This will be part of David Anthony’s new book for sure…
Back migration into Africa by Eurasians
Two preprints/papers.
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals:
Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.
Basically, this paper concludes that Eurasian back-migration related to Europeans/West Asians seems to be around 30% of Sub-Saharan African ancestry. They carry about 30% of the Neanderthal ancestry of Eurasians.
Then, a preprint that uses a pretty sophisticated method, Ancient Admixture into Africa from the ancestors of non-Africans:
Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.
This paper estimates 35-40% back-migration from the ancestral proto-Eurasian population, with less (~20%) in African hunter-gatherers. This paper didn’t detect Neanderthal ancestry and argues that the back-migration predates the West vs East Eurasian split. It plausibly argues African effective population sizes are inflated by the admixture event.
The two results here clearly contradict the details.
Recent human origins in 2021
I wrote three long pieces for my Substack:
- Yo mama’s mama’s mama’s mama… etc.
- Our African origins: the more we understand, the less we know ($).
- What happens in Denisova Cave stays in Denisova Cave… until now ($).
I’m thinking about where I’m going to go in relation to this topic, and i think it may be in the direction of Eurasian back-migration to African and what we know now.
Also, I’m at nearly 60 podcasts after more than a year of the Substack. Please remember to rate it positively.
What Sahul tells us about world genetic history
The paper Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul came out a few months ago. It’s fine. But one thing jumped out at me:
All estimated effective population size curves show a bottleneck around 60–70 ka, as found for European and Asian populations (supplementary fig. 16, Supplementary Material online). Around 50 ka, estimated effective population sizes for populations from Wallacea and Sahul are between 1,671 and 2,100 individuals, and between 2,540 and 2,999 individuals in Eurasia and 9,506 individuals in Africa. All divergence dates for Wallacea/Sahul groups from Africa, represented by Yoruba genomes, show similar results (74 ± 4.2 ka, supplementary fig. 17, Supplementary Material online). We note here that this date is older than that obtained between Eurasian and African genomes (66.5 ± 3.7 ka), a result previously reported and interpreted as a potential methodological bias or the signal of an even earlier human migration from Africa (Malaspinas et al. 2016; Mallick et al. 2016; Pagani et al. 2016; Bergstrom et al. 2017).
First, the bottleneck precedes the massive expansion after 60 ka. Second, perhaps there was Eurasian back-migration into Africa and that’s impacting the difference coalescence dates? Basically, the Yoruba can be thought as a population strongly influenced by “out-of-Africa” gene flow.
Women at war
The new Wheel of Time television show has a scene where an Aiel woman totally smashes a half a dozen male soldiers with her skilled usage of her spears (this deployment of spears comes from the books, where the Aiel women do fight). The scene was well done overall, and some pathos was added by the fact that she was in labor (this is from the book too). But watching it I couldn’t help but think of this piece, Male and Female Athletic Performance: Worlds Apart. Here’s a relevant chart:
Here are the ones that jumped out to me re: male strength advantage:
– Grip strength, 57%
– Total upper strength, 90%
– Punch power, 162%
It’s a fantasy TV show. But I really hope that people aren’t taking the wrong lessons from this. I remember here some idiotic Late Night TV show host asking Scarlett Johansson how she fought so well, and ScarJo laughed it off and said “they make me seem tough,” as she found the question ludicrous.
Open Thread – 12/11/2021 – Gene Expression
Peggy Mohan’s Wanderers, Kings, Merchants is a strange book for a reader of this weblog. The author is really fixated on retroflex consonants, but she’s also aware of the latest archaeogenetic work. It’s a pretty academic work, and if you aren’t interested in questions like how Sanskrit evolved along with early Dravidian languages, it’s not for you, but I think Mohan’s book illustrates a possible future for synthetic interdisciplinary research. I’d like to see more of this.
Defund the Police Meets the Crime Wave. Crime is coming close to my friend’s Leighton Woodhouse’s life (he lives in Oakland). It looks like the Democrats really want the Republicans to win again on “tough on crime.” This shit is not sustainable.
There is now a TV series based on The Wheel of Time. I haven’t read these books since I was a literal teenager, and I do not personally feel the source material is rich enough to really produce anything comparable to Game of Thrones. Obscure fact: this series is set in our far future, in a post-apocalyptic world.
The Man in the Lineup – Alice Sebold’s best-selling account of her own rape was headed for the big screen. Then the film’s unlikely producer started asking questions. The author of The Lovely Bones isn’t going to live this down.
Charles C Mann recently appear ed on the UL podcast. We talked for nearly an hour and a half; there is a lot to talk about. Please rate the podcast on Apple or Stitcher. One thing Charles mentioned to me privately is that it was fun to talk to me because I’d read his books and actually knew his writing. That struck me as funny, but it’s not like I’m Terry Gross, I don’t just talk to anyone. Usually, I am interested in talking to the person for a reason.
Thanksgiving squabbles are a feature, not a bug – How eternally unsettled debates are the lifeblood of the republic. This is on my Substack.
Dark Horse out of the Steppe – Fishing the Sintashta, Scythians and Sarmatians out of obscurity.
Ten Thousand Years of Patriarchy
Alice Evans has a long write-up of some of her ideas about the origins of patriarchy, Ten Thousand Years of Patriarchy:
Patriarchy has persisted for at least ten millennia. Cereal-cultivation, the plough and irrigation increased agricultural yields, enabling a taxable surplus, state-formation and social stratification across much of Eurasia. Land and herds were inherited by men, who maintained lineage purity by guarding women.
Eurasia then underwent an important divergence. South Asia and the Middle East saw tightening endogamy (caste and cousin marriage), alongside religious authoritarianism. The more visible the woman, the greater the suspicion and moral ambiguity. By preventing rumour, men preserved piety, honour, and inclusion within vital kinship networks. East Asia remained exogamous, while Europe became increasingly nuclear, democratic, and scientific. But as long as women laboured on family farms (lacking both economic independence and their own social organisations), this global variation in kinship, institutions and religion may not have made an enormous difference.
I was one of the people Alice corresponded with, so I knew the general outlines, but this is a massively interesting effort, and work in progress.
How much smarter are white Democrats than white Republicans?
In the conversation between Coleman Hughes and Charles Murray, there was a point where they mooted the idea that white Democrats are smarter than white Republicans. Since the realignment of the Trump era, this seems to be a major issue, as college-educated white Democrats have become more Democrat and liberal, while non-college whites less so.
I’ve looked at this before, but I’ll look at it again, using GSS’s WORDSUM variable. Correlating with IQ at 0.70 the vocab test is decent if imperfect. I looked at the distribution in non-Hispanic whites from 2016 onward (race(1) hispanic(1) year(2016-*)) for WORDSUM, and broke it into the bottom 30%, middle 50%, and top 10%. Then I looked at distributions within each political/ideological class (column) and the proportions of each political/ideological class within the vocabulary bracket.
| Row = 100% | Column = 100% | ||||||
| 30th% in vocab | 60th% in vocab | 10th% in vocab | 30th% in vocab | 60th% in vocab | 10th% in vocab | ||
| Lib | 22 | 58 | 20 | 19 | 27 | 45 | |
| Mod | 38 | 54 | 8 | 43 | 32 | 25 | |
| Cons | 30 | 61 | 9 | 39 | 41 | 31 | |
| Dem | 27 | 57 | 16 | 31 | 37 | 53 | |
| Ind | 43 | 46 | 10 | 23 | 13 | 15 | |
| Rep | 31 | 61 | 8 | 46 | 49 | 32 |
Stem-human gene flow into Neanderthals
The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals:
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.
The standard model is that 500-750,000 years ago the ancestors of African (modern) stem humans and Neandersovans diverged, and that’s that before the recent admixture and assimilation. But it’s pretty clear there were contacts between stem lineage and Neandersovans before the recent expansion of the African lineage. Neanderthals acquired lots of neat genes from our lineage, and we probably acquired stuff from them too.
(note that I think there were old modern lineages that disappeared)
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…