Open Thread, 4/17/2018

Almost done with She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. To be honest I’m a little relieved that there wasn’t that much focus on the “perversions” of heredity. Lots of interesting stuff. This is definitely a book that scientists and lay people could benefit from.

Carl is a great writer so he makes rather abstruse concepts clear and engaging to nonspecialists. As for those of us who have our noses close to the ground, we sometimes lose the bigger perspective. There is a lot of interesting research that he surfaces in She Has Her Mother’s Laugh that I wasn’t very familiar with, though I had probably read about it or seen it in one of his columns (or Ed Yong’s).

Met a lot of cool people, and touched base with others who I knew ahead of time, at the AAPA 2018. Compared to ASHG or even SMBE the conference was very white. I guess that’s why there were all the diversity sessions?

Lee & I

I had a lot of discussions with Lee Berger about science on a broad philosophical level. Unfortunately, specialization is such that it can be hard to communicate across disciplines such as human genomics and paleoanthropology. But as Lee brings enough samples into the open to do some real statistics I think that will change how constrained to the elect paleoanthropological knowledge is.

Braai

Lee’s son introduced me to the concept of South African barbecue. I haven’t had any yet, but I’m curious about it.

Lee will be on this week’s episode of The Insight. Again, please subscribe on iTunes, Stitcher, Google Play. The last episode with Stuart Ritchie was our most successful yet in terms of traffic. We’re suspecting that Lee’s episode will do quite well as well. People keep finding the podcast by chance. We really need reviews to get featured by iTunes!

Spencer and I will probably shift back to a two-person conversation next week. We should probably do an AMA again soon.

Was There a Civilization On Earth Before Humans? Very interesting piece, especially for those of us who have read science fiction. But my issue is straightforward: humans have scrambled biogeography so much in such a short amount of time. I think any other industrial species would have done the same. Even after they went extinct, the phylogeographic chaos they wrought would remain.

It seems very likely that all Australian marsupials descend from one South American ancestor species. The explosive emergence of very different placentals all across Australia simultaneously in the fossil record would be quite suspicious (or red deer descendants in New Zealand).

I spent some time with the people who were associated in some way with the Reich lab a fair amount during the AAPA meeting. I also talked to a few friends about what they thought about David’s op-ed and book. It’s no surprise that there are legitimate human population geneticists considering writing a response of some sort. It’s also no surprise that even critics of David within the population genetics community think that the Buzzfeed op-ed was so bad that it makes it harder for them say something, as the water has been nuddied.

In some ways the reaction has made one of David’s major points: population geneticists need to offer their unvarnished opinions, rather than cosigning people in other fields who mangle their findings.

Some people feel that David “threw me under the bus” in his now infamous chapter. I don’t see it that way.

As many of you know (if you subscribe to my total content feed you know) I have a few other blogs, one of them Brown Pundits. It actually receives substantial traffic from India now. It will be “interesting” to say the least.

A population genetic interpretation of GWAS findings for human quantitative traits. Stuck in the weeds of ancient DNA these past few years I haven’t been paying attention to the storm of GWAS and PRS approaching.

Signatures of negative selection in the genetic architecture of human complex traits.

12 thoughts on “Open Thread, 4/17/2018

  1. Looks like my comment has vanished – may be (and hopefully) related to the server being apparently down just as it was completed.

    Saw your Brown Pundits post about 1500 years ago as the time endogamy set in for many groups, which differs from 2000-3000 years ago given by Reich for a south Indian vysya community: is this specific to Vysyas or a margin of error?

    Does population bottleneck really mean what wikipedia says it means – because I interpreted Reich using this definition (I am reading his book now), and I got the impression that he uses a different definition (that a small group of people suddenly have too many descendants).

    Thanks for your time.

  2. i don’t see your comments in trash either? ;-(

    i think the 1,500 figure is when all groups stopped mixing. i believe that some may have stopped earlier. though it could be noise with sample size too.

    re: bottleneck. it just means that the number of breeding individuals is small. that number is really important for long-term of a population. later pop size not as big of an issue (small or large).

  3. I was curious about the endogamy issue as well. Does that mean that less than 1% of the group outmarried over that time, or that they were so effective at banishing anyone who didn’t marry within the group that it shows up like that? Or both?

  4. Thanks very much. Embarrassingly I had interpreted bottleneck in the wikipedia sense, that there was a drastic reduction in population at some time due to some catastrophe.

    (Only the first comment, it turned out, vanished, which was due to the server issue. The second appeared after an unusually long delay, in which time I assumed it was gone).

  5. I just saw a new study came out with the finding that the Polynesian sweet potato and the South American populations stopped interbreeding at least 111,500 years ago – potentially even earlier going by choroplasts. If this holds up this would mean that South Americans and Polynesians independently domesticated the sweet potato, and the best evidence of pre-Columbian contact between Polynesians and South America is gone. Wild sweet potatoes reached Polynesia by rafting on their own – not something which is unknown among wild relatives of the plant.

  6. “humans have scrambled biogeography so much in such a short amount of time”

    As Chris D. Thomas writes in Inheritors of the Earth: How Nature Is Thriving in an Age of Extinction this scrambling also helps nature grow and diversify in a very fast way.

  7. In case you haven’t seen this yet:

    [link removed, sorry, i don’t want to give that creep more pagerank!]

    (starring you).

  8. Some pretty interesting fossil work I happened to read and worth a readover from early this year (rather overshadowed by epic adna!) on the emergence of the form of the modern human brain (I would guess all spurred on by the major Jebel Irhoud re-dating from last year, and re-analysis of their form as presenting an archaic braincase with a modern retracted and small face):

    http://advances.sciencemag.org/content/4/1/eaao5961“Modern humans have large and globular brains that distinguish them from their extinct Homo relatives…Our data show that, 300,000 years ago, brain size in early H. sapiens already fell within the range of present-day humans. Brain shape, however, evolved gradually within the H. sapiens lineage, reaching present-day human variation between about 100,000 and 35,000 years ago. This process started only after other key features of craniofacial morphology appeared modern and paralleled the emergence of behavioral modernity as seen from the archeological record. “

    In this analysis, AMH classified skulls between 300kya-115kya overlap with Neanderthals from 75kya-40kya on globularity. Present day humans are highly variable (partly product of higher sample size?); the range of present day humans varies from samples overlapping AMH 36-10 kya and only slightly more globular than Neanderthals, up to samples as much more globular from AMH 36-10 kya as AMH 36-10 kya are from Neanderthals. (Fig 2 and Fig 3).

    “It is intriguing that the evolutionary brain globularization in H. sapiens parallels the emergence of behavioral modernity documented by the archeological record. First, the emergence of the Middle Stone Age is close in time to the currently earliest known fossils of early H. sapiens that had large brains but did not exhibit any major changes to (outer) brain morphology. Second, as the H. sapiens brain gradually became more globular, features of behavioral modernity accumulated gradually with time. Third, at the time when brain globularity of our ancestors fell within the range of variation of present-day humans, the full set of features of behavioral modernity had accumulated at the transition from the Middle to the Later Stone Age in Africa and from the Middle to the Upper Paleolithic in Europe around 50,000 to 40,000 years ago.”

  9. A slightly different analysis of endocranial shape mid last year between a smaller sample of Neanderthals, <115kya AMH and recent AMH (and no very early AMH or Homo Erectus) or is presented here:
    https://link.springer.com/chapter/10.1007%2F978-4-431-56582-6_2 (a chapter of a larger work on paleoneurology via digital endocasts)

    In this instance (Fig 2.20), no single dimension of globularity is found. A dimension PC1 tracks relatively shorter, broader, slightly higher brains distinguished recent people (Japanese, Indians and Europeans) from both of <115kya AMH *and* Neanderthals, looks to peak in recent European samples. Another PC2 places distinguishes on one end recent Japanese together with relatively taller brains in contrast to Neanderthals at the other end with relatively longer, broader, flatter brains, and Europeans and early <115kya AMH intermediate. (PC2 is "associated with relatively larger cerebellum and parietal regions" relative to other regions of the brain). Here PC1 looks something like globularisation A and PC2 like globularisation B, rather than a single phenomenon.

    Studies probably generate varying results because of varying landmarks and varying sample composition (e.g. second is heavy on recent AMH). In either case, whether globularisation is one phenomena or two, there is some agreement on high diversity of AMH on brain shape, relative to differences against Neanderthals.

    Mainly noteworthy is that the first of these two studies fails to find a singular AMH brain shape that predates estimates dates at which our species coalesces. Instead finds that this evolution towards a more globular brain was ongoing at points during and after expansion of AMH as a global species ;), where AMH appears to have been evolving as a structured population, and while AMH cultures show variable evidence of features of behavioural modernity.

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