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Thursday, September 21, 2017

Ancient genomes from Neolithic North Africa (Fregel et al. 2017 preprint)


Over at bioRxiv at this LINK. The paper includes three ancient North African Y-haplogroup results: two instances of E-M35 from the Early Neolithic (5300-4800 BCE) and a singleton T-M184 from the Late Neolithic (3780-3650 BCE). Emphasis is mine:

Abstract: One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.


Fregel et al., Neolithization of North Africa involved the migration of people from both the Levant and Europe, bioRxiv, Posted September 21, 2017, doi: https://doi.org/10.1101/191569

Tuesday, September 19, 2017

R1a-M417 from Eneolithic Ukraine!!!11


A new version of Mathieson et al. 2017 has just been posted at BioRxiv [LINK]. It includes more samples. One of these new samples is a male from an Eneolithic Sredny Stog culture site on the Pontic (Ukrainian) steppe who belongs to Y-haplogroup R1a-M417 (ID I6561 from Alexandria in the ADMIXTURE bar graph below). This is huge, obviously with major implications for the peopling of large parts of Eurasia. Why? Because of this. Here's the new abstract:

Abstract: Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2000 years before the migration that replaced much of northern Europe's population.



Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted September 19, 2017, doi: https://doi.org/10.1101/135616

By the way, I don't want to toot my own horn too much, but looking back, some of my comments in the discussion about the first version of Mathieson et al. 2017 were awesome. See here and here.

Three new Yamnaya, all from Ukraine, but sadly all females.

Expected the Mesolithic/Neolithic R1a/R1b in Ukraine, and it would've been good to see some Yamnaya males from there, because some are likely to be R1a-M417.

But it's nice to see that Bulgarian MLBA R1a/U5a sample. Interesting date for R1a to be in the Balkans: 1750-1625 calBCE (3400±30 BP).

...

It can't be a coincide that all of their Yamnaya samples from Ukraine are females.

I reckon they're holding the males back for their South Asian paper.

I'm surprised they let the Bulgarian MLBA R1a out of the bag, because that's a big clue about what we'll see in BA Ukraine.

Update 20/09/2017: I put together a spreadsheet with the key details for the samples in this paper (click on the image below to open it). I'm not sure which of the individuals are new, because many of the IDs have been changed. A spreadsheet with the original set of samples is located here.


See also...

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

Monday, September 18, 2017

Ancient IBD/cM matrix analysis offer


I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output.

A Bronze Age dominion from the Atlantic to the Altai

I can do this for $15 (USD) per individual. Please e-mail the data and money (via PayPal) to eurogenesblog [at] gmail [dot] com. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.

I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread below so that they can be discussed and analyzed further.

Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.

Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.

So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.

The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.

Indeed, Past 3 can do a lot of interesting things with matrix files; anything from linear models to rotating three dimensional plots. If you'd like to repeat the linear models from my above linked to blog post, then choose the relevant two columns in your matrix and go Model > Generalized Linear Model. You should see something like this.


Moreover, a matrix with the 3000+ public samples can be gotten here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.

Friday, September 15, 2017

Modern-day Greeks & Italians vs Mycenaeans


What are the historical and linguistic implications of these qpAdm mixture models, apart, of course, from the most obvious? Please share your thoughts in the comments below. By the way, I tried a wide variety of ancients only models for the Greeks and Italians and these were statistically the most sound. If you're wondering who the Roman outlier is, see here.

Mycenaean
Minoan_Lasithi 0.780±0.044
Srubnaya 0.220±0.044
P-value 0.909333794
chisq 7.595
Full output

vs

Greek
Iran_ChL 0.090±0.071
Mycenaean 0.478±0.103
Slav_Bohemia 0.432±0.077
P-value 0.461783732
chisq 12.820
Full output

Italian_Bergamo
Anatolia_BA 0.239±0.057
Iceman_MN 0.332±0.054
Unetice 0.429±0.030
P-value 0.764439946
chisq 9.112
Full output

Italian_Tuscan
England_Roman_outlier 0.118±0.115
Mycenaean 0.521±0.147
Unetice 0.361±0.059
P-value 0.741956816
chisq 9.402
Full output

Sicilian_East
Bell_Beaker_Germany 0.222±0.077
England_Roman_outlier 0.210±0.134
Mycenaean 0.567±0.163
P-value 0.504442682
chisq 12.285
Full output

Sicilian_West
England_Roman_outlier 0.216±0.121
Mycenaean 0.503±0.135
Unetice 0.281±0.056
P-value 0.808464904
chisq 8.516
Full output

See also...

Ancient Greeks and Romans may have imported a whole new genetic cline into Europe (or not)

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Wednesday, September 13, 2017

How the Corded Ware people Indo-Europeanized southern Scandinavia


Over at the American Journal of Archaeology at this LINK. Below is the paper abstract. Emphasis is mine.

In this article, we approach the Neolithization of southern Scandinavia from an archaeolinguistic perspective. Farming arrived in Scandinavia with the Funnel Beaker culture by the turn of the fourth millennium B.C.E. It was superseded by the Single Grave culture, which as part of the Corded Ware horizon is a likely vector for the introduction of Indo-European speech. As a result of this introduction, the language spoken by individuals from the Funnel Beaker culture went extinct long before the beginning of the historical record, apparently vanishing without a trace. However, the Indo-European dialect that ultimately developed into Proto-Germanic can be shown to have adopted terminology from a non-Indo-European language, including names for local flora and fauna and important plant domesticates. We argue that the coexistence of the Funnel Beaker culture and the Single Grave culture in the first quarter of the third millennium B.C.E. offers an attractive scenario for the required cultural and linguistic exchange, which we hypothesize took place between incoming speakers of Indo-European and local descendants of Scandinavia’s earliest farmers.

Rune Iversen, Guus Kroonen, Talking Neolithic: Linguistic and Archaeological Perspectives on How Indo-European Was Implemented in Southern Scandinavia, American Journal of Archaeology Vol. 121, No. 4 (October 2017), pp. 511–525, DOI: 10.3764/aja.121.4.0511

See also...

The puzzle of the early Corded Ware grave

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

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

Two starkly different Neolithic traditions in the Lower Volga basin


Recent papers in English dealing with the Neolithic transition on the Caspian steppe aren't easy to find, but I managed to dig one up at Documenta Praehistorica: Initial stages of two Neolithisation models in the Lower Volga basin by Alexander Vybornov.

The author describes two highly contrasting Neolithic traditions in this region; one that is essentially a ceramic Mesolithic culture, no doubt practiced by local foragers, and the other a pastroralist culture, probably brought to the steppe by migrants from the south.

I think it's possible that these migrants could have been the main source of the, thus far imprecisely characterized, Caucasus-related ancestry in the potentially Proto-Indo-European Khvalynsk and Yamnaya peoples (see here). But it's hard to argue either way until someone sequences DNA from a few relevant skeletons.

In this paper, two groups of ancient sites located in the Lower Volga River basin are analysed. The first group is linked to the emergence of the oldest pottery in this region, which is one of the most ancient in Europe. The presence of this feature of the ‘Neolithic package’ can be dated to the middle of the 7th millenium BC. A production economy is a particular feature of the second group of sites, which can be dated to the end of the 6th millenium BC. This is one of the earliest pieces of evidence of the existence of domesticated species in Eastern Europe. These two groups of sites show the initial stages of two Neolithisation models in the Lower Volga basin.

...

The Neolithisation process in the southern part of the Low Volga region during 6500–5500 BC did not include a producing economy. From the point of view of European researchers, sites of this period could be attributed only to the ‘ceramic Mesolithic’. In the eastern European scientific world, pottery is regarded as a marker of the beginning of the Neolithic era (Oshibkina 1996), which is why these sites were classified as Neolithic.

...

The origin of Prikaspiiskaya culture is reckoned to be connected with the Lower Don region. Some migration from Western Asia could also have occurred. Thus, the Prikaspiiskaya sites in the Lower Volga region represent the second Neolithisation model proposed for this area. The model is connected with the appearance of a producing economy in the milieu of Prikaspiiskaya culture.

Alexander Vybornov, Initial stages of two Neolithisation models in the Lower Volga basin, Documenta Praehistorica, Vol 43 (2016), DOI: http://dx.doi.org/10.4312/dp.43.7

Tuesday, September 12, 2017

Three key late comers in prehistoric Greece: steppe ancestry, horses and millet


A review paper at Archaeological and Anthropological Sciences posits that millet and horses arrived in what is now Greece together during the Bronze Age (see here). The author suggests that they may have been introduced via contacts with cultures to the north/northeast of Greece or directly by migrants from the Eurasian steppe. Considering the recent discovery via ancient human DNA that steppe ancestry also spread into the southern Balkans and Mycenae during the Bronze Age (see links below), I'd say the latter scenario is much more likely. I'd also add that millet and horses were probably part of an economic and cultural package expanding along with early Indo-European speakers throughout Eurasia at the time (note, for instance, how important horses are to the early Indo-European pantheon). Here's the review abstract. Emphasis is mine.

Abstract: Archaebotanical evidence for Panicum miliaceum is reviewed for prehistoric Greece including published and unpublished recent finds, providing a basis for exploring the context of the appearance of millet in Greece, the timing of its introduction and cultivation, and its significance in terms of contacts, movement of people, and cultural identity as expressed through culinary practice and food consumption. To this end, the archaeobotanical record is examined together with human isotopic, archaeozoological, and artefactual evidence. Millet is introduced to the northern part of Greece sometime during the end of the 3rd millennium bc and established as a widely used crop during the Late Bronze Age. Isotopic evidence suggests that millet consumption during the Late Bronze Age was not widespread but confined to certain regions, settlements, or individuals. Millet is suggested to reach Greece from the north after its spread westwards from China through Central Asia and the steppes of Eurasia. The timing of the introduction of millet and the horse in northern Greece coincide; the possibility therefore that they are both introduced through contacts with horse breeding cultures cultivating millet in the north and/or northeast is raised. Intensified contact networks during the Bronze Age, linking prehistoric northern Greece to central Europe and the Pontic Steppes, would have opened the way to the introduction of millet, overland via river valleys leading to the Danube, or via maritime routes, linking the Black Sea to the north Aegean. Alternatively, millet could have been introduced by millet-consuming populations, moving southwards from the Eurasian steppes.

Valamoti, S.M., Millet, the late comer: on the tracks of Panicum miliaceum in prehistoric Greece, Archaeol Anthropol Sci (2016) 8: 51. https://doi.org/10.1007/s12520-013-0152-5

See also...

Steppe invaders in the Bronze Age Balkans

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

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

Monday, September 11, 2017

The story of Y-haplogroup Q


Over at Molecular Genetics and Genomics at this LINK. I wonder how the Q1a Khvalynsk guy (see here) fits into this story?

Abstract: The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.


Huang, YZ., Pamjav, H., Flegontov, P. et al., Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia, Mol Genet Genomics (2017). https://doi.org/10.1007/s00438-017-1363-8

See also...

Phylogeography of Y-haplogroup Q3-L275

Comic relief from Russia (Klejn et al. 2017)


I kid you not, the map below was published in a recent discussion paper in the European Journal of Archaeology. It was put together by two highly experienced Russian academics: archaeologist Leo Klejn and geneticist Oleg Balanovsky. Pretty crazy, huh?


It surely must rank as one of the most naive, awkward and inadvertently comical attempts to debunk the Kurgan Proto-Indo-European theory that I have seen anywhere, and I've seen some really dumb sh*t in this context in the comments at this blog.

Klejn and Balanovsky are actually arguing that Yamnaya-related ancestry did not spread from the Pontic-Caspian steppe to most of the rest of Europe, but rather from somewhere around modern-day Finland to most of the rest of Europe, including the Pontic-Caspian steppe.

Obviously, this is impossible, and the reasons for this are explained by Klejn's co-authors and discussion opponents in the paper. Basically, the very specific type of genetic structure fixed in the Yamnaya population of the Early Bronze Age Pontic-Caspian steppe did not exist in Northeastern Europe prior to the arrival of the Corded Ware people in the region, and they, in all likelihood, came from the Pontic-Caspian steppe, because some of the earliest Corded Ware samples are practically identical to those from the Yamnaya horizon.

Here's a figure from the recent Mathieson et al. 2017 preprint that illustrates this very neatly with an ADMIXTURE analysis. Remarkably, the Globular Amphora Culture (GAC) people, who lived on the northwest edge of the Pontic-Caspian steppe just prior to the formation of the Corded Ware Culture across much of Northern Europe, showed, at best, trace amounts of the Yamnaya-specific genetic component. On the other hand, the early Corded Ware individual from what is now Latvia (Latvia_LN) appears almost indistinguishable from the average Yamnaya folks.


Hopefully, Klejn and Balanovsky have now given up on their highly original theory about the expansion of the Yamnaya genetic signal after looking over the data from Mathieson et al. 2017. But from running this blog and having to deal with copious amounts of stupid sh*t in the comments, I know how exceedingly difficult it is for some people to finally bury their pet theories, no matter how at odds with reality they are, so I guess we'll see.

Citations...

Klejn et al., Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?, European Journal of Archaeology, Published online: 28 July 2017, doi:10.1017/eaa.2017.35

Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted May 9, 2017, doi: https://doi.org/10.1101/135616

See also...

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

A plausible model for the formation of the Yamnaya genotype

Sunday, September 10, 2017

Your ancient ancestry #1


This is the first of a series of guides to modeling your ancient ancestry with the Global 10/nMonte2 method.

I do already have a user guide for running Global 10 and Basal-rich K7 data with nMonte and 4Mix (see here). However, in this series I’m going to recommend specific models that produce results similar to those from my experiments with other methods, such as qpAdm, as well as from scientific literature. Hopefully, this will help users achieve more sensible and accurate outcomes, and avoid problems such as overfitting.

Let’s start with models for modern-day Europeans that focus on Yamnaya-related ancestry, which very likely represents a genetic signal of early Indo-European dispersals during the Early to Middle Bronze Age from the Pontic-Caspian steppe.

It’s now clear via a wide range of methods that about half of the genomes of modern-day Eastern and Northern Europeans, and up to about a quarter of the genomes of modern-day Southern Europeans, are derived from such Yamnaya-related sources. Any tests dealing with ancient European substructures that don’t, one way or another, reflect this robust inference must be considered inadequate.

So if my models are to be useful, then this is what they must show. And indeed they do. Here are a few examples focusing on modern-day and ancient England, in chronological order:

England_Iron_Age
Yamnaya_Samara 49.75
Barcin_N 32.3
Hungary_HG 17.95

distance%=0.5318 / distance=0.005318

England_Roman
Yamnaya_Samara 45.65
Barcin_N 33.35
Hungary_HG 21

distance%=0.4668 / distance=0.004668

England_Anglo-Saxon
Yamnaya_Samara 44.95
Barcin_N 31.6
Hungary_HG 23.45

distance%=0.5409 / distance=0.005409

English_Cornwall
Yamnaya_Samara 44.55
Barcin_N 36.95
Hungary_HG 18.5

distance%=0.3699 / distance=0.003699

English_Kent
Yamnaya_Samara 45.2
Barcin_N 36.85
Hungary_HG 17.95

distance%=0.4875 / distance=0.004875

The full output is available in a zip folder HERE. I’m not claiming that these ancestry proportions are perfect, especially for Southern Europeans, who generally have very complex ancestry, but they do make a lot of sense.

One obvious problem with the Global 10 is that some of its dimensions, or PCs, exaggerate affinity between modern-day and Mesolithic Europeans. This is especially true for PC6. Hence, to try and mitigate this problem I decided to remove PC6 from the Global 10 datasheet used in my analysis.

To try these models on your own genome, remove PC6 from your Global 10 coordinates file, and use the data text files provided in the zip folder linked to above. It’s best to rely on the datasheets specifically designed for your ethnic group or region of Europe. But feel free to tweak my models. There’s no harm in experimenting if you’re cautious and sensible about it. Indeed, using Iberia_HG or Loschbour along with Hungary_HG appears to produce more accurate outcomes for many Western Europeans.

The important, but often neglected, point to keep in mind is that I designed the Global 10 to help replicate results from more reliable but technically less accessible methods, and not to challenge any generally accepted models.

In the near future, a wider choice of ancient samples should enable me to fine tune and improve the models. For instance, a slightly more eastern-shifted forager reference population than Hungary_HG, such as the yet to be published Lithuanian Narva samples (see here), will probably shift the results slightly for Northeast Europeans, perhaps by bringing down their Yamnaya-related ancestry proportions by a few per cent.

Moreover, adding a wide range of yet to be published Middle to Late Neolithic European samples, such as those from the Globular Amphora Culture (GAC), should prove an interesting exercise.

See also...

Global 10: A fresh look at global genetic diversity

Wednesday, September 6, 2017

Banned commentators list


People listed below aren't allowed to make posts in the comments section at this blog. If they do, their posts will be removed as soon as I see them. Moderation will be turned on when necessary to block banished commentators from returning.

batman

xyyman

I'll be updating the list regularly as more people are banned, which is highly likely. To make sure that you don't make it onto the list, think twice before you post a comment. Follow the blog rules [see HERE] and make an effort to understand the basics of what is being discussed before you join the discussion.

If, perhaps, you're frustrated that your pet theory isn't working out, then come up with a better pet theory. But whatever you do, don't troll here. Also please note, discussions with banned commentators are forbidden, and those who break this rule will also be banned.

Monday, September 4, 2017

Female mobility and exogamy as the main drivers of foreign admixture during the Late Neolithic/Early Bronze Age shift in Central Europe (Knipper et al. 2017)


The paper is still embargoed. I'll update this post after I've read it. The press release is here. Who wants to bet that this is exactly what happened on the Eneolithic/Early Bronze Age steppe?

Corina Knipper et al., Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe, PNAS (2017). www.pnas.org/cgi/doi/10.1073/pnas.1706355114

Update 05/0/2017: I just had a quick look at the paper. It's not as comprehensive as I had hoped, because it lacks Y-chromosome and genome-wide data. But anyway, the authors do make a strong case for male patrilocality and abundant female exogamy at the sites in question. Below is the paper abstract. Emphasis is mine:

Human mobility has been vigorously debated as a key factor for the spread of bronze technology and profound changes in burial practices as well as material culture in central Europe at the transition from the Neolithic to the Bronze Age. However, the relevance of individual residential changes and their importance among specific age and sex groups are still poorly understood. Here, we present ancient DNA analysis, stable isotope data of oxygen, and radiogenic isotope ratios of strontium for 84 radiocarbon-dated skeletons from seven archaeological sites of the Late Neolithic Bell Beaker Complex and the Early Bronze Age from the Lech River valley in southern Bavaria, Germany. Complete mitochondrial genomes documented a diversification of maternal lineages over time. The isotope ratios disclosed the majority of the females to be nonlocal, while this is the case for only a few males and subadults. Most nonlocal females arrived in the study area as adults, but we do not detect their offspring among the sampled individuals. The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC. The persisting residential rules and even a direct kinship relation across the transition from the Neolithic to the Bronze Age add to the archaeological evidence of continuing traditions from the Bell Beaker Complex to the Early Bronze Age. The results also attest to female mobility as a driving force for regional and supraregional communication and exchange at the dawn of the European metal ages.

See also...

A plausible model for the formation of the Yamnaya genotype

Corded Ware women more mobile than their men (Sjögren et al. 2016)

Eneolithic pastoralism in the Lower Volga but maybe not at Dereivka


I'm reading a couple of papers on the Eneolithic in Eastern Europe. They're relevant to the discussions we've been having recently in the comments about the origins of pastoralism on the Pontic-Caspian steppe. I wonder what the implications of the results in these papers might be for the Proto-Indo-European homeland debate?

New insights into the subsistence economy of the Eneolithic Dereivka culture of the Ukrainian North-Pontic region through lipid residues analysis of pottery vessels

Simona Mileto, Elke Kaiser, Yuri Rassamakin, Richard P. Evershed

DOI: https://doi.org/10.1016/j.jasrep.2017.03.02

Abstract: The Dereivka site of the North-Pontic forest-steppe has been widely investigated because of its potential as a centre for horse domestication (Levine, 1990; Telegin, 1986). Despite the significant archaeological evidence available, Dereivka is considered a contradictory and complex site (Rassamakin, 1999: 143) due to a range of challenges connected with reconciling the various lines of available archaeological evidence. Consequently, a generally acceptable subsistence economic model has still to be developed, with contrasting theories remaining unresolved. This paper presents new results of organic residues analyses from the site. Forty potsherds were submitted to biomolecular and stable carbon and hydrogen isotope analyses and the results discussed in relation to previously published zooarchaeological evidence (Bibikova, 1986; Levine, 1999; Kaiser, 2010). The findings offer a further perspective on the overall subsistence economic strategies of the community, particularly in relation to the exploitation of the horse. Significantly, the biomolecular and stable carbon isotope results confirmed that Dereivka community consumed horse products predominantly, together with smaller proportions of ruminant and non-ruminant products. Interestingly, although ruminant adipose fats were recovered from some vessels, evidence of ruminant dairy product exploitation was insignificant, with only one residue displaying a possible ruminant dairy fat origin. Hydrogen isotope analysis of lipids was applied to investigate equine milk processing in pots (Outram et al., 2009) but these analyses did not offer significant new insights.

On the chronological aspect of productive economy origin in the Lower Volga region

Aleksandr A. Vybornov, Markku Oinonen, Natalia S. Doga, Marianna A. Kulkova, Aleksandr S. Popov

DOI: http://dx.doi.org/10.15688/jvolsu4.2016.3.1

Abstract: The Lower Volga region territory plays a large part in studying the origin of producing economy. It is particularly important to determine the time of this process commencement. The researchers assumed the coexistence of the late Neolithic and Early Eneolithic monuments in this area. On that basis they highlighted the Neo-Eneolithic period. The researchers dated it to the middle of the 5 millennium BC. They associated this period and the emergence of producing economy at the territory under discussion. The weak point of this hypothesis was a small number of radiocarbon dates on this issue. Obtained after 2007, the radiocarbon dates on the Neolithic and Eneolithic monuments in the Lower Volga region demonstrate a 500-year chronological gap between them. That is why the hypothesis of the Neo-Eneolithic period is not confirmed. At the same time there is a reason to believe that the Late Neolithic and the Caspian Sea region culture coexisted during 5800-5500 BC. However, the referring of the Caspian Sea region culture to the Eneolithic suffers from the lack of evidence that its carriers were familiar with metal. There is also no evidence that they had cattle breeding. The situation changed after studying the Oroshaemoye I archaeological site in the Lower Volga region in 2014-2015. Cultural layer with materials from only the Caspian Sea region culture was found there. This increases the significance of the monument. The bones of domestic sheep and goats were found in this cultural layer. This is the first significant evidence of producing economy existing among the population of the Lower Volga region. AMS radiocarbon dates 4800 and 4700 BC were obtained from domestic sheep bones from this site. Thus, it is possible to make a reasoned conclusion that producing economy had being formed in the Lower Volga region among the carriers of the Caspian Sea region culture. This process can be reliably dated to the beginning of the 5 millennium BC.

See also...

Two starkly different Neolithic traditions in the Lower Volga basin

Wednesday, August 30, 2017

R1b-V88: out of the Balkans and into Africa?


Late last year I tentatively suggested that R1b-PF6279/V88, also known as R1b1a2, and formerly as R1b1c, may have entered Africa from Iberia, rather than from the Near East as is generally accepted, because of its presence in an Early Neolithic sample from Iberia (see here).

This is now looking a lot more plausible due to the recent discovery that the eastern Balkans was home to Mesolithic foragers belonging to R1b-PF6279/V88 (see page 122 here and discussion here) and indeed a pre-Neolithic R1b hotspot (see Mathieson et al. 2017 and González-Fortes et al. 2017). Note also the continued absence of R1b in the growing selection of prehistoric samples from Anatolia and the Levant.

So here's a theory that I think is worth considering for the time being: R1b-V88, and perhaps even R1b, originated in an as yet unsampled Balkan population, dating to the Upper Paleolithic and ancestral to the so called Villabruna cluster (see here), that eventually contributed ancestry to all present-day Europeans, as well as many present-day Asians and, via an Iberian route, Africans. Is there any archaeological evidence for the existence of such an Upper Paleolithic group in the Balkans?

Saturday, August 26, 2017

The pseudo-steppe theory: last line of defense against the inevitable


A popular tactic used by those none too pleased with the presence of Bronze Age steppe or Yamnaya-related ancestry in South Asians is to claim that this ancestry isn't actually from the steppe. Thus, they call it "pseudo-steppe" ancestry.

This theory is based on the assumption that a population very similar to Yamnaya formed independently in South Asia, or at least as part of a cline of such ancestry running from South Asia to the Eastern European steppe.

At best, this is highly speculative and, at worst, insane; a last ditch attempt to counter mounting genetic evidence backing the Aryan Invasion Theory (AIT), or, if you're politically correct, Aryan Migration Theory (AMT). But it gets traction for the time being, including, unfortunately, among some Indian scientists (see here), simply because of the lack of ancient DNA data points for Central and South Asia.

However, we do have Iran_HotuIIIb, a Mesolithic or Neolithic forager from the Hotu Cave near the southeastern coast of the Caspian Sea in modern-day Iran. This location is not in Central Asia per se, but pretty damn close by anyone's standards, because it's next door to the Turkmenistan border.

Below is a map that I put together to illustrate the absurdity of the pseudo-steppe theory. Note that Iran_HotuIIIb is located between Yamnaya and present-day Brahmins from northern India, so if you're a proponent of the pseudo-steppe theory you'd expect him to pack quite a bit of Yamnaya-like ancestry, right? Well, he shows a slither, but much less than the Brahmins. How is this possible geographically and temporally, without a migration from the steppe to India some time after Iran_HotuIIIb was alive? Realistically, it's not.


The ancestry proportions on the map are based on an easily reproducible ADMIXTURE analysis. The test was run in unsupervised mode, but I designed the dataset to help the algorithm flesh out the so called Early Bronze Age steppe (Steppe_EBA) component. The full Q output is available in this spreadsheet.


In fact, there are several ways to show that present-day South Asians share relatively recent and direct ancestry with Bronze Age Eastern Europeans, including, for example, with a haplotype test (see here). But I'd say that a well designed ADMIXTURE analysis is an especially effective way of doing it, because both a strength and weakness of ADMIXTURE is that it's sensitive to ethnic-specific genetic drift. Thus, the so called ancestral populations that it infers are often just exaggerated signals of relative inbreeding, isolation, and/or rapid expansions experienced by founders of ethnic groups.

Clearly, my Steppe_EBA component is a signal of a relatively small, young founder population expanding rapidly across and out of the Eurasian steppe during the Bronze Age. That's because it peaks at extreme levels in genetically and archaeologically closely related Bronze Age steppe populations, such as Afanasievo, Poltavka and Yamnaya, and their recent descendants, such as Andronovo, Corded Ware and Srubnaya. In other words, ADMIXTURE has probably managed to pick up the genetic signal of a Bronze Age ethnic group.

This signal also shows up at relatively high frequencies in many geographically disparate Indo-European speakers, such as the Indian Brahmins and Icelanders. That's obviously good news for those of us who favor the Eastern European steppe as the Proto-Indo-European homeland.

Among the other ancients, those that plausibly can't have ancestry from the EBA steppe because they're too old, it's only seen at high levels in such populations as Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), and Ancient North Eurasians (ANE). In other words, populations that contributed in a big way to the formation of the Bronze Age peoples of the Eastern European steppe.

It's important to understand also that my ADMIXTURE analysis isn't anything particularly original. Iran_HotuIIIb shows essentially the same behavior in this standard Principal Component Analysis (PCA) of West Eurasian populations, sitting just south of present-day South Central Asians (SC_Asia). This, of course, is out of whack with geography, and, again, can only be explained by significant gene flow from the north into South Central Asia after Iran_HotuIIIb's time.


See also...

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

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

Friday, August 25, 2017

The focus turns to the Kazakh steppe


As we wait for more ancient data to be released, here are a couple of interesting quotes from an interview with Harvard's David Reich at Lapham's Quarterly (for the whole thing see here). Emphasis is mine:

I spent the morning corresponding with an archaeologist in Kazakhstan. We’re trying to do genetics in the Bronze Age and the pre–Bronze Age variants in Kazakhstan.

...

We’d like to characterize the genetic variation in Kazakhstan because it’s a key connection point between the regions south of the Hindu Kush mountains, Iran and India in the south, the steppes in Russia in the north, in China in the East; it’s all mixing up there. And we’re trying to understand the connections. It’s a place of movement and migration, and understanding the genetics is interesting. So that was my morning, and then I spent some hours talking with colleagues today in the laboratory about ancient farmers of Israel and Iran that we have some data from.

It looks like this interview was done a while ago, because he's talking about samples from Iran and Israel that have already been published, so I'd say the Kazakhstan data will be part of the upcoming ancient DNA paper on South Asia.

See also...

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

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

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

Tuesday, August 22, 2017

Last South Asian qpAdm crapshoot


I had one last go at modeling South Asians with qpAdm using ancient samples from the Eurasian steppe and Iran before the (imminent?) publication of more proximate and relevant ancient data from Central and South Asia. Indeed, I used the updated qpAdm methods from Lazaridis et al. 2017 (ie. I packed the right pops with 16 outgroups), and, initially, the exercise was an utter failure.

The normally successful (p-value >0.05) model with Han, Neolithic farmers from Iran (Iran_N), Onge, and Early/Middle Bronze Age herders from the Eurasian steppe (Steppe_EMBA), turned out either infeasible or a really bad fit (for instance, see here). Clearly, something important was missing.

However, using Sarmatian_Pokrovka instead of Steppe_EMBA, as proxy for Bronze Age Eastern European ancestry, and the Lebbo (from Borneo) instead of Han and Onge, as a stand-in for Ancestral South Indian (ASI) ancestry, worked well enough, at least for the South Asian populations that I chose to run. Why? No idea. Feel free to speculate in the comments.

But importantly, unlike the Indo-Iranians, Dravidian speakers from India - Gond, Kapu and Malayan - could be modeled successfully without any ancient Eastern European admixture. No need to explain why this is so important.

Brahmin
Iran_N 0.277±0.042
Lebbo 0.304±0.037
Sarmatian_Pokrovka 0.418±0.045
P-value 0.293270281
chisq 15.229
Full output

Gond
Iran_N 0.095±0.061
Lebbo 0.905±0.055
Sarmatian_Pokrovka 0.001±0.063
P-value 0.785177372
chisq 8.836
Full output

Kalash
Iran_N 0.373±0.042
Lebbo 0.137±0.038
Sarmatian_Pokrovka 0.489±0.047
P-value 0.0661709327
chisq 21.356
Full output

Kapu
Iran_N 0.324±0.054
Lebbo 0.573±0.053
Sarmatian_Pokrovka 0.104±0.060
P-value 0.945176825
chisq 6.027
Full output

Kol
Iran_N 0.310±0.055
Lebbo 0.539±0.053
Sarmatian_Pokrovka 0.151±0.058
P-value 0.929121312
chisq 6.429
Full output

Malayan
Iran_N 0.192±0.062
Lebbo 0.738±0.056
Sarmatian_Pokrovka 0.071±0.066
P-value 0.774189887
chisq 8.983
Full output

Pathan
Iran_N 0.354±0.038
Lebbo 0.154±0.034
Sarmatian_Pokrovka 0.492±0.041
P-value 0.21064991
chisq 16.757
Full output

Tajik_Pomiri
Iran_ChL 0.319±0.043
Lebbo 0.143±0.035
Sarmatian_Pokrovka 0.538±0.052
P-value 0.835612167
chisq 8.121
Full output

Interestingly, using Caucasus Hunter-Gatherers (CHG) instead of Iran_N, as proxy for Neolithic Near Eastern input into South Asia, also worked, while, at the same time, potentially lowering the ancient Eastern European ancestry proportions (although not if we assume that the early Indo-Iranians moving into South Asia had a higher ratio of CHG-related admixture than the Pokrovka Sarmatians).

But it's impossible to say whether this is meaningful, because I had to remove CHG from the outgroups to add it to the reference populations. Also, this model is less parsimonious geographically, because South Asia is much closer to Iran than to the Caucasus, therefore there's no need to assume at this stage that the Neolithic farmers moving into South Asia were more like CHG than Iran_N.

Brahmin
CHG 0.399±0.060
Lebbo 0.366±0.036
Sarmatian_Pokrovka 0.236±0.071
P-value 0.18924389
chisq 17.224
Full output

Gond
CHG 0.120±0.045
Lebbo 0.880±0.045
P-value 0.735236332
chisq 10.362
Full output

Kalash
CHG 0.527±0.056
Lebbo 0.204±0.034
Sarmatian_Pokrovka 0.269±0.064
P-value 0.434945033
chisq 13.168
Full output

Kapu
CHG 0.404±0.044
Lebbo 0.596±0.044
P-value 0.815283592
chisq 9.241
Full output

Kol
CHG 0.383±0.072
Lebbo 0.602±0.053
Sarmatian_Pokrovka 0.015±0.080
P-value 0.780646206
chisq 8.897
Full output

Malayan
CHG 0.218±0.045
Lebbo 0.782±0.045
P-value 0.773142044
chisq 9.849
Full output

Pathan
CHG 0.517±0.046
Lebbo 0.219±0.031
Sarmatian_Pokrovka 0.264±0.053
P-value 0.954914864
chisq 5.746
Full output

Tajik_Pomiri
CHG 0.387±0.054
Lebbo 0.126±0.035
Sarmatian_Pokrovka 0.486±0.062
P-value 0.780117456
chisq 8.904
Full output

And now, we wait. I don't know when we'll see the first big ancient DNA paper on South Asia. Hopefully this year, and hopefully at bioRxiv first, so we can have a robust discussion about its conclusions before the final version appears in a journal. Apparently the Broad MIT/Harvard team is close to getting something out. If anyone has info about this paper, feel free to post it in the comments.

See also...

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

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

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

Saturday, August 19, 2017

Genetic and archaeological continuity from Khvalynsk to Yamnaya


Over a year ago, using the D-stats/nMonte method of mixture modeling (see here), I noticed that Yamnaya did not appear to be simply a two-way mixture between Eastern European and Caucasus Hunter-Gatherers (EHG and CHG, respectively), but the result of a much more complex process:

Using the most plausible reference samples currently available - almost all of them older than Yamnaya, and thus unlikely to skew the results with Yamnaya admixture - reveals the following models for the two Yamnaya sets from Kalmykia and Samara, respectively.

Yamnaya_Kalmykia
Khvalynsk 57.7
Kotias 28.3
Hungary_EN 12.9
Ulchi 1.1
AfontovaGora3 0
Anatolia_Neolithic 0
Karelia_HG 0
Loschbour 0
MA1 0
Motala_HG 0

distance%=1.9125 / distance=0.019125

Yamnaya_Samara
Khvalynsk 56.75
Kotias 26.4
Hungary_EN 10.85
Karelia_HG 4.4
Loschbour 1.6
AfontovaGora3 0
Anatolia_Neolithic 0
MA1 0
Motala_HG 0
Ulchi 0

distance%=2.1354 / distance=0.021354

Very interesting but hardly surprising. Essentially what we're seeing there is potentially very strong genetic continuity from the Eneolithic to the Early Bronze Age on the Pontic-Caspian Steppe. In other words, from Khvalynsk to Yamnaya.

However, at some point between the Eneolithic and the Early Bronze Age, the steppes saw a major influx of extra CHG, represented by the ~27% of Kotias-related admixture. Considering the relevant uniparental data, with lots of Y-HG R1b and no Y-HG J among Yamnaya males, I'd say this CHG came with women.

Also, the relatively high admixture related to early Hungarian Plain farmers (Hungary EN) is a fairly curious detail that has not been reported before. If real, it probably represents gene flow from the Neolithic and/or Chalcolithic Balkans to the Pontic-Caspian Steppe. Again, in all likelihood it mostly came with women, perhaps from Tripolye-Cucuteni and/or Varna communities.

The reason I mention this now is because I can reproduce basically the same model using the updated qpAdm methodology described recently in Lazaridis et al. 2017, which relies on a relatively large number (≥16) of ancient genomes/populations as outgroups (see here), and, in my experience, causes many formerly successful models to fail miserably (P-value dives from >0.05 to <0.05). Note that in my dataset Khvalynsk is now labeled Samara_Eneolithic, Kotias as CHG, and Hungary_EN as Hungary_N.

Yamnaya_Kalmykia
CHG 0.334±0.044
Hungary_N 0.115±0.031
Samara_Eneolithic 0.550±0.032
P-value 0.419775785
chisq 13.368
Full output

Yamnaya_Samara
CHG 0.267±0.040
Hungary_N 0.130±0.027
Samara_Eneolithic 0.603±0.030
P-value 0.300777879
chisq 15.106
Full output

Here's a formerly successful model in which Steppe_EMBA (a grouping which includes Afanasievo, Poltavka, Russia_EBA and Yamnaya) is posited as a mixture between EHG and Chalcolithic farmers from the Zagros Mountains in what is now Iran. It clearly fails when I use CHG as one of the outgroups.

Steppe_EMBA
EHG 0.544±0.020
Iran_ChL 0.456±0.020
P-value 0.00279643007
chisq 31.553
Full output

vs.

Steppe_EMBA
CHG 0.310±0.034
Hungary_N 0.121±0.023
Samara_Eneolithic 0.568±0.025
P-value 0.50194795
chisq 12.316
Full output

Now, tight statistical fits are great, but they don't always reflect reality, especially when fine scale genetic structure is being tested. So does my model have any support from archeology? In other words, does archaeological data show continuity between Khvalynsk and Yamnaya (Pit-Grave culture)? According to Morgunova and Turetskij 2016 it does. Emphasis is mine:

Abstract: The aim of the paper is to provide the research results concerning the Pit-Grave culture sites of the south Ural region, which is a part of the Volga-Ural interfluve. The Pit-Grave culture developed mostly out of the Khvalynsk Eneolithic culture at the turn of the 5th–4th millennium cal BC. People of the Sredny Stog and forest-steppe Eneolithic cultures from the Middle Volga region also influenced the Pit-Grave culture. The paper considers the radiocarbon data (more than 120 dates), specifies the periodization of the Pit-Grave culture of the Volga-Ural interfluve, singles out the three stages of its development. The chronology of the culture is determined 3900–2300 cal BC. The authors provide new information about the Pit-Grave economy. Paleopedology, palynology, anthropology, metallography, ceramic technical, and technological analyses were used together with archaeological methods to make a more detailed description of the culture.

...

A number of steppe Eneolithic features remained at the Repin stage. The cultural continuity between the Pit-Grave, Khvalynsk, and Sredny Stog Eneolithic cultures was proved by the following features: skeletons in crouched supine position with bent legs to the left or to the right, heads at the eastern sector of burials, ochre coverage with high or low density, multiple burials, egg-shaped ceramics with neck and crushed shell impurity. Technical and technological analysis of pottery was another evidence demonstrating the pottery continuity between the Khvalynsk and Repin traditions (Vasilyeva 2002; Salugina 2005). Big soil burial grounds were substituted by individual burials under the barrow. The spread of local production copper articles was a distinctive feature of the Pit-Grave culture. This was the phenomenon, which archaeologists consider to be the beginning of the Early Bronze Age in steppe of Eastern Europe.

Morgunova N. and Turetskij M., Archaeological and natural scientific studies of Pit-Grave culture barrows in the Volga-Ural interfluve, Estonian Journal of Archaeology, Vol. 20, Issue 2, doi: 10.3176/arch.2016.2.02

Friday, August 18, 2017

So far so good for the Kurgan hypothesis


This is basically what I'm seeing in the ancient DNA published to date. Thus, the Kurgan hypothesis or steppe theory, which, of course, posits that the Proto-Indo-European homeland was on the Pontic-Caspian steppe, is looking really good at this stage. Indeed, unless there are some ancient DNA shocks on the way from, say, Anatolia or the Caucasus, that might buck the trend, then this one's in the bag.

See also...

A Bronze Age dominion from the Atlantic to the Altai

A homeland, but not the homeland #2

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

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

Wednesday, August 16, 2017

A homeland, but not the homeland #2


Back in May, in a post titled A homeland but not the homeland, I said this:

It seems increasingly likely that ancient DNA has identified a massive expansion, or a series of expansions, from Mesopotamia and/or surrounds in basically all directions dating to the Chalcolithic (ChL) and Bronze Age (BA). This phenomenon is mainly characterized by the simultaneous spread of:

- Iran_ChL-related genome-wide ancestry

- Y-haplogroup J

- South Caspian-specific mitochondrial haplogroups such as R2 and U7

In the same post I also included a list of ancient populations that showed at least two of these characteristics. I can now add two more populations to this list: the Minoans and Mycenaeans.

- Anatolia_BA, Western Turkey, 2836-1800 calBCE (Lazaridis et al. 2017)

- Egyptian mummies, Middle Egypt, 776-2 calBCE (Schuenemann et al. 2017)

- Iran_ChL, Western Iran, 4839-3796 calBCE (Lazaridis et al. 2016)

- Levant_BA, Northwestern Jordan, 2489-1966 calBCE (Lazaridis et al. 2016)

- Minoans, Crete, Greece, 2900-1700 BCE (Lazaridis et al. 2017)

- Mycenaeans, Greece, 1700-1200 BCE (Lazaridis et al. 2017)

- Sidon_BA, Southern Lebanon, 1750-1600 BCE (Haber et al. 2017)

Out of all of these groups, only the Mycenaeans are generally accepted to have been speakers of an Indo-European language. However, they differ from the others in that they harbor minor but significant ancestry from a source, or multiple sources, closely related to Yamnaya, Sinatshta and other Bronze Age peoples of the Pontic-Caspian steppe (see here).

Possible question for the discussion in the comments: what does this say about where the Mycenaeans got their Indo-European language? Also, who wants to bet that Bronze Age samples from the Indus Valley Civilization will too make it onto my list?

See also...

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

Monday, August 14, 2017

CHG or no CHG in Bronze Age western Iberia?


Here's what Martiniano et al. had to say recently in regards to the genetic shifts in what is now Portugal, western Iberia, during the Bronze Age that they saw in their ancient DNA data:

A recurring feature of ADMIXTURE analyses of ancient northern Europeans is the appearance and subsequent dissemination within the Bronze Age of a component (teal) that is earliest identified in our dataset in HGs from the Caucasus (CHG). Unlike contemporaries elsewhere (but similarly to earlier Hungarian BA), Portuguese BA individuals show no signal of this component, although a slight but discernible increase in European HG ancestry (red component) is apparent. D-Statistic tests would suggest this increase is associated not with Western HG ancestry, but instead reveal significant introgression from several steppe populations into the Portuguese BA relative to the preceding LNCA (S4 Text, S6 Table).

...

In the present analysis, fineSTRUCTURE has identified the 3 Portuguese Bronze Age individuals as a genetically distinct population (S23 Fig). When compared to Central or Northern European populations such as Ireland [11], the degree of discontinuity between the Neolithic and Bronze Age in Portugal is not pronounced. However, despite the small sample size we have evidence suggesting complete discontinuity at the level of Y-chromosome lineages with all 3 male Bronze Age samples presenting derived alleles at marker M269.

Although in ADMIXTURE analysis we were not able to observe the presence of the CHG-related cluster in the ancestry proportions of the Portuguese Bronze Age samples, with D(Mbuti, X; Portuguese MN/LNCA, Portuguese BA) we find support for CHG/Yamnaya related introgression and also an increase in EHG [Eastern European Hunter-Gatherer] ancestry.

Despite the authors' conclusion that steppe-related admixture was present in their Portuguese BA samples, the ambiguity created by their ADMIXTURE analysis encouraged some heated debates in the comments at this blog and elsewhere about whether their findings were legitimate, and also suggestions that the Portuguese BA R1b-M269 Y-chromosomes were not derived from the steppe.

To try and put this debate to bed, at least on this blog, let's run the same samples with the qpAdm mixture modeling algorithm. I don't want to get into the details here about the difference between ADMIXTURE and qpAdm, because I don't feel it's something that I can explain accurately. But, suffice to say that qpAdm is a more direct way of estimating ancestry proportions, so, in my experience, it's less likely to lose minor but significant admixture signals in a well thought out and put together analysis.

First up, I need to test whether these Portuguese BA (Portugal_BA) individuals can be modeled as a two-way mixture between EHG and Portuguese Late Neolithic farmers (Portugal_LN).

Portugal_BA
EHG 0.093±0.036
Portugal_LN 0.907±0.036
P-value 0.0102798873
chisq 20.015
Full output

Nope, they can't. But what happens if I add CHG to the model?

Portugal_BA
CHG 0.106±0.048
EHG 0.042±0.042
Portugal_LN 0.852±0.042
P-value 0.0367007784
chisq 14.946
Full output

The statistical fit improves, but it's still lousy, which perhaps suggests that I need a temporally more proximate CHG-related reference sample. How about Yamnaya?

Portugal_BA
Portugal_LN 0.849±0.045
Yamnaya_Samara 0.151±0.045
P-value 0.0725988319
chisq 14.371
Full output

That's not too bad. But let's try a more proximate Yamnaya-related population: Bell Beakers from Germany. Note that some of these Beakers belonged to Y-haplogroup R1b-M269(P312+), which is the most common Y-chromosome lineage among present-day Iberians.

Portugal_BA
Bell_Beaker_Germany 0.328±0.089
Portugal_LN 0.672±0.089
P-value 0.109643502
chisq 13.065
Full output

Somewhat better, and we could probably keep going like this, improving the fits each time, with more relevant reference samples if they were available, like, say, late Beakers from what is now France. I suspect also that using more westerly Hunter-Gatherers than EHG, perhaps from what is now Ukraine, might significantly improve the second model. In any case, my qpAdm analysis provides strong evidence that, unlike Portugal_LN, Portugal_BA harbored CHG-related ancestry that was probably mediated via Yamnaya- and Beaker-related groups.

Citation...

Martiniano R, Cassidy LM, Ó'Maoldúin R, McLaughlin R, Silva NM, Manco L, et al. (2017) The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet 13(7): e1006852. https://doi.org/10.1371/journal.pgen.1006852

See also...

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

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Saturday, August 12, 2017

The Iron Age Iranian (?)


After the recent publication of Bronze Age genomes from present-day Greece and Portugal, you'd have to be a desperate fool not to accept that the Pontic-Caspian steppe in Eastern Europe is the most likely homeland of all surviving branches of the Indo-European language family. I don't want to say I told you so, but, well, I told you so (see here).

Yes, we're still waiting for those ancient genomes from South Asia. But don't expect any surprises when they do arrive, probably in a couple of months. Indeed, if you've still got a thing for the Out-of-India Theory (OIT), then it might be time to start looking around for a different hobby than following ancient DNA results. My advice is try meditation.

Thus, pending the sequencing of Hittite and other bona fide early Indo-European genomes from Bronze Age Anatolia, which should be able to help pinpoint the Proto-Indo-European (as opposed to just the Late Proto-Indo-European) Urheimat to the satisfaction of most, I suggest that we shift focus in the comments here in a big way, and, instead of wasting time arguing whether the early Indo-European expansions from the steppe happened, we get stuck into the details of how they happened.

Worthy subjects of discussion in this context, I'd say, are a couple of intriguing ancient West Asian individuals whose genotypes are now available for download at the Reich Lab website: Kumtepe4 from Chalcolithic Anatolia and F38 from an Iron Age burial at Tepe Hasanlu in what is now Iran.

Let's start with F38, whose genome was originally published back in 2016 as part of Broushaki et al. (see here):

Furthermore, our male Iron Age genome (F38; 971-832 BCE; sequenced to 1.9x) from Tepe Hasanlu in NW-Iran shares greatest similarity with Kumtepe6 (fig. S21) even when compared to Neolithic Iranians (table S20). We inferred additional non-Iranian or non-Anatolian ancestry in F38 from sources such as European Neolithics and even post-Neolithic Steppe populations (table S20). Consistent with this, F38 carried a N1a sub-clade mtDNA, which is common in early European and NW-Anatolian farmers (3). In contrast, his Y-chromosome belongs to sub-haplogroup R1b1a2a2, also found in five Yamnaya individuals (17) and in two individuals from the Poltavka culture (3). These patterns indicate that post-Neolithic homogenization in SW-Asia involved substantial bidirectional gene flow between the East and West of the region, as well as possible gene flow from the Steppe.

In other words, it's almost certain that F38 had recent ancestry from elsewhere than the South Caspian region, and probably from the Pontic-Caspian steppe.

However, interestingly, when F38 was alive, Tepe Hasanlu was more likely to have been an ethnically Hurrian or Urartian site, rather than an Iranian one, and the Iron Age settlement there has a fascinating and tragic final story (see here).

Also, F38 shows a great deal of genetic similarity to three Early Bronze Age (EBA) samples from Kura-Araxes culture burials in what is now Armenia (labeled together as Armenia_EBA). Indeed, one of these Kura-Araxes individuals belongs to Y-haplogroup R1b, albeit to a different subclade than F38. Moreover, Kura-Araxes people are hypothesized to have been early speakers of Hurro-Urartian languages.

This is where Armenia_EBA and F38 cluster in my Principal Component Analysis (PCA) of ancient and present-day West Eurasian populations. Right click and open in a new tab to enlarge:


Like four peas in a pod, right? Not necessarily, because this outcome might be a simple coincidence. And, in fact, that's what my qpAdm analysis suggests. Using no less than 16 ancient outgroups, I found that the models below produced the best fits. Obviously, Anatolia_BA stands for Anatolia Bronze Age, CHG for Caucasus Hunter-Gatherer, Iran_ChL for Iran Chalcolithic, and Tepecik_Ciftlik_N for Tepecik Ciftkik Neolithic.

Iran_IA F38 (2-way)
Iran_ChL 0.815±0.066
Poltavka_outlier 0.185±0.066
P-value 0.72807065
chisq 10.457
Full output

Iran_IA F38 (3-way)
Anatolia_BA 0.122±0.107
Iran_ChL 0.717±0.098
Poltavka_outlier 0.161±0.070
P-value 0.773758066
chisq 8.989
Full output

Armenia_EBA (2-way)
CHG 0.582±0.042
Tepecik_Ciftlik_N 0.418±0.042
P-value 0.817374811
chisq 9.210
Full output

Admittedly, a more systematic and exhaustive search might be able to dig up even better fitting models and show that F38 does share recent ancestry with Armenia_EBA. But in any case, after running these tests, I'm now certain that F38 had significant admixture from the European steppe, probably via a population very similar to Poltavka_outlier.

On the other hand, I'd say that if Armenia_EBA had any steppe ancestry, then it's only a few per cent, and likely from a less northern-shifted source than Poltavka_outlier. This is what the 2-way models look like on the same PCA as above. Armenia_EBA and F38: so similar, yet potentially so different.


F38's probable steppe connection, of course, suggests that he was at least partly of Indo-European origin, and possibly a speaker of an Iranic language, because the Poltavka culture has been associated by some scholars with early Indo-Iranians.

Unfortunately, I don't have a decent enough diploid version of F38's genome to test his fine scale genetic affinities with a haplotype analysis. So I'd say that the most useful thing I can do, that wasn't already done in Broushaki et al., is to run an Identical-by-State (IBS) affinity test. This method is generally pretty good at picking up recent ethnic-specific genetic drift. These are F38's top 25 matches out of over 100 present-day populations:

Georgian 0.676468
Armenian 0.676024
Abkhasian 0.675791
Iranian_Jew 0.675418
Iraqi_Jew 0.675224
Lezgin 0.675124
Cypriot 0.674942
Greek 0.674824
Kurdish 0.674795
Uzbek_Jew 0.674770
Azeri_Jew 0.674701
Greek_Macedonia 0.674700
Italian_South 0.674556
Kosovar 0.674489
Chechen 0.674463
Sicilian_East 0.674334
Turkish 0.674315
Sicilian_West 0.674247
Sephardic_Jew 0.674198
North_Ossetian 0.674125
Kumyk 0.674045
Romanian 0.674017
Greek_Peloponnese 0.673945
Iranian 0.673911
Yemenite_Jew 0.673875

The top three hits are from the Caucasus, which I suspect is due to F38's high ratio of CHG-related ancestry. Iranian and Iraqi Jews are both in the top five, probably because they're relatively similar to Iran_ChL. Armenians are the highest scoring Indo-European speakers, but Kurds also make the top ten, and it's interesting to see several different Greek and Italian groups in the top 25. No idea what that might mean though? To wrap things up, I'll suggest a few questions for the ensuing discussion in the comments:

- Was F38 an Hurro-Urartian or Indo-European, or an Hurro-Urartian with some Indo-European ancestry? If Indo-European or partly Indo-European, then what type? Armenian, Cimmerian, Iranian, or...?

- Is F38's R1b1a2a2 lineage a reflection of his potential Poltavka ancestry from the steppe or Kura-Araxes ancestry from the Caucasus?

- What explains F38's strong affinity to many modern-day European groups?

- Does the southern, non-Eastern European Hunter-Gatherer (EHG), part of Yamnaya's ancestry perhaps derive from a Bronze Age South Caspian population closely related to F38 and rich in R1b1a2a2?

Nah, I'm just trolling with that last one. I thought I'd save some of you the trouble. Let's be honest, what are the chances that this will ever pan out? I'll give it a probability of 5%.

See also...

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

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Yamnaya-related migrations into Iberia: infiltration rather than invasion (Martiniano et al. 2017)

Thursday, August 10, 2017

Basal-rich K7 & Global 10 updates (10/08/2017)


I've updated the Basal-rich K7 spreadsheet and the Global 10 datasheets with a plethora of ancient individuals and populations, including Anglo-Saxons, British Celts (labeled England_IA), Minoans, Mycenaeans, Bronze Age Iberians and many more.

Basal-rich K7 spreadsheet

Global 10 main datasheet

Global 10 ancient averages datasheet

Please keep in mind that the K7 can be somewhat conservative with minor ancestry proportions, especially Ancient North Eurasian (ANE) admixture, and low coverage samples can behave in odd ways in the Global 10. So when modeling ancestry with ancient samples it might be useful to stick to high coverage individuals that show consistent results. If you don't know what the Basal-rich K7 and Global 10 are, then these links will be useful.

The Basal-rich K7

Global 10: A fresh look at global genetic diversity

An nMonte and 4mix guide for the participants of the Basal-rich K7 and/or Global 10 tests

Tuesday, August 8, 2017

Pots were people in Bronze Age southern Central Asia too


New archaeological evidence of potentially significant Bronze Age migrations from the Eurasian steppe into present-day southern Turkmenistan is coming to light thanks to the Archaeological Map of the Murghab Delta (AMMD) project. The new findings are discussed in a paper in Quaternary International available here or here. From the paper:

Adding to the number of questions was the fact that the AMMD project also recorded hundreds of small campsites, particularly in the northern distal reaches of the fan, that bore ceramics [my note: called Incised Coarse Ware or steppe ware] unlike those of other Murghab communities, but with unmistakable affinities to the so-called Andronovo cultural group occupying regions to the north and east during this same period (Cattani, 2008; Cattani et al., 2008; Cerasetti, 2008, 2012). These campsites are interpreted as representing the influx of a new socio-cultural group of mobile pastoralists who began to occupy first more remote areas and gradually move toward more physical and subsistence integration with settled farming groups in the Murghab (Cerasetti et al., in press; see also; Rouse and Cerasetti, 2014). However, the question of whether such encounters upset a careful ecological balance struck by Murghab farming settlements for over a millennium, or whether they were merely coincidental with environmental changes, could not be sufficiently addressed with the coarseness of survey data; targeted research agendas were (and are) still needed to address such questions specifically. Nonetheless, up to this point, it is clear that at the end of the Bronze Age, major social, demographic, and environmental changes were coinciding.

Southern Turkmenistan is, of course, not too far away from South Asia, which was also potentially a target of large scale Bronze Age migrations from the Eurasian steppe that may have brought Indo-European languages to the region. Archaeological evidence of such population movements into South Asia is, for now, apparently minimal or, as some claim, even non-existent. However, ancient DNA evidence in favor of the so called Aryan Invasion or Migration Theory (AIT/AMT) is rapidly building up (see here). By the way, if you're wondering about the title of this post then this might help: "Kossinna's Smile" (Heyd, 2017).

Citation...

Rousea and Cerasetti, Micro-dynamics and macro-patterns: Exploring new archaeological data for the late Holocene human-water relationship in the Murghab alluvial fan, Turkmenistan, Quaternary International, Volume 437, Part B, 5 May 2017, Pages 20-34, https://doi.org/10.1016/j.quaint.2015.12.021

See also...

Maybe first direct hints of Yamnaya-related gene flow into South Central Asia

Swat Valley "early Indo-Aryans" at the lab

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

Wednesday, August 2, 2017

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)


Over at Nature at this LINK. Why is the presence of steppe admixture in Mycenaeans important? And why does it matter if the Minoans already had a lot of ancestry from the Caucasus or surrounds? Because Mycenaeans were Indo-Europeans and Minoans weren't. I'm still reading the paper and will update this entry regularly over the next few days. Below is the abstract and, in my opinion, a key quote. Emphasis is mine.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean [1, 2], and most of the remainder from ancient populations related to those of the Caucasus [3] and Iran [4, 5]. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia [6, 7, 8], introduced via a proximal source related to the inhabitants of either the Eurasian steppe [1, 6, 9] or Armenia [4, 9]. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

...

The simulation framework also allows us to compare different models directly. Suppose that there are two models (Simulated1, Simulated2) and we wish to examine whether either of them is a better description of a population of interest (in this case, Mycenaeans). We test f4(Simulated1, Simulated2; Mycenaean, Chimp), which directly determines whether the observed Mycenaeans shares more alleles with one or the other of the two models. When we apply this intuition to the best models for the Mycenaeans (Extended Data Fig. 6), we observe that none of them clearly outperforms the others as there are no statistics with |Z|>3 (Table S2.28). However, we do notice that the model 79%Minoan_Lasithi+21%Europe_LNBA tends to share more drift with Mycenaeans (at the |Z|>2 level). Europe_LNBA is a diverse group of steppe-admixed Late Neolithic/Bronze Age individuals from mainland Europe, and we think that the further study of areas to the north of Greece might identify a surrogate for this admixture event – if, indeed, the Minoan_Lasithi+Europe_LNBA model represents the true history.

Lazaridis, Mittnik et al., Genetic origins of the Minoans and Mycenaeans, Nature, Published online 02 August 2017, doi:10.1038/nature23310

Update 03/08/2017: This is my own Principal Component Analysis (PCA) of the Minoan and Mycenaean samples, which are freely available at the Reich Lab website here. The Armenian angle for the eastern admixture in Mycenaeans looks forced. The trajectory of this admixture obviously runs from Northern or Eastern Europe to the Minoans. If it did arrive from Armenia, then realistically only via a heavily steppe-admixed population. Right click and open in a new tab to enlarge:


Update 05/08/2017: Much like Lazaridis et al., I ran a series to qpAdm analyses to find the best mixture model for the Mycenaeans. However, just to see what would happen, unlike Lazaridis et al., I didn't group any of the archaeological populations into larger clusters based on their genetic affinities. The three models below stood out from the rest in terms of their statistical fits.

Mycenaean
Minoan_Lasithi 0.786±0.049
Sintashta 0.214±0.049
P-value 0.96574059
chisq 6.030
Full output

Mycenaean
Corded_Ware_Germany 0.210±0.043
Minoan_Lasithi 0.790±0.043
P-value 0.961238695
chisq 6.198
Full output

Mycenaean
Minoan_Lasithi 0.791±0.043
Srubnaya 0.209±0.043
P-value 0.950419642
chisq 6.558
Full output

So it's essentially the same outcome as the one obtained by Lazaridis et al., because Sintashta and Srubnaya are part of their Steppe_MLBA cluster, while Corded Ware is part of their Europe_LNBA cluster, and it's these clusters that, along with Minoan_Lasithi, provided their most successful mixture models for the Mycenaeans. But it's nice to see Sintashta at the top of my results, because it fits so well with the long postulated archaeological links between Sintashta and the Mycenaeans (for instance, see here).

By the way, here's what I said back in May when the Mathieson et al. 2017 preprint came out (see here). So things are falling into place rather nicely.

The same paper also includes the following individual from present-day Bulgaria dated to the start of the Late Bronze Age (LBA), which is roughly when the Mycenaeans appeared nearby in what is now Greece:

Bulgaria_MLBA I2163: Y-hg R1a1a1b2 mt-hg U5a2 1750-1625 calBCE

This guy is the most Yamnaya-like of all of the Balkan samples in Mathieson et al. 2017, and, as far as I can see based on his overall genome-wide results, probably indistinguishable from the contemporaneous Srubnaya people of the Pontic-Caspian steppe. He also belongs to Y-haplogroup R1a-Z93, which is a marker typical of Srubnaya and other closely related steppe groups such as Andronovo, Potapovka and Sintashta. So there's very little doubt that he's either a migrant or a recent descendant of migrants to the Balkans from the Pontic-Caspian steppe.

See also...

Modern-day Greeks & Italians vs Mycenaeans

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