search this blog

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