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

Open Thread – 11/29/2021 – Gene Expression

The The Aristocracy of Talent: How Meritocracy Made the Modern World is a fast read. Recommended.

I’ve been too busy to do an “Open Thread” and now that I do stuff similar for my Substack…well, you know the drill. That being said, South & SC Asian neolithic ancestry in Steppe Eneolithic. The big issue here is the space of graphs is big. Is this the best option? Sarazm seems to post-date the emergence of the proto-Yamnaya genetic matrix as outlined by David Anthony in his interview with me.

Also, I’m going to block some people who seem to have started trolling if you don’t stop (you know who you are, you are not a regular).

Finally, anyone have suggestions for people I should have on the podcast? I have a lot recorded already…

23 thoughts on “Open Thread – 11/29/2021 – Gene Expression

  1. Ancient proteome could turn out to be interesting in Homo phylogeny. Last year it made Antecessor being an ancestor unlikely. Maybe it can help clarify subclades of Erectus.

  2. Peter Turchin would be a good listen for the podcast, if you haven’t already had him on. I hear he has another book or two on the horizon…

  3. i’ll try and have richersen on


    More on multi-level selection (like your latest substack) every chance that you get. Especially guidance on reading on the subject.

    Has anyone tried to “fit” those personality traits to the old standbys like greed, hubris, narcissism, etc.?

  4. Could you please provide a small guide on what I could read to get a better understanding of genetics? Maybe a textbook which hasn’t fallen too far behind current thought. I much prefer learning from a physical book, because screens give me headaches. Much gratitude for you and your community here sharing information.

  5. Re; South Asian related ancestry in Steppe_Eneolithic, I think where I would criticize that graph is just from a quick look seems like there are lots of minimal drift edges to nodes labelled things like “IndiaN”, where I’m not sure they really imply that there is lot of shared drift or where the mystery node was actually living.

    The topic of the IranN/CHG like ancestry in the Steppe has become very contrarian lately, with some people in a way that seems reactionary to the academics trying to “Europeanize” the Steppe_Eneolithic component as much as possible (“It is purely a European component that has existed in the Steppe since the Mesolithic!”), and then others trying to emphasize wider links (because it makes plausible some other potential linguistic links). I don’t think this will be much solved without further new adna. I really hope we see what the Kelteminar culture was like, and whether it is at all plausible that they were part of a sphere that contributed to the Steppe_Eneolithic.

    It does seem like from Davidski’s Global 25 that there are links between the Sarazm_Eneolithic with both the Indus_Periphery and present day South Asian samples beyond what would be found for a model of TKM_Neolithic (Turan Neolithic) and CHN_Tarim_EMBA (North Eurasian HG).

  6. Very interesting paper on Neandersovan blood groups, deficiencies of which may have contributed to their extinction in the face of homo sapiens:

    This little section stood out to me:

    “Consolidation of an African origin for Neanderthal and Denisova

    First, the analysis of archaic blood groups anchors the lineage of Eurasian Neanderthals and Denisovans to Africa via: the absence of the antigen combination RhC, RhE, K, Fya, Jkb and S (14% of sub-Saharan African populations, 0.06% in non-African populations [10]), the presence of a double-dose of ancestral forms of the RH, Kell, Duffy, Kidd, MNS and Diego blood groups (respectively the haplotype Dce/Dce, KEL*02/*02, KEL*06/*06, FY*02/*02, JK*01/*01, MNS*04/*04 and Memphis form of Band 3 system [8, 41, 42], and RHD, RHCE variants phylogenetically linked or presently exclusive to African clusters and populations [31]. These features are in accordance with a Neanderthal and Denisovan gene pool pre-dating the exit of Homo sapiens from Africa [43].”

    How exactly does any of this mean that Neandersovans originated from an African source? Particularly the last two items, the authors seem to be implying because Neandersovans share “ancestral” alleles with Africans that the former stem from the latter, but aren’t they ignoring the obvious fact that Neandersovans are an outgroup to any living African? So who’s to say the common ancestor of Neandersovans+Homo Sapiens didn’t live in Eurasia?

  7. Possibly a sign that adna papers are scarce, but I thought this was an interesting preprint on the effect of admixture on pigmentation in an isolated Caribbean population that’s mostly a two-way mixture of Native Caribbean and West African diaspora:

    They look at the effect of transition from largely African->Native American ancestry independent of variations in SLC24A5, SLC45A2, OCA2, and find that for sample who are ancestral on SLC24A5, SLC45A2, OCA2, the Melanin Index (of skin pigmentation) goes from about expected 62 in 0% Native American (i.e. close to 100% African), to what would be expected to be 37 in 100% Native American (which is beyond the maximum range, at 90%). (OCA2 is isolated out due to the individuals with albinism in their panel, whose variation they also study).

    (That graphic: )

    They find that the effect of derived SLC24A5 and SLC45A2, independent of ancestry, contributes -6 and -3 MI respectively.

    (They note this is consistent with expectation: “The effect size for SLC24A5A111T is consistent with previously reported results of -5 melanin units for African-Americans and -5.5 for the admixed inhabitants of the Cape Verde islands. Reported effect sizes for continental Africans are both higher and lower (-7.7 to -3.6). The estimated effect size in the CANDELA study (GWAS of combined admixed populations from Mexico, Brazil, Columbia, Chile and Peru), only about -2 melanin units, is an outlier.”)

    Kind of interesting in its own right, but for comparison, they included some Europeans and East Asian MI levels, at 21 and 25 MI. Lower than other studies have found, but it’s kind of useful as a baseline for comparison to their sample.

    So on a baseline on that, for ancient people, before these variants swept, we might expect Europeans who were ancestral on SLC24A5 and SLC45A2 to be around 30 MI. About twice the East Asian:European difference they found here, or half the expected European:Native American difference. A European with SLC24A5 but ancestral on SLC45A2 might be expected to be similar to the East Asian mean. Not as large an effect as I would’ve expected. (All disregarding any other variants that may have been more or less common in ancient people).

    (MI 62 in the samples with 0% Native American admixture who are almost completely African is roughly as expected from 54 in African-Americans and those about 14-18% European and the MI measurement here.)

    It’s a pretty small study sample size, but it’s interesting to actually see the direct measurable interaction of the MI and ancestry, and reassuring to see some validation of effect sizes of the specific alleles between multiple studies. When it comes UKBiobank or other large GWAS samples, thinking about it I’m not actually sure what they’re measuring when it comes to pigmentation scores, whether it’s self-reported or what (which would be sort of a weak thing to measure), and its more abstract what it actually means.

  8. Actually, though, I think you’d probably double that if it is per copy, which I think it is, so that is maybe a larger effect.

  9. Recommendations? Check out Alexander Adams ( @AdamsArtist ), artist and art critic. He is English and his recent books look at “artivism”.

    Tho’, he hangs out with an “angsty” conservative crowd. Also, I’m not a paying subscriber.

    Here is a recent podcast he was part of:

  10. Also, I’m going to block some people who seem to have started trolling if you don’t stop (you know who you are, you are not a regular).

    Sorry about my recent outbursts of walls of text. In millennial-speak, I was triggered by “Nazi-baiting.” I will now return to observe and learn mode.

    Also, might I suggest my hobby horse, Martin van Creveld? Aside from military topics, he opines widely on social, civilizational, and even feminism issues of contemporary concern. He is in Israel, so it’d have to be remote.

  11. How about Greg Cochran? Haven’t heard much from him since his initial reactions to the pandemic. Always interesting.

  12. Anand Giridharadas’s premise that foundations, NGOs, and philanthropy institutions (not to mention governments) have been captured by elites immersed in, and dedicated to neo-liberal corporatism, preclude the consideration of capitalism’s (especially the global variety) role in the creation and exacerbation of wealth inequality may have merit. However, how is placing indigenous people on the foundation board (on the idea that they know more about what they need than do the minions of the elites) going to bring forth “the” solutions? If the indigenous people knew how to effect solutions to wealth and power inequality, they wouldn’t have come to the attention of the foundations and NGOs in the first place.

  13. – Europeans more resistant to anthrax.

    “New research from the Cornell College of Veterinary Medicine has revealed how humans evolved greater resistance against anthrax multiple times during history: when they developed a diet of more ruminants, and when agricultural practices took hold.

    Anthrax grabbed the nation’s attention when it was used in bioterrorism attacks in 2001, but the disease has haunted humans for much longer. Over millennia, humans and anthrax have co-evolved. According to a study in Nature Communications from the lab of Charles Danko, this resulted in humans, particularly humans of European descent, evolving fewer anthrax receptors that allow the disease to take hold in the body.”

    In the wake of “Guns, Germs and Steel” there was a fashion online for talking about “European diseases” originally from domestic animals impacting the Americas though most were were pan-Old World and probably not particularly more common in Europeans, and domestic animals are not necessarily most frequent source of zoonotic post-agriculture diseases (for an example, possibly Covid-19, if we accept the wet market version of events). But maybe anthrax was, because of more herding.

    Perhaps this would replicate in long term herding populations (Mongolians, Arabians?).

  14. Study from last year that might be interesting to some – – “The shaping of immunological responses through natural selection after the Roma Diaspora”. Whole genome sampling of Roma and Romanians, and compared and identified shared natural selection between them to exclusion of NW India. Various immune pressures are shared.

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