R1b Z2103. R1b Z2103's TMRCA is 5400 BP according to yfull which is 3400 BC. Not 5000-6000 BC.

pricinfix said...

@Davidski

True; founder effect can play a part. Is there any way that we can estimate the split time — of Yamnaya and Afanasievo — from autosomal DNA? Any technique or tool for this you know?

Archi said...

@Joey

It is clear that you yourself do not understand a word in what you write. What do you mean by EDAR? Who are you writing about? Understand, if you yourself do not understand what you are writing, then no one here understands all the more. Your proposals are incomprehensible to anyone at all, you do not decipher them, you do not provide any data, as if what you are mistakenly saying is clear to everyone.

Tigran said...

Regarding the ANE situation in Asia it seems like there was a proto ANE population of ydna C1a2/C1b guys. Those lineages were wiped out by East Eurasian K2b/P either from China or SE Asia creating ANE. ANE after mixing with more West Eurasian females had this ancestry diluted. Eventually they were forced out of North Asia by ydna C2b Baikial Neolithic guys. Does that seem right?

Rob said...

@ Tigran
Well for a start Baikal Neolithic is mostly Hg N

Archi said...

@Tigran

"Regarding the ANE situation in Asia it seems like there was a proto ANE population of ydna C1a2/C1b guys."

Nonsense. You always write erroneous statements. C1a2/C1b had nothing to do with proto ANE at all.

"Those lineages were wiped out by East Eurasian K2b/P either from China or SE Asia creating ANE."

Nonsense. You do not know how to read, K2b/P have never been from East Asia or SE Asia, they do not have the Denisovan component that appeared in Tianyuan, who came to East Asia, and even more so they do not have the Southern Denisovans from SE Asia, which Tianyuan does not have. ANE is the northern Central Eurasian component, conditionally related to the western branch, but not the Western Eurasian.

There was only migration from the West to Eastern Eurasia in the Paleolithic, and all the similarities in Eastern Eurasia to ANE are associated with the influence of ANE on Eastern Eurasia due to the migration of early ANE-like components, one example of which is Yana. This can be seen not only in genetics, but also in all other sciences, anthropology, archeology, etc.

"ANE after mixing with more West Eurasian females had this ancestry diluted. Does that seem right?"

Completely wrong. You don't seem to be reading scientific articles. And in them it is clearly written that Yana belongs to the Western Eurasian branch (more precisely, to the Central Eurasian) and Ust-Ishim, which was in Western Siberia (Central Eurasia) even before the division into western and eastern branches, and he belonged to K2a.

Samuel Andrews said...

@princinix,

The origin of Proto-Indo Europeans was around 5000-4500 BC. The split between Yamnaya and Afansievo ancestors happened later sometime in 4000-3000 BC.

Foxvillager said...

@ Epoch


What do you think happened to these BA people?Elp-Hilversum culture's?They assilimated in the later Western Germanic and more specific to Weser-Rhine speakers?

Tigran said...

@ Archi

That's the biggest cope I've ever seen.

pricinfix said...

@Samuel Andrews

Yes, Yamnaya and Afanasievo split can happen between 4000 B.C. and 3000 B.C. The exact time of separation is an important clue in determining the PIE homeland; its sad that nobody has estimated it precisely. Autosomal DNA can help in estimating when the divergence exactly happened. Do you know how to estimate it? F statistics and branch length estimation can be helpful for it, I suppose — don't know how to do it though.

Sofia Aurora said...

FOLKS SORRY TO BREAK OUT OF THE SCOPE OF THE POST, BUT HAVE YOU LEARNED THESE NEWS?
https://siberiantimes.com/other/others/news/sensational-find-of-a-250000-year-old-milk-tooth-found-inside-the-denisova-cave-in-siberia/


https://mobile.twitter.com/IAET_SBRAS__NAP/status/1311923676519051267

Aram said...

Tigran

P or even K2b are not from East Asia. P moved to Siberia via Central Asia.
That theory about SE Asia is obsolete and wrong.

Davidski said...

@pricinfix

Afanasievo and Yamnaya are one and the same population in terms of genome-wide ancestry. There's no clear autosomal split there.

Arza said...

There a two new videos with Stamov:

https://www.youtube.com/watch?v=KzAL0ssXwgc
https://www.youtube.com/watch?v=2Glrz8sUOMg

Does anyone here know Bulgarian and could say if he revealed anything new?

Ric Hern said...

@ pricinfix

Maybe you should look at the Lower Don River during the Eneolithic...

Cy Tolliver said...

@Tigran

If P does really have a SE Asian origin, why doesn't the earliest P sample, Yana at 31,000 ybp, have any SE Asian specific drift? All he shows is a vague extra affinity to East Eurasians relative to other ancient West Eurasians. Yana could possibly be mixed with EE but so far (to my knowledge) there's nothing linking him genetically to any particular subset of EEs. IIRC correctly from the original paper, his EE ancestry looked like it was even more basal than Tianyuan.

epoch said...

@Bessarion

I really don't know. The magnificent large structures on the Veluwe - such as the 6 km long rows Epe-Niersen barrows - show continuous use up until the early Iron Age.

What I am curious about is how well established the idea is that proto-Germanic is a combination of two different branches of IE dialects, based on the fact that Germanic languages show many isoglosses with Balto-Slavic languages while being a Kentum-language.

Maybe it means something in this discussion. Also, I am by no means an expert here.

Archi said...

@Arza

It was already.

https://eurogenes.blogspot.com/2020/08/fascinating-stuff.html?showComment=1598269506039#c489431518986999224

Arza said...

@ Archi

These videos were uploaded less than 2 weeks ago (20 Oct 2020).

Arch Hades said...

@ Michalis

Mainland Greeks can't have that much "Near Eastern" ancestry...as in post Mycenaean ancestry from the Near East. Maybe 10% i would guess, which would have come in some time between the Greco-Persian Wars and the fall of Constantinople and Byzantium to the Turks. So "some time" here being a span of about 2,000 years, which is understandable. The Natufian component that is 10-15% in Southern Italy or Cyprus is maybe ~3%~ in modern mainland Greeks and this is about 30% or more of the ancestry in Levantine populations and ancient Canaanites. As for the Cypriots, it's ridiculous to think the general population there was ever identical to Myceneans. My guess is they were a very "Eastern" genetically Greek populace in antiquity.

Regarding the Imperial "Romans", well modern Southern Italians are more European than they are. It seems to me these people mostly just died out. So my guess is modern Southern Italians are just Samninite-Greco-Phoenician hybrids with some small Medieval North African and even possibly very small Medieval Germanic ancestry.

Modern Mainland Greeks. Well they're just Bronze age Greeks + some very modest "general" Bronze age and later Levantine or Anatolian ancestry over the course of thousands of years, mixed with some considerably stronger Slavic ancestry thanks to the Slavic expansion. Basically in Greece the Anatolian true Neolithic farmer ancestry has gone down since Myceanean times, Mesolithic European Hunter-Gatherer ancestry has increased as well as Caucasus Hunter Gatherer ancestry. That's why Greeks shift more Northern and Eastern compared to the Bronze age Greeks.

Lastly, we should be careful to believe that the Classical Greeks were absolutely Identical to the Bronze age Greeks. The Crete_Armenoi sample from Laz 2017 might indicate Greeks a little after the Bronze age were starting to get more genetically North and Eastern shifted like modern Greeks. Perhaps the Dorians are responsible for this, i'm not sure. But i'm definitely not sold the classical Greeks will be identical to the Mycenaeans.

ambron said...

Arza, around 17 minute there is a board with I2a1a2b.

Michalis Moriopoulos said...

@Arch Hades

Are you on Anthrogenica? We discuss this topic a lot over there (in depth) so you might want to check it out.

Mainland Greeks don't have as much post-BA Near Eastern influence as the islanders, obviously, but they still require Anatolia MLBA-like ancestry in my models. The MLBA reference is the best we got until something decent from IA Anatolia comes out. I don't know how or when this got to the Balkans but I suspect medieval Balkan Greeks had a lot more of it before the Slavic migrations.

The Crete Armenoi sample is low quality so I'm content to ignore it. We do have the Empuries samples from the IA that cluster with Mycenaeans so obviously the BA profile survived into the Classical Era. The BIG question then is did different types of Balkan and Aegean Greeks co-exist with this Mycenaean profile at the time. We just don't know. There might have already been Near Eastern and north-shifted Greeks living in other parts of the circum-Aegean and that's what I hope is soon revealed. Your point about a pre-Slavic northern shift is well-taken. Sorcelow on AG often posits the possibility of a haplogroup E-bearing northern-shifting influence coming into Greece after the BA. That's certainly possible and, indeed, might even be tied to Dorians.

On the Imperial Romans: Southern Italians are very similar to them so I couldn't disagree more. There might have been some northern influences in the mix, but Southern Italians are basically the same type of people as the Imperial Romans. In fact, an East Med profile persisted even in Central Italy well into the Middle Ages. You do begin to see it diluted with more northern influences after Late Antiquity, but there is definitely continuity there. We don't have any ancient samples from Southern Italy right now, but don't expect any surprises. You're going to see a lot of West Med Latin-like people there before Greek and Phoenician. And by the Hellenistic era, it's going to be crawling with people like Al Pacino.

Foxvillager said...

@ Arch Hades

Cyprus was a bronze age Anatolian kingdom with the name Alashiya before Greeks and Pheonecians colonized it.Their autosomal DNA is still today mostly BA Anatolian associated.They clushter first with Cappadocian Greeks,Greek islanders and Cretans and then with Levantines.Ofc there are kits and samples who might shifting closer to the northern levantines but overall their ancesty is Anatolian and that's the reason they are very close with Cappadocian Greeks and Greek Islanders because all of them share the BA Anatolian genetic make up.It begins from Pontic Greeks and even Armenians(thought Armenian are more Arslantepe) and catches Greek islands,Mainland Greece and goes even to South Italy,Sicily.Ofc many of them do not have simply BA Anatolian admixture but also BA/IA Levant especially Greek islanders and Cretans.Also Cyprus has a decent steppe DNA for such a small and isolated island i am wondering if its coming from Greeks,Anatolians or maybe even Phohenicians.

Foxvillager said...

@ Michalis

South Italians inclunding Sicilians are a combination of Pre-Greek(Italic people)+ Greeks-Myceneans plus additional Anatolian/Levant/North African input depends region.As for the lovely actor Pacino he does not look Greek imo.

Foxvillager said...

@ Epoch

I think Elp and later northwestblock were BB hotspots and assilimated by the arrival Celts and Germanics forming the Belgian and Frankish ethnicities.Belenux,Northern France,Western Germany(Rhineland,Saarland,Hesse,Rihneland Palatinato etc) are all descended mostly by these people who are a combination of Gauls and Franks and ofc the assilimated BB pockets that cathed catched in the northwest area of modern Belenux-Friseland... and its obvious also from some R1b lineages and clades that you cannot find among other Germanics.

Cy Tolliver said...

@ Sam Andrews

A while back I remember you saying you were going to start working with Admixtools yourself - have you downloaded it yet and done any work with it? I've always been impressed with your general commentary here which seems to be informed strictly by your own G25 work and close readings of the latest academic papers. I feel like you would have even more powerful insights if you were working directly yourself with things like DStats, qpAdm, qpGraph, etc.

BTW, are you on Anthrogenica?

Joey said...

@Archi

Derived EDAR causes the incisor shoveling found in those remains, and the only derived EDAR in the area and timeframe is from Steppe Maykop. As its a variant associated with East Asian populations, assuming it came from the Caucasus side and not the Central Asian ancestry of Steppe Maykop doesnt make sense. Can you name a sample from the same timeframe from the vicinity that also carries the derived EDAR variant other than the Steppe Maykop sample? The EDAR variant didnt just drop from the sky, so wondering if it could be related to the one and only sample from the same timeframe and area also carrying it is not as crazy as youre acting like it is.

You can just not answer by the way, no reason to go toxic. Not the first time either.

Vladimir said...

What nonsense is published in scientific journals. I assume that this article was sponsored by Carlos 🤣

https://www.biorxiv.org/content/10.1101/2020.11.02.364521v1

Copper Axe said...

Funniest thing you will read all week:

https://www.biorxiv.org/content/10.1101/2020.11.02.364521v1

Check how they explain the spread of Indo-European languages as well for a fun bonus.

Samuel Andrews said...

@Davidski, Rob, All.

This is about Corded Ware and Bell beaker.

Based on archeaology & ancient DNA, it seems to me the each case the Kurgan tribes conquered native communities/populations then absorbed their populations. I think this is why admixture happened immediately and was complete in only 300-500 years in most cases. I'd like to get your opinions on this.

I know Rob you dis agree. But, how else do you explain why almost Neolithic cultures in Northern Europe disappeared at the same time Corded Ware appears? Not every single one. But just about every single one. This supports the idea that Corded Ware destroyed native settlements and took their land. But then also absorbed the native population which can explain why farmer admixture became widespread and significant in Corded Ware so quickly.

Y DNA further supports this. As Y DNA was basically an ethnic marker for both Kurgan and many Neolithic farmers. The fact, the mixed populations of 3rd millenium BC Europe almost all have Kurgan Y DNA is further evidence it was the Kurgan tribes who absorbed the native populations not the other way around.

Corded Ware Swiss have Farmer Y DNA and elevated farmer ancestry. There's Y DNA I1 in Scandinavia which is of farmer origin. Welzin Bronze age had mostly Y DNA I2a and low Kurgan ancestry. But, these are exceptions.

Rob said...

Stanov mentions/ lists I2a1b, which in ISOGG 2020 is I2a2a-M223 (ISOGG 2016); which is in likelihood is the I2a2a1b1 already present in Bulgaria Yamnaya, DD2, etc
He also mentions someting about Trojans ..

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