Out of Africa

[pmokeefe]

This video from Jan 2022 discusses the "Out of Africa" theory.
Seminar by Professor Chris Stringer: Some current issues in the later stages of human evolution.

[Asjkqwop774]

What are the datasets/software used for that graphic?


How about technical issues like correction for admixture?

More technical issues with f3 statistics here.

What happened to eurasiadna, are they banned or smth, I can't click on their profile.. Anyways, I thought that all modern humans should be equidistant from chimpanzees given the split time from all modern humans to chimps is the same w/ 0 post-split admixture and that any difference in divergence from pan is due to individual-level, chance mutation, so how on earth could any "population" be closer or further, and is the difference statistically significant

[Asjkqwop774]

f3 outgroup tells how close 2 populations are to each other?

[Billyh]

f3 outgroup tells how close 2 populations are to each other?

Relative to how close they are to another population, I believe so.

[Billyh]

What happened to eurasiadna, are they banned or smth, I can't click on their profile.. Anyways, I thought that all modern humans should be equidistant from chimpanzees given the split time from all modern humans to chimps is the same w/ 0 post-split admixture and that any difference in divergence from pan is due to individual-level, chance mutation, so how on earth could any "population" be closer or further, and is the difference statistically significant

I've always heard that equatorial populations went through less mutations than populations in different climates than chimpanzees, which is why Africans and Onge are ever so slightly closer to Chimpanzees. It was a thing people did sometimes on GEDMatch with the primate samples, usually just to troll. Doesn't really make a lot of sense in hindsight though as only a small portion of our DNA has been connected to phenotypic traits, and all of the phenotypic differentiation we've gone through in the past 4 million years seems to just completely make that irrelevant.

Screenshot 2022-11-28 221559.png

[Kale]

I've always heard that equatorial populations went through less mutations than populations in different climates than chimpanzees, which is why Africans and Onge are ever so slightly closer to Chimpanzees. It was a thing people did sometimes on GEDMatch with the primate samples, usually just to troll. Doesn't really make a lot of sense in hindsight though as only a small portion of our DNA has been connected to phenotypic traits, and all of the phenotypic differentiation we've gone through in the past 4 million years seems to just completely make that irrelevant.

I have nothing to back it up, but my first thought intuitively would be immune system. I bet a good chunk of DNA is devoted to that.
New environment (Eurasia) requires new immune system adaptations, distancing Eurasian populations from tropical primates and humans who's immune systems would retain some similarities due to similar environment?

[pmokeefe]

I have nothing to back it up, but my first thought intuitively would be immune system. I bet a good chunk of DNA is devoted to that.
New environment (Eurasia) requires new immune system adaptations, distancing Eurasian populations from tropical primates and humans who's immune systems would retain some similarities due to similar environment?

A few papers on human adaptations to tropical rainforests:
Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest (2019)

Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers (2018)

Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia (2022)

Note that there are a wide variety of habitats in both Africa and Eurasia and there have also been wide swings in climate in the past 100,000 years ( multiple "green Sahara"l periods; periods with drastically smaller tropical rainforests, etc).

[TuaMan]

I have nothing to back it up, but my first thought intuitively would be immune system. I bet a good chunk of DNA is devoted to that.
New environment (Eurasia) requires new immune system adaptations, distancing Eurasian populations from tropical primates and humans who's immune systems would retain some similarities due to similar environment?

I believe there is some indication of positive selection on Neanderthal variants in Eurasians that are related to immune response. However, I wonder if relaxed selection in OoA was more important in terms of differentiaton between OoA and Africa. Tropical Africa has loads of serious infectious diseases - malaria, sleeping sickness, dengue and yellow fever, roundworm, etc. That intense of a disease burden would put a constraint on different paths natural selection could go, since any variation that cropped up that either dinged immunity against those diseases in some way, or even if neutral, would get naturally selected against very quickly. In OoA though, that intense selective pressure would mostly go away, so evolution could proceed in different ways.

Some good, comparative exome sequencing looking for evidence of natural selection over the past 50,000-60,000 years in Eurasians and Africans would be interesting in this respect.

[DudeTheDud]

I've always heard that equatorial populations went through less mutations than populations in different climates than chimpanzees, which is why Africans and Onge are ever so slightly closer to Chimpanzees. It was a thing people did sometimes on GEDMatch with the primate samples, usually just to troll. Doesn't really make a lot of sense in hindsight though as only a small portion of our DNA has been connected to phenotypic traits, and all of the phenotypic differentiation we've gone through in the past 4 million years seems to just completely make that irrelevant.

Screenshot 2022-11-28 221559.png

Eurasians slightly Neanderthal shifted, Oceanians slightly Denisovan shifted compared to Eurasians. Makes sense. What paper is this from?

[Asjkqwop774]

I've always heard that equatorial populations went through less mutations than populations in different climates than chimpanzees, which is why Africans and Onge are ever so slightly closer to Chimpanzees. It was a thing people did sometimes on GEDMatch with the primate samples, usually just to troll. Doesn't really make a lot of sense in hindsight though as only a small portion of our DNA has been connected to phenotypic traits, and all of the phenotypic differentiation we've gone through in the past 4 million years seems to just completely make that irrelevant.

Screenshot 2022-11-28 221559.png

Sorry I reply kinda late, I don't go here that often. I think the PCA with Africans closest to chimpanzees, Eurasians (-Oceanians) intermediate, and Oceanians furthest is because the PCA is defined by neanderthal/denisovan variation. Since Oceanians are high in archaic ancestry, they share more derived alleles with neanderthals/denisovans so are shifted right on the axis, and Africans lacking or having very little neanderthal/denisovan ancestry do not share as many derived alleles with them so are closer to chimp on there. Regarding the gedmatch thing, could the fact that these primates score like 90%+ SSA be due to the fact that these populations have the largest gene pool/genetic diversity? Since these calculators aren't designed to work on non-humans, so the populations that have the largest gene pools on these calculators end up as "dumpster bins" for any ancestry that doesn't fit well with any of the components, kinda like how neanderthals/denisovans also score mostly SSA even though they are closer to Eurasians or how ancient Eurasian samples sometimes score SSA noise. Onge being closer to chimp is new to me, as far as I know they are standard Eurasian and one of the most bottlenecked groups on Earth.