search this blog

Tuesday, February 20, 2018

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)


At last, after many months of waiting, the paper that I've been calling the Bell Beaker Behemoth will finally appear at Nature today or tomorrow, depending on your time zone [Update: the paper is here]. The accompanying dataset is already online, and it's twice as big as what the paper's bioRxiv preprint promised, packing 400 new samples from Neolithic, Copper Age and Bronze Age Europe (freely available via the Reich Lab here).

I'll incorporate these samples into my collection of ancients very shortly, and then put them through their paces in the usual and new ways.

Nevertheless, despite the much larger and more varied new dataset, I know for a fact that the conclusions in the paper are the same as those in the preprint (which we discussed here). The authors tentatively accept the archaeologically-based academic consensus that the Bell Beaker phenomenon originated in Copper Age Iberia. But they admit that they can't find evidence in their ancient DNA data that its expansion across much of the rest of Europe was accompanied by significant gene flow from Iberia, and thus driven by migration.

However, they do see in their data a large-scale migration of Central European Beakers to Western Europe around 2500 BC, bringing with them, amongst other things, steppe or Yamnaya-related admixture to the region for the first time. Many of the new samples are from the British Isles - where the impact of this migration was profound, resulting in at least a 90% turnover of the population - and they appear to have been collected specifically to reaffirm this conclusion.

How exactly this massive population turnover came about isn't known yet. But early indications from other parts of Europe, where similar population shifts have been inferred from ancient DNA for the Late Neolithic/Early Bronze Age period, are that plague epidemics and deadly violence may have been important factors (see here and here).

I don't have a strong opinion about the place of origin of the Beaker cultural package, and I don't find the Iberian model entirely satisfying, mostly because it doesn't gel with the latest ancient DNA data. On the other hand, I've made up my mind as to who the Central European Beakers rich in steppe ancestry and also Y-haplogroup R1b-M269 were, and you can read about that here.

What are your thoughts after looking over the new samples? It's a big dataset alright, but does it do justice to the massive and complex Bell Beaker phenomenon? If not, then what's missing? Who's actually happy that the puzzle of the origin of the Beakers has now been solved? Feel free to let me know in the comments below.

Update 21/02/2018: I've updated the Global 25 datasheets with most of the ancient samples from Olalde et al. 2018 and Mathieson et al. 2018 (see list here).

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

See also...

Who's your (proto) daddy Western Europeans?

Sunday, February 18, 2018

C for Cheddar Man (?)


A new preprint has just appeared at bioRxiv on the Mesolithic to Neolithic transition and resulting massive population shift in Britain. It features genome-wide data from six Mesolithic and 67 Neolithic individuals, including the famous Cheddar Man.

Population Replacement in Early Neolithic Britain by Brace et al.

The peculiar thing about this preprint is that it doesn't list the Y-haplogroups of the male ancients. However, it's been rumored for a while that Cheddar Man belongs to Y-haplogroup C (for instance, see here). Has this now been confirmed officially anywhere?

On a related note, the guys at DNAGeeks have been working on a range of Cheddar Man products (see here). So for a few bucks you can get yourself a Cheddar Man tee or wall print based on this arty depiction of the Mesolithic British forager. Yes, his resemblance to pop icon Prince is indeed uncanny.


Thursday, February 15, 2018

Modeling genetic ancestry with Davidski: step by step


There are many different ways to model your genetic ancestry. I prefer the Global25/nMonte method (see here). This is a step by step guide to modeling ancient ancestry proportions with this simple but powerful method using my own genome.


As far as I know, the vast majority of my recent ancestors came from the northern half of Europe. This may or may not be correct, but it gives me somewhere to start, so that I can come up with a coherent model. If you don't have this sort of information, because, perhaps, you were adopted, then just look in the mirror, and work from there. Like I say, it's not imperative that you know anything whatsoever about your ancestry, because your genetic data will do the talking, but you do need a model when modeling.

In scientific literature nowadays, Northern Europeans are often described as a three-way mixture between Yamnaya-related pastoralists, Anatolian-derived early farmers, and Western European Hunter-Gatherers (WHG). So let's see if this model works for me. Obviously, if it does, then it'll confirm the information that I have about my origins, but it might also reveal finer details that I'm not aware of. The datasheet that I'm using for this model is available here.

[1] distance%=6.9025 / distance=0.069025

Davidski

Yamnaya_Samara 53.9
Barcin_N 30.75
Rochedane 15.35
Tepecik_Ciftlik_N 0

Yep, the model does work, with a fairly reasonable distance of almost 7%. The ancestry proportions more or less match those from scientific literature and the plethora of analyses that I've featured at this blog on the topic. Please note that I've kept things very simple, using only four reference populations and individuals as proxies for four distinct streams of ancestry. But I've put my own twist on this Neolithic/Bronze Age model by including two populations from Neolithic Anatolia (Barcin_N and Tepecik_Ciftlik_N), just to see what would happen. The WHG proxy is Rochedane.

Admittedly, though, my Yamnaya cut of ancestry appears somewhat bloated at over 53%, and the model's distance is a little higher than what I normally see for really strong models. So let's check if I can get a better fitting and more sensible result by adding a slightly more easterly forager proxy than Rochedane: Narva_Lithuania.

[1] distance%=5.9331 / distance=0.059331

Davidski

Yamnaya_Samara 45.75
Barcin_N 31.45
Narva_Lithuania 22.8
Rochedane 0
Tepecik_Ciftlik_N 0

The statistical fit does improve, and when given a choice between Rochedane and Narva_Lithuania, the algorithm picks the latter as the only source of extra forager input in my genome.

What could this mean? It might mean that a large part of my ancestry derives from the Baltic region. Actually, I know for a fact that this is true. But even if I had no idea about my genealogy, this result would be a very strong hint about my genetic origins. Indeed, let's follow this trail and try to further improve the fit of the model by adding a more relevant Yamnaya-related proxy, such as early Baltic Corded Ware (CWC_Baltic_early).

[1] distance%=5.444 / distance=0.05444

Davidski

CWC_Baltic_early 54.95
Barcin_N 26.7
Narva_Lithuania 18.35
Rochedane 0
Tepecik_Ciftlik_N 0
Yamnaya_Samara 0

Holy shit! To be honest, I wasn't expecting this sort of resolution and accuracy, and I can't promise that everyone using the Global25/nMonte method will see such incredibly nuanced outcomes, but this isn't a fluke. It can't be, because it gels so well with everything that I know about my ancestry. Please note also that I belong to Y-chromosome haplogroup R1a-M417, which is a lineage intimately associated with the Corded Ware expansion across Northern Europe (for instance, see here).

But of course, the Baltic and nearby regions haven't been isolated from migrations and invasions since the Corded Ware times. For instance, at some point, probably during the Bronze Age, Uralic-speaking peoples moved west across the forest zone of Northeastern Europe and into the East Baltic and northern Scandinavia. It's generally accepted that they brought Siberian admixture with them (see here). Moreover, from the Iron Age to the Middle Ages, East Central Europe was under intense pressure from a wide range of nomadic steppe groups with complex ancestry, such as the Sarmatians, Avars, Huns, and Mongolians. Did any of these peoples leave their mark on my genome? At the risk of overfitting the model, let's explore this possibility by adding a few more reference populations.

[1] distance%=5.444 / distance=0.05444

Davidski

CWC_Baltic_early 54.95
Barcin_N 26.7
Narva_Lithuania 18.35
Han 0
Mongolian 0
Nganassan 0
Rochedane 0
Sarmatian_Pokrovka 0
Tepecik_Ciftlik_N 0
Yamnaya_Samara 0

Nothing changes when I add the Han Chinese, Mongolians, Nganassans (an Uralic people from Siberia), and Sarmatians to the model. But what about if I throw in the only ancient Slav in my datasheet?

[1] distance%=2.9904 / distance=0.029904

Davidski

Slav_Bohemia 85.9
CWC_Baltic_early 7.7
Narva_Lithuania 6.4
Barcin_N 0
Rochedane 0
Tepecik_Ciftlik_N 0
Yamnaya_Samara 0

Considering that the vast majority of my recent ancestors were Poles, thus a Slavic-speaking people from near the Baltic, this outcome makes perfect sense. And check out the new distance! But the problem now is that I'm overfitting the model by using two very similar and probably very closely related references, CWC_Baltic_early and Slav_Bohemia. And overfitting should be avoided at all costs. So it might be useful to break up this effort into two models: one focusing on the Neolithic and Bronze Age, and the other on the Iron Age and Middle Ages. I'll do that soon, but not just yet, because there are still too few Iron Age and Medieval samples available from the Baltic region and surrounds for meaningful analyses of this type.

For a more technical guide to running Global25-type data with nMonte, please refer to this post at my other blog by regular commentator Onur: An nMonte and 4mix guide for the participants of the Basal-rich K7 and/or Global 10 tests.

Tuesday, February 6, 2018

Unleash the power: Global 25 test drive thread


Ancestry modeling enthusiasts, feel free to do your best (or worst) with these datasheets and share the output, whatever it might be, in the comments below:

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

Global 25 PAST datasheet

The Global 25 is a more powerful version of the Global 10 ancestry analysis (see here). If all goes well in the comments, it'll soon be offered for free to those who already have Global 10 coordinates. After that, we'll see what happens.


Below is a quick attempt to model Samara Yamnaya with its Global 25 coordinates using nMonte2. Hmmm...interesting stuff.

[1] distance%=2.4936 / distance=0.024936

Yamnaya_Samara

Samara_Eneolithic 71.15
Armenia_EBA 13.6
CHG 12.6
Iran_LN 2.65
ALPc_MN 0
Anatolia_BA 0
Anatolia_ChL 0
Armenia_ChL 0
Baden_LCA 0
Balaton_Lasinja_CA 0
Baltic_HG 0
Barcin_N 0
Blatterhole_HG 0
Blatterhole_MN 0
Boncuklu_N 0
EHG 0
Greece_N 0
Greece_Peloponnese_N 0
Iran_ChL 0
Iran_N 0
Koros_EN 0
Koros_HG 0
LBKT_MN 0
LBK_EN 0
Levant_BA 0
Levant_N 0
Narva_Estonia 0
Narva_Lithuania 0
SHG 0
Starcevo_EN 0
TDLN 0
Tepecik_Ciftlik_N 0
Tianyuan 0
Tisza_LN 0
Tiszapolgar_ECA 0
Vinca_MN 0
WHG 0

Obviously, this makes a lot of sense, but it's somewhat different from my recent models of Samara Yamnaya using methods based on formal stats (see here and here). In the end, only ancient DNA from the steppes and Caucasian-Caspian region will settle this issue when enough of it is sampled.

Update 10/02/201: As per our discussion in the comments, in most cases it might be useful to restore the variance of the raw data (like in the datasheets here and here). This can be done with the EigenScale.R script available here. You'll also need a text file of the relevant eigenvalues, available here. Instructions on how to call the R script are here. Below is the same model of Samara Yamnaya as above, except using the "restored" data. The result is very similar, albeit a little cleaner.

[1] distance%=3.8086 / distance=0.038086

Yamnaya_Samara

Samara_Eneolithic 70.35
Armenia_EBA 14.9
CHG 14.75
ALPc_MN 0
Anatolia_BA 0
Anatolia_ChL 0
Armenia_ChL 0
Baden_LCA 0
Balaton_Lasinja_CA 0
Baltic_HG 0
Barcin_N 0
Blatterhole_HG 0
Blatterhole_MN 0
Boncuklu_N 0
EHG 0
Greece_N 0
Greece_Peloponnese_N 0
Iran_ChL 0
Iran_LN 0
Iran_N 0
Koros_EN 0
Koros_HG 0
LBKT_MN 0
LBK_EN 0
Levant_BA 0
Levant_N 0
Narva_Estonia 0
Narva_Lithuania 0
SHG 0
Starcevo_EN 0
TDLN 0
Tepecik_Ciftlik_N 0
Tianyuan 0
Tisza_LN 0
Tiszapolgar_ECA 0
Vinca_MN 0
WHG 0

See also...

Modeling genetic ancestry with Davidski: step by step

Mitogenomes from the Iron Age South Baltic (Stolarek et al. 2018)


Over at Scientific Reports at this LINK. And yes, full genomes of many of the samples are on the way. Emphasis is mine:

Abstract: Despite the increase in our knowledge about the factors that shaped the genetic structure of the human population in Europe, the demographic processes that occurred during and after the Early Bronze Age (EBA) in Central-East Europe remain unclear. To fill the gap, we isolated and sequenced DNAs of 60 individuals from Kowalewko, a bi-ritual cemetery of the Iron Age (IA) Wielbark culture, located between the Oder and Vistula rivers (Kow-OVIA population). The collected data revealed high genetic diversity of Kow-OVIA, suggesting that it was not a small isolated population. Analyses of mtDNA haplogroup frequencies and genetic distances performed for Kow-OVIA and other ancient European populations showed that Kow-OVIA was most closely linked to the Jutland Iron Age (JIA) population. However, the relationship of both populations to the preceding Late Neolithic (LN) and EBA populations were different. We found that this phenomenon is most likely the consequence of the distinct genetic history observed for Kow-OVIA women and men. Females were related to the Early-Middle Neolithic farmers, whereas males were related to JIA and LN Bell Beakers. In general, our findings disclose the mechanisms that could underlie the formation of the local genetic substructures in the South Baltic region during the IA.

Stolarek et al., A mosaic genetic structure of the human population living in the South Baltic region during the Iron Age, Scientific Reportsvolume 8, Article number: 2455 (2018) doi:10.1038/s41598-018-20705-6

Friday, February 2, 2018

Early Baltic Corded Ware form a genetic clade with Yamnaya, but...


This is what Mittnik et al. 2018 say about a couple of their Corded Ware, or Baltic Late Neolithic (Baltic_LN), samples from what is now Lithuania:

Computing D-statistics for each individual of the form D(Baltic LN, Yamnaya; X, Mbuti), we find that the two individuals from the early phase of the LN (Plinkaigalis242 and Gyvakarai1, dating to ca. 3200–2600 calBCE) form a clade with Yamnaya (Supplementary Table 7), consistent with the absence of the farmer-associated component in ADMIXTURE (Fig. 2b). Younger individuals share more alleles with Anatolian and European farmers (Supplementary Table 7) as also observed in contemporaneous Central European CWC individuals [2].

We can add a third early Baltic Corded Ware sample, Latvia_LN1, to this list, because this individual was also shown to lack the above mentioned farmer-associated component in ADMIXTURE by Jones et al. 2017.

However, in my Principal Component Analysis (PCA) of ancient West Eurasia, all three samples fall just "northwest" of Yamnaya, along with one German Corded Ware outlier, and form a separate cluster that is shifted slightly closer to European hunter-gatherers and farmers. Hence, Plinkaigalis242 and Gyvakarai1 only form a clade with Yamnaya to the limit of the resolution in the analysis by Mittnik et al., but aren't exactly identical to Yamnaya. The relevant datasheet is available here.


So what might this mean? Possibly that the ancestors of this Corded Ware trio "absorbed" trace forager and/or farmer admixture as they migrated from the Pontic-Caspian steppe to the East Baltic. Or it could mean that they came from a more westerly part of the Pontic-Caspian steppe where people harbored slightly elevated forager and/or farmer ancestry relative to Yamnaya.

More sampling of Eneolithic and Early Bronze Age (EBA) burial sites on the Pontic-Caspian steppe, particularly north of the Black Sea, will probably solve this mystery. Please note, however, that we already have an Eneolithic sample from the Pontic-Caspian steppe that not only packs extra farmer admixture over Yamnaya, but also belongs to Y-haplogroup R1a-M417, which is a marker intimately associated with the Corded Ware expansion (see here).

By the way, this is how the Corded Ware set from Mittnik et al. behaves in another of my PCA, which is designed to focus on entho-linguistic-specific genetic drift in Northern Europe. I don't usually run samples older than the Bronze Age in this analysis, the reason being that they often don't share enough genetic drift with modern-day Europeans to produce meaningful output. And to be honest, I'm not quite sure what to make of these results. But it's probably not a coincidence that the Scandinavian Corded Ware (CWC_Battle_Axe) individual clusters so strongly with the Nordic Iron Age and modern-day Scandinavian samples. The relevant datasheet is here.


See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Modern-day Poles vs Bronze Age peoples of the East Baltic

The genetic history of Northern Europe (or rather the South Baltic)

Tuesday, January 30, 2018

Indian smoke and mirrors


On January 4 this year Hindi newspaper Dainik Jagran published a so called special feature on Indo-European languages. In fact, the article claimed to be giving its readers a sneak peak at the results from the upcoming and much anticipated archaeogenetics paper on the northern Indian Harappan site of Rakhigarhi. [LINK]

I knew about this article when it first came out, because it was mentioned in a few off topic comments on this blog, like this one by commentator Sanuj.

Latest news on the Rakhigarhi results, published in a prominent Hindi paper, also quoting Niraj Rai, the lead geneticist working on it. It is essentially saying that researchers, both foreign and Indian have established that India is home of the Indo-European family and that the aDNA from Rakhigarhi is a close match to North Indian Brahmins. The results are to be published in a leading journal soon.

I deleted these comments soon after I saw them, not only because they were off topic, but also because they made absolutely no sense whatsoever.

Why? For one, because over the past year or so I've managed to gather a little bit of intel on the Rakhigarhi paper from very reliable sources, and all indications were that the results would show significant ancient population movements from West Asia and Eastern Europe to India, and not the other way around.

Moreover, thanks to already published ancient DNA from outside of South Asia, it's obvious that there were significant population movements from West Asia and Eastern Europe to India, and not the other way around. The one exception to this rule is the migration of the Romani (Gypsy) people from northern India to Europe, but this is irrelevant to the topic at hand, because it didn't have much of an impact on the genetic structure or linguistics of Europeans.

So why have I now decided to give Dainik Jagran my full attention? Well, because commentator Sanuj recently resurfaced in another comment thread and said this...

They have been hinting at the outcome, you are just not ready to listen to what they are hinting at, this Jagran article is a case in point. By the way Jagran is the most widely read newspaper in India, and is one of the most credible - rated by Reuters-BBC.

Yep, he's correct: Dainik Jagran is a huge and well respected newspaper.

Please note, however, that the chances of India being confirmed the Indo-European homeland thanks to the ancient DNA from Rakhigarhi are zero; not just low, not almost zero, but zero. Anyone with a generally healthy mind and the ability to be more or less objective in this matter has to admit that this is indeed the case. So why would one of the biggest and most respected Indian newspapers publish such utter crud?

It's an intriguing question to say the least. Moreover, was Niraj Rai actually interviewed by the reporter from Dainik Jagran? If he was, did he really say what he's claimed to have said, or was he grossly misrepresented? If the latter, has he sought a correction? If not, why not? Have the western scientists who are collaborating with Rai asked him what the fig is going on, and have they sought a correction? If not, why not?

Does anyone know if Dainik Jagran has since published a correction, or at least a letter from Rai straighting things out?

Admittedly, I have no idea what's going on now with the Rakhigarhi study and paper; the trail went cold months ago. But whatever it is, it's something peculiar. That's because I find it extremely unlikely that any newspaper, let alone one of the top newspapers in India, would be allowed to get away with misrepresenting and indeed inverting, either by design or mistake, the outcome of such a major international project.

See also...

Best of Davidski on South Asian population history

Monday, January 29, 2018

Paleoeuropeoid (steppe herder) infiltration into South Central Asia during the Bronze Age (Dubova et al. 2016)


I don't usually take cranial studies very seriously, mostly because they have a history of being way out of the ballpark. However, Interaction between Steppe and Agricultural Tribes during the Bronze Age: Morphological Aspects by Dubova et al. 2016 is, at the very least, a decent read. A preprint of this paper is freely available at Academia.edu HERE. One day, hopefully in the not too distant future, we'll see a paper like this based on ancient genomes. And I'm pretty sure that the results won't look much different. Emphasis is mine:

Abstract: Here we discuss the results of research conducted on the variability of anthropological features of the populations of Turkmenistan, Uzbekistan, Tajikistan, Pakistan, China, etc., from the Late Stone Age and Bronze Age. A detailed analysis was carried out on 85 craniological series from burial grounds at Gonur and Buston VI (see Table 1). We examined skulls from the steppe, forest-steppe, desert, and semi-desert areas of Central Asia, Ural, Siberia and the North Caucasus. Factor analysis was used to explore the data obtained. Four factors, describing more than 70% of craniological variations, were extracted. The first factor (describing 29.6% of variability) differentiated groups according to the lengthwise sizes of the head and face, mostly taking into consideration cranial breadth, bezygomatic diameter, and orbit width, as well as minimum frontal diameters, upper face and nose heights. The second factor (17.4% of variability) differentiated groups mainly according to facial height, nose and orbit heights. The highest loadings of the third factor, which determined 14.9% of variability, considered important characteristics such as cranial length and breadth, and the fourth factor (10,4% of variability) – nose breadth. As a result, we identified two major anthropological groups: the first comprising North Kazakhstan, South Siberia, Altai, and Ural-Volga, populations with larger latitudinal proportions of the head and face, as well as a smaller width of the forehead, upper face height, and height of the nose; and the second comprising the southern territories, including the majority of the populations of Iran, Pakistan, the Indus valley, and the southern regions of Uzbekistan, Tajikistan, and Turkmenistan as well, who had the opposite combination of features: long and narrow heads, high, narrow faces and noses, and round orbits. The analysis conducted has enabled us to affirm that Southern Turkmenistan manifestations of minimal impurities with regard to anthropological components, which could be linked to pastoral surroundings, were not seen prior to the middle of the 2nd millennium BC.

...

New data has shed light on the interaction between the steppe pastoralists and the sedentary farmers. Cranial series from the southern regions of Central Asia, representing populations where the features of agricultural and pastoral cultures are combined (Kokcha III, Buston VI, Karaelematasai, and Patmasai, Djarkutan), have been clearly located between ‘typical’ farmers (Hasanlu, Gonur, Mohendjo Daro, Pakistani Timargarha and Butkara) and series from the territory of Kazakhstan, southern Siberia, and the Volga-Ural region. At the same time, Gonur skulls, from the necropolis situated in and around ruins of early buildings, and the Buston VI series, as well as those from later layers of Tepe Hissar in Iran, have been identified as having large transversal dimensions while maintaining the same height-sizes of traits of subjects uncovered from earlier periods at the same monuments. This might be connected primarily to the general brachicephalization processes manifested at that time. But it is also likely that this was the result of a gradual penetration of groups from the Eurasian Steppe to the south, which was initially random but then became increasingly common with frequent mating between steppe groups and farmers. The term “infiltration” best characterizes this process of mixing. It should be noted that the currently available archaeological materials from Gonur Depe reveal that around such major proto-urban centers (which Gonur was at the end of the 3rd-2nd millennium BC) already by the middle of the 2nd millennium BC herders were indigenous, as evidenced by small settlements of cattle breeders in the vicinity of the city walls (see for example: Hiebert & Moore, 2004; Cattani, 2004). In addition, separate (sporadic) steppe pottery fragments have been unearthed from some areas of the site and its surrounding smaller settlements (Sarianidi & Dubova, 2010, pp. 39-42). However, we must particularly emphasize that at Gonur (i.e., in Southern Turkmenistan) manifestations of minimal impurities in anthropological components, which could be linked to pastoral surroundings, were not seen prior to the middle of the 2nd millennium BC.

Another important point to bear in mind is that in the southern regions of Central Asia there were no Bronze Age sites (or earlier ones), where the presence of the so-called ‘Protoeuropean’ anthropological type (a massive variant with a large sized head, low and wide face, rectangular orbits, and with a flattening of the upper part of the face) was fixed. This variant has only been described by researchers in the northern regions of Central Asia. The groups with a small proportion of the ‘Paleoeuropeoid’ anthropological component in their composition reached southern regions in the Bronze Age. The most prevalent among them still being the Mediterranean type. Such a situation, of course, leads to an increase in mixed populations (i.e., in later groups including those of the Iron Age) with the characteristics presented in both groups becoming increasingly mixed (e.g. Mediterranean traits).

Dubova N.A., Junusbayev S.M., Saipov A.B., Interaction between Steppe and Agricultural Tribes during the Bronze Age: Morphological Aspects, Int. Journal of Anthropology – Vol. 31 – n.1-2 – 2016, DOI: 10.14673/IJA2016121026

See also...

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts

Descendants of ancient European (fair?) maidens in Central Asia's highlands

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Saturday, January 27, 2018

mtDNAwiki on "Steppe folk" mtDNA and Indo-Iranian origins


Fascinating stuff from Samuel at mtDNAwiki. Emphasis is mine:

Steppe folk were people who resided in what are today Southern Russia and Eastern Ukraine between 6,000 and 4,000 years ago. They were very different from the Anatolian farmers I discussed earlier.

Ancient DNA shows that, between 3000 and 2000 BC, Steppe folk migrated en masse into Northern Europe, Central Asia and Siberia. Shortly afterwards, Steppe folk settled in South Europe, South Asia (India, Afghanistan, etc.), and Iran.

They contributed huge chunks of ancestry to countless modern ethnic groups. Modern-day Europeans are for the most part a two-way mixture between Steppe folk and European Neolithic farmers (who were mostly of Anatolian origin).

...

As much as 33% of Tajik mtDNA really does derive from Eneolithic/Bronze Age Eastern Europe. No doubt about it. Yes, Tajiks are an exception, because they have a lot more Steppe mtDNA than essentially all other South Central Asians. However, significant frequencies of Steppe mtDNA exist in every population in this region. For example, the mtDNA in the Kalasha, a small ethnic group from the Hindu Kush, is mostly made up of founder effects involving Steppe mt-HGs U4a1, U4b1a4, U2e1h, and J2b1a. Each of these haplogroups has been found in remains from Eneolithic/Bronze Age Eastern Europe.

Typical European haplogroups such as U5a1a1, H2a1, T1a1, H5a1, H6a1, J1b1a1, J2b1a, H7b, etc. consistently pop up in every South Central Asian population. Realistically, none of these haplogroups are more than 10,000 years old. Indeed, all of them are likely to be less than 7,000 years old. The European-related mtDNA in South Central Asia isn’t derived from distant, Paleolithic shared ancestry between Europeans and Asians. It’s recent stuff from the Steppe.

For over a decade Y-haplogroup R1a-M417 perplexed many geneticists because it was the most common Y-haplogroup in two geographically very distant peoples; Balto-Slavs of Eastern Europe and Indo-Aryans of South Asia. But thanks to ancient DNA, it has now been confirmed that R1a-M417 is an European Steppe lineage which expanded both west and east from the Pontic-Caspian Steppe between 4,600 and 3,500 years ago.

Interestingly, I’ve found mtDNA haplogroups which correlate very well with R1a-M417; meaning that they either exist in South Asians & Eastern Europeans, or in South Asians & ancient Central and Eastern Europeans rich in R1a-M417, such as the Corded Ware and Srubnaya peoples.

J1c1b1a: Russia, Ukraine, Hungary, Romania, Denmark, UK, Spain, Tajik, India. Srubnaya (R1a-Z93), Corded Ware (R1a-M417).
H2a1a: Russia, Hungary=2, Finland, Britain, Ireland, France, Pathan, Tajik=16, Turkey, Siberia. Eneolithic Ukraine (R1a-M417), Bronze age Scotland, Unetice.
H5e1: Russia=2, Hungary, Greece, Tajik=3.
T1a1b: Russia=4, Poland=3, Hungary=2, Iran=2, Turkey, Tajik=4, India. Bronze age Latvia, Sycthian=2.
N1a1a1a1: Estonia=3, Finland=2, Italy, Turkmen, India=2. Sintashta, Sycthian, Sarmatian.
K2a5: Estonia, Ireland, Iran, Sindhi, Pathan, India. Corded Ware Germany, Corded Ware Sweden.
U4b2: Russia, Ukraine, Sweden, Spain, Burosho, Tajik, India.
U4b1a4: Kalash, Tajik, Iran, Siberia=3. Catacomb, Sycthian.
U2e1h: Kalash=3, Tajik=8, Siberia, Italy. Sintashta, Potapovka

The most important mt-HGs here are U2e1h, H2a1a, U4b1a4, T1a1b, and N1a1a1a1. They directly link modern Indo-Iranian speakers in Asia with Eneolithic/Bronze age Eastern Europeans generally considered by historical linguists and archaeologists to be Proto-Indo-European- or Proto-Indo-Iranian-speakers (i.e. Sintashta and Potapovka).

When I put all of this data together, and saw the undeniable links between modern-day Indo-Iranian speakers and Eneolithic/Bronze Age Eastern Europeans, I was amazed. The results confirmed to me, beyond any doubt, that the ancient migrations from the western Steppe deep into Asia long hypothesized by historical linguists and archaeologists did happen. Indo-Iranian languages really did originate in Eastern Europe, probably in what is now Ukraine, then took the long journey all the way to the Indian Subcontinent.

Case in point: ancient DNA sample I6561. That’s his lab ID, but he’s a man who died in what is now Ukraine ~5,500 years ago. He belonged to Y-HG R1a-M417 and mt-HG H2a1a. Today H2a1a is most common in the Tajik people of South Central Asia. The most common Y-HG in Tajiks, and many of their neighbors, such as Pashtuns, Kalasha, northern Indians, etc. is R1a-M417.

All of the evidence suggests that Mr. I6561 belonged to a PIE community whose descendants would go on to settle lands that stretch all the way from modern-day Norway to India. His people are important founders of countless modern ethnic groups; Russians, Czechs, Tajiks, Pashtuns, Indians, and so on. Oh yeah, and also the ancient Scythians, who dominated much of Asia around 500 BC, derived directly from his people. Pretty amazing.

...

It’s been known for a while, via archaeological data, that Steppe folk traded with these farmers. But now, thanks to ancient DNA, it’s clear that they exchanged more than just goods. Enneolithic and Bronze Age genomes from what are now Ukraine, Romania, and Bulgaria show that the Steppe and farmer folks began mixing by at least 4400 BC.

Hence, when Steppe folk expanded both west and east, they took with them at least a little Anatolian admixture. This is also true for the Steppe folk who went to South Asia. Several of the mt-HGs that I labeled “Steppe” are in fact Anatolian mt-HGs that the Steppe folk acquired through admixture with farmer peoples before their mass migrations. These include mt-HGs H1b1, H5a1, H7b, J1c1b1a, J2b1a, N1a1a1a1, K1b1a1, HV6, and HV9.

It’s often said, in scientific literature as well as on various genetic blogs and forums, that the Steppe folk who moved into South Asia didn’t harbor any Anatolian ancestry. But my mtDNA data easily debunks this claim. South Asians do indeed carry some Anatolian-derived mtDNA which they, in all likelihood, acquired from their Steppe ancestors.

See also...

Another look at the genetic structure of Yamnaya

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts

Descendants of ancient European (fair?) maidens in Central Asia's highlands

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Thursday, January 25, 2018

Unadmixed Basal Eurasians lived throughout the Near East ~45-15 KYA?


Below is a map from a recent review paper at Trends in Genetics by Melinda A. Yang and Qiaomei Fu titled Insights into Modern Human Prehistory Using Ancient Genomes.


It's somewhat speculative and an abstract of geographic realities (note that the ancient "Karelia" population is placed several thousand miles east of Karelia, in Northern Asia as opposed to Northeastern Europe). Nevertheless, the fact that the authors chose to illustrate the home of the so called Basal Eurasians as a rather large range in the middle of the Near East, rather than something more remote and limited, like, say, a small part of the Arabian Peninsula or even North Africa, is interesting.

Indeed, they seem to suggest that post-Basal Eurasian Near Eastern populations took shape not as a result of the expansion of Basal Eurasians across the Near East, but rather due the migration of northern foragers (labeled EUR on the map) from Eastern Europe to the Near East. Like I say, no doubt this is based on some guesswork, and needs to be confirmed with more sampling from the ancient Near East, but still noteworthy that it made it onto the map.

Citation...

Melinda A. Yang and Qiaomei Fu, Insights into Modern Human Prehistory Using Ancient Genomes, https://doi.org/10.1016/j.tig.2017.11.008

See also...

Villabruna cluster =/= Near Eastern migrants