Open Thread, 04/12/2019

Just a reminder for people to check in on The Insight this week. Lots of talk about Denisovans between Spencer and myself. We’ve also got a follow-up podcast scheduled with a researcher working in Denisovan genomics in a few weeks (we’re on Spotify now by the way).

Our three new hires at George Mason economics. These look good.

Sri Lanka Suicide Bombings Targeting Christians Kill Hundreds. The most likely culprits seem to be a jihadist group active in southern South Asia.

A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. I think the “Crusader genes” are hard to find in the Near East because the collapse of the Latin kingdoms was gradual enough that “Franks” and their scions mostly managed to get out and go back to Western Europe.

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants.

Anxious Times In Pakistan’s Pagan Valley.

Why One-Third Of Biologists Now Question Darwinism. I’m writing a response to this piece for The Federalist. Rather than a response to Intelligent Design, I want to represent what evolutionary biology really is.

Evidence for Early European Neolithic Dog Dispersal: New Data on South-Eastern European subfossil dogs from Prehistory and Antiquity Ages.

17 thoughts on “Open Thread, 04/12/2019

  1. A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. I think the “Crusader genes” are hard to find in the Near East because the collapse of the Latin kingdoms was gradual enough that “Franks” and their scions mostly managed to get out and go back to Western Europe.

    I’d love to read your thoughts (even if speculative) on the two apparently admixed-individuals.

  2. Got an internal server error when I made the above comment. So I re-commented, but wrote over it after seeing the first one appear anyway.

  3. would appreciate if others told me about the errors too if they see them. i think the archives on this blog or something is getting too large to serve pages? the traffic load is pretty modest. so i think it’s some changes/plugins that are memory hogs.

  4. twinkie, i think the mixed individuals are probably the offspring of western men and eastern christian women. intermarriage between these groups is recorded, especially btwn armenians and western christians. i think because the fathers were ‘franks’ they were raised as such, as western latin rite christians speaking proto-french. i believe they left little impact because these chrtistians left the holy land as the muslims conquered state after state.

  5. @Twinkie, of the 2 ‘admixed’ individuals SI-41 actually matches the set of Southeast Iberians from between 400ad-1600ad from the recent paper on historical Iberia. I don’t think he’s recently admixed, certainly not anything involving the populations they talk about.

    In a way its understandable they didn’t get this, since this is very recent, but that they didn’t test the sample with any published NW or African sources is less understandable.

    The Southern Italian like individual SI-53 may genuinely be recently admixed, buuut he’s pretty close to the range of existing Southern Italian samples, and their evidence for being recently admixed is not very strong (its not like they’ve exactly got a diploid genome with a neat division between European and Lebanese ancestry or something). I expect that as more Southern European ancient DNA rolls in, we’ll also find it doubtful he’s admixed and also within the range of post Roman Southern Europe. But its at least a possibility that for SI-53 they got it right.

  6. armenians

    That was my first thought when I read about the two admixed ones. I’ve always been fascinated by Turcopoles, so the mixed or non-Frankish buried with the Crusaders was very intriguing.

    Thank you for your thoughts.

  7. there is a tendency of turning white muslims into brown people due to their religion. we know the geopolitical/social reasons for this.

    now i see a milder counter-trend where dark-skinned christians whose families have been so for centuries are turned western colonizer/white (from your twitter)

    I’d say a corresponding trend (or maybe “a milder other-way trend”). It’s doing the same race-change thing for the same geopolitical/social reasons. The second trend does not go against (counter to) the first. It extends it.

  8. Can someone clarify what people mean by the term “Darwinism”? I’ve always been confused about how this word is used.

    Is it a code-word for evolutionary theory as a whole? Or some kind of straw-man opponent for creationists who ignore all developments in biology since Darwin’s era, and choose to attack evolutionary theory based on a literal read of Darwin’s (pre-genetics) writings?

  9. Different people mean different things. Some mean your first, some your second, and some other things. Neo-Darwinism is sometimes used to specifically mean modern theory.

  10. @Matt

    Regarding your response to my question on PCA comparisons in the previous 4/15 Open Thread. Yes, I was aware that Fst is probably a simpler method of comparing distance between populations, however isn’t Fst highly skewed by extreme drift and bottlenecks, which could muddle attempts at unbiased comparative analysis?

  11. Curious if there are any signals of natural selection that are different between castes in South Asia. For example, are there HLA adaptations in Scheduled Castes who were exposed to pathogens for many generations that other castes were comparatively speaking insulated from?

  12. “Can someone clarify what people mean by the term “Darwinism”?”

    Often the term is used to refer to social Darwinism, a political economic doctrine that sees “survival of the fittest” to be the natural order of things and thus a justification for why the well to do deserve their well being. Social Darwinism is often seen as going hand in hand with Eugenics which is also not a popular concept at the current time (although it was once seen as a progressive idea).

    Even when not used in that narrow manner, it is often a term chosen to evoke the negative reaction associated with that ideology, and some creationists actually think that people who believe in evolution are also, necessarily, social Darwinists, even though that isn’t accurate.

  13. @Mick, ah, I suppose I can see the reasoning there, in theory, PCA could allow you to find a dimension that represents drift particular to one particular population and allow you to estimate distances between populations without that (though that wouldn’t really be distance between two populations as such the way a direct Fst is).

    Though in practice kind of difficult as it seems like PCA sometimes undershoot and overshoot certain dimensions (I guess population specific drift can reduce the degree to which a population is detected by PCA as on a common drift dimension sometimes?), and PCA dimensions are abstract adn don’t necessarily really represent periods of drift or anything like that so much, as far as I know?

  14.“A 5,000-year-old barley grain discovered in Finland changes understanding of livelihoods” – Pitted Ware Culture (“Inuit of the Baltic”) also liked their barley. I wonder if they actually practiced agriculture as link suggests, or whether this is really about trading for grain…?“We have long been aware that complex societies emerged in Llanos de Moxos in southwestern Amazonia, Bolivia, around 2,500 years ago, but our new evidence suggests that humans first settled in the region up to 10,000 years ago during the early Holocene period,””

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