Substack cometh, and lo it is good. (Pricing)

Open Thread – 06/07/2022 – Gene Expression

I feel I may have read Ancient China and its Enemies: The Rise of Nomadic Power in East Asian History but I don’t recall reading it. So I’m reading it.

Please check out my Substack open thread.

America spends a lot more on schools than on police – And in international terms, our funding of both is very average. Matt Yglesias’ beat seems to be saying things that are easy to look up but no one bothers to say?

How did Etruscan, a language that has been dead for 2,000 years, give rise to the third letter of our alphabet?

The biocultural origins and dispersal of domestic chickens.

The Red-Pilling of Liberal America.

Polygenic Transcriptome Risk Scores Can Translate Genetic Results Between Species.

13 thoughts on “Open Thread – 06/07/2022 – Gene Expression

  1. “saying things that are easy to look up but no one bothers to say”
    Some mix of incompetence, laziness, and perverse incentives for the guilty.

  2. Regarding The Red-Pilling of Liberal America…If cities in California and Texas are anything like DC, it’ll take the death of innocent women, particularly of the tribe, for them to change anything.

  3. Anyone know of any interesting aDNA papers coming up on the horizon? I remember reading from Eurogenes a year or two ago about a supposed paper on Old Kingdom Egyptian samples coming out in the near future but that seems to have been a dud.

  4. “Larry Krasner, Philadelphia’s cantankerous district attorney, has developed a habit of browbeating critics in town hall meetings with appeals to ‘the science’ and how his in-house criminologist can give people the real numbers if they really want them.” [from the Red Pill article]

    Wow, am I getting flashbacks to David Halberstram’s The Best and the Brightest. Robert McNamara would browbeat everyone with data, data, and more data. Unfortunately, it was, um, inaccurate. People lower in the hierarchy knew what the higher-ups wanted to hear and gave it to them. About six years too late, he got wise to what was going on.

  5. In the world of physics, some papers are being held up because of issues about co-authoring with Russian institutions in light of the Ukraine war. CERN has frozen new paper releases for that reason, for example. I don’t know if something similar is happening in the world of aDNA papers.

  6. “The biocultural origins and dispersal of domestic chickens.”

    Turns out that the whole thing was the pursuit of Chicken Soup With Rice:

  7. This seems like a potentially particularly adjacent Razib’s interests type and study – https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.24566 – “As the political, economic, military, and cultural center of the early Yuan Dynasty, Xanadu attracted people from all over the world. It was thriving and prosperous, composed of residents with different customs and religious beliefs from different social strata. Genetic analysis of Xanadu’s residents provides a valuable approach for inferring processes of population movement and exchange during the Yuan period.”

    “As the capital of the Yuan Dynasty, Xanadu was a prosperous city with international influence. The nine skeletons from the Zhenzishan cemetery reflect the high genetic diversity of Xanadu’s residents, with clear differences in paternal and maternal origins. The maternal lineages of these residents were mainly East Asian with some western Eurasian features, while the paternal lineages were mainly western Eurasian with fewer East Asian features. These results contribute to a better understanding of the Mongolian Empire’s impact on the migration and mixture of people across the Eurasian continent.”

    The Mongol or post Mongol Era in more rural/hinterland settings often involved different dynamics to what is found here.

  8. I’m astonished to learn that Nick Patterson doesn’t get paid. That’s just not right.

  9. A future adna lecture for those interested in Near Eastern genetics (the Southern Arc is coming!):

    https://iias.huji.ac.il/event/david-reich-lecture

    Lecture by Prof. David Reich – “The Genetic History of the Southern Arc: A Bridge between West Asia & Europe”“The lecture will be held at the Israel Institute for Advanced Studies at 11am on Tuesday, 12 July 2022.”

    “We present an integrative genetic history of the Southern Arc, an area divided geographically between West Asia and Europe, but which we define as spanning the culturally entangled regions of Anatolia and its neighbors, in both Europe (Aegean and the Balkans), and in West Asia (Cyprus, Armenia, the Levant, Iraq and Iran). We employ a new analytical framework to analyze genome-wide data at the individual level from a total of 1,320 ancient individuals, 731 of which are newly reported and address major gaps in the archaeogenetic record. We report the first ancient DNA from the world’s earliest farming cultures of southeastern Anatolia and northern Mesopotamia, as well as the first Neolithic period data from Cyprus and Armenia, and discover that it was admixture of Natufian-related ancestry from the Levant—mediated by Mesopotamian and Levantine farmers, and marked by at least two expansions associated with dispersal of pre-pottery and pottery cultures—that generated a pan-West Asian Neolithic continuum. Our comprehensive sampling shows that Anatolia received hardly any genetic input from Europe or the Eurasian steppe from the Chalcolithic to the Iron Age; this contrasts with Southeastern Europe and Armenia that were impacted by major gene flow from Yamnaya steppe pastoralists.

    In the Balkans, we reveal a patchwork of Bronze Age populations with diverse proportions of steppe ancestry in the aftermath of the ~3000 BCE Yamnaya migrations, paralleling the linguistic diversity of Paleo-Balkan speakers. We provide insights into the Mycenaean period of the Aegean by documenting variation in the proportion of steppe ancestry (including some individuals who lack it altogether), and finding no evidence for systematic differences in steppe ancestry among social strata, such as those of the elite buried at the Palace of Nestor in Pylos.

    A striking signal of steppe migration into the Southern Arc is evident in Armenia and northwest Iran where admixture with Yamnaya patrilineal descendants occurred, coinciding with their 3rd millennium BCE displacement from the steppe itself. This ancestry, pervasive across numerous sites of Armenia of ~2000-600 BCE, was diluted during the ensuing centuries to only a third of its peak value, making no further western inroads from there into any part of Anatolia, including the geographically adjacent Lake Van center of the Iron Age Kingdom of Urartu. 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. The demographic significance of Anatolia on a Mediterranean-wide scale is further documented by our finding that following the Roman conquest, the Anatolian population remained stable and became the geographic source for much of the ancestry of Imperial Rome itself.”

    Comment: Anatolia was just too damn populous and the Indo-Europeans coming via Europe could do nothing, demographically? It’s where Cavalli-Sforza’s hypothesis that the demographic bulk was too large to be displaced (except by similarly sized large farmer populations) really held true? A contrast with the places that were in the same ecozone and where farmers had low/declining populations. But these places would later grow to host huge farming populations, much later in history…

    Mycenaeans also show a situation where steppe ancestry autosomally is uncorrelated with social status… Though this isn’t surprising as it was true on a more compressed scale in Britain (albeit there we’d guess admixture is not very frequent where autosomally teh “King of Stone Henge”, the Amesbury Archer, I14200) was in significantly more EEF than the Beakers as a whole. Although he probably got his admixture in France/Switzerland and not England. It’ll be interesting to see if this is true y-dna wise as well (unlike in other regions)… the one Mycenaean male published so far being a J2a (I9041) and contemporary Greeks lack of R dominance, would both suggest that steppe y-dna would lose its association too, conforming to a scenario where patrilineal bonds broke down in favour of collaboration between lineages and assimilation into IE speaking, perhaps because the requirements of the more complex society favoured it. But we’ll know when we see it.

    Direct migration by the Yamnaya as far as Northwestern Iran – not just getting to NW Iran via Central Asia! We have already had Bronze Age dna that his indicated that this is happening, in the form of one sample – which is I4243 at 2300 BCE. That sample seemed to have nothing to do with the Corded Ware/Sintashta so, the hypothesis there was that the desertification conditions on the steppe around 2400-1900 BCE drove the Yamnaya/post-Yamnaya Catacomb culture south, and then they were later replaced on the steppe by the Lola Culture from Central Asia (admixed ANE-Yamnaya type guys) and more substantially by the Sintashta from the northern forests, who then go onto move into Central Asia in another wave. So it’s nice to see that the idea of a pulse into NW Iran is confirmed and not just an outlier…

    (Kind of confirms why the Corded Ware matter more for our dna today than the Yamnaya; the Yamnaya migrated out to places where the population was already big, but the potential for growth was much lower, or places like Central Asia where it would forever remain low, while the Corded Ware took over Northern Europe where population was low, but there was enormous agricultural productivity in its future. Possibly even population of Yamnaya descendents certainly might have boomed above Corded Ware, for a few hundred years, but then…)

    It’s interesting that NW Iran is specified – did this wave then peter out and not move further east into Central Asia? Steppe ancestry is largely absent from the BMAC/Gedrosia Zone sampled by Narasimhan in his paper. Though culturally a language could’ve continued to spread eastwards through this zone. Even more tentatively; might this potentially help explain any shared linguistic features identified through a putative Indo-Graeco-Armenian grouping of IE? Generally the Indo-Balto-Slavic grouping is more strongly maintained, but there are some authors who’ve argued for shared features between Indo-Graeco-Armenian. Did the movement of Yamnaya->Armenia and NW Iran have anything to do with the movement to Greece? Certainly Graeco-Armenian is commonly recognised, so it seems difficult to have a movement to Greece be totally independent of a movement to Armenia from the steppe giving rise to Armenian…

    I believe they may also be arguing that the Yamnaya receive different CHG related ancestry from West Asia at different times, presumable a later one with a little Anatolian, and an earlier one without any?

  10. A preprint (https://www.biorxiv.org/content/10.1101/2021.10.23.465563v1.full) on ancient Koreans just got published, for anyone with interest: https://www.cell.com/current-biology/fulltext/S0960-9822(22)00916-2“Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea” (paywall, the preprint is free)

    Press: https://drolab.co.uk/1700-year-old-korean-genomes-show-genetic-heterogeneity-in-three-kingdoms-period-gaya/“Six out of eight ancient individuals were genetically closer to modern Koreans, modern Japanese, Kofun Japanese (Kofun genomes are contemporaneous with individuals from the study), and Neolithic Koreans. The genomes of the remaining two were slightly closer to modern Japanese and ancient Japanese Jomons. “This means that in the past, the Korean peninsula showed more genetic diversity than in our times,” says Gelabert.

    “The individual genetic differences are not correlated to the grave typology, indicating that the social status in the Three Kingdoms Korea would not be related to genetic ancestry. We have observed that there is no clear genetic difference between the grave owners and the human sacrifices”

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