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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, July 12, 2019

Getting the most out of the Global25


The first thing you need to know about the Global25 is that I update the relevant datasheets regularly, usually every few weeks, but they're always at these links:

Global25 datasheet (scaled)

Global25 pop averages (scaled)

Global25 datasheet

Global25 pop averages

Each sample has a population code and an individual code. The population codes represent the countries, ethnic groups and/or archeological affinities of the samples, and I often modify these codes to suit my needs. On the other hand, the individual codes are unique to most of the samples and I usually don't change them.

So if you'd like to know more details about the samples try searching for their individual codes via a decent online search engine. Basic information about many of the samples is also available in the "anno" files here.

The main purpose of the Global25 is to provide data for mixture modeling. In other words, for estimating ancestry proportions, both ancient and modern (see here). This can be done on your computer with the R program and the nMonte R script, or online with the Global25 nMonte Runner, which I discuss below.

If you don't have R installed on your computer, you can get it here, while nMonte is available here. For this tutorial please download nMonte and nMonte3, and store them in your main working folder (usually My Documents).

Once you have R set up, make sure its working directory is the same place where you stored nMonte. You can check this in R by clicking on "File" and then "Change dir". Additionally, you'll need two nMonte input files in the working directory titled "data" and "target". Examples of these files are available here. We'll be using them to test the ancient ancestry proportions of a sample set from present-day England.

Before you can begin the analysis you need to first call the nMonte script by typing or copy pasting source('nMonte.R') into the R console window, and then hitting "enter" on your keyboard. This is what you should see in the R console window afterwards.


To start the mixture modeling process, type or copy paste getMonte('data.txt', 'target.txt') into the R console window, hit "enter", and wait for the results. After a short time, probably less than a minute or two, you should see this output.


The data and target files contain population averages, and, as you can see, the results that these population averages produced were in line with what one would expect from such a model focusing on the genetic shifts in Northern Europe during the Late Neolithic. Very similar ancient ancestry proportions have been reported for the English and other Northern Europeans recently in scientific literature.

However, when focusing on exceptionally fine-scale genetic variation that isn't reflected too well in the Global25 population averages, a more effective strategy might be to use multiple individuals from each reference population and let nMonte3 aggregate and average the inferred ancestry proportions.

This is often the case when attempting to model ancestry proportions for more recent periods, such as the Middle Ages. So let's try this with the English sample set using a modified data file, which is available here.

Replace the old data file with the new one in your working directory, and, like before, copy paste into the R console window the following two commands, hitting "enter" after each one: source('nMonte3.R') and getMonte('data.txt', 'target.txt'). This is what you should eventually see.


It's difficult to say how accurate these estimates are. But they look more or less correct considering the limited and less than ideal reference samples. For instance, the individuals labeled SWE_Viking_Age_Sigtuna are supposed to be stand ins for Danish and Norwegian Vikings, but they're a relatively heterogeneous group from Sweden, possibly with some British or Irish ancestry, so they might be skewing the results.

However, I'll be adding many more ancient samples to the Global25 datasheets as they become available, including lots of new Vikings, which should greatly improve the accuracy of these sorts of fine-scale mixture models.

An alternative to the R-based approach is the online Global25 nMonte Runner [LINK]. This is a free tool, and easy to work with via several drop down menus, but users must become sponsors to unlock all of its available features. To run an analysis follow these three steps:
1) use the first drop down menu to pick the reference populations of your choice (up to four are allowed for free users)

2) move down to the second set of the drop down lists and either pick a test population that is already in the system or copy paste a set of Global25 coordinates into the space labeled "Enter/Paste Sets of Coordinates - Scaled and Comma-separated"

3) feel free to experiment with the additional options if you're game and willing to part with a little cash to help pay for the site.


However, it's important to note that the Global25 is a Principal Component Analysis (PCA), so it makes good sense to also use it for producing PCA graphs. To do this just plot any combination of two or three of its Principal Components (PCs) to create 2D or 3D graphs, respectively. This can be done with a wide variety of programs, including PAST, which is freely available here.

To produce a 2D graph, open a Global25 datasheet in PAST, choose comma as the separator, highlight any two columns of data, click on the "Plot" tab and, from the drop down list, pick "XY graph". Below is a series of graphs that I created in exactly this way. I also color coded the samples according to their geographic origins. This was done by ticking the "Row attributes" tab.


PAST can also be used to run PCA on subsets of the Global25 scaled data to produce remarkably accurate plots of fine-scale population structure. To try this create a new text file with your choice of populations from the Global25 scaled datasheet, open it with PAST and choose Multivariate > Ordination > Principal Components Analysis. I've already put together several datasheets limited to European, Northern European, West Eurasian and South Asian populations. They're available at the links below along with more details on how to run them with PAST.

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

The South Asian cline that no longer exists

And if you're fond of tree-like structures as a means to describe fine-scale genetic variation, please check out this blog post...

Global25 workshop 4: a neighbour joining tree

Wednesday, July 10, 2019

Global25 workshop 4: a neighbour joining tree


Phylogenetic trees are easy to produce, but there's an infinite number of ways to run them, and, depending on the input data you're using, some methods are a lot more effective than others. In this tutorial I'm going to demonstrate one method that has worked well for me when looking at the fine scale genetic relationships between ancient and present-day human populations with my Global25 data.

To get started download this datasheet, plug it into the PAST program, which is freely available here, then select all of the columns by clicking on the empty tab above the labels, and choose Multivariate > Clustering > Neighbour joining. Here's a screen cap of me doing just that...


Then, from the tabs on the right, choose Chord as the similarity index and MAR_Iberomaurusian, the most distinct unit in the datasheet, as the root. PAST offers an exceptionally large range of similarity indices and they generally produce similar results, but, in my experience, Chord creates among the most visually pleasing outcomes when dealing with fine scale genetic substructures.


This is the tree you should see after exporting the image via the graph settings tab in PAST, and, if you like, rotating it 90 degrees with an image editing software of your choice. Note the fairly substantial differences between the populations from Northwestern Europe, which are often difficult to tease apart in such analyses.


If you have your own Global25 coordinates you can add them to my PAST-compatible datasheet to see where you cluster in this tree. And, of course, you can design your own PAST-compatible datasheets and trees with any combination of populations and/or individuals from the Global25 text files at the links below. It's easy; just copy paste the coordinates of your choice into an empty text file, open it with PAST and then save it with the dat extension to create a new PAST datasheet. But make sure never to mix up the scaled and non-scaled coordinates.

Global25 datasheet (scaled)

Global25 pop averages (scaled)

Global25 datasheet

Global25 pop averages

An important point to keep in mind when running these sorts of analyses is that PAST and other such programs need enough genetic differentiation to latch onto in order to produce meaningful results. Thus, even when studying the relationships between very closely related populations, it's not just useful to include a root population or individual, but also some near and far related groups to help the analysis algorithm flesh out the key genetic substructures.

To be honest, I don't really know whether using the Chord index and rooting the tree with MAR_Iberomaurusian is the best way to run a neighbour joining tree analysis of ancient and present-day West Eurasian genetic variation. What do you think? Feel free to let me know in the comments.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

The South Asian cline that no longer exists

Getting the most out of the Global25

Genetic ancestry online store (to be updated regularly)

Sunday, July 7, 2019

Open thread: How did steppe ancestry spread into the Biblical-era Levant?


It's likely that at least two of the Philistines from Feldman et al. 2019 harbor relatively recent steppe ancestry. They're labeled ASH067 and ASH068 in the paper. The former individual is a male who belongs to Y-chromosome haplogroup R1, which appears to be R1b-M269 judging by the data from the relevant BAM file.

This is just the second instance of Y-haplogroup R1 from the pre-Crusades Levant, and, of course, neither R1 nor R1b-M269 appear in the Near Eastern ancient DNA record prior to the expansions of the Yamnaya and other closely related pastoralist groups from the steppes and forest steppes of Eastern Europe.

So how did the Yamnaya-related ancestry spread into the Biblical-era Levant? Did it come via Anatolia, the Caucasus and/or the Mediterranean?

To try and answer this question I analyzed separately the genome-wide data for ASH067 and ASH068 with qpAdm, relying on outgroup and reference populations that weren't featured in the qpAdm runs in the Feldman et al. paper. I also limited the analyses to what were in my view the most proximate two- and three-way solutions in terms of chronology and geography.

The models with the best statistical fits, each labeled with their "tail probs", are available in a zip file here. From my experience with qpAdm, I'd say that the most useful models generally show comparably high tail probs but low chisq values and standard errors. Please note also that I discarded all of the models with at least one standard error higher than 0.2 and/or based on less than 100K SNPs.

As far as I can see, these two are among the very best outcomes. Bell_Beaker_FRA are nine samples associated with the Bell Beaker culture (BBC) from what is now France. Interestingly, the BBC population was rich in Y-haplogroup R1b-M269.

Levant_ISR_Ashkelon_IA1_ASH067
Bell_Beaker_FRA 0.116±0.059
GRC_Minoan 0.507±0.111
Levant_ISR_Ashkelon_LBA 0.377±0.117
tail prob 0.530432
chisq 9.018

Levant_ISR_Ashkelon_IA1_ASH068
Bell_Beaker_FRA 0.237±0.044
GRC_Minoan 0.763±0.044
tail prob 0.943265
chisq 4.736

In my opinion, these models basically confirm that both ASH067 and ASH068 harbor Yamnaya-related ancestry. It's heavily diluted and minor, but it's there. Admittedly, even after looking over the qpAdm output several times, I'm still not quite sure how their ancestors acquired this ancestry. But for the time being, Mediterranean Europe appears to be the most plausible proximate source one way or another. Any thoughts about that? Feel free to share them in the comments below.

See also...

Evidence of European ancestry in the Philistines

R1b-M269 in the Bronze Age Levant

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

Wednesday, July 3, 2019

Evidence of European ancestry in the Philistines


The abstract below has just appeared at the European Nucleotide Archive (see here), so I'm guessing that the relevant paper and accompanying ancient genome-wide data will be published within weeks if not days. Emphasis is mine:

The ancient Mediterranean port-city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a dramatic cultural change between the Late Bronze- and the early Iron- Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples”. Here, we report genome-wide data of ten Bronze- and Iron- Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European related admixture. Interestingly, this genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze- to Iron- Age transition in Ashkelon but did not leave a long-lasting genetic signature.

Update 4/7/2019: The paper is now available at Science Advances [LINK]. One of the Ashkelon ancients, who also shows a relatively high level of European ancestry, belongs to Y-Chromosome haplogroup R1 (probably R1b-M269). I've updated my Global25 datasheets with the new samples. Look for the Levant_ISR_Ashkelon prefix. Same links as always...

Global25 datasheet (scaled)

Global25 pop averages (scaled)

Global25 datasheet

Global25 pop averages

This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation. The relevant datasheet is available here. Based on these results, it's tempting to think that the European ancestry in the Philistines may have been of Greek provenance. But keep in mind that this is just a two dimensional view and a simplification of reality. I'll have more to say about the ancestry of these individuals and the origins of the Philistines in future blog posts.

See also...

Five foot Philistines

How did steppe ancestry spread into the Biblical-era Levant?

Monday, July 1, 2019

Almost everything you ever wanted to know about the Xiaohe-Gumugou cemeteries


I'm reading an interesting and very comprehensive new archeological thesis about the Tarim Basin mummies. It's freely available via Uppsala University's DiVA portal here:

Shifting Memories: Burial Practices and Cultural Interaction in Bronze Age China: A study of the Xiaohe-Gumugou cemeteries in the Tarim Basin

The author, Yunyun Yang, has some suggestions for the future direction of research on the topic:

1. Analysis of Y chromosomal DNA on the males from 4th-1st layers of the Xiaohe cemetery: it is not clear if they were genetically distinct from the Afanasievo (and Yamnaya) males, and consistent to the Andronovo males.

2. More research on ancient DNA of the six males buried in type I the sun-radiating-spokes graves: the six males were so different in the Gumugou cemetery, and we don't know who they were. In this study, it has been suggested that they came from the parallel Andronovo horizon, and preserved some of their original social identities.

3. Analysis of the white sticky materials painted on the dead’s hair, faces, and bodies: it is not clear what this material is. It might be application of dairy/milk products with some holy functions. And the interesting point is why the dead was painted on such materials, for holy reasons, and/or was embalmed that way for preventing decay of the dead bodies?

4. Research on the use of Ephedra plants: Ephedra twigs were common and important in both cemeteries. Were they related to the “Soma” in ancient India (Vedas) and/or “Haoma” in ancient Iran (Avesta)? Were the Ephedra twigs related to the body painting (whitish sticky materials painting on skins of the dead)? Was there a common use of Ephedra plant in more nomadic groups in the Eurasian Steppe?

5. Research on the comparisons between the Andronovo burials and the stone circular-kerbs with stone-pits in Xinjiang: a major obstacle to such research is the language barriers, with the material published in English, Chinese and Russian. Such research is, however, essential to understand the conjunction of the geographical areas, the expansion of nomadic groups, the spreading of horses and wagons (linked to the noble groups of the Shang Dynasty (1600-1046 BCE) in central China), the formation of the Silk Road in this area (till the expansion of Han Dynasty (206 BCE-220 CE)), the moving of Indo-Iranians, the expansion of Scythians (900 BCE-400 CE), etc.

I agree, but I'd also add that we need a good number of ancient Y-chromosome and genome-wide samples from across space and time in the Tarim Basin, including and especially from attested Tocharian-speaking communities. That's really the only way to figure out whether the Tarim Basin mummies belonged to the speakers of Indo-Iranian or Tocharian languages, and whether the latter were introduced into the region by migrants from the Afanasievo culture.

Citation...

Yang, Yunyun, Shifting Memories: Burial Practices and Cultural Interaction in Bronze Age China: A study of the Xiaohe-Gumugou cemeteries in the Tarim Basin, URN: urn:nbn:se:uu:diva-386612

Update 2/7/2019: OK, it looks like there's a paper coming soon with Iron Age samples (~200 BCE) from eastern Xinjiang. As far as I know, this was likely to have been a Tocharian-speaking region at the time. In any case, BAM files for the samples have already been uploaded to the European Nucleotide Archive and the accompanying text suggests that they harbor Yamnaya-related ancestry (see here).

See also...

Another look at the ancient mtDNA from Xiaohe, Tarim Basin

On the doorstep of India

The mystery of the Sintashta people

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

Friday, June 28, 2019

On the origin of the Gravettians (Bennett et al. 2019 preprint)


Over at bioRxiv at this LINK. No major surprises, as far as I can see. From the preprint, emphasis is mine:

The Gravettian technocomplex was present in Europe from more than 30,000 years ago until the Last Glacial Maximum, but the source of this industry and the people who manufactured it remain unsettled. We use genome-wide analysis of a ~36,000-year-old Eastern European individual (BuranKaya3A) from Buran-Kaya III in Crimea, the earliest documented occurrence of the Gravettian, to investigate relationships between population structures of Upper Palaeolithic Europe and the origin and spread of the culture. We show BuranKaya3A to be genetically close to both contemporary occupants of the Eastern European plain and the producers of the classical Gravettian of Central Europe 6,000 years later. These results support an Eastern European origin of an Early Gravettian industry practiced by members of a distinct population, who contributed ancestry to individuals from much later Gravettian sites to the west.

...

The mitochondrial haplogroup of BuranKaya3A was determined to belong to an early branch of the N lineage, N1.

...

In addition, the N1 of BuranKaya3A carries three of the eight mutations occurring prior to N1b, a rare haplogroup most highly concentrated in the Near East, yet appearing broadly from western Eurasia to Africa. The descendants of the N1b node include N1b2, currently found only in Somalia [22], and N1b1b, found in nearly 10% of Ashkenazi Jewish haplogroups [23]. These three mutations allow us to place BuranKaya3A on a lineage apart from that which has been proposed to later enter Europe from Anatolia during the Neolithic (N1a1a) [24]. Among ancient samples, the mitochondrial sequence of an 11,000-year-old Epipalaeolithic Natufian from the Levant (“Natufian9”) [25] is also a later derivative of this N1b branch.

...

From the reads mapping to the Y chromosome, six out of six Single Nucleotide Polymorphisms (SNPs) that overlap with diagnostic sites for Y-haplogroup BT all carry the derived allele, allowing a minimum assignment to BT, which has origins in Africa, with additional derived alleles suggesting an eventual placement of CT or C, found in Asia and the Epipalaeolithic Near East [25]. Additional ancestral alleles make an assignment of C1a2 or C1b, which appear in UP Europe [1], unlikely (see Table S3 for a summary and comparative placement of Palaeolithic Y-haplogroups, and Supplementary Data 1 for a complete list of Y diagnostic SNPs).


Bennett et al., The origin of the Gravettians: genomic evidence from a 36,000-year-old Eastern European, bioRxiv, posted June 28, 2019, doi: https://doi.org/10.1101/685404

Monday, June 24, 2019

Genetic substructures and adaptations in Lithuanians (Urnikyte et al. 2019)


Over at Scientific Reports at this LINK. Apparently, the genotype data from this paper will be available at figshare in just over three months (see here). Among other things, the paper makes some interesting points about the relationship between the genetic ancestry of Lithuanians and their language:

Partial genetic isolation of the Lithuanians is a possible explanation for the structure results observed. Until the late Middle Ages, the eastern Baltic region was one of the most isolated corners of Europe [27]. Moreover, after the fall of the Roman Empire in the 5th century, the eastern Baltic region was spared by the subsequent population movements of the Migration Period [26,28], which allowed the most archaic of all the living speaking Indo-European languages [1] to survive. Thus, Lithuanians could retain their cultural identity.

Urnikyte et al., Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data, Scientific Reports volume 9, Article number: 9163 (2019), DOI: https://doi.org/10.1038/s41598-019-45746-3

See also...

Fresh off the sledge

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

It was always going to be this way

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

Saturday, June 15, 2019

Not Bell Beaker, not Corded Ware, but...the SGBR complex


I'd be very grateful if someone could explain to me what this new paper at the Proceedings of the Prehistoric Society journal was actually about.

Citation...

Furholt, Martin, Re-integrating Archaeology: A Contribution to aDNA Studies and the Migration Discourse on the 3rd Millennium BC in Europe, Proceedings of the Prehistoric Society, Published online: 10 June 2019, DOI: https://doi.org/10.1017/ppr.2019.4

See also...


Sunday, June 9, 2019

Genetic continuity across the millennia in central Poland


Apparently, ancient DNA and anthropological research on the populations of what is now central Poland suggests strong genetic continuity in the region since the Neolithic or even Mesolithic. Science in Poland has a news feature about the soon to be published study (see here). Below are a few quotes from the article. Emphasis is mine:

How were the people in Poland changing over the centuries, from the early Middle Ages to the 19th century? Did the Slavs migrate to our territories, or are they indigenous? The 3D scanning project and digital access to skulls, skeletons and DNA from human remains from central Poland is expected to help answer these questions.

...

Research shows that the shape of the cerebral part of the skull has changed over the centuries - people in the early Middle Ages had more elongated heads. This interesting phenomenon has not been fully explained yet. "There are many theories on this subject, but it is not known whether this was a microevolutionary genetic change, or perhaps an environmentally conditioned one, associated with a reconstruction of the skull as a consequence of the chewing apparatus being relieved" - he adds.

Researchers are also trying to assess the level of diversity of the population living in the territory of present-day Poland during that period and whether migrants from other areas of Europe, for example from Scandinavia, appeared here. "There is the topic of participation of Scandinavian groups in the creation of the Polish State. Such groups indeed penetrated Poland, they could be hired warriors. But I think that, for example, we can probably put aside the hypothesis that Mieszko I was Scandinavian" - the researcher says.

The features, the variability of which anthropologists study, include the height of the body. We already know that, for example, people in the early Middle Ages in Poland were relatively tall, similar to Poles in the 1960s. Later there was a clear decline in body height, lasting until the 19th century.

...

There are already first conclusions from the research of the team from the Biobank Laboratory and the Department of Anthropology. The researchers believe that in the case of the population living in Kujawy there was a surprisingly strong genetic continuity, dating back to the time of the first farmers, 7.5 thousand years ago.

"It seems that we are dealing with an interesting genetic continuation in the population living in Kujawy from the early Middle Ages to the 19th century. The roots of these populations probably reach the Neolithic, perhaps even the Mesolithic" - the scientist suggests.

Source: 3D scans of skulls and a collection of ancient DNA will be available on the information platform e-Czlowiek.pl

See also...

They came, they saw, and they mixed

Saturday, June 1, 2019

They came, they saw, and they mixed


Y-chromosome haplogroup N is strongly associated with Uralic-speaking populations. That's probably because it was a salient feature of the gene pool of the earliest Uralic speakers, and it went with them as they migrated across northern Eurasia. However, some of its younger subclades appear to have spread with the speakers of Indo-European and Turkic languages.

For instance, N-Y10931 seems to be a marker of the Rurikids, a Varangian dynasty that, according to most sources, ruled the Kievan Rus in what are now Russia and Ukraine. And the Kievan Rus was a lose medieval political federation in which Slavic, Finnic (west Uralic) and Germanic languages were probably spoken. The latest on the genetic genealogy of the Rurikids was presented a couple of days ago at the Centenary of Human Population Genetics conference in Moscow, and there's an abstract of the talk available here (download the PDF and scroll down to page 84).

I'm not aware of any Rurikids among the thousands of ancients in my dataset, or even of any samples belonging to N-Y10931. But I do have the genome of someone who belongs to N-Y4339, which, as per the abstract linked to above, is proximally ancestral to N-Y10931. Not only does this person come from Viking Age Scandinavia, but he was buried in a crouched position typical of Slavic funerary customs of the time.

The individual in question is vik_84001. His genome was published recently along with a paper on the population structure of the Swedish town of Sigtuna way back when it was a Viking stronghold (see here). This is where his Y-chromosome sequence, labeled ERS2540883, is positioned on the YFull Y-chromosome phylogenetic tree. Click on the image to go to YFull.


However, the result is likely to be compromised to some extent by missing data. If so, it's possible that vik_84001 does indeed belong to N-Y10931 and ought to be sitting near or even among that cluster of Russian samples (Rurik descendants?) at the bottom of the page.

In any case, vik_84001 seems to be the closest individual in the ancient DNA record to a Rurikid. The Principal Component Analysis (PCA) below is based on my Global25 data. It features 13 other Viking Age individuals from Sigtuna alongside vik_84001 (look for the black dots). Interestingly, despite his eastern Y-haplogroup, vik_84001 is one of the few Sigtuna ancients who clusters strongly with present-day Swedes.
But here's what happens when I model his ancestry proportions with the Global25/nMonte method using a wide range of reference populations from Northern and Eastern Europe. The Swedes in this model are the same as those in the PCA.

vik_84001
Swedish,84.6
Ingrian,9.2
Russian_Tver,6.2

Belarusian,0
Estonian,0
Finnish,0
Finnish_East,0
Karelian,0
Latvian,0
Mordovian,0
Russian_Kostroma,0
Russian_Kursk,0
Russian_Orel,0
Russian_Pinega,0
Russian_Smolensk,0
Russian_Voronez,0
Ukrainian,0
Vepsian,0

[1] "distance%=2.3778"

Yep, despite his position in the PCA, vik_84001 shows a strong signal of ancestry related to the present-day populations of northwestern Russia. I'm not sure what this means exactly, but it's certainly fascinating stuff. And, by the way, I usually wouldn't use so many similar reference populations in a single Global25/nMonte model because of the problem of "overfitting", but in some cases it's OK to do so if the nMonte algorithm has enough recent genetic drift to latch onto.

See also...

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

Fresh off the sledge

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

It was always going to be this way

Conan the Barbarian probably belonged to Y-haplogroup R1a

Tuesday, May 28, 2019

North African ancestry in a British Bell Beaker?


A new thesis uploaded to the University of Huddersfield Repository suggests that there might be "Near Eastern/North African ancestry in a Bell Beaker individual from northeastern England" (see here).

If true, this wouldn't be a shocking outcome, but certainly an interesting one. Do any of the British Beakers in the Global25 datasheets show this type of ancestry?

See also...

A Bell Beaker superhighway

The Boscombe Bowmen

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

Friday, May 24, 2019

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


Genes don't speak languages, people do. Thus, associations between genetic markers and languages may often not be easy to discern, especially with time. This is the case when it comes to Y-chromosome haplogroup N and the Hungarian language.

I briefly discussed this problem not long ago in the context of new ancient DNA samples from medieval Hungary (see here). Today, a detailed paper on the topic by Post et al. was published at Scientific Reports (open access here). It brings together evidence from modern and ancient DNA, linguistics and archeology to argue that Hungarian was introduced into the Carpathian Basin during the Middle Ages by migrants from near the Ural Mountains rich in Y-haplogroup N3a4-B539. Below is the paper abstract, emphasis is mine:

Hungarians who live in Central Europe today are one of the westernmost Uralic speakers. Despite of the proposed Volga-Ural/West Siberian roots of the Hungarian language, the present-day Hungarian gene pool is highly similar to that of the surrounding Indo-European speaking populations. However, a limited portion of specific Y-chromosomal lineages from haplogroup N, sometimes associated with the spread of Uralic languages, link modern Hungarians with populations living close to the Ural Mountain range on the border of Europe and Asia. Here we investigate the paternal genetic connection between these spatially separated populations. We reconstruct the phylogeny of N3a4-Z1936 clade by using 33 high-coverage Y-chromosomal sequences and estimate the coalescent times of its sub-clades. We genotype close to 5000 samples from 46 Eurasian populations to show the presence of N3a4-B539 lineages among Hungarians and in the populations from Ural Mountain region, including Ob-Ugric-speakers from West Siberia who are geographically distant but linguistically closest to Hungarians. This sub-clade splits from its sister-branch N3a4-B535, frequent today among Northeast European Uralic speakers, 4000–5000 ya, which is in the time-frame of the proposed divergence of Ugric languages.


Post et al., Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia, Scientific Reports 9, Article number: 7786 (2019), DOI: https://doi.org/10.1038/s41598-019-44272-6

See also...

Fresh off the sledge

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

It was always going to be this way

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

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

Sunday, May 19, 2019

Who were the people of the Nordic Bronze Age?


Ancient DNA has revealed that large scale migrations and population replacements have often accompanied major cultural changes in prehistoric Europe. But, for now, my opinion is that the formation of the archeologically ostentatious Nordic Bronze Age wasn't associated with any significant foreign gene flow into Scandinavia. I've tested this as best as I could with the few relevant ancient samples that are currently available.


For instance, below are among the most successful qpAdm mixture models that I was able find for various ancient Scandinavian groups dating back to the local Middle Neolithic (MN) period. The Nordic Bronze Age population is represented by three individuals labeled Nordic_BA. Unfortunately, the guy pictured above, from the famous Borum Eshøj barrow burial in what is now Denmark, didn't make the cut. For more details about my sampling and labeling strategies refer to the text file here.

Nordic_MN_B
CWC_CZE 0.822±0.059
POL_Globular_Amphora 0.178±0.059
chisq 14.478
tail prob 0.341086
Full output

SWE_Battle_Axe
CWC_Baltic_early 0.662±0.028
POL_Globular_Amphora 0.338±0.028
chisq 11.234
tail prob 0.591189
Full output

Nordic_LN
Nordic_MN_B 0.928±0.069
SWE_TRB 0.072±0.069
chisq 12.139
tail prob 0.516307
Full output

Nordic_BA
Nordic_LN 0.851±0.061
SWE_TRB 0.149±0.061
chisq 10.897
tail prob 0.619475
Full output

It's impossible to successfully model the ancestries of Nordic_MN_B and SWE_Battle_Axe simply with the populations that were living in Scandinavia before them. Therefore, it's likely that they were migrants or the recent descendants of migrants to Scandinavia. But there's nothing surprising about that, because they're archeologically associated with the Corded Ware culture (CWC), which has always been seen as intrusive to Scandinavia from the south and east.

Conversely, it's easy to produce statistically sound mixture models for both Nordic_LN and Nordic_BA exclusively with earlier Scandinavian populations. Indeed, based on the outgroups or right pops that I'm using, Nordic_LN is almost indistinguishable from Nordic_MN_B, and the same can be said of Nordic_BA in regards to Nordic_LN.

Of course, if I mixed and matched reference populations from across prehistoric Europe, I could probably come up with some spectacular statistical fits even without the need for any Scandinavians. Essentially that's because Nordic_LN and Nordic_BA are closely related to many earlier and contemporaneous peoples living all the way from the Atlantic facade to the Ural Mountains. My point, however, is that this isn't crucial, despite the dearth of ancient samples from Scandinavia.

This is how things look in a Principal Component Analysis (PCA) of Northern European genetic variation based on my Global25 data. Strikingly, Nordic_MN_B, SWE_Battle_Axe, Nordic_LN and Nordic_BA more or less recapitulate the cluster made up of present-day Swedish samples. The relevant datasheet is available here.
Granted, two of the Nordic_BA samples sit just south of the Swedes, no doubt due to their slightly higher ratios of Neolithic farmer (SWE_TRB-related) ancestry, but this is also an area of the plot that many present-day Danes call home (not shown, because I don't have any suitable academic Danish samples to run).

I'll eat my hat if it turns out that Scandinavia experienced a major population shift (say, more than a collateral ~10%) during the LN and/or BA periods. And I'll post a clip of it online too.

See also...

The Trundholm sun chariot was found in a peat bog on the island of Zealand, Denmark, in 1902. It's thought to be an Indo-European religious artifact dating back to the Nordic Bronze Age; a representation of a horse pulling the sun and perhaps also the moon in a spoked wheel chariot. So one way or another it appears to be a reference to the Divine Twins mythos. Click on the image for more...


Thursday, May 16, 2019

Fresh off the sledge


As things stand, the closest individual to a Proto-Uralic speaker in the ancient DNA record is arguably OLS10 from an Iron Age tarand grave in what is now Estonia. I say that because:

- isotopic data suggest that OLS10 wasn't born where he died, and considering his elevated Siberian ancestry relative to earlier and most contemporaneous Baltic ancients, he was very likely a migrant to the Baltic region from the east

- the tarand grave tradition appears to be specifically a Finnic (west Uralic) phenomenon that probably spread from the Volga-Oka region, which is just west of where most people place the Proto-Uralic homeland

- OLS10 belongs to Y-chromosome haplogroup N-L1026, a paternal marker that is especially closely associated with Uralic-speaking populations and probably only appeared in the East Baltic region during the transition from the Bronze Age to the Iron Age

You can find more background info about OLS10 and other relevant samples in Saag et al. 2019 (see here). This is where he sits in my Principal Component Analyses (PCA) focusing on fine scale Northern European genetic diversity. The relevant datasheets are available here and here, respectively.



Note that OLS10 doesn't cluster strongly with any ancient or modern populations. To investigate this in more detail I ran a series of two-way qpAdm analyses, testing tens of ancient individuals and populations as potential admixture sources. These two models stood out above the rest in terms of their statistical fits, chronology and overall plausibility.

Baltic_EST_IA_0LS10
Baltic_EST_BA 0.826±0.045
RUS_Sintashta_MLBA_o1 0.174±0.045

chisq 12.527
tail prob 0.564048
Full output

Baltic_EST_IA_0LS10
Baltic_EST_BA 0.683±0.102
RUS_Mezhovskaya 0.317±0.102

chisq 13.811
tail prob 0.463864
Full output

Please note that RUS_Sintashta_MLBA_o1 isn't representative of the Sintashta culture population as a whole. It's a group of the most extreme genetic outliers among the Sintashta samples, and they may or may not have been Uralic speakers (see here). Interestingly, the Mezhovskaya culture population is generally associated with the Ugric branch of the Uralic language family.

I was also able to closely replicate these results with the Global25/nMonte method; down to almost one per cent. However, the statistical fits (distances) are poor, probably because the reference populations aren't the real mixture sources. This is in line with the fact that their Y-haplogroups are Q1a, R1a and R1b, rather than any type of N.

Baltic_EST_IA:0LS10
Baltic_EST_BA,83.8
RUS_Sintashta_MLBA_o1,16.2

distance%=4.7955

Baltic_EST_IA:0LS10
Baltic_EST_BA,69.8
RUS_Mezhovskaya,30.2

distance%=3.5783

I do realize that two Bronze Age samples from Bolshoy Oleni Ostrov, Kola Peninsula, belong to N-L1026, but adding them to my mixture models doesn't help. Little wonder, because the Kola Peninsula lies within the Arctic Circle, and I'm pretty sure that OLS10 and his N-L1026 came from somewhere just north of the mixture cline marked on the map below. Unfortunately, I can't test this directly yet due to the scarcity of ancient samples from this region.


See also...

It was always going to be this way

On the association between Uralic expansions and Y-haplogroup N

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

Saturday, May 11, 2019

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


I've started analyzing the ancient genotype data from the recent Saag et al. paper on the expansion of Uralic languages and associated spread of Siberian ancestry into the East Baltic region. The paper is freely available here and the data are here.

I really like the paper, but I don't agree with the authors' claim that the appearance of Y-chromosome haplogroup N in what is now Estonia and surrounds during the Iron Age is "not matched by a clear shift in autosomal profiles". In my opinion it certainly is, and, as one would expect, it's a shift towards a genetic profile typical of western Uralic speakers.

I'd say that the easiest way to find this signal is with a Principal Component Analysis (PCA) focusing on fine scale genetic substructures within Northern Europe, like the one below. The relevant datasheet is available here.


Note that the East Baltic Iron Age samples, all from burial sites in what is now Estonia, appear to be peeling away from their Bronze Age predecessors and overlapping strongly with present-day Estonians, who are Uralic speakers. Indeed, the PCA suggests to me that the formation of the greater part of the present-day Estonian gene pool took place in the East Baltic during the transition from the Bronze Age to the Iron Age. That is, when Uralic languages are generally accepted to have arrived in the region from near the Ural Mountains in the east.

I was also able to closely replicate these outcomes with my Global25 data using the method described here. However, in this effort, present-day Estonians are clearly more western than the Estonian Iron Age samples (EST_IA), which might be due to the presence of low level Germanic ancestry in Estonia dating to the medieval period. The relevant datasheet is available here.


Interestingly, the Estonian Bronze Age samples (EST_BA) come from stone-cist graves which are widely hypothesized to have been introduced to the East Baltic from the Nordic Bronze Age civilization. I even recall reading a paper on the topic which claimed that the remains buried in such graves were those of Proto-Germanic-speaking Scandinavian migrants. Well, I haven't had a chance to study these samples in any great detail yet, but considering that in both of the PCA above they're overlapping strongly with Latvian Bronze Age samples (LVA_BA) and sitting far away from the nearest Scandinavians, I'd say they're probably of local stock from way back.

See also...

It was always going to be this way

On the association between Uralic expansions and Y-haplogroup N

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

Thursday, May 9, 2019

It was always going to be this way


The native peoples of the East Baltic - Estonians, Latvians and Lithuanians - are genetically alike and their paternal gene pools are dominated by the same two Y-chromosome haplogroups: R1a and N3a.

Linguistically, however, Estonians are a world apart from Latvians and Lithuanians. That's because the Estonian language belongs to the Uralic language family, which has an obvious North Eurasian character. On the other hand, Latvian and Lithuanian are both classified as Indo-European languages, along with the vast majority of other European languages.

The Uralic and Indo-European language families may or may not descend from the same ancestral tongue, but even if they do, their relationship is very distant.

So how is it that Estonians came to speak a Uralic language? As far back as I can remember, the basic explanation accepted by most people was that Uralic speech arrived in what is now Estonia and neighboring Finland during the Bronze Age with migrants, or perhaps invaders, rich in N3a from somewhere around the Ural Mountains. Conversely, Latvians and Lithuanians were generally assumed to have retained the Indo-European speech of their R1a-rich forefathers from the Pontic-Caspian steppe, who colonized much of Eastern Europe north of the steppe during the Late Neolithic.

Ancient DNA has now uncannily corroborated these theories (for instance, see Mittnik et al. 2018 and, published today, Saag et al. 2019). All it took was a handful of samples from a few relevant sites. I think that's awesome; I love it when sensible, long-standing hypotheses are validated by cutting edge science.

I'll have a lot more to say about the spread of Uralic languages and Uralian genes to the East Baltic when I get my hands on the genotype data from the new Saag et al. paper. I also have a post coming soon about the Nordic Bronze Age. Stay tuned.


Update 10/05/2019: Uralic-specific genome-wide ancestry did make a signifcant impact in the East Baltic

See also...

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

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)

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

Tuesday, May 7, 2019

The execution


Around 2,800 BCE, in what is now southern Poland, a family group of fifteen individuals associated with the Globular Amphora culture (GAC) were massacred. They were probably captured and executed, because each victim was killed with a blow to the head from the same type of weapon, possibly a stone axe, and lacked defensive wounds. The dead were mostly women and children. They were buried in a mass grave, but with great care and very likely by someone who knew them well.

This Late Neolithic mass grave is the focus of a new ancient DNA and archeological research paper at PNAS by Schroeder et al. (see here). The authors tentatively attribute the massacre to the Corded Ware culture (CWC) people, who were expanding rapidly at the time across much of Europe from their homeland on the Pontic-Caspian steppe.


The CWC people may or may not have been responsible; we'll never know for sure. The perpetrators could just as easily have been a competing GAC family group.

In any case, it's interesting to see that the GAC males belong to Y-chromosome haplogroup I2a-L801. This is today a rather uncommon subclade of I2, and almost exclusively found in Germanic-speaking populations, especially Scandinavians. To me this suggests that some Polish GAC males were incorporated into Indo-European-speaking CWC populations that ended up in Scandinavia, and their paternal lineages eventually became a part of the Proto-Germanic gene pool. Admittedly, though, that's just one of many possible scenarios.

See also...

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

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)

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

Sunday, May 5, 2019

Conan the Barbarian probably belonged to Y-haplogroup R1a


A fresh batch of Iron Age genomes from across the Eurasian steppe is about to be published along with a new paper at Current Biology. The manuscript, titled Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance, is still under review but freely available here.

Most of the male ancients, including two Cimmerians from the North Pontic steppe, in what is now Ukraine, belong to Y-chromosome haplogroup R1a. Wasn't Conan the Barbarian supposed to be a Cimmerian? From the preprint, emphasis is mine:

The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western/Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in Eastern Hunter-Gatherer (EHG) ancestry in the Early Iron Age Ponto- Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.

...

Out of the 31 samples of this study, 16 are male, and with sufficient Y-chromosome coverage for haplogroup assignment (Table S2). R1a (43%) and I (27%) are the two most frequent Y- chromosome hgs in present-day Ukrainians [142]. R1a is also the predominant lineage among Cimmerians, Scy_Ukr and ScySar_SU in our data, and present among Scy_Kaz as well. Thus, although acknowledging our small sample size, the individuals sampled from archaeological context associated with Scythian identity do not appear to stand out from the context of other groups living in the region before and after them. One notable difference from the present is the absence of hg N, nowadays widespread in the Volga-Uralic region and West Siberia as well as among Mongols and Altaians [165-167]; however, this result is consistent with the absence of hg N among Bronze Age and Eneolithic males from the Steppe [168]. In context of their claimed Altaian homeland it is interesting to note that one Scy_Ukr and the single Sar_Cau sample belong to the Q1c-L332 lineage which is a sub-clade of hg Q1c-L330 that today has peak frequency of 68% in Western Mongolians [169] and occurs at 17% in South Altaians [170] while being very rare (<1%) in East European populations and absent elsewhere (https://www.yfull.com/tree/Q-L330/).


Järve et al., Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance, Current Biology (preprint), Posted: 6 Mar 2019, http://dx.doi.org/10.2139/ssrn.3346985

Update 12/07/2019: The paper has just been published and is freely available at Current Biology [LINK].

See also...

The mystery of the Sintashta people

On the association between Uralic expansions and Y-haplogroup N

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

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...

Thursday, April 25, 2019

Some myths die hard


Ancient DNA tells us that the Bronze Age wasn't kind to the indigenous populations of Central Asia. It seems to have wiped them out totally. Indeed, Central Asia might well be the only major world region in which native hunter-gatherers failed to make a perceptible impact on the genetics of any extant populations.

Before the Neolithic transition, much of Central Asia was home to hunter-gatherers closely related to those of nearby western Siberia. During the Neolithic, agriculturalists and pastoralists from the Near East gradually moved into the more arable parts of southern and eastern Central Asia, eventually giving rise to the Bactria Margiana Archaeological Complex, or BMAC, and other similar communities.

It's not clear what their relationship was like with the native hunter-gatherers in these areas. But they did mix with them in varying degrees. This is obvious because genome-wide genetic ancestry characteristic of the Botai people, who hunted and eventually domesticated horses on the Kazakh steppe during the 4th millennium BCE, and were probably the archetypal Central Asians for their time, is found at significant levels in a number of later samples from Central Asian farmer and pastoralist sites, such as Dali, Gonur Tepe and Sarazm.

Thus, even though the Neolithic transition did have a big impact on Central Asia, and clearly led to large scale population replacements in some parts of the region, this was just the beginning of these population shifts. Moreover, in some cases the expanding farmer and pastoralist populations seem to have acquired significant indigenous Central Asian ancestry and spread it with them.

The precise geographic extent of the relatively unique Botai-related ancestry in prehistoric Eurasia is still something of a mystery. But to give you a general picture of where it was found from around 6,000 BCE to 2,000 BCE, here's a map with info about samples with significant levels of this type of ancestry from a wide range of sites in space and time.


Going by this map, I'd say it's safe to infer that the Botai-related ancestry was a major feature of practically all forager populations living between the Caspian Sea and the Altai Mountains. It was also present in the Early Bronze Age (EBA) pastoralist population associated with the Steppe Maykop archeological culture of Eastern Europe, so it may have already been in Europe as early as 3,800 BCE, because that's when the Steppe Maykop culture first appeared.

It's an interesting question where the ancestors of the Steppe Maykop herders came from. I once simply assumed that they were closely related to the Maykop people who lived in the Caucasus Mountains. But it's now clear that the populations associated with these two similar cultures were starkly different, with the Maykop people being basically of Near Eastern origin and lacking any discernible Botai-like ancestry. My guess for now is that the Steppe Maykop herders were in large part the descendants of the Kelteminar culture population from just east of the Caspian Sea, but we'll see about that when more ancient DNA comes in.

The other great mystery is what eventually happened to the Steppe Maykop people. Around 3,000 BCE, their culture vanished from the archeological record and their particular genetic signature disappeared from the steppe ancient DNA record. Where did they go? Did they migrate back east?

I don't know, but at about that time other Eastern European steppe herders, those associated with the Yamnaya and Corded Ware archeological cultures, began to stir and migrate in big numbers in basically all directions, including into Steppe Maykop territory. Indeed, unlike the Steppe Maykop population, these groups weren't closely related to any contemporaneous or earlier Central Asians. But they ended up moving into Central Asia, and in a big way too.

Their impact all the way from the Ural Mountains to what are now China and India was profound. For instance, not only did they end up totally replacing the Botai people, but also their horses. For more details on this topic check out the Youtube clip here. I have a strong suspicion that the same sort of thing happened to the aforementioned Steppe Maykop people. In other words, they may have been forced out from the Eastern European steppe, and perhaps sought shelter in the Caucasus Mountains?

Admittedly, I'm not offering anything new here. I just wanted to emphasize a few key points, because I'm still seeing some confusion online about the population history of Central Asia, and especially how it relates to the population history of Europe, and also the Proto-Indo-European homeland question. Make no mistake, thanks to the ancient DNA already available from Central Asia, we can confidently infer the following:

- the chance that the ancient European populations associated with the Yamnaya, Corded Ware and other closely related archeological cultures formed as a result of migrations from Central Asia is zero

- the chance that the Proto-Indo-European homeland was located in Central Asia is zero

- the chance that present-day Europeans, by and large, derive from any ancient Central Asian populations is zero

See also...

Central Asia as the PIE urheimat? Forget it

The Steppe Maykop enigma

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

Monday, April 22, 2019

R1b-M269 in the Bronze Age Levant


The new Harvard genotype datasets that I blogged about recently include a couple of potentially very useful samples from the Levant dated to 1400-1100 BCE. Search for IDs I2062 and I1934 in the anno files here. They're both from an archeological paper about a Late Bronze Age (LBA) burial site in what is now Israel that was published back in 2017 (see here).

Surprisingly, individual I2062 is listed in the anno files as belonging to Y-haplogroup R1b1a1a2, which is also known as R1b-M269. The reason that this is a surprise to me is because R1b-M269 is closely associated with the Bronze Age expansions of pastoralists from the Pontic-Caspian steppe in Eastern Europe, and these expansions didn't impact the Levant in any direct or significant way.

The Y-haplogroup assignment may or may not be correct. Sometimes the Y-haplogroups in these sorts of datasheets are indeed wrong. Unfortunately, as far as I know, the BAM file for I2062 isn't available anywhere online, so I can't check whether he does really belong to R1b-M269. But, intriguingly, his autosomes do show a subtle signal of Yamnaya-related ancestry from the Pontic-Caspian steppe that is missing in earlier ancients from the Levant.

To characterize his genome-wide ancestry, I first ran a series of unsupervised and supervised analyses with the Global25/nMonte3 method (using this datasheet). For the sake of simplicity, I narrowed things down to the mixture models below based on three reference populations each. Levant_ISR_C is made up of Chalcolithic samples from Israel. The identities of the other reference sets should be obvious to most readers. If confused, feel free to ask for more details in the comments below.

Levant_ISR_MLBA:I2062
Levant_ISR_C,66.8
IRN_Seh_Gabi_C,27
Yamnaya_RUS_Samara,6.2

[1] distance%=1.8905

Levant_ISR_MLBA:I2062
Levant_ISR_C,66.2
Kura-Araxes_ARM_Kaps,30.2
Yamnaya_RUS_Samara,3.6

[1] distance%=2.0856

Levant_ISR_MLBA:I2062
Levant_ISR_C,67.8
Kura-Araxes_RUS_Velikent,31.8
Yamnaya_RUS_Samara,0.4

[1] distance%=2.1738

To further confirm the reliability of my models, I tested them with the formal statistics-based qpAdm software. As far as I can tell, the output from qpAdm looks very solid across the board.

Levant_ISR_MLBA_I2062
IRN_Seh_Gabi_C 0.193±0.052
Levant_ISR_C 0.710±0.038
Yamnaya_RUS_Samara 0.098±0.026

chisq 9.304
tail prob 0.67676
Full output

Levant_ISR_MLBA_I2062
Kura-Araxes_ARM_Kaps 0.249±0.076
Levant_ISR_C 0.681±0.051
Yamnaya_RUS_Samara 0.071±0.035

chisq 11.101
tail prob 0.52032
Full output

Levant_ISR_MLBA_I2062
Levant_ISR_C 0.661±0.042
Kura-Araxes_RUS_Velikent 0.339±0.042

chisq 7.979
tail prob 0.844942
Full output

Admittedly, even though I2062 can be modeled with Yamnaya-related admixture, he doesn't need to be. Indeed, his ratio of this type of ancestry varies significantly between the models, from around 10% to nothing. This appears to be dependent on the geography of the non-Levant and non-Yamnaya reference populations; the closer they are to the Pontic-Caspian steppe, the smaller the ratio of Yamnaya-related ancestry in I2062. I'd describe this as an artifact of the isolation-by-distance phenomenon, and it totally makese sense, but it prevents me from confirming beyond any doubt that I2062 does harbor genome-wide steppe ancestry. Unfortunately, individual I1934 doesn't offer enough data to be analyzed with the same methods.

Samples associated with the Kura-Araxes or Early Transcaucasian culture are particularly strong references for the eastern ancestry in I2062. This probably isn't a coincidence, and it might also explain his Y-haplogroup, because, at its maximum extent, the territory occupied by the Kura-Araxes culture stretched all the way from the Pontic-Caspian steppe to the southern Levant. The map below is from Wilkinson 2014.

See also...

Downloadable genotypes of present-day and ancient DNA data

Early chariot riders of Transcaucasia came from...

R-V1636: Eneolithic steppe > Kura-Araxes?