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

Open Thread – 11/07/2021 – Gene Expression

In the mid-2000’s I read a bunch of books on the history of Catholicism in the US. One of the most memorable of those books was Jay P Dolan’s In Search of an American Catholicism: A History of Religion and Culture in Tension.

If you haven’t, please write a positive review of the Unsupervised Learning podcast. The more positive reviews, the better it is for exposure, etc. etc.

Some links on the Substack too. Also, a new paid piece, Heritability of height: the long and the short of it. Using genetics to make historical and cultural inferences are popular, obviously, but the interplay between genetics and evolution are just as interesting to me. Obviously.

I interviewed Eric Berger about SpaceX. Most of the discussion focused on his book, Liftoff: Elon Musk and the Desperate Early Days That Launched SpaceX. I’m generally pro-Musk, so I recommend the book. If you want a negative treatment, just read the rest of the media!

Parent-of-origin effects in the UK Biobank.

Genetic and chemotherapeutic causes of germline hypermutation.

America Needs a New Scientific Revolution.

Replace the Proposed New California Math Curriculum Framework – Open Letter to Governor Gavin Newsom, State Superintendent Tony Thurmond, the State Board of Education, and the Instructional Quality Commission. This is a “whitepill.” Lots of people I respect on this list, even people with a reputation as being very much on the Left.

11 thoughts on “Open Thread – 11/07/2021 – Gene Expression

  1. There’s a lot of billionaires in the US where I think they’re basically replaceable (albeit with another billionaire). If Bezos had never existed, we’d probably still have some pretty excellent e-commerce sites with fast delivery (although e-books might be even less well-developed).

    But I don’t get that impression with Musk. Without Musk, rocketry in the US would be radically different, and not in a good way. And you can see the difference in the fact that both Bezos and Richard Branson started rocketry companies around the same time, and neither of them is even remotely as capable or effective as Musk’s company.

  2. I am starting to think that maybe Homo Erectus evolved from a migrant Habilis population in western Asia.

  3. Ancient genome analyses shed light on kinship organization and mating practice of Late Neolithic society in China

    Chao Ning (et al) applies Harald Ringbauer and colleagues’ low coverage RoH method to Chinese ancient dna (“In order to identify if the Pingliangtai individuals were descended from some degree of recent inbreeding, we estimated the ROH of selected genomes in our study following a approach implemented in Ringbauer et al. (Ringbauer et al., 2020a) “). Nice because that is a bit of a gap in the paper Ringbauer published recently (which was based on the adna set available pre-publishing of ancient Chinese genomes).

    Excavated a Longshan era set of burials (approx 2000 BCE), and found that 3/4 were related to each other, and 1/4 was from a consanguinous first cousin marriage union.

    Also applied to all available other Chinese Central Plain data (33 samples) and found large population size with only one Han era individual who seemed potentially to be a second-cousin offspring.

    So this suggests that consanguinity was probably really neither hugely more common nor less common in Han or pre-Han populations than in samples of a comparable age in Europe or West Asia (e.g. Unetice Culture or EBA Italy or Roman Era). Possibly some consanguinity, but far from the sort of thing where Henrich’s regression based on a sample heavily skewed by contemporary Islamic cultures from South and West Asia and North Africa would predict rates like 1/6 first-cousin marriage (15%, what his regression predicted with zero “centuries under the Medieval Churches”). It kind of adds to the picture where we find strongly elevated cousin marriage rates either a) on quite small islands (thing upcoming papers on Greek islands in the Bronze Age and Malta in the Bronze Age relate to this), or b) under very specific cultural circumstances (the Andes at a specific time, and, emerging at some unknown point, it seems much of the Islamic world).

    Although tentatively its possible it could have been higher in Longshan Era or some cultures within that horizon? Larger samples of these things might allow a bit more comparison of a finer scale of how common different degrees of consanguinity might have been in the Han Empire vs Rome, or Longshan vs contemporary cultures in Europe / Levant / Anatolia.

    Think the authors here also tie their findings around kinship and burial to a hypothesis that this relates to a transition from a clan based society (maybe based around a patrilineage?) towards a society more built around a general extended family within an early state.

  4. I mentioned previously here about an event on Marija Gimbutas legacy, and this talk (“Marija Gimbutas: A Magnificent Vindication”) is uploaded onto YouTube:

    It’s good really for an overview of the full history of IE homeland theories, as given here by James Mallory (which is a bit more nuanced than “Gimbutas invented kurgan theory and invented the idea of the Pontic-Caspian steppe origin” without in any sense negating her contribution). And really of interest for the recent paper on the evidence that the first domesticated horses were MLBA era DOM2 horses, David Anthony gives his thoughts on expansion of the horse.

    DA does marshall some evidence for horse use by the Yamnaya, and particularly mentions some new evidence for horse riding by Yamnaya as seen in skeletal pathologies.

    *But* to my mind, he doesn’t really seem to grapple with the consequences of the recent paper – states “Yamnaya horses have a role to play in the IE expansion”. However part of the point of the recent paper is that Corded Ware horses have *no* ancestry linked to steppe horses. They’re not bringing horses with them at all, just seem to be using whatever horses are around. That is not really consistent with the idea that Yamnaya (or proto-CWC if we prefer) already had horses which they’d bred, who were so strongly differentiated from various native horses to be strongly preferred.

    He is asked this directly by the audience at 1 hour 21, and… sort of dodges it. He does talk about them Corded Ware adopting local Northern European horses without steppe horse ancestry, but… just to say its fascinating that they did this. Which sort of dodges the idea of why; if pre-Yamnaya cultures had domesticated, bred horses which they people were the first to domesticate, and people like the Globular Amphora presumably didn’t, then why are are Corded Ware adopting these Northern-Central European horses instead?

    DA’s comments on the Gimbutas narrative also described it as “partially vindicated” in context of hinting that the bits he thought were not so strongly vindicated were the idea of IE being more patriarchal and more violent contrasted to egalitarian, pacifistic previous societies. Although the full comments in the video probably better conveys his view than I am here.

  5. I’m currently reading _Kindred: Neanderthal Life, Love, Death and Art_ by Rebecca Wragg Sykes. It’s pretty good. She starts every chapter with some impressionistic prose (which I find annoying), but she does pack in quite a bit of information.

  6. Just as another afterthought to my comment on DA’s responses to the Gimbutas lecture and in case anyone has any other thoughts around the topics involved: In balance to his comments about Gimbutas narrative, he does mention at the end the ideas about the Indo-European koryos (in context of a positive comment on the idea of Gimbutas as using comparative mythology to identify past social structures in combination with archaeology, after his slightly negative comment on some parts of her narrative).

    The koryos idea does seem like its worth pursuing, but kind of hard to quantify as a main reason for IE expansion. To me the Bohemian CWC data look like a sustained and steady male bias in admixture between CWC and other Central European groups about 1/40 or 1/33 reproductive events per generation for close to 500 years (not so much like a big event that happens in one or two generations). Plausible then that the koryos practice might drive it, but how much weight does it get over economic factors?

    CWC look like an expanding group that has recently experienced high population growth from a new economy (in the way Anthony describes in the video). Probably spoke a fairly undifferentiated language and practice similar cultural rituals. A different and more mobile mode of subsistence that may have helped them to colonize some central areas that were abandoned due to declining soil quality*. Also speculatively slightly greater immunity to plague. So how much remains to be explained? Koryos may have played a role, just hard to quantify. May even have played a negative role, causing infighting and death among early CWC, and possibly they would have even demographically and genetically expanded more without as much raiding culture.

    *Declining soil fertility, does seems to be the current view on Late Neolithic agricultural decline in North and Central Europe – soil exhaustion rather than climate. See Rowly-Conwy – May explain why later colonized places like Orkney or Southwestern Ireland may have had more enduring agriculture over time. Plus Orkney has had the advantages of use of seaweed as fertilizer, and mild Gulf Stream climate may have helped for overwintering animals.

    Focus on soil fertility hypothesis may help explains why this happened more in Northern Europe; as EEF expanded to the north, the primary productivity drops, but also dropped the nitrogen fixing crops. Broad beans, chickpeas, lentils.

    A soil fertility view also centers role of rivers and marshes in early civilization. Proto-civilization is found sometimes in hills, like in Central Europe and Southern Spain, Unetice and El Argar, but enduring early proto-civilization seems around rivers and marshes. Perhaps rivers and marshes that flooded and brought rich nutrients out gave enduring fertility without need to migrate to new soils, allowing sustained economic growth generation after generation. So simple farming communities->civilization.

    Maybe the scientists can test this with sedimentary adna. E.g. Sampling different deep soil layers in relatively unexcavated sites (if there are any!) and test for the presence of crop dna over time. Probably a dream with some major technical issues tho.

  7. @Matt

    Thanks for keeping tabs on the presentation. Nice that it’s been uploaded.

    The decline of the late Early Helladic/EBA Greece has also been partially connected to the factors you mentioned. Could be that these argued for late EBA – early MBA migrating/invading groups (if we keep seeing them in the aDNA as we tentatively have so far at least) found an opportunity there too, rather than being the sole cause, then helped things move along.

  8. @Matt I’ve always assumed soil fertility was a factor since very early on when we started having good data about the timing of first wave Neolithic rise and fall, but the literature directly examining the hypothesis does seem to be sparse. You idea regarding how this could be tested is a good one.

  9. @ohwilleke, thanks. I probably misrepresented things and implied it was a new idea, definitely not, just one that as far as I can tell from a bit of reading seems be closer to the dominant idea now, and one that I paid probably not enough attention to before. (Sounds like you’ve probably had the better reading and thinking about this idea for a while).

    @forgetful cheers, interesting comment on that factor in EBA Greece.

  10. Razib: Another South Asian child prodigy:

    “How a 12-Year-Old From New Jersey Became the Youngest Chess Grandmaster Ever: Abhimanyu Mishra and his father booked one-way tickets to Hungary for a chance at history. ‘You will never be 12 years old again.’” By Joshua Robinson and Andrew Beaton | Nov. 9, 2021 • Appeared in the November 10, 2021, print edition as ‘A Mission to Become Grandmaster.’

  11. Paper on ancient dna in El Argar got released –

    Quick hot-take on what El Argar paper shows from a skim:

    – Only one clear East Med + North Africa related outlier among El Argar… They think he has no local ancestry but he has R1b, so possibly part of a R1b network… ZAP002, who “clusters with Sicily EBA”.

    – That said, they do think there’s Iran_N like ancestry only in El Argar… But, also argue it might just be due to better statistical data. El Argar looks like less steppe ancestry than the North.

    – The one y-dna E1b sample from La Bastida site doesn’t seem to have anything special going on in PCA though they note its late in time in the sequence.

    – They think they’ve found a slightly different ancestry structure in SE Iberia, with contributions from Magdalenian HG and Levant_N/Iran_N which are lacking in N Iberia.

    – El Argar look slightly low in steppe ancestry compared to North BA, whether they have Iran_N ancestry or not, despite replacement of y chromosome.

    – f4 stat shows almost complete association or R1b-M269 with steppe ancestry. Only for two I2a from the Copper Age pre-Bell Beaker “megasite” Valencia de la Concepcion, Montelirio this is not true. But both of these samples also have very low levels of SNPs and the ones from the site who have high substantial SNPs aren’t like this. It seems unlikely that it would just happen to be the samples with low quality data that show this signal though!

    – As with some previous work in the Baltic and Central Europe, they find a collapse in the observable autosomal:X chromosome bias for steppe ancestry over time: To assess a potential sex bias in the steppe-related ancestry contribution as postulated previously (7), we applied distal and proximal qpAdm models (text S8) to the X chromosome and autosomes (Fig. 6B and table S2.22). As males contribute, on average, only one-third of the X chromosomes to the next generation (75), a lower proportion of any ancestral component on the X chromosome than on the autosomes would thus be indicative of male bias concerning the respective component (76, 77). In turn, if the ancestral component is statistically higher on the X chromosome, this indicates a female bias. On the basis of this rationale, we do not observe significant male bias in steppe-related ancestry using either distal or proximal sources (Fig. 6B and table S2.22). The fact that the male bias is not detectable could be indicative of an already balanced ancestral component in both sexes, as is reflected in the work of Mittnik et al. (77), where the male bias in the steppe component is only detected in Corded Ware, but no longer in Bell Beaker or BA populations.

    Seems to me like there is some work required to look at what happens over time with these X:A signals. I still have a vague notion that while possibly they held true in Latin America for 500 years due to a structured social system, they might not exist in the same way in the Indo-European expansions in a slightly longer term, where kinship could be more important than autosomal ancestry (or “race”) in determining who can reproduce with who. Although the y-chromosome may preserve the steppe ancestry expansion, I have some vague notion that if the later shuffling around with the admixed populations often involved males with more autosomal EEF reproducing with females with more steppe, then over many generations the signal might collapse. No clear idea if that’s possible or not.

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