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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?
Citation...

Antonio et al., Stable population structure in Europe since the Iron Age, despite high mobility, bioRxiv, posted May 16, 2022, doi: https://doi.org/10.1101/2022.05.15.491973

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.

Citation...

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: https://doi.org/10.1101/2022.05.13.491805

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: https://doi.org/10.1101/2022.05.04.490594

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.


In any case, this will be my last post on the topic, and the only place where I'll allow commentary related to it. Please try not to stray too far from reality.

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.



Citation...

Marnetto et al., Ancestral genomic contributions to complex traits in contemporary Europeans, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.01.046

See also...

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

Mainstream media BS: Europeans owe their height to Asian nomads

Thursday, February 10, 2022

Mainstream media BS: Europeans owe their height to Asian nomads


From a recent Daily Mail article by some clown named Sam Tonkin:

Present day Europeans owe their blue eyes to hunter gatherers, their height to Asian nomads and their blonde hair to Anatolian Neolithic farmers, a new study suggests.

...

Most of the contemporary European genetic makeup was shaped by movements that occurred in the last 10,000 years when local hunter gatherers mixed with incoming Anatolian farmers — from present-day Turkey — and Asian nomads, or Pontic Steppe pastoralists.

The latter originated from what is now parts of Bulgaria, Romania, Moldova, Ukraine, Russia and Kazakhstan.

Haha.

Bulgaria, Romania, Moldova and Ukraine are European countries. The relevant parts of Russia and Kazakhstan are also located in Europe.

Obviously, the author is referring to the Yamnaya herders who lived on the Pontic-Caspian steppe, which is obviously in Eastern Europe.

I blame Johannes Krause for this.

See also...

Matters of (basic) geography

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

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

Wednesday, February 9, 2022

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


Over at Current Biology at this LINK. Here's the summary:

The contemporary European genetic makeup formed in the last 8,000 years when local Western Hunter-Gatherers (WHGs) mixed with incoming Anatolian Neolithic farmers and Pontic Steppe pastoralists. 1–3 This encounter combined genetic variants with distinct evolutionary histories and, together with new environmental challenges faced by the post-Neolithic Europeans, unlocked novel adaptations. 4 Previous studies inferred phenotypes in these source populations, using either a few single loci 5–7 or polygenic scores based on genome-wide association studies, 8–10 and investigated the strength and timing of natural selection on lactase persistence or height, among others. 6,11,12 However, how ancient populations contributed to present-day phenotypic variation is poorly understood. Here, we investigate how the unique tiling of genetic variants inherited from different ancestral components drives the complex traits landscape of contemporary Europeans and quantify selection patterns associated with these components. Using matching individual-level genotype and phenotype data for 27 traits in the Estonian biobank 13 and genotype data directly from the ancient source populations, we quantify the contributions from each ancestry to present-day phenotypic variation in each complex trait. We find substantial differences in ancestry for eye and hair color, body mass index, waist/hip circumferences, and their ratio, height, cholesterol levels, caffeine intake, heart rate, and age at menarche. Furthermore, we find evidence for recent positive selection linked to four of these traits and, in addition, sleep patterns and blood pressure. Our results show that these ancient components were differentiated enough to contribute ancestry-specific signatures to the complex trait variability displayed by contemporary Europeans.

This is a fascinating effort, but I'm not taking it too seriously until I see the results reproduced with several cohorts from very different parts of Europe. The reason being is that at least some of the outcomes might be specific to Estonia, and reflective of its own peculiar recent population history.

For example, the authors find that among Estonians blond hair and blue eyes show a high association with Anatolian farmer ancestry (see table S4).

Now, some people might be surprised by this link between light pigmentation and Near Eastern ancestry. However, I'm not, because I know that quite a few Estonians, especially northwest Estonians, harbor recent north German and/or Scandinavian ancestry.

Obviously, north Germans and Scandinavians are some of the blondest haired and lightest eyed people in Europe. But they also have more Anatolian farmer ancestry than Estonians. So it might well be that in Estonia these traits are strongly linked with recent Germanic ancestry rather than ancient Anatolian ancestry.

In fact I'm willing to bet that this is indeed the case. I'm also willing to bet that blond hair and blue eyes won't show a strong association with Anatolian farmer ancestry in other European countries, but rather with steppe herder ancestry or even, in some cases, minor Siberian admixture.

Citation...

Marnetto et al., Ancestral genomic contributions to complex traits in contemporary Europeans, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.01.046

See also...

Mainstream media: Europeans owe their height to Asian nomads

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

Wednesday, February 2, 2022

The PIE homeland controversy: February 2022 status report


I think we'll see the emergence of two main competing proto-Indo-European (PIE) homeland theories over the next few years:

- a homeland in the Eneolithic North Caucasus, and the spread of Anatolian languages into West Asia with Maykop-related ancestry

- a homeland in the North Pontic region, possibly within the Eneolithic Sredny Stog archeological culture, and the spread of Anatolian languages into West Asia via the Balkans.

Both theories have support from ancient DNA. Some of it has already been published (for instance, see here).

At this point, I can see myself firmly in the North Pontic camp, even if it turns out that North Pontic-related ancestry only made a fleeting impact on Bronze Age Anatolia.

After all, there's no direct relationship between genes and languages, so to prove that Anatolian languages came from the North Pontic, there's no need for North Pontic-related ancestry to persist in Anatolia, as long as we have solid evidence that people with this type of ancestry moved there at the right time.

In my mind, for now, the Maykop culture provides an excellent explanation for non-Indo-European influences in PIE, and there's no need to make it Indo-European speaking, let alone PIE speaking.

See also...

The PIE homeland controversy: June 2021 status report