Open Thread, 12/02/2019

Evolution and Selection of Quantitative Traits is available on Kindle format. I have most population and quantitative genetics texts, but these are not optimal for portability. They are big and heavy. Evolution and Selection of Quantitative Traits is not cheap, but it’s over 1,000 pages. Merry Christmas to me!

Dante is sequencing my whole genome. As in, the process has begun! I will be posting a Dropbox link to the VCF file at a minimum since I promised I would post it if I had it done about ten years ago.

People ask me of Dante is legit. I purchased my kit in early June. So it’s been a while, but the results are now coming back (my father in law got his back about a month ago). So Dante does get around to it eventually.

Since it’s CyberMonday, MyHeritage, 23andMe, Ancestry, Family Tree DNA, all have sales.

Since it’s CyberMonday, I should mention that Jennifer Doudna’s A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution is on sale.

Big deal of 2019: ancient DNA confirms the link between Y-haplogroup N and Uralic expansions. Seems right.

In Prince Andrew Scandal, Prince Charles Emerges as Monarch-in-Waiting. When you are making Charles look like he has gravitas.

The last (porn) picture shows: Once dotted with dozens of adult cinemas, L.A. now has only two. They’re like James Monroe, who continued to dress in the style of the Revolutionary era long after it was out of fashion.

Distinct genetic variation and heterogeneity of the Iranian population. Iran seems to have gotten the “steppe” between 2000 and 1000 BC.

Alanis Morissette Isn’t Angry Anymore. But ‘Jagged Little Pill’ Rages On. OK, Boomer, you are finally retiring, and Generation X editors are making the calls about the nostalgic retrospectives.

Does Who You Are at 7 Determine Who You Are at 63? Back when Netflix was still DVDs I binge-watched this. Didn’t watch the last installment.

Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity.

A bird’s-eye view of Italian genomic variation through whole-genome sequencing.

The Typical American Lives Only 18 Miles From Mom.

The impact of global selection on local adaptation and reproductive isolation.

Brad Gobright, a Throwback Climber on the Fringes of a Sport. We are a crazy species.

The Ironic Loss of the Postmodern BEST Store Facades.

An animal society based on kin competition, not kin cooperation.

Kindle paper-white is on sale for CyberMonday. I decided to get one to check it out. I do a lot of reading on my Fire, but the battery life…

What to read on it? The Great Cauldron: A History of Southeastern Europe, The Boundless Sea: A Human History of the Oceans, and Cognitive Gadgets: The Cultural Evolution of Thinking. My “stack” is getting thick, and I like long long books. But it is what it is.

Kamala Harris aide bolts to Bloomberg campaign. The whole thing is funny. I dislike Kamala’s authoritarian streak. Like Young Pompey.

A fully phased accurate assembly of an individual human genome.

Why Russia’s pagan Udmurts are feared.

With Brutal Crackdown, Iran Is Convulsed by Worst Unrest in 40 Years. Not to sound Marxist, but it looks like problems with the base may result in a change in the ideological superstructure.

19 thoughts on “Open Thread, 12/02/2019

  1. I wanted to thank you for The Insight, I loved listening. I haven’t seen any new episodes in my feed since the last season ended. Do you have plans to start another season?

    2+
  2. Kamala Harris aide bolts to Bloomberg campaign.

    Perhaps the aide thinks that the Harris campaign won’t be writing checks in a few months. But Bloomberg is worth billions and says he’s going to spend $100 million of his own money.

    0
  3. Razib, how do you manage to get meaningful use out of textbooks on the Kindle? My experience with eReaders is that the mono screen and limited resolution make them useful for text-only documents, and that’s about it. Figures or graphs are almost unusable. What am I missing?

    0
  4. Razib, how do you manage to get meaningful use out of textbooks on the Kindle? My experience with eReaders is that the mono screen and limited resolution make them useful for text-only documents, and that’s about it. Figures or graphs are almost unusable. What am I missing?

    you are correct. but i don’t get textbooks that need to be graph/figure heavy. the equation rendering in walsh & lynch seems to be OK.

    I wanted to thank you for The Insight, I loved listening. I haven’t seen any new episodes in my feed since the last season ended. Do you have plans to start another season?

    yeah, 8 episodes are recorded. so there will be a season three for sure. can’t tell you on when…

    0
  5. Looking forward to the next season of The Insight.

    Listening to The Insight, and reading this blog, inspired me to get my own DNA tested, and it made sense to me to start with the kit from Insitome. Although getting the Neanderthal results was interesting, on the whole I have to say the Regional Ancestry report was… rather underwhelming. It seemed less detailed than, e.g., the ones on sale today.

    But with the “sequence once, query often” model, can we expect more ancestry-related apps anytime soon?

    0
  6. “Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity” is a really nice paper in filling in sampling gaps.

    Excerpt putting the main PCA and ADMIXTURE results from the paper side by side, followed by some similar PCA made from the Eurogenes Global25, using published data for some comparison with groups not in their PCA:

    https://imgur.com/a/oTklpvN

    In Fig 1 from the paper, PCA samples have labels coloured by language family, with Vietnam samples also getting a green dot. While in Fig 2a, all samples are coloured by dots labels indicating country. E.g. if a sample has a blue label in Fig 1 This is a little hard to read in terms of inferring which population is which but a interesting schema. Would be a good complement to the paper’s PCA to also have had one with labelled populations as well.

    My PCA using Eurogenes data tends to show that the Burmese are samples are somewhat clinal between the Oakaie Bronze Age sample (pretty Northern Han like, or rather, Naxi/Yi like) and a Kharia like population. Though the history may not be exactly like this.

    The Han in Eurogenes set for whatever reason are a small Northern Han cluster, and a more diverse cluster that includes samples who are closer to Kinh Vietnamese than the Han N China cluster (most “Southern” Han are about 80% of the total distance from most “Northern” Han to Kinh; what country they are from I do not know). Cambodians in Eurogenes include about 3-4 who look “Austroasiatic” and one who seems fairly Southern Han like in ancestry with some ancestry like the other 3-4.

    0
  7. Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history

    https://www.biorxiv.org/content/10.1101/470583v1.abstract

    Page 22 of the PDF, Table 1 – Number, size distribution and sum of ROH (above and below 1.5Mb) across global regions and according to population.

    When looking at the far right colummn “Total Sum of ROH < 1.5 Mb" (which is supposed to be an indicator for ancient bottleneck signatures in a population's genome – the greater amount of short ROH, the more profound bottlenecks were in a population's deep pre-history, whereas larger amounts of longer ROH tracts indicate much more recent inbreeding), West African groups tend to have scores around 100. Europeans are in the 250 range, East Asians around 320. Interestingly, Horn African pops are in the 130 range, much closer to the West African mean than the European, despite the fact these groups are in the range of 40-50% West Eurasian themselves. So why isn't their total amount of short ROH more in the 170-180 range?

    0
  8. @Mick, my understanding (and Razib can correct me if I’m wrong) is that although “OoA” ancestry does increase short RoH (because OoA populations went through a stronger bottleneck than African) in East Africans, it doesn’t do so in proportion to OoA ancestry but at a lower clip, because the OoA ancestry is also partially breaking up short RoH from (less harsh) bottlenecks that African populations have been through themselves. OoA populations are not simply a bottlenecked version of African populations alone but descend from a parallel population history from the true ancestral population Africans also descend from, with a harsher bottleneck in OoA?

    0
  9. i heard a rumor on twitter about BGI and creating a genomic bioweapon and that david mittelman is going to “out” them?? is any of that true?

    0
  10. “Kindle paper-white is on sale for CyberMonday.”

    Tried it. But, I didn’t like the interface. When Southwest Airlines returned my Fire HDX I returned the Paper White to Amazon.

    The HDX has such a fabulous screen, newer Fires don’t come close to it. If my Fire ever dies, I will migrate to a tablet of some sort.

    0
  11. “Not to sound Marxist, but it looks like problems with the base may result in a change in the ideological superstructure.”

    We keep hoping. But, until the doctor declares it is dead, and a stake is driven through its heart, we will not be at ease.

    0
  12. @Matt, that actually sounds like a very reasonable explanation. Just looking at the African American samples in that table, both are right around 90 mean sums of ROH < 1.5, noticably lower than the "pure" West African Yoruba, Igbo pops, and AAs are on average around 20-25% European or so. In fact, it looks like all the more blatantly mixed African populations have means well below 100 – the Eastern African Niger Congo speakers (a mix of West-African related Bantus, Nilotes, and Cushites) are in the 85-90 range, and the Southern African and Khoe San pops (complex mixes of San hunter-gather, Bantu, Cushitic, and in some cases European ancestry) in the 60-90 range (I'm presuming the high amounts of super diverged San ancestry is what drives the mean downwards in pops rich in that ancestry).

    Though on the flip side, the Wolof, Jolof, and Fula are around 105, perceptibly higher than Yoruba/Igbo. I suspect in this case, the recent Eurasian admixture (within the last 2,000 years) these groups have received from Berber populations is actually boosting their mean sums up proportional to their actual level of Eurasian autosomal ancestry, because the small, short-ROH dense fraction of OoA ancestry isn't large enough to have a "scrambling" effect on the short ROH variation of the African side of their ancestry, so Eurasian short ROH just gets straight added on to their totals?

    And I liked this last sentence of your post: "OoA populations are not simply a bottlenecked version of African populations alone but descend from a parallel population history from the true ancestral population Africans also descend from, with a harsher bottleneck in OoA." This aligns well with what we've seen in several studies the past few years positing deep divergence times between Africans and Eurasians as far back as 100,000 years ago, well before the great OoA bottleneck typically dated 50,000-70,000 years BP.

    0
  13. Slight update to my comment above re “Extensive ethnolinguistic diversity in Vietnam…”, there actually is a table of populations, giving the population each number corresponds to, in their supplement, so placing this side by side with the PCA makes it easy to see which populations are present: https://imgur.com/a/Sqkve2T

    For example pop 73 is Han_NC, 74 is Han_SC, and 78 is Lahus, so you can see many of those Sino-Tibetan speakers from China in the plot who do cluster fairly closer to Kinh than Han_NC are from the Han_SC cluster and not just Lahu (but this population label also has a fair few samples who are much closer to Han_NC cluster). Thai population from Vietnam is close to Dai speakers, without the additional drift towards India in the Thai_T (Thailand) samples labelled in red. Etc.

    0
  14. On kin competition, the link says “By forming social groups of non-kin, females increase their chances of successful reproduction, while avoiding the indirect fitness cost of competition among sisters.

    One Sentence Summary: We describe the first known example of an animal society based on avoidance of kin competition rather than on promotion of kin cooperation.”

    First known example, but it might be an explanation of how unrelated female bonobos cooperate to dominate males, all of whom are related.

    0

Leave a Reply

Your email address will not be published. Required fields are marked *