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Showing posts with label Northern Europe. Show all posts
Showing posts with label Northern Europe. Show all posts

Friday, November 10, 2023

Wielbark Goths were overwhelmingly of Scandinavian origin


When used properly, Principal Component Analysis (PCA) is an extraordinarily powerful tool and one of the best ways to study fine-scale genetic substructures within Europe.

The PCA plot below is based on Global25 data and focuses on the genetic relationship between Wielbark Goths and Medieval Poles, including from the Viking Age, in the context of present-day European genetic variation.


I'd say that it's a wonderfully self-explanatory plot, but here are some key observations:

- the Wielbark Goths (Poland_Wielbark_IA) and Medieval Poles (Poland_Middle_Ages) are two distinct populations

- moreover, the Wielbark Goths form a relatively compact Scandinavian-related cluster and must surely represent a homogenous population overwhelmingly of Scandinavian origin

- on the other hand, the Medieval Poles form a more extensive and heterogeneous cluster that overlaps with present-day groups all the way from Central Europe to the East Baltic, and that's because they are likely to be in large part of mixed origin

- I know for a fact that at least some of these early Poles harbor recent admixture, because their burials are similar to those of Vikings and their haplotypes have been shown to be partly of Scandinavian origin (see here)

- one of the Wielbark females is an obvious genetic outlier (Poland_Wielbark_IA_outlier), and basically looks like a first generation mixture between a Goth and a Balt.

Please note that the PCA is only based on relatively high quality genomes, so as not to confuse the picture with spurious results and noise. Also, all outliers with potentially significant ancestry from outside of Central, Eastern and Northern Europe were removed from the analysis. The relevant datasheet is available here.

However, sanity checks are always important when studying complex topics like fine-scale genetic ancestry. To that end I've prepared a graph based on f3-statistics of the form f3(X,Cameroon_SMA,Estonia_BA)/(X,Cameroon_SMA,Ireland_Megalithic), that reproduces the key features of my PCA. The relevant datasheet is available here.

Polish groups from the Middle Ages are marked with the MA suffix, while the Iron Age Wielbark Goths are marked with the IA suffix.

If you're wondering why I plotted the f3-statistics that I did, take a look at this (all groups largely of Scandinavian origin are emboldened):

f3(X,Estonia_BA,Cameroon_SMA)
Poland_Legowo_MA 0.226406
Poland_Ostrow_Lednicki_MA 0.225996
Poland_Plonsk_MA 0.225017
Poland_Trzciniec_Culture 0.224215
Poland_Lad_MA 0.224142
Poland_Viking 0.223838
Poland_Niemcza_MA 0.223659
Poland_Weklice_IA 0.223549
Poland_Kowalewko_IA 0.222584
Poland_Pruszcz_Gdanski_IA 0.222324
Sweden_Viking 0.222091
Russia_Viking 0.222042
Poland_Maslomecz_IA 0.221914
Norway_Viking 0.221825
Denmark_EarlyViking 0.221257
Denmark_Viking 0.221174
England_Viking 0.220979

f3(X,Ireland_Megalithic,Cameroon_SMA)
Poland_Maslomecz_IA 0.219816
Poland_Weklice_IA 0.219501
Denmark_Viking 0.2192
Poland_Kowalewko_IA 0.219176
Poland_Ostrow_Lednicki_MA 0.218916
Norway_Viking 0.218854
Poland_Pruszcz_Gdanski_IA 0.218684
Sweden_Viking 0.218626
Denmark_EarlyViking 0.218529
England_Viking 0.218308
Russia_Viking 0.217999
Poland_Viking 0.217914
Poland_Plonsk_MA 0.217756
Poland_Lad_MA 0.217719
Poland_Legowo_MA 0.21765
Poland_Niemcza_MA 0.217001
Poland_Trzciniec_Culture 0.216551

Interestingly, the Middle Bronze Age samples associated with the Trzciniec Culture (Poland_Trzciniec_Culture) show a closer genetic relationship to Medieval Poles than to Wielbark Goths or Northwestern Europeans. This is indeed the case both in terms of genome-wide and uniparental markers, including some very specific lineages under Y-chromosome haplogroup R1a.

But that's a much more complex issue that I'll leave for another time. So please stay tuned.

See also...

Slavs have little, if any, Scytho-Sarmatian ancestry

Friday, August 27, 2021

R1a vs R1b in third millennium BCE Central Europe (Papac et al. 2021)


R1a-M417 and R1b-L51 are by far the most important Y-chromosome haplogroups in Europe today. More precisely, R1a-M417 dominates in Eastern Europe, while R1b-L51 in Western Europe.

It's been obvious for a while now, at least to me, that both of these Y-haplogroups are closely associated with the men of the Late Neolithic Corded Ware culture (CWC). Indeed, in my mind they're the main genetic signals of its massive expansion, probably from a homeland somewhere north of the Black Sea in what is now Ukraine.

I'm still not exactly sure how the east/west dichotomy between R1a and R1b emerged in Europe, but, thanks to a new paper by Papac et al. at Science Advances, at least now I have a working hypothesis about that. Below is a quote from the said paper, emphasis is mine:

Our results suggest that the Y-lineage diversity in early CW males was supplanted by a nonrandom process [selection, social structure, or influx of nonlocal R1a-M417(xZ645) lineages] that drove the collapse in Y-chromosomal diversity. A simultaneous decline of Y-chromosomal diversity dating to the Neolithic has been observed across most extant Y-haplogroups (64), possibly due to increased conflict between male-mediated patrilines (65). We view that changes in social structure (e.g., an isolated mating network with strictly exclusive social norms) could be an alternative cause but would be difficult to distinguish in the underlying model parameters.

Right, so even though the CWC was clearly a community of closely related groups, there must have been some competition between its different clans. And since these clans were highly patriarchal and patrilineal, this competition probably led to different paternal lineages dominating different parts of the CWC horizon, with M417 becoming especially common in the east and L51 in the west.

Of course, the expansions of post-Corded Ware groups, such as the M417-rich Slavs in Eastern Europe and L51-rich Celts in Western Europe, were also instrumental in creating Europe's R1a/R1b dichotomy, but obviously these groups were in large part the heirs of the CWC.

By the way, most of the samples from Papac et al. are already in the Global25 datasheets linked here. Look for the labels listed here. Below is a plot made from the Global25 data courtesy of regular commentator Matt.
Citation: L. Papac, M. Ernée, M. Dobeš, M. Langová, A. B. Rohrlach, F. Aron, G. U. Neumann, M. A. Spyrou, N. Rohland, P. Velemínský, M. Kuna, H. Brzobohatá, B. Culleton, D. Daněček, A. Danielisová, M. Dobisíková, J. Hložek, D. J. Kennett, J. Klementová, M. Kostka, P. Krištuf, M. Kuchařík, J. K. Hlavová, P. Limburský, D. Malyková, L. Mattiello, M. Pecinovská, K. Petriščáková, E. Průchová, P. Stránská, L. Smejtek, J. Špaček, R. Šumberová, O. Švejcar, M. Trefný, M. Vávra, J. Kolář, V. Heyd, J. Krause, R. Pinhasi, D. Reich, S. Schiffels, W. Haak, Dynamic changes in genomic and social structures in third millennium BCE central Europe. Sci. Adv. 7, eabi6941 (2021).

See also...

On the origin of the Corded Ware people

Understanding the Eneolithic steppe

Conan the Barbarian probably belonged to Y-haplogroup R1a

Saturday, November 7, 2020

Slavic-like Medieval Germans


The samples labeled DEU_MA_Krakauer_Berg in the Principal Component Analysis (PCA) plot below are from a recent paper by Parker et al. at Scientific Reports. Their remains were excavated from a Medieval cemetery in the now abandoned village of Krakauer Berg in eastern Germany.

Krakauer sounds sort of like Kraków, doesn't it? That's probably not a coincidence, especially considering how these people behave in my analysis. To see an interactive version of the plot, paste the coordinates from the text file here into the relevant field here.

See also...

Yamnaya-related ancestry proportions in present-day Poles

Warriors from at least two different populations fought in the Tollense Valley battle

Viking world open analysis and discussion thread

Tuesday, September 8, 2020

Warriors from at least two different populations fought in the Tollense Valley battle


I can't get the genotype data from the Burger et al. paper. The lead authors, Joachim Burger and Daniel Wegmann, aren't replying to my emails.

But they were gracious enough to release the BAM files for each of their samples, and these files can be converted to genotype data. So I've included ten of the Tollense Valley warriors (DEU_Tollense_BA) in the Global25 datasheets (see here).

The claim in the paper that these warriors "represent an unstructured population" is absolutely false and extremely naive.

Below are a couple of Principal Component Analysis (PCA) plots produced with Vahaduo Global25 views. The samples are labeled according to their Y-chromosome haplogroups. To see interactive versions of the same plots, paste the Global25 coordinates from the text file here into the relevant fields here.


These warriors are not a single unstructured population, because they cover too much ground in the above plots for that to be possible. It's clear to me that they represent at least two different groups from Central Europe and surrounds.

Of course, this would be a lot easier to work out if Burger et al. cared to supply more information about each of the warriors, such as their attire, weapons, circumstances of death, and so on. It's a complete mystery to me why this wasn't included in the paper, and the authors are refusing to talk to me, so it's unlikely that I'll ever be able to get it from them.

In the absence of such crucial archeological and anthropological data, I don't want to speculate too much, and get overly creative, but here are a couple of possible scenarios to explain the ancient DNA results:
- this may have been a battle between two Central European armies, one rich in Y-haplogroup R1b and the other rich in Y-haplogroup I2a, as well as their allies or hired help, including warriors from Eastern Europe belonging to Y-haplogroup R1a

- or perhaps it was an invasion from the east by warriors rich in Y-haplogroup R1a, and it was a success, with the local armies, rich in Y-haplogroups R1b and I2a, losing the battle and suffering most of the casualties.

I'm sure that one day someone will attempt to undertake a decent multidisciplinary study of this epic battle, and we'll at least have a rough idea about what happened. Or not.

Citation...

Burger et al., Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years, Current Biology, Available online 3 September 2020, https://doi.org/10.1016/j.cub.2020.08.033

See also...

Genetic and linguistic structure across space and time in Northern Europe

Saturday, December 14, 2019

Avalon vs Valhalla revisited


Pictured below is a new version of my Celtic vs Germanic genetic map. It's based on the same Principal Component Analysis (PCA) as the original (which can be seen here), but more focused on Northwestern Europe and produced with a different program.


To see the interactive online version, navigate to Vahaduo Custom PCA and copy paste the text from here into the empty space under the PCA DATA tab. Then press the PLOT PCA button under the PCA PLOT tab. For more guidance, refer to the screen caps here and here.

To include a wider range of populations in the key, just edit the data accordingly. For instance, to break up the ancient grouping into more specific populations, delete the Ancient: prefix in all of the relevant rows. This is what you should see:


Conversely, you can leave the ancient sample set intact and instead reorder the present-day linguistic groupings into, say, geographic groupings. To achieve this just delete all of the linguistic prefixes, such as Celtic:, Germanic:, and so on. You should end up with a datasheet like this and plot like this.

Of course, you can design your own plot by using any combination of the ancient and present-day individuals and populations that I've already run in this PCA. Their coordinates are listed here. Indeed, if you're in the possession of your own Celtic vs Germanic PCA coordinates, you can add yourself to the plot. And if you're not, see here.

It's also possible to re-process PCA data via the SOURCE tab. But I don't recommend doing this with the Celtic vs Germanic data, which are derived from a fine scale analysis and don't pack much variation. On the other hand, Global25 data are ideal for such re-processing. I made the plots below from subsets of Global25 coordinates available in a zip file here. To see how, refer to the screen caps here and here.




See also...

Modeling your ancestry has never been easier

Getting the most out of the Global25

Modeling genetic ancestry with Davidski: step by step

Monday, November 25, 2019

Viking Age Iceland


I finally managed to get some of the Icelandic ancients from Ebenesersdóttir et al. 2018 into the Global25 datasheets (see here). Better late than never. Look for the"ISL_Viking_Age" prefix. Below is a screen cap of a Principal Component Analysis (PCA) with the new samples. It was done with an online Global25 PCA runner freely available here.


The individuals classified as unadmixed Gaels and Norse by Ebenesersdóttir et al. generally also look like it based on their Global25 coordinates.

The mixture models below, using all of the populations from the Global25 "modern pop averages scaled" datasheet, were run with an online tool freely available here. Note that the ADD DIST COL option is set to 1X. This is a useful feature for modeling the fine scale ancestry of samples that are derived from very similar populations.






See also...

They came, they saw, and they mixed

Commoner or elite?

Who were the people of the Nordic Bronze Age?

Wednesday, July 17, 2019

Viking invasion at bioRxiv


A new preprint featuring hundreds of Viking Age genomes has appeared at bioRxiv [LINK]. Titled Population genomics of the Viking world, it looks like a solid effort overall, although I'm skeptical about its conclusions. I might elaborate on that in the comments below, but I'll have a lot more to say on the topic if and when I get to check out the ancient genomes with my own tools. Details about the new samples, including their Y-chromosome haplogroup assignments, are available here. Below is the abstract, emphasis is mine:

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Margaryan et al., Population genomics of the Viking world, bioRxiv, posted July 17, 2019, doi: https://doi.org/10.1101/703405

See also...

They came, they saw, and they mixed

Who were the people of the Nordic Bronze Age?

Asiatic East Germanics

Monday, July 15, 2019

Asiatic East Germanics


Around a third of the ancient individuals in my dataset associated with East Germanic-speaking cultures show obvious ancestry from Central and/or West Asia.

This shouldn't be too surprising, considering, for instance, the well documented contacts between East Germanic tribes and the Avars, Huns, Sarmatians and other nomadic groups that streamed into Europe from the Asian steppes during the Migration Period. It's a topic that I've raised before at this blog (see here).

But the curious thing is that very little, if any, of this ancestry has percolated down to present-day Europeans.

The easiest way to show this is with a Principal Component Analysis (PCA) based on my Global25 data. The relevant PCA datasheet can be downloaded here. Basic details about the ancient samples in the analysis are available here.

Some of the Northeastern European populations, particularly the Uralic speakers, appear to be attracted to the Hunnic cluster. However, this is mostly an artifact of pre-Migration Period east to west population expansions in the far north of Europe, probably including those of the Proto-Uralians (see here).

So how is it that, despite ruling over vast areas of Europe for hundreds of years, the East Germanics appear not to have contributed significantly to the present-day European gene pool? My theory is that, much like the Avars and Huns, they were militarily and demographically overwhelmed by the ascending groups around them, such as the Slavs, and they simply went extinct.

To wrap things up, here's a basic qpAdm mixture model designed to test for Hunnic-related ancestry in a few Eastern and Northern European populations of interest. Note the significant slice of this type of ancestry in the likely early Goths of the Chernyakhiv culture. Is it real? Feel free to share your thoughts in the comments below.

UKR_Chernyakhiv
DEU_MA 0.863±0.038
Hun_Tian_Shan 0.137±0.038
chisq 12.525
tail prob 0.325466
Full output

Swedish
Baltic_EST_IA 0.126±0.078
DEU_MA 0.849±0.073
Hun_Tian_Shan 0.025±0.020
chisq 8.338
tail prob 0.595877
Full output

Ukrainian
Baltic_EST_IA 0.121±0.064
DEU_MA 0.857±0.060
Hun_Tian_Shan 0.022±0.017
chisq 11.458
tail prob 0.322956
Full output

Estonian
Baltic_EST_IA 0.597±0.069
DEU_MA 0.373±0.064
Hun_Tian_Shan 0.030±0.017
chisq 15.739
tail prob 0.107361
Full output

See also...

Conan the Barbarian probably belonged to Y-haplogroup R1a

More on the association between Uralic expansions and Y-haplogroup N

Uralic-specific genome-wide ancestry did make a signifcant impact in the East Baltic

Friday, May 3, 2019

Inferring the linguistic affinity of long dead and non-literate peoples: a multidisciplinary approach


Ancient DNA has treated us to many surprises in recent years. But it has also uncannily corroborated some well established hypotheses that were formulated decades ago from historical linguistics and archeological data. One such hypothesis is that the population associated with the Late Neolithic Corded Ware culture (CWC), and its myriad offshoots, spoke early Indo-European languages and spread them across much of Europe and into the Indian subcontinent.

Below is a series of figures in which I explain why the CWC and its likely close relative, the Sintashta culture, are widely regarded as early Indo-European-speaking cultures, even though their languages aren't attested. To view the images at their maximum size, right click on the thumbs and choose "open link in a new tab".




It's a damn shame that we still don't know where the modern domesticated horse lineage ultimately came from. I'm pretty sure that it came from the Pontic-Caspian steppe, but I was hoping this would be confirmed in the latest paper on horse genomics published today at Current Biology: Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Nope, the topic wasn't even covered, and no wonder, because the sampling strategy in the paper didn't allow it to be. What we desperately need are samples associated with such archeological cultures as Khvalynsk, Repin, Sredny Stog and Yamnaya. Maybe next time, eh?

See also...

Monday, December 3, 2018

On the trail of the Proto-Uralic speakers (work in progress)


Historical linguists have long posited that Fennoscandia was a busy contact zone between early Germanic and Uralic languages. The first ancient DNA samples from what is now Finland have corroborated their inferences, by showing that during the Iron Age the western part of the country was inhabited by a genetically heterogeneous population closely related to both the Uralic-speaking Saami and Germanic-speaking southern Scandinavians.

The samples were sequenced and analyzed by two different teams of researches, and their findings published recently in Lamnidis et al. and Sikora et al. (see here and here, respectively).

This is how most of these ancients, whose remains were excavated from the Levanluhta burial site dated to 300–800 CE, behave in a Principal Component Analysis (PCA) based on my Global25 data. Levanluhta_IA are the Saami-related samples, while Levanluhta_IA_o is an Scandinavian-like outlier. Baltic_IA is an Iron Age individual from what is now Lithuania from the recent Damgaard et al. paper (see here). Note the accuracy of the Global25 data in pinpointing their genetic affinities and also the trajectory of the Levanluhta_IA cluster, which seems to be "pulling" towards Levanluhta_IA_o.



The Saami and Levanluhta_IA are clear outliers from the main Northern European cluster. There are two reasons for this: excess East Asian/Siberian-related ancestry and Saami-specific genetic drift. However, this eastern admixture and genetic drift are shared in varying degrees by other North European populations, especially those that also speak Uralic languages, and this is why they appear to be "pulling" towards the Saami/Levanluhta_IA clusters in my PCA. Thus, what this suggests is that the expansion of Uralic languages across Northeastern Europe was intimately linked with the spread of Siberian-related ancestry into the region.

This idea has been around for a long time and is now becoming even more widely accepted (see here). However, Lamnidis et al. also featured samples from a likely pre-Uralic (1523±87 calBCE) burial site at Bolshoy Oleni Ostrov in the Kola Peninsula, present-day northern Russia, and, perhaps surprisingly, found that they showed even more Siberian-related ancestry than Levanluhta_IA. So what's going on?

I'm confident that this discrepancy can be explained by multiple waves of migrations from the east into Northeastern Europe, possibly before, during and after the time of the people buried at Bolshoy Oleni Ostrov, by pre-Uralic, para-Uralic and/or Proto-Uralic-speaking populations.

Consider the following qpAdm output, in which Levanluhta_IA is just barely modeled successfully as a two-way mixture between Levanluhta_IA_o and Bolshoy_Oleni_Ostrov. The statistical fit improves significantly with the addition of Glazkovo_EBA as a third mixture source. This is an ancient population from near Lake Baikal dated to 4597-3726 BC from the aforementioned Damgaard et al. paper.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.468±0.036
Levanluhta_IA_o 0.532±0.036
chisq 19.129
tail prob 0.0854706
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.241±0.092
Glazkovo_EBA 0.162±0.059
Levanluhta_IA_o 0.597±0.046
chisq 7.756
tail prob 0.734966
Full output

For the sake of being complete, I also tested whether Levanluhta_IA_o could be substituted by other similar ancient samples from the neighborhood, including those associated with the Battle-Axe and Corded Ware cultures. There's not much to report; qpAdm returned poor statistical fits and/or implausible ancestry proportions (for the full output from my runs, see here). Baltic_IA did produce a statistically sound model, but with excess Glazkovo_EBA-related ancestry. I also had to drop Bolshoy_Oleni_Ostrov from the analysis to make things work, which suggests to me that the result shouldn't be taken too literally.

Levanluhta_IA
Baltic_IA 0.677±0.034
Glazkovo_EBA 0.323±0.034
chisq 8.547
tail prob 0.741095
Full output

So as far as I can see, the western ancestry in Levanluhta_IA is likely to be mostly of Germanic origin, and thus Indo-European, meaning that it's logical to look east, perhaps far to the east, for the source of its Uralic ancestry. This might seem like a complicated and uncertain task, considering that Levanluhta_IA could well be at least a thousand years younger than the first entry of Uralic speakers into Fennoscandia. However, take a look what happens when I substitute Glazkovo_EBA with a variety of Uralic-speaking populations from around the Ural Mountains, which is where the Proto-Uralic homeland is generally considered to have been located.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.210±0.091
Khanty 0.283±0.090
Levanluhta_IA_o 0.507±0.035
chisq 7.007
tail prob 0.798532
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.193±0.098
Levanluhta_IA_o 0.495±0.035
Mansi 0.312±0.100
chisq 7.884
tail prob 0.7237
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.300±0.065
Levanluhta_IA_o 0.337±0.072
Mari 0.363±0.121
chisq 8.393
tail prob 0.677705
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.238±0.084
Levanluhta_IA_o 0.553±0.036
Nenets 0.209±0.067
chisq 7.210
tail prob 0.78181
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.302±0.069
Levanluhta_IA_o 0.324±0.081
Udmurt 0.373±0.135
chisq 9.195
tail prob 0.60393
Full output

All of these models look great, and easily rival the best model with Glazkovo_EBA. Moreover, they make good sense in terms of linguistics. The only problem is that they're anachronistic, because the Uralic-speaking reference populations are younger than Levanluhta_IA. So I can't be certain that they reflect reality without corroboration from ancient DNA. It might turn out, for instance, that a Glazkovo_EBA-like population was already present somewhere deep in Europe before or during the time of Bolshoy_Oleni_Ostrov, while no such population existed around the Ural Mountains until the time of Levanluhta_IA.

By the way, it might be important to note that the present-day Finnish samples in my dataset can't be modeled as a mixture between Levanluhta_IA and Levanluhta_IA_o. But they can be modeled as a mixture between Baltic_IA and Levanluhta_IA. I don't know which part of Finland they're from exactly; probably all over the place, so it'd be useful to test regional Finnish populations to see how they behave in such models. Of course, Finns aren't Saamic speakers, they're Finnic speakers, and they're probably the result of a more recent Uralic expansion into Fennoscandia than the one that gave rise to the Saami.

Finnish
Baltic_IA 0.671±0.076
Levanluhta_IA 0.329±0.076
chisq 14.114
tail prob 0.293508
Full output

Damgaard et al. didn't report the Y-haplogroup for Baltic_IA, but the word round the campfire is that this individual belonged to N1c, which is today the most common Y-haplogroup among Uralic speakers. Obviously, we need a lot more ancient DNA to sort all of this out, but things are already looking pretty much as expected. Stay tuned for new posts in this series following the publication of more ancient DNA relevant to this fascinating topic.

See also...

How did Y-haplogroup N1c get to Bolshoy Oleni Ostrov?

The Uralic cline in the Global25

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

Sunday, September 16, 2018

Celtic vs Germanic Europe


I have a feeling that ancient DNA from post-Bronze Age Northwestern Europe will be coming thick and fast from now on. To get the most out of such data I've designed a new Principal Component Analysis (PCA) that does a better job of separating the Celtic- and Germanic-speaking populations of Europe than my previous efforts of this sort (see here and here). Below are two different versions of the same PCA. The relevant datasheet is available here.

And here's a Discrimination Analysis (LDA) plot based on the 25 principal components. It further differentiates many of the populations along the east > west cline of genetic diversity.


The difference between the Germanic Anglo-Saxons and the Celtic and Roman Britons of what is now eastern England is obvious. The Anglo-Saxons could pass for Scandinavians, while the Celts and Romans both cluster between the Irish and French. This makes good sense, and is exactly what I was looking for. It's also interesting to see the presumably Celtic-speaking Hallstatt samples from Bylany, Czechia, clustering with the Belgians.

Update 14/12/2019: Pictured below is a new version of my Celtic vs Germanic genetic map. It's based on the same Principal Component Analysis (PCA) as the original, but more focused on Northwestern Europe and produced with a different program.


To see the interactive online version, navigate to Vahaduo Custom PCA and copy paste the text from here into the empty space under the PCA DATA tab. Then press the PLOT PCA button under the PCA PLOT tab. For more guidance, refer to the screen caps here and here.

To include a wider range of populations in the key, just edit the data accordingly. For instance, to break up the ancient grouping into more specific populations, delete the Ancient: prefix in all of the relevant rows. This is what you should see:


Conversely, you can leave the ancient sample set intact and instead reorder the present-day linguistic groupings into, say, geographic groupings. To achieve this just delete all of the linguistic prefixes, such as Celtic:, Germanic:, and so on. You should end up with a datasheet like this and plot like this.

Of course, you can design your own plot by using any combination of the ancient and present-day individuals and populations that I've already run in this PCA. Their coordinates are listed here. Indeed, if you're in the possession of your own Celtic vs Germanic PCA coordinates, you can add yourself to the plot. And if you're not, see here.

It's also possible to re-process PCA data via the SOURCE tab. But I don't recommend doing this with the Celtic vs Germanic data, which are derived from a fine scale analysis and don't pack much variation. On the other hand, Global25 data are ideal for such re-processing. I made the plots below from subsets of Global25 coordinates available in a zip file here. To see how, refer to the screen caps here and here.




See also...

Modeling your ancestry has never been easier

Getting the most out of the Global25

Modeling genetic ancestry with Davidski: step by step

Tuesday, September 26, 2017

The beast among Y-haplogroups


A lot has been written about Y-haplogroup R1a over the years. Sadly, most of it was wrong, such as its posited Pleistocene origin in the Indian subcontinent and subsequent migration to Europe.

In all likelihood, R1a was born somewhere in North Eurasia. More importantly, its R1a-M417 subclade, which encompasses almost 100% of modern-day R1a lineages, no doubt came into existence somewhere on the Pontic-Caspian (or Western) steppe in what is now Ukraine and southern Russia just 7,000-6,000 years ago.

And within a couple of thousand years it expanded in almost all directions, probably on the back of the early Indo-European dispersals (see here), to cover a massive range from Scandinavia to South Asia. It is the beast among Y-haplogroups.


The most common subclade of R1a-M417 in South Asia today is R1a-Z93, and, realistically, it couldn't have arrived there earlier than about 2,000BC. So much for the Pleistocene.

See also...

Y-haplogroup R1a and mental health

The Poltavka outlier

Yamnaya isn't from Iran just like R1a isn't from India

Friday, May 12, 2017

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


All of the post-Middle Neolithic samples from the recent Mittnik et al. and Saag et al. preprints on the ancient population history of the Baltic region belonged to Y-chromosome haplogroup R1a. And most of them belonged to the R1a-M417 (R1a1a) subclade that makes up almost 100% of the R1a lineages in the world today. This is what the results look like in a table (the sample IDs are of my own design):


Earlier samples from the same region belonged to Y-haplogroups I2a and R1a, but this was a subclade of R1a defined by the YP1272 mutation that is extremely rare today even in Northeastern Europe.

And now shifting our focus west of Scandinavia: all but two of the post-Middle Neolithic samples from around the North Sea from the recent Olalde et al. preprint on the Bell Beaker phenomenon and ancient population history of Northwest Europe belonged to Y-chromosome R1b, and more specifically to the R1b-M269 (R1b1a1a2) subclade, which makes up almost 100% of the R1b lineages in the world today. Here's a table:


Earlier samples from the same region belonged to Y-haplogroups I2a, I, G2a and CF, and most of the instances of I and the CF would probably be classified as I2a if not for missing data.

Interestingly, despite the R1a vs R1b dichotomy between these post-Middle Neolithic obvious newcomers to the Baltic and North Sea regions, respectively, they were very similar in terms of overall genetic structure, obviously closely related, starkly different from Middle Neolithic Northern Europeans, and in all likelihood mainly derived from the same homeland that was not located in Northern Europe.

So can we locate this homeland with any degree of certainty, you might wonder? In fact, you might ask, isn't this a futile search for the time being, as we await ancient DNA from many prehistoric Eurasian populations?

Not at all, because when attempting to answer this question we're bounded by two key constraints: the exceptionally high frequencies of R1a and R1b in the post-Middle Neolithic Baltic and North Sea samples, and their close genetic affinity to earlier and contemporaneous populations from the Pontic-Caspian steppe, part of which is due to significant Caucasus Hunter-Gatherer (CHG) admixture that was lacking in Middle Neolithic Northern Europeans.

Indeed, to date, the Pontic-Caspian steppe is the only region where both R1a and R1b have been found in ancient remains from the same sites dating to the Mesolithic, Neolithic and Eneolithic. Here's a table based on results from Mathieson et al. 2015 and 2017. The R and R1 might really be R1a or R1b if not for missing data.


The Pontic-Caspian steppe also abuts the Caucasus foothills, and we know that CHG admixture was a major feature of its inhabitants from at least the Eneolithic. So odds are, and make no mistake, these are indeed excellent odds, that the homeland we're looking for was on the Pontic-Caspian steppe.

But of course I2a has also been recorded in prehistoric samples from the Pontic-Caspian steppe. So, you might ask, why did the populations migrating out of the steppe belong to R1a and R1b, and why did some of them seemingly carry only R1a while others only R1b? This can be explained by local founder effects on the steppe due to patrilocality. Moreover, it's possible that some groups moving out of the steppe did carry high frequencies of I2a, but they're yet to enter the ancient DNA record. [Edit: Maybe they already have? See here]

Now, the aforementioned post-Middle Neolithic newcomers to the Baltic and North Sea regions are most certainly in large part the direct ancestors of modern-day Northern Europeans, speaking languages belonging to the three daughter branches of late Proto-Indo-European (PIE): Balto-Slavic, Celtic and Germanic. It's highly unlikely that languages ancestral to these present-day languages were spoken by Middle Neolithic farmers, nor introduced into Northern Europe after it was colonized by the migrants from the Pontic-Caspian steppe.

What this strongly suggests is that the Pontic-Caspian steppe was also the late PIE homeland.

But, you might argue, the Pontic-Caspian steppe may have just been the expansion point for some of the late PIE language branches. No, that won't work. For one, modern-day populations speaking languages belonging to all other late PIE branches, such as Armenian, Greek, Indo-Iranian and Italic, show signals of the same population expansion from the Pontic-Caspian steppe that gave rise to modern-day Northern Europeans, in the form of Yamnaya-related genome-wide genetic admixture and appreciable frequencies of Y-chromosome haplogroups R1a-M417 and/or R1b-M269.

Some of these signals are certainly due to fairly recent admixture from Northern Europeans, like in much of Greece as a result of the Slavic expansions during the Early Middle Ages, but most cannot be explained in this way.

Secondly, Balto-Slavic, Celtic and Germanic are not more closely related to each other than to some of the other late PIE branches. For instance, Balto-Slavic is considered far more closely related to Indo-Iranian than to Celtic, which is generally seen as a sister branch to Italic. Therefore, if Balto-Slavic and Celtic derive from a homeland on the Pontic-Caspian steppe, then logically this is also where we should look for the origins of Indo-Iranian and Italic.

So as far as the late PIE homeland is concerned, thanks to ancient DNA, the debate is now practically over. But the PIE homeland debate is still wide open, or so we're told.

Apparently, Mathieson et al. 2017 aren't comfortable with putting the PIE homeland on the Pontic-Caspian Steppe because they can't find any evidence in their ancient DNA dataset of a significant migration through the Balkans that would potentially bring Anatolian languages from the Pontic-Caspian steppe to Anatolia. From the paper:

One version of the Steppe Hypothesis of Indo-European language origins suggests that Proto-Indo European languages developed in the steppe north of the Black and Caspian seas, and that the earliest known diverging branch – Anatolian – was spread into Asia Minor by movements of steppe peoples through the Balkan peninsula during the Copper Age around 4000 BCE, as part of the same incursions from the steppe that coincided with the decline of the tell settlements. [51] If this were correct, then one way to detect evidence of it would be the appearance of large amounts of characteristic steppe ancestry first in the Balkan Peninsula, and then in Anatolia. However, our genetic data do not support this scenario. While we find steppe ancestry in Balkan Copper Age and Bronze Age individuals, this ancestry is sporadic across individuals in the Copper Age, and at low levels in the Bronze Age. Moreover, while Bronze Age Anatolian individuals have CHG/Iran Neolithic related ancestry, they have neither the EHG ancestry characteristic of all steppe populations sampled to date [20] , nor the WHG ancestry that is ubiquitous in southeastern Europe in the Neolithic (Figure 1A, Supplementary Data Table 2, Supplementary Information section 1). This pattern is consistent with that seen in northwestern Anatolia [11] and later in Copper Age Anatolia [23], suggesting continuing migration into Anatolia from the East rather than from Europe.

And this...

On the other hand, our data could still be consistent with the Steppe-Balkans-Anatolia route hypothesis model, albeit with constraints. It remains possible that populations dating to around 1600 BCE in the regions where the Indo-European Luwian, Hittite and Palaic languages were spoken did have European hunter-gatherer ancestry. However, our results would require that such ancestry was not ubiquitous in Bronze Age Anatolia, and was perhaps tightly linked to Indo-European speaking groups. We predict that additional insight about the genetic origins of the potential speakers of early Indo-European languages will be obtained when ancient DNA data become available from additional sites in this key period in Anatolia and the Caucasus.

But I'd say the authors are taking that one particular version of the Steppe Hypothesis way too seriously. They might even be implying things that the creator(s) of the said hypothesis never posited.

Why do they seemingly expect a massive surge of steppe admixture into the Balkans during the Copper Age? If the steppe people are just shooting through the Balkans on their way to Anatolia, why would they leave a lot of admixture along the way? And if the locals are abandoning their tell settlements and running for the hills as far away from the oncoming steppe invaders as they can, how exactly would they acquire steppe admixture? Osmosis or what?

The Balkans is not Northern Europe, and the hypothesized migration of the proto-Anatolians from the Pontic-Caspian Steppe to Anatolia through the Balkans was never, as far as I know, meant to parallel the massive Corded Ware expansion across Northern Europe. In other words, why should all of the early Indo-European expansions have been of the same character, especially considering that they moved into such starkly different areas of Eurasia?

Indeed, as Mathieson et al. 2017 point out in the quote above, the evidence for the fleeting presence of steppe peoples in the Copper Age Balkans is in their dataset. For instance, in their Varna 1 sample set from Bulgaria, three out of the five individuals show significant steppe admixture. One of these individuals is almost 50% Yamnaya-like. Surely, there's really no need to expect anything more than that when looking for signals of a proto-Anatolian migration from the Pontic-Caspian Steppe to Anatolia.

In fact, even though I do appreciate the incredible work these guys are doing and the data they're making available to myself and everyone else, I suspect that there's a little bit of, shall we say, schadenfreude going on here.

They sequenced all of three Early Bronze Age Anatolians of obscure origin (are they actually suspected Anatolian speakers, like Luwians?), and apparently it's a big deal that they can't find any steppe admixture in Early Bronze Age Anatolia. Come on.

And then we're offered just three Yamnaya samples from the Pontic Steppe in Ukraine. One happens to be a massive outlier towards the Caucasus. Wow, what are the chances of that? And guess what, all three of these Yamnayans are females, so of course we're left wondering about the Y-haplogroups of the Yamnaya males on the Pontic Steppe. What happened to the males? Next paper, that's what.

Update 19//05/2017: Please note that the authors are not holding back any Yamnaya males from Ukraine for a future paper, as per my claim in the last paragraph above. They used what they had for the time being.

Update 21/05/2017: Actually, I suspect that we already have a population from the Bronze Age steppe in the ancient DNA record with a high frequency of Y-haplogroup I2a. See here.

See also...

R1a-M417 from Eneolithic Ukraine!!!11

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

Eastern Europe as a bifurcation hotspot for Y-hg R1

Globular Amphora people starkly different from Yamnaya people

Sunday, January 22, 2012

Eurogenes' North Euro clusters - phase 2, final results


This is a continuation of my ChromoPainter analysis of Europeans from north of the Pyrenees, Alps and Balkans (see here). To obtain the most accurate results possible on my laptop, I increased the burn-ins and iterations in fineSTRUCTURE to 500K each (5 hour run in all, which is all I'm willing to put this machine through). The end product looks very similar to my initial analysis, in which I explored the data at 200K burn-ins and iterations. What I think this shows is that the results are robust, and I doubt they'd change much even after a couple of days of running fineSTRUCTURE.

Indeed, as mentioned in my previous blog entry, this appears to be the most detailed and accurate cluster analysis of this part of Europe produced anywhere to date. There are 21 clusters in all, with at least 20 looking like strong signals of genetic substructures across North, West, Central and East Europe (see spreadsheet for individual classifications). They include:

pop0 - West Finnish1: This is a pair of reference individuals, most likely from Western Finland, judging by their PCA and ADMIXTURE results. They are either from the same community, or have a very similar mix of very specific ancestries.

pop1 - Erzya + Moksha: This includes all of the Erzya and Moksha in the project, plus a Russian with recent Erzya ancestry. It's closely related to ethnic Russian clusters that stretch from Northwest Russia to near the Volga, and also to the Estonian cluster.

pop2 - South/Central Finnish: This is the largest Finnish cluster, and that's probably more than just the result of sampling bias. I would say that the greater part of the Finnish population would belong to this type of cluster, which occupies regions of highest population density within the country.

pop3 - Fenno-Scandian: This cluster includes a Northern Swede, a Swede with probable recent Finnish ancestry, and Finns with probable recent Swedish influence. I have a feeling that Finland Swedes and Aland Islanders would also be placed here more often than not.

pop4 - Northwest Russian/Southeast Finnish: Although this cluster includes only two individuals, it's definitely much more than just the result of two relatively closely related samples being in the same run. I'd hazard a guess that Northwest Russians with, say, significant Ingrian ancestry, would land here, and so would Finns with recent Russian ancestry.

pop5 - West Finnish2: Based on PCA and ADMIXTURE results, most of these Finns likely come from Western Finland, probably from places like Southern Ostrobothnia. They possibly also have some Swedish influence.

pop6 - West German: This cluster is based on individuals from Western and Northwestern Germany. It also includes a Dutchman, Austrian and people of mixed origin, like a Dane with French and German ancestry, and Americans with British, German, Scandinavian and/or Polish ancestry. In other words, this is where Northwestern Europe meets Central Europe.

pop7 - Vologda Russian: Most of the Vologda Russians from the HGDP land here, so this appears to be a local cluster. Judging from its phylogeny, it looks like a mix of North Slavic, Baltic and Finnic influences.

pop8 - East Finnish: All the project and reference Finns with substantial ancestry from new settlement areas of Eastern Finland appear in this cluster. No wonder then, that this is the cluster with the highest chunk count in this analysis.

pop9 - Estonian: This is a mixed cluster, including individuals from Estonia, and, as far as I know, Russians with substantial ancestry from near Estonia. As mentioned above, it's closely related to the Erzya + Moksha, Northwest Russian and Vologda clusters. However, it's clearly much more western than any of these clusters (for instance, see the PCA below), which suggests Germanic influence in its makeup.

pop10 - Cornish: Almost all of my Cornish samples from the 1000 Genomes Project feature in this very local cluster, which shows the highest chunk count among the Western European samples. The overall results suggest a lack of outbreeding in recent times.

pop11 - French/Belgian: Interestingly, this cluster includes the bulk of the French samples, a French Canadian, and two Belgians. On the other hand, the most northerly French are placed in the more cosmopolitan Northwest European cluster (see below).

pop12 - Lithuanian: All of the more or less pure Lithuanians fall in this cluster. Those that don't are a reference sample from Behar et al. 2009, who always appears very Belorussian like in other analyses, and here sits in the East Slavic cluster, and a project member with recent German ancestry (LIT3). The Western European influence carried by the latter pushes him into the Polish/West Ukrainian cluster, despite not having any documented Polish or Ukrainian ancestry.

pop13 - Northwest Russian: This cluster appears to be made up of Russians who have more Finnic, and/or perhaps Eastern Baltic, ancestry than the individuals in the East Slavic cluster. In other words, it's more northerly, less westerly, and more closely related to the Finnic-speaking Erzya, Moksha and Estonians.

pop14 - Irish + West British: Most Irish individuals fall in this cluster, as well as British samples from Western Scotland and Wales. It's tempting to correlate this cluster with Celtic genetic ancestry in the Isles.

pop15 - South/West Scandinavian: This is basically a Norwegian and Southern Swedish cluster. It also features Swedes from other parts of the country who most likely have some German, Walloon and/or French influence.

pop16 - East German: This cluster includes individuals with significant or even overwhelming Germanic ancestry, but also with very clear Western Slavic input. One of the individuals here is of mixed Polish, German and Swedish ancestry, which pretty much sums up the character of this cluster in a modern context. The presence of two Hungarians from Behar et al. 2009. isn't surprising, because Hungary was settled by both Germanic and Western Slavic groups from the early Middle Ages until modern times.

pop17 - Northwest European: I had reasonable hopes of breaking up this large cluster into a couple of units at least. However, that did not happen, and I don't think it will unless I obtain more samples from the relevant areas of Europe, like Holland and specific parts of the UK. I think the main reason this cluster failed to budge was because of its cosmopolitan nature. In other words, the samples here include some of the most outbred in the analysis, and this, coupled with the fact that they carry very similar ancestral components, means that fineSTRUCTURE doesn't have anything to latch onto to create divisions.

pop18 - East Scandinavian: This could also be called a Swedish cluster. It's almost entirely made up of Swedes, usually from Eastern or Southeastern Sweden, and/or occasionally with recent Finnish influence.

pop19 - Polish/West Ukrainian: The vast majority of the Poles fall in this cluster, and about half of the Ukrainians from Yunusbayev et al. 2011. Most of these Ukrainians appear to be from the Lviv district in the west, and some might even have fairly recent Polish and/or German ancestry. In fact, I would say the latter is a good bet for UkrLv240Y, who shows large Western European segments on several chromosomes.

pop20 - East Slavic: All of the Belorussians cluster here, and so do Russians from near Belorussia and Ukraine, and almost half of the Ukrainians from Yunusbayev et al. 2011 (those who show more easterly genetic characteristics). An individual of mixed Polish and Lithuanian ancestry also makes an appearance here, suggesting that one of the main factors differentiating this cluster from the Polish/West Ukrainian group is a higher level of Baltic admixture in the former.

pop21 - East Central European:
This cluster is based on most of the Hungarians in my dataset, but it also includes a number of Western and Southern Slavs, often with significant German ancestry. Not surprisingly, this cluster shows very high affinity with both the East German and Polish/West Ukrainian clusters.

Let's now move on to some graphics. Below, in order of appearance, are the following: raw data coancestry matrix, showing the placement of individual samples; aggregate coancestry matrix, showing the populations (or clusters) described above; pairwise coincidence matrix, which is useful for spotting very recent ancestral ties; a PCA plot of the 21 clusters. More detailed ChromoPainter/fineSTRUCTURE PCAs of Western Europe can be found at this link.





Finally, those of you who wish to run your own experiments with the ChromoPainter datasheets from this analysis can download them here. Please note, the sheets don't reveal any raw or traits/disease data.

Friday, January 13, 2012

Eurogenes' North Euro clusters - phase 1, exploring the data


I have some preliminary results from a new intra-North Euro cluster analysis, using a cutting edge tool called ChromoPainter. More than 400 samples and 270K SNPs were tested, in linkage mode, and then the output processed in fineSTRUCTURE at 200K burn-ins and iterations. Like I say, the results should be treated as preliminary, but they already look better than any other cluster analysis I've ever seen dealing with Europe north of the Alps, Pyrenees and Balkans. The algorithm identified 21 clusters, with most located in Eastern and Northeastern Europe (see spreadsheet for details). Below are two plots showing how the clusters relate to each other via a tree diagram and heat maps – the first shows an aggregate view, and the second the individual samples.





It's interesting that the Baltic Finns seem to create clusters at a drop of a hat, but they also share the highest number of chunks, and the longest chunks, than any other group. Indeed, all of the Finnish clusters are closely related, and many of the individuals, especially from East Finland, even look like distant relatives on the heat map (note the ultra-hot, blue squares). On the other hand, the large Northwestern European cluster, featuring samples from across the UK, as well as from several nearby countries, is holding firm, and might be tough to break up in this analysis.

I have some theories about the reasons for the obvious genetic homogeneity and diversity in Western Europe, and these include the effects of the Black Death. It decimated many populations in the western half of the continent, thus encouraging migrations into emptied areas, and eventually leading to more open, mobile societies. It's an interesting subject, and I might write much more on it in the future. Meantime, here's a PCA plot from the ChromoPainter chunk counts data. Note the large distances spanned by groups from Northern and Eastern Europe, and the tight bundle of samples from the west, mostly from the UK, Ireland, France and the Low Countries. Interestingly, and perhaps counter-intuitively, it's the closely related Finns who take up most of the space on the plot.



The first component picked up by this PCA appears to be an Atlantic one. It peaks in the Cornish samples, but shows similar levels in all the British, Irish, French, Dutch and Belgians (post-Black Death mobility?). If we are to assume that I identified the component correctly, then it appears as if the East Finns, Vologda Russians, Erzya from the Middle Volga, and Lithuanians are the least “Atlantic” samples in this analysis. These groups, especially the East Finns, also happen to act like relative genetic isolates in many of my experiments (such as ADMIXTURE and MDS analyses). Thus, it seems they've been sheltered from significant gene flow from outside in recent times, including from the west, like German emigration to East Central Europe and Scandinavian influence in Western and Southwestern Finland.