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Friday, August 12, 2022

Mediterranean PCA update

I updated my Principal Component Analysis (PCA) of Mediterranean populations with most of the ancient Jewish samples from the Waldman et al. preprint. To view intereactive versions of the plots paste the data from here into the PCA DATA field here and press PLOT PCA. The ancient Jews are labeled DEU_MA_Erfurt.

See anything interesting? I'm again seeing more complexity than claimed by Waldman et al., but what would I know anyway?

See also...

My take on the Erfurt Jews

Greeks in a Longobard cemetery

Tuesday, June 21, 2022

My take on the Erfurt Jews

I had a quick look at the genotype data from the recent Waldman et al. preprint focusing on the ancestry of early Jews from Erfurt, Germany. My impression is that the genetic origins of these Jews are somewhat more complex than claimed in the manuscript.

Indeed, I'd say the Waldman et al. characterization of the Erfurt Jews as a three-way mixture between populations similar to present-day Lebanese, South Italians and Russians doesn't exactly reflect reality.

Unlike Waldman et al., I designed an ADMIXTURE analysis that separated East Asian ancestry into East Asian and Siberian clusters, and also included Mediterranean and North African clusters. The output is available in a spreadsheet HERE. Below is a bar graph based on some of the output.
Now, keeping in mind that ADMIXTURE is not a formal mixture test, and that it estimates ancestry proportions from inferred populations, as opposed to ancient groups that actually existed, here are some key observations:

- in terms of fine scale ancestry, the Erfurt Jews show enough variation to be divided into three or four clusters, as opposed to just two as per Waldman et al.

- some of the Erfurt Jews show excess "Mediterranean" ancestry, while others excess "North African" ancestry, and this cannot be explained with ancestral populations similar to Lebanese and/or South Italians, but rather with significant gene flow from the western Mediterranean and possibly North Africa

- several of the Erfurt Jews show relatively high levels of "East Asian" ancestry that cannot be explained by admixture from Russians, or even any Russian-like populations, because such populations almost lack this type of ancestry, and instead show significant "Siberian" admixture

- as far as I can see, there are no correlations between any of the observations above and the quality of the samples. That is, low coverage doesn't appear to be causing the aforementioned excess "Mediterranean", "North African" and/or "East Asian" ancestry proportions.

Investigating this in more detail with, say, formal statistics will take some time. But I was able to reproduce the results from the above ADMIXTURE run using several somewhat different datasets, so that's something.

It seems to me that Waldman et al. want a simple and elegant model to explain the data, which is understandable, but I do think they should at least expand their ADMIXTURE analysis to include "Siberian", "Mediterranean" and "North African" clusters, and go from there depending on what they find.


Waldman et al., Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century, bioRxiv, posted May 16, 2022, doi:

See also...

Mediterranean PCA update

Saturday, June 18, 2022

David Reich on the origin of the Yamnaya people (!?)

Harvard's David Reich is doing a talk next month about the genetic history of West Asia and nearby parts of Europe. This is a quote from an online abstract of the talk (found here).

The impermeability of Anatolia to exogenous migration contrasts with our finding that the Yamnaya had two distinct gene flows, both from West Asia, suggesting that the Indo-Anatolian language family originated in the eastern wing of the Southern Arc and that the steppe served only as a secondary staging area of Indo-European language dispersal.

If this is actually what David Reich is going to claim then I'd say his team has a lot of work to do before they put out their paper on the topic.

First of all, Yamnaya did not have two distinct gene flows from West Asia. I don't even know what that means exactly, but there's no way that this statement is correct no matter how one interprets it.

In fact, the Yamnaya population formed on the Pontic-Caspian steppe from earlier groups native to this part of Eastern Europe, such as the people associated with the Sredny Stog culture.

That is, there were no migrations from West Asia into Eastern Europe that can be claimed to have been instrumental in the emergence of the Yamnaya population. On the other hand, Yamnaya may have been significantly influenced by cultural impulses from West Asia, but this is nothing new.

In terms of deep population structure, the Yamnaya genotype can be described as a mixture between Eastern European and West Asian-related genetic components. However, these Asian-related components were already in Europe thousands of years before Yamnaya came into existence.

Indeed, soon to be published ancient DNA shows that hunter-gatherers very similar to the Yamnaya people, packing quite a lot of West Asian-related ancestry, lived in the Middle Don region (just north of the Pontic-Caspian steppe) well before 5,000 BCE (see here).

So, did the West Asian ancestors of these Middle Don hunter-gatherers speak Proto-Indo-European, or, as David Reich calls it, Indo-Anatolian? Keep in mind that most linguists put the birth of Indo-Anatolian around 4,000 BCE, which is actually the Sredny Stog period.

Moreover, in underlining Anatolia's supposed impermeability to exogenous migration, David Reich is arguing against things that no one worth their salt ever claimed. That's because the spread of Indo-Anatolian speakers into Anatolia has never really been described by archeologists and linguists as a massive migration, but rather as an infiltration into lands already heavily populated by the Hattians (for instance, see here).

We may have already seen the genetic evidence of this infiltration in the presence of steppe Y-chromosome haplogroup R-V1636 in a Chalcolithic burial at Arslantepe (see here and here). Let's wait and see what else crops up over the next few years as many more ancient Anatolian genomes are sequenced by David Reich and colleagues.

See also...

Wednesday, May 18, 2022

Geography is hard (for some)

It's that time of the academic year again when bioRxiv is inundated with ancient DNA preprints. I'm not complaining, but I almost spat out my coffee when I saw this map in one of the new manuscripts (here).
What's the logic behind labeling almost all of Eastern Europe as "Steppe", and instead labeling just Czechia, Hungary and Slovakia as "Eastern Europe"? In my opinion those three countries, plus Poland, are better described as East Central Europe anyway.

It seems to me that many people working at the highest level in population genetics simply don't know what the Eurasian steppe is. They appear to see it as a continent of its own, when, in fact, it's a topographical feature and ecoregion that straddles the continents of Europe and Asia. That's why it's called the Eurasian steppe, and it's made up of three main parts: the Pontic-Caspian steppe of Eastern Europe, the Kazkah steppe of Central Asia, and the Eastern steppe of Mongolia.

Here's the same map with a few corrections (in red). Much better, don't you think?

Antonio et al., Stable population structure in Europe since the Iron Age, despite high mobility, bioRxiv, posted May 16, 2022, doi:

See also...

Matters of geography

Tuesday, May 17, 2022

Genome-wide data from medieval German Jews (Waldman et al. 2022 preprint)

Over at bioRxiv at this LINK. Here's the abstract:

We report genome-wide data for 33 Ashkenazi Jews (AJ), dated to the 14th century, following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ and have substantial Southern European ancestry, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried the same nearly-AJ-specific mitochondrial haplogroup and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. However, the Erfurt bottleneck was more severe, implying substructure in medieval AJ. Together, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.

It's nice to finally see some ancient Jewish genotypes on the way, but there's a bit of a problem with this preprint.

The fact that the authors are using modern-day Russians to model Eastern European-related ancestry in these Ashkenazi ancients from Central Europe tells me that they're somewhat confused.

They did this because some of the Jews harbor significant Slavic ancestry and minor but perceptible East Asian ancestry, and Russians are Slavs who carry some Siberian ancestry, which is closely related to East Asian ancestry. Thus, broadly speaking, in terms of the right mix of DNA, Russians do the job.

However, as per the preprint, based on historical data, these Jews probably sourced their Slavic ancestry from Bohemia, Moravia and/or Silesia, and the Slavic speakers in these regions carry very little, if any, East Asian or Siberian ancestry. I'm sure the authors can verify this claim without too much trouble.

Ergo, it's likely that the Erfurt Jews received their Slavic and East Asian admixtures from different sources, and possibly at different times.

I'd like to see Waldman et al. tackle this issue properly. I suspect that if they do, they might discover something interesting and perhaps unexpected about the ethnogenesis of Ashkenazi Jews.

See also...

My take on the Erfurt Jews

Mediterranean PCA update

Saturday, May 7, 2022

Population genomics of Stone Age Eurasia (Allentoft et al. 2022 preprint)

Over at bioRxiv at this LINK. It'll take me a few days to read this manuscript properly. Here's the abstract:

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.

Allentoft et al., Population Genomics of Stone Age Eurasia, bioRxiv, posted May 06, 2022, doi:

See also...

Understanding the Eneolithic steppe

Saturday, March 12, 2022

Lousy intel

I don't like discussing current events and politics here, but it's impossible to ignore what is happening in Eastern Europe.

It's a tragedy and catastrophe for both Ukraine and Russia. It's also likely to have a negative impact on ancient DNA research, Indo-European studies, and thus also on this blog.

I'm seeing a lot of confusion online about why Russia invaded Ukraine, but I don't think it's very complicated.

After getting the better of the West in recent years, Russia finally overreached and made a massive tactical blunder, in large part because of lousy intel. More broadly, I also see this as the Soviet Union's dead cat bounce moment.

Russia will now have to reinvent itself, possibly as China's junior partner or even vassal state.

As for the "special military operation", Russia's initial plan was to achieve a quick, relatively bloodless victory, followed by a military parade in Kyiv. But obviously that's not going to happen.

Russia's back up plan, if we can call it that, seems to be to keep pushing into Ukraine at any cost, and hope that the Ukrainians finally tap out. But right now that looks like a long shot.

Thursday, February 24, 2022

A unified genealogy of modern and ancient genomes (Wilder Wohns et al. 2022)

Over at Science at this LINK. Broadly speaking, this looks like a more sophisticated version of something that I tried about five years ago (see here).
I wonder if they got the idea from me? Honestly, I wouldn't be surprised if they did. But like I say, their methods are way more advanced.

Keep in mind, however, that for now, their analysis includes 3601 modern genomes and just eight ancient genomes. That's because they can only run super high quality ancient sequences. The ratio of ancient genomes will no doubt rise rapidly over the next few years, and that's when things will get really interesting.

Below are some screen caps from a clip accompanying the paper, freely available here. This is the caption to the movie:

Spatio-temporal dynamics in human history. This movie shows the estimated geographic locations of ancestors of Human Genome Diversity Project, Simons Genome Diversity Project, Neanderthal, Denisovan, and Afanasievo samples over time. Each dot represents an edge in the tree sequence of chromosome 20, where the time and geographic location of the parent and child nodes of the edge have been estimated. The locations of edges at each point in time are plotted along the great circle between the parent and child nodes. Edges are colored by the region of the descendants of the child node. If an ancestral lineage has ancestors in multiple regions, its color is the average of the respective colors of each region.

See also...

Haplotype-based PCA of West Eurasia and Europe

Monday, February 21, 2022

The Pict

KD001 is the first undeniable Pictish sample in my dataset, courtesy of Dulias et al. 2022. Thanks to Altvred for processing the files.

This is how KD001 behaves in my Celtic vs Germanic Principal Component Analysis (PCA). Looks kind of Irish, doesn't he?

To see an interactive version of the plot, paste the coordinates from here into the relevant field here.

See also...

Celtic vs Germanic Europe

Avalon vs Valhalla revisited

When did Celtic languages arrive in Britain?

Monday, February 14, 2022

Blond hair is only indirectly associated with Anatolian ancestry in Estonia...duh

In a recent paper about complex traits in Europeans, Marnetto et al. found that blond hair and blue eyes showed a relatively high association with ancient Anatolian ancestry.

This is a somewhat curious finding considering that ancient Anatolians weren't particularly blond haired or blued eyed, and that's probably an understatement.

However, the Europeans that Marnetto et al. based their analysis on were Estonians. And in Estonia ancient Anatolian ancestry peaks in the west and north, probably because this is where Estonians have the most Germanic and Finnish ancestry.

Germanic and Finnish populations are somewhat richer in ancient Anatolian ancestry than Estonians, and, unlike ancient Anatolians, they're often exceptionally blond haired and blue eyed.

So it makes sense that, in Estonia at least, ancient Anatolian ancestry is associated with blond hair and blue eyes, but only indirectly so. The more direct link is between Germanic and Finnish ancestry and blond hair and blue eyes.

I feel that Marnetto et al. should've investigated this, and they also should've made it clear that the associations they found won't necessarily be seen in other European countries.

For the doubters out there, and I know there are at least a few of you, below is a series of Principal Component Analyses (PCA) showing how Estonians compare to other populations from around the Baltic Sea, as well as to present-day Turks from central Anatolia.

Note that, by and large, the same Estonians who show more affinity to the Germanic and/or Finnish individuals are also shifted slightly closer to the Turks, and this is because they harbor elevated ancient Anatolian ancestry. The relevant datasheets are available here.


Marnetto et al., Ancestral genomic contributions to complex traits in contemporary Europeans, Current Biology (2022),

See also...

Ancient ancestry and complex traits in Estonians (Marnetto et al. 2022)

Mainstream media BS: Europeans owe their height to Asian nomads