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Angela
23-12-18, 16:45
It's a very interesting paper. Why'd they have to drop it now? :)

See:
Laurits Skov et al

https://www.biorxiv.org/content/biorxiv/early/2018/12/21/503995.full.pdf

"Strong selective sweeps before 45,000BP displaced archaic admixture across the human X chromosome"

"The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust'-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event."

From Lazaridis:
"A very intriguing paper by @SkovLaurits (https://twitter.com/SkovLaurits) et al.. Could Basal Eurasians be the non-Neandertal-admixed pop. that contributed to Ust'Ishim? If so, all non-Africans could have some fixed B.E. ancestry (and a few in the Near East extra B.E. above the baseline)."

bicicleur
23-12-18, 19:55
So, after our forfathers mixed with Neanderthals somewhere in SW Asia, they went to another place where they mixed with mondern humans with these mutations in the X-chromosome but without Neanderthal admixture, and only after this 2nd admixture event, they spread all over Eurasia?

There were modern humans in Europe, like the Bohunician and the Perigordian since +/- 48 ka, but they probably went extinct when Aurignacians expanded.
Aurignacians arrived in Europe around 44 ka and expanded all over Europe around 39 ka, replacing earlier modern humans in Europe.
The earliest modern humans in Europe might not have had these X-chromosome mutations, while Aurignacians (and early Kostenkians ca 42 ka) did.

Would a combination of diluted Neanderthal admixture and X-chromosome mutations have given our forfathers the ability to replace all other humans in Eurasia?

Angela
23-12-18, 20:08
So, after our forfathers mixed with Neanderthals somewhere in SW Asia, they went to another place where they mixed with mondern humans with these mutations in the X-chromosome but without Neanderthal admixture, and only after this 2nd admixture event, they spread all over Eurasia?

There were modern humans in Europe, like the Bohunician and the Perigordian since +/- 48 ka, but they probably went extinct when Aurignacians expanded.
Aurignacians arrived in Europe around 44 ka and expanded all over Europe around 39 ka, replacing earlier modern humans in Europe.
The earliest modern humans in Europe might not have had these X-chromosome mutations, while Aurignacians (and early Kostenkians ca 42 ka) did.

Would a combination of diluted Neanderthal admixture and X-chromosome mutations have given our forfathers the ability to replace all other humans in Eurasia?

I've only skimmed it (I'll read it in depth after Christmas), but that's what it seems like to me. What selective pressure drove these mutations, however, so that they overwhelmed this "archaic" admixture? In other words, what do they "do"?

bicicleur
23-12-18, 20:19
I've only skimmed it (I'll read it in depth after Christmas), but that's what it seems like to me. What selective pressure drove these mutations, however?

it's a 3 stage expansion : out of Africa, out of SW Asia, out of India, and the latter were our forfathers

and yes, we got rid of a lot of Neanderthal DNA, not only by drift and natural selection, but also by admixture with other modern humans

Angela
23-12-18, 20:46
it's a 3 stage expansion : out of Africa, out of SW Asia, out of India, and the latter were our forfathers
and yes, we got rid of a lot of Neanderthal DNA, not only by drift and natural selection, but also by admixture with other modern humans

Still, what replaced it had to be more advantageous, yes?

Razib Khan has posted on it.

See:
https://www.gnxp.com/WordPress/2018/12/23/drivers-of-the-selection-for-ghosts-in-the-genome/?utm_source=dlvr.it&utm_medium=twitter

The other alternative seems to be that it's really archaic ancestry on the X which came roaring back after the admixture with Neanderthals and erased the Neanderthal signal?

"We hypothesize that our observations are due to meiotic drive in the form of an inter-chromosomal conflict between the X and the Y chromosomes for transmission to the next generation. If an averagely even transmission in meiosis is maintained by a dynamic equilibrium of antagonizing drivers on X and Y, it is possible that the main bottlenecked out-of-Africa population was invaded by drivers retained in earlier out-of-Africa populations. If this hypothesis is true, the swept regions represent the only remaining haplotypes from such early populations not admixed with Neanderthals."

"This strange evolutionary genetic process then may have preserved a genetic relic within the human genome. But on Twitter Iosif Lazaridis (https://twitter.com/iosif_lazaridis/status/1076558671713390592)suggests that perhaps the donor population were “Basal Eurasians,” and all non-Africans may have some Basal Eurasian ancestry, with Near Easterners exhibiting more than baseline ancestry (presumably through later admixture)."

Either way, these alleles were clearly more advantageous, and still would like to know what they control.

Some good stuff in there about the X. I don't know enough about the X, and have to remedy that.

Gnarl
02-01-19, 13:54
Well, Basal Eurasians I or II would seem to be the go-to for this one. I am not sure why the primary theory seems to be introgression from a previous out-of-Africa event, would not a second migration out of Africa be more plausible? Or are the introgressing genes more divergent?

Is it possible that the replaced genes were Neanderthal or other archaic genes that had poor compatibility with our genes?

berun
02-01-19, 14:56
Maybe the answer is more simple, maybe as happens many times in many regions there were 'clans' which mixing with 'locals' and others that prefered to set up an apartheid-like system. If the admixed clans would fit less in the ecosystem their DNA would go in such a way, well X is like another continent.

halfalp
02-01-19, 18:51
What's really frustrating about Neanderthals, the closest Sapiens we have admixed with Neanderthal to almost 11% of his Genome is Oase 1, and this guy, didn't countribute at all to modern humans... Other than that, we have multiple individuals that shows Neanderthal Genome, but way after Neanderthal dissapear, so we dont have any clue, when, where and with who admixture happened. The same goes with Denisova into Papuans, did they mix with a Southeast Asian Denisovan or with an Altai-related one. Those are questions that interest me a lot. Because looking at Native Americans and East Asians part of Neanderthal, it's definitly not just Oase 1, or Ust-Ishim. We missed a magnificient proxy that could be exciting.

bigblob
06-01-19, 13:01
Neanderthal hybrid was found in Portugal and dated 24 000 years:

https://en.wikipedia.org/wiki/Lagar_Velho_1

bicicleur
06-01-19, 15:13
Neanderthal hybrid was found in Portugal and dated 24 000 years:

https://en.wikipedia.org/wiki/Lagar_Velho_1

I'm afraid this info is outdated.

bigblob
07-01-19, 12:34
Well there is a lot of controversy about the Lapedo child, with one lot claiming the Lapedo child is a modern human with Neanderthal affinities. Others claim its a Neanderthal/modern human hybrid.