Re-reading The Turks in World History as I’m thinking about my next post in my series on the Eurasian steppe for Substack.
What’s going on?
23 thoughts on “Open Thread – 9/15/2022 – Gene Expression”
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Re-reading The Turks in World History as I’m thinking about my next post in my series on the Eurasian steppe for Substack.
What’s going on?
Comments are closed.
Regarding Turks, I have noticed that most Turkish nationalists during the establishment of Turkey were from the Balkans. Not even necessarily Balkan Turks(who themselves were most likely Albanian/Slav/Greek three-four generations prior) but of very recent Albanian or Slavic descent. It was as if the US collapsed and the founders of the American rump state in New England were all children of Latino and Asian immigrants. Very fascinating phenomenon.
Lewontinism 2.0?
https://www.eupedia.com/forum/threads/42828-disconnecting-the-link-between-(European)-DNA-and-Identity-and-Belonging?p=657666#post657666
Some questions about Turks if anyone can answer
– Is it true proto Turks descended from Huns?
– Do eastern Turkish people and black sea Turkish people have little Turkic ancestry?
– How much Turkic ancestry do Balkan Turks have?
– How much Turkic ancestry do Azeris have?
– In what region or part of Azerbaijan is the Turkic ancestry found highest in Azeris?
– Who have more Turkic ancestry? NW Turkish people or SW Turkish? How much Turkic ancestry do they both have?
– Do northern Caucasians(people from northern Caucasus) have Turkic ancestry?
Hi, Razib. What do you think about WHG origins? Where do you think they come from originally? They seem to be intrusive into western Europe, but WHGs outside of Italy can be modeled as a mixture of Italian WHG + some other stuff. Then again, we don’t have super ancient (25,000-15,000 year old) Balkans samples, maybe they came from the Balkans early on and settled into Italy so the later ones in Italy like Grotta Continenza weren’t as admixed by movements between 16,000 and 10,000 years ago.
Then again, the Black Sea region also holds some promise.
What do you think: Italy? Balkans? Black Sea? or something else? Or no opinion yet?
@Seeker
If I remember correctly Razib has said in the past that Black Sea Turks are identical to Pontic Greeks, indicating conversion to Islam and thus adopting Turkish identity rather than having any Turkic ancestry.
I was listening to the Ethan Strauss episode. “…biggest selection pressure is height.” I have also heard that the among NBA players there is no correlation with height and performance. If that is true, it sounds like these 2 claims can go hand in hand because all possible impact the height factor alone could have had on basketball performance has been fully milked at the NBA level due to the selection pressure that Ethan Strauss mentions. Is there a name for a phenomenon where the impact of one variable is completely used up to the point no more can be extracted anymore? Is fixation the correct term or is it something else? I haven’t formally learned stats so all I know is from reading things here and there.
Also, regarding the cultural reference: the joker had schemes, so I don’t think that was the best analogy.
conditioning on the collider or range restriction
@Seeker
“Is it true proto Turks descended from Huns?”
I think the proto Turks were definitely part of the Huns, but unlikely to be the ruling dynasty. I’ve asked Atwood about the language of the Xiongnu, and he said Xiongnu definitely were not a “Altaic” speaking due to lacking vowel harmony and the names of the Chanyu/Darguo are not Turkic, Mongolic, or Tungusic.
Christopher Atwood thinks that some form of Paleo-Siberian language was kind of an high culture language in the eastern steppe. He said that earliest recorded form of Mongolic like the Tuoba language has many Paleo-Siberian features, and the dichotomy between the words for year in Mongolian of on and jil, and likewise with the earliest recorded forms of Turkic languages.
Also of interest is the Jie people during the Sixteen Kingdoms and Five Barbarians period of China, Jie are described as Caucasoid people, yet linguistic evidence points to them speaking some form of Yeniseian language.
@Sean
The last of the relatively un-admixed ANE?
@dingbat
I don’t know. But the Jie might have been Iranic or Tocharian elements of the Xiongnu Empire.
https://www.nature.com/articles/s41562-022-01438-z – “Genetic footprints of assortative mating in the Japanese population”
“We robustly replicated the GPD estimate for adult height in the European-ancestry population as a sanity check (θheight in UKB = 0.030 and 0.030 for the current and previous studies, respectively). The GPD estimate of BMI in our work was slightly higher than in the previous study (θBMI in UKB = 0.0079 and 0.0001 for the current and previous studies, respectively). It is noteworthy that the GPD estimates for adult height were relatively higher than those for BMI in both European-ancestry and Japanese populations (that is, θheight in EAS = 0.0073 and θBMI in EAS = 0.0067). However, the GPD estimate for adult height was not as high in Japanese compared with the European-ancestry cohort. This result was consistent with previous epidemiological reports, in which the correlation of height between spousal pairs in Western countries was higher than those in non-Western regions. “
“Our study has several limitations. One potential limitation is that we did not assess AM in educational attainment (EA), as such information was not collected in BBJ, a hospital-based biobank. In European-ancestry populations, EA is among the traits strongly influencing AM, but it is also associated with common diseases and cognitive traits”
https://link.springer.com/article/10.1007/s00438-022-01955-6 – “Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations” – “Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia.”
“The Selection Landscape and Genetic Legacy of Ancient Eurasians” (https://www.biorxiv.org/content/10.1101/2022.09.22.509027v1?rss=1, razib’s pinboard) is potentially interesting way to separate out those findings from the general big “Population Genomics of Stone Age Eurasia” paper.
One thing I still complain about old news from the previous preprint, but addressed to a new method in this version that they give in Fig4c, is how they find that:
“In addition to the above reconstructions of genetic traits among the ancient individuals, we also estimated the contribution from different ancestral populations (EHG, CHG, WHG, Yamnaya and Anatolian farmer) to variation in polygenic phenotypes in present-day individuals, leveraging the exceptional resolution offered by the UK Biobank genomes to investigate this. We calculated ancestry-specific polygenic risk scores based on chromosome painting of the >400,000 UKB genomes, using ChromoPainter (Fig. 4C, Supplementary Note 2g). This allowed us to identify if any of the ancient ancestry components were over-represented in modern UK populations at loci significantly associated with a given trait, and also avoids exporting risk scores over space and time.”
Essentially they estimate that within UK Biobank, Yamnaya related segments have more tall height alleles and EEF lower height alleles (or rather segments around “tall” variants have more Yamnaya ancestry).
And they seem to interpret this in the main paper in light of a general argument over the paper that ancient components and not post-admixture selection explains variation in modern populations (e.g. introduction claims: “These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago.”.
But this interpretation as applied simply to UKBiobank, may fly in the face of the finding by Mashaal Sohail on the same Biobank – https://elifesciences.org/articles/39702 –
“Interestingly, the north-south genetic cline in the UK tracks the height gradient in the opposite direction than in Continental Europe (Figure 2—figure supplements 2 and 4) “ (e.g. more genetically northern/steppe persons are shorter “and after correcting with principal components, we do not observe any evidence of residual stratification in comparison with the 1000 genomes data (Figure 2a,c). “
e.g. which would mean that people with more steppe ancestry people within UKBiobank, tended to have slightly lower height.
Importantly all this is calculated on exactly the same Neale lab height related polygenic risk score, and on exactly the same population. (Incidentally Sohail also found that in 1000G comparing TSI, IBS, GBR and CEU, there was very limited dispersal in these scores).
I don’t know how they can reconcile this with a claim that recent post-BA selection doesn’t impact height.
In fact it’s actually compatible with post-admixture selection, as in the paper by Marnetto et al. Indeed the authors responsible for that section actually say such in their supplement:
“From this bootstrapping exercise we can conclude whether a difference in allele frequencies in ancient populations contributed to phenotypic variation today. Unsurprisingly, with a large enough sample size most phenotypes will show differences in ancestral contributions for this, usually due to drift or founder effects. However, this goes further than just reporting risk scores for ancient populations, because we are looking directly at coalescent tracts in the British population. We can conclude that “ancestry X contributes higher genetic risk for phenotype Y in the test population”. On the other hand, because we have used independent LD blocks to select SNPs to include in the PRS calculation, the requirement for independence is met when we bootstrap with loci (Figure S2h.2). A positive result here is therefore much stronger, showing a systematic over/under-representation of an ancestry at loci affecting a given trait, beyond what is expected given the correlation among individuals. This points towards selection as an explanation.”
I have no doubts that Yamnaya had taller genetic height than the EEF populations, and that tall height variants today still show a greater association with Yamnaya ancestry, but all this is very different from the idea that we can explain height genetics between populations with genome-wide Yamnaya ancestry mainly or only, or draw a simple regression between these two. A bit can be attributed to ancient populations, but surely not all of it.
@Matt
I think the general idea has been brought up here before (I might have even directly asked you but I err forget right now) but would this cline correlate with combined Anglo-Saxon + French-like vs British-like ancestry per the additional, broad conclusions of the recent paper? If the putative French-like was similar to the British-like in height (Irish population not as tall as you might expect from their steppe-related admixture, close to if not the maximum of existing populations, relative to other European populations?), this could be at least partially driven by excess Anglo-Saxon-related admixture too rather than just selection within the UK as well? So you end up with subpopulations with somewhat lower steppe but also greater direct ancestry from a population that had greater height than the others involved.
The Balkans is an interesting case as well because the well-known region of particularly great height (though the Balkans also seems taller in general than you’d expect from a basic model, relative to other regions) seems to traditionally encompass populations with varying amounts of steppe-related admixture, including areas of north Albania where that component drops quite a bit (I think to a large extent due to different levels of early Slavic-like admxiture) in comparison to their direct Montenegrin/Serbian neighbors.
The situation within Europe, of generally similar ancestral components at different percentages, does seem more complex in many of its details.
@Forgetful, it seems like it should be. (Which does make me think it would have been useful to see the ancients here projected on Biobank UK PCA, which is the one they didn’t do. But that would only be extra confirmation). Maybe some direct phenotype comparison like the Southern Arc paper using GWAS for height and maybe also Hirisplex on these two sets of samples – Iron Age and Early Medieval – could test the ideas that there was differentiation between the CNE/WBI related populations on height, hair pigmentation etc.
Also re; those Balkan populations is another place where the relationships are somewhat different perhaps. And that gets on to Grasgruber’s argument that ydna haplogroup I should be linked to greater height. Which I find doubtful as it’s somewhat evident in males and females (who, uh, don’t bear an Y chromosome). But test it in UK Biobank! You have the sample size! (Which again is maybe linked to the contention that the height gradient in the UK is not explained by steppe ancestry).
@Matt
“And that gets on to Grasgruber’s argument that ydna haplogroup I should be linked to greater height.”
That kind of argument always felt a bit iffy but a within population comparison like you’re suggesting would still be nice since those older between population comparisons I recall (not sure if it’s the one you’re referring to here or another paper that also made a similar argument but I recall the argument floating around) seem a bit too confounded by other factors to be too meaningful I feel.
In the Balkan case, you also have some extreme variation in the kind of I frequencies that reach very high levels in Bosnia but much much lower ones in those parts of northern Albania/Albanian-inhabited Montenegro where great height seems to be traditionally the case (even if height hypothetically follows a bit of a north to south cline, being greater in the relative north, within that west Balkan area) so I’m not sure how much can be said about it.
@Forgetuful; Yeah, because of those regional patterns, I guess ideally you’d look at male and female heights and this y-haplogroup in a pan-European Biobank with a focus on the southeast, but we only have what we have…
(On that tangent and why I go on about it so much, I’m not really opposed to the idea of Yamnaya ancestry still having some bearing on height today at all btw, it’s just when you get these things that go
“Well, Sardinians have about 5% Yamnaya ancestry and are 168.5cm, Spanish have 28% and are 174cm, Dutch have 47% and are 183cm… Therefore Yamnaya were 200cm tall (6 foot 7) on average and EEF were 166 cm”
which is basically what saying that these differences are largely explained by deep ancestry with little to no role of subsequent selection.
Whereas when I regress on the ancestry and estimated heights from measured bone lengths of actual Steppe admixed skeletons (using the data put up by Marciniak and Mathieson’s paper) where you can look at the correlation between steppe:EEF:WHG ancestry and height, to identify the associated between them, the covariates would indicate that for the measured CA->EBA skeletons, came up with an estimate of 3 inches difference between Barcin and Yamnaya or 2.5 inches between WHG and Yamnaya. The Corded Ware skeletons with 60-70% steppe ancestry were taller but just weren’t consistently *that* much taller than the neolithic farmers. It’s entirely possible this is somewhat suppressed more in the Yamnaya group than the others by poor quality CA->EBA nutrition (despite the claim that steppe ancestry groups had improved diet compared to farmers) but I doubt that this suppression was so extreme that a genetic difference of ~14 inches was reduced to being closer to ~3 inches size…)
Selection from Yamnaya ancestry which was eventually separate from the ancestry itself.
>We also find psychological trait scores with evidence for
overdispersion related to mood instability and irritability, with Western Hunter-gatherers generally showing lower genetic scores for these traits than Neolithic Farmers.
>Interestingly, loci associated with overdispersed mood-related polygenic phenotypes recorded among the UK Biobank individuals (like increased anxiety, guilty feelings, and irritability) showed an overrepresentation of the Anatolian farmer ancestry component;
Mental differences linked with Anatolian ancestry, more stoic WHGs.
>and the WHG component showed a strikingly high contribution to traits related to diabetes.
WHGs were bad at processing sugar.
>We also found that the ApoE4 effect allele (increased risk for Alzheimer’s disease) is preferentially found on a WHG/EHG haplotypic background
Interesting.
>Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago.
Not surprising. Yamnaya were taller than farmers. But as I said before in the post, after the mixture, the trajectory of Yamnaya ancestry and the height genes brought by them could have differed.
And by differed I mean separated. No reason to keep selecting for more Yamnaya ancestry when they could select indirectly for the (probably Yamnaya provided to a great extent) height genes by more directly selecting for the taller phenotype.
Related – https://www.biorxiv.org/content/10.1101/2022.09.23.509097v1 – “Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations”
“By using the largest ancient genome dataset from the Stone Age, along with new Medieval and post-Medieval genomes, we show that many of the genetic risk variants for MS rose to higher frequency among pastoralists located on the Pontic Steppe, and were brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the Steppe population, and later in Europe, likely driven by pathogenic challenges coinciding with dietary and lifestyle environmental changes. This study highlights the critical importance of this period as a determinant of modern immune responses and its subsequent impact on the risk of developing MS in a changing environment.”
MS is Indo-European?
Probably.
Recently uploaded ENA Abstracts
https://www.ebi.ac.uk/ena/browser/view/PRJEB55327?show=reads (uploaded 10/08/2022) –
“Ancient DNA sequences from 27 Neanderthals from Chagyrskaya and Okladnikov Cave in Siberia”
“Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans, but the social organization of Neanderthal communities remains poorly understood. Here, we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave and two from Okladnikov Cave – making this the largest genetic study of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second degree relatives, indicating that at least some of the individuals lived at the same time. Up to a third of these individuals’ genomes occur in long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.”
Large Neanderthal samples. Cool.
https://www.ebi.ac.uk/ena/browser/view/PRJEB53899 – 2022-08-01 –
“Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1347 CE, and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10-40%. It is assumed that this high mortality affected the gene pools of these populations. Firstly, local population crashes reduced genetic diversity. Secondly, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the aetiological agent (Yersinia pestis). Thirdly, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods; (i) prior to the plague striking Trondheim in 1349 CE, (ii) the 17th-19th century, and (iii) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.”
Isles migrants into Norway prior to 1349? Might fit with the entangled history of Norway and Britain in the Middle Ages?
Following up on that second abstract, the detail from SMBE 2019 – https://smbe.org/smbe/SMBE2019Meeting/www.smbe2019.org/media/1058/smbe-2019-abstract-book.pdf – “Despite the relatively small sample sizes of our dataset, our results validate with the hypothesis that the second plague pandemic played a significant role in shaping the genomic diversity of Trondheim – something expected given the large estimated change in population size that occurred during this period. In particular, our data is compatible with a major decrease in migration from previous population sources (e.g. the British Isles) during this time, consistent with the decrease in Trondheim’s political and economic importance. The average proportion of ancestry derived from British Isles decreases from ~30-40% in the pre-1349 samples, to under 5% in the post-1349 samples.”