That Neanderthal question.

slowburner · 10-05-2014 11:39am

Some intriguing reconstructions of various hominids. There is a selection to view in the slideshow towards the end of the page.
http://www.smithsonianmag.com/science-nature/bringing-human-evolution-life-180951155/?no-ist

slowburner · 20-06-2014 10:40am

The Spanish team believe the more primitive population could be an ancient human species called Homo antecessor, which lived in Europe around one million years ago. “They could be the stem group before the split between Neanderthals and modern humans,” Prof. Arsuaga said.

http://www.thehindu.com/sci-tech/science/neanderthal-faces-emerge-from-gloom-of-spanish-cave/article6132901.ece

dubhthach · 20-06-2014 10:48am

That's based purley on mtDNA. The sample from Spain (400k old) is probably Homo heidelbergensis

dubhthach · 03-07-2014 11:15am

It appears that Tibetans get their high altitude "tolerance" from the Denisovans.

http://arstechnica.com/science/2014/07/tibetans-altitude-tolerance-may-have-come-from-our-extinct-relatives/

http://www.unz.com/gnxp/a-vindication-of-multi-regionalism-in-adaptation-not-ancestry/

slowburner · 24-06-2015 9:45am

Modern human had a recent Neanderthal relative.

See here

Wibbs · 24-06-2015 1:43pm

Another aspect I've wondered about and it doesn't seem to come up at all, is do any late Neandertal samples show modern human sequences? Was the gene flow all one way? I'd be very surprised if it was. Though generally speaking in such societies it's usually the women who move from group to group. So AMA woman moves in with Neandertals and Neandertal women move in with the AMA's. I recall reading that the flow seems to have been from their men to our women, maybe our guys to their gals didn't produce(or rarely) viable young? It seems that while we clearly could have kids together we were sufficiently distant that such pairings caused viability issues in successive generations.

Regardless more and more my previous contention that these weren't rare and isolated events is looking likely. I'd bet it was happening pretty often, but the dilution of their legacy has sped up(maybe since agriculture kicked off). If you go back to relatively recent ancient DNA in the three odd thousand year old Otzi the iceman he has much higher Neandertal admixture than people related to him living today, or anyone else. 6-7% IIRC. Ye he was "only" 3000 years closer to the event(s), an event that going on current knowledge would have been over at the latest by 20,000 years ago. This latest 40,000 year old dude had nearer 9% and more importantly whole chunks of intact Neandertal sequences. Again it'll be interesting to see if any late Neandertals show up with our gene's in them. After all the hook up that shows up in 40,000 year guy's genes would have resulted in the first generation of kids being more 50/50 percentage wise. OK genes don't work that precisely at all, you could have one kid with one kid with 80% and another with 10% of either parent, but still, if one of those kids were sequenced they could look like a Neandertal with lots of AMA genes.

The social aspect would be fascinating with these "mixed marriages". How were they regarded, how were the kids regarded? Where they integrated, or where these couplings the result of outcasts from both groups hooking up? Sadly that's something we'll likely never get even a sniff of.

dubhthach · 24-06-2015 8:23pm

I could be wrong but I recall a discussion at some stage which proposed that Male Neanderthal/Female Homo Sapien cross could have potential issues due to Neanderthal skull shape versus Homo Sapien hip structure. Of course any hybrid would be intermediate in form between both parents.

tac foley · 24-06-2015 8:29pm

Trust me on this one - you only have to walk down the high street in our local town to see the results of this cross-breeding at first eye.

The Neanderthaler hasn't gone away, he, AND she, are still very much with us.

tac

slowburner · 27-11-2018 12:44pm

Neandertals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neandertals and humans interbred, as evidenced by Neandertal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neandertal ancestry is ∼12% higher in East Asian individuals relative to European individuals.

Full text (pdf) here;
https://www.biorxiv.org/content/biorxiv/early/2018/08/30/343087.full.pdf

Wibbs · 27-11-2018 6:26pm

East Asians also show Denisovan genes and again at high enough percentages(IIRC some populations show up to 10%). Which along with other research seems to show that the older idea that we only got it on on occasion and rarely is not the full story and it looks more likely that there were quite the few hanky panky events going on throughout Eurasia. Which makes much more sense. Humans of any sort were rare in the landscape back then, mating choices would be limited enough. Paleo folks of all types show quite narrow genetics and even physical evidence in the bones of genetic defects higher than normal for today and later populations.

*aside* those Andaman islanders who killed the American that were in the news last week. One bit I noted in one report was that Andaman islander genetics showed no Denisovan ancestry, though their genetics weren't "African", but more related to the Asians more locally to them. I can't find any data on Neandertal admixture. Now if they don't show Denisovan and they colonised the islands between 15-20,000 years ago(not 60,000 as most outlets report) what's going on there? Where they part of a group that stayed along the coasts, never went inland and met Denisovans, while those they left behind went inland and did and that's why they have their genes? Or is it possible Denisovans might have been around after 20,000 years ago and the Andaman folks were out of the mix by then? Might explain the higher levels of Denisovan genes in modern Asian populations. They are closer to the admixture event.

It also brings up musings like though Andaman folks look far more African than Asian today, that maybe back then Asians looked more like Africans and the phenotype we think of when we think of Asians is a more "recent" thing? After all going on current genetic clocks and research, blond hair in modern Europeans is only around about 15,000 years and blue eyes isn't that much older(Some Neandertals appear to have had pale eyes and light, even red hair, but they're different genes to ours)

dubhthach · 27-11-2018 10:33pm

Tibetans carry a specific gene variant which is advantageous for living at attitude (Tibetan plateau and all that). It would seem that basically they have undergone selection for this variant due to the advantage it gives them. Anyways it originates in Denisovan's. In other populations with partial Denisovan ancestry (such as Melanesians) this specific variant wasn't perserved as it didn't offer any evolutionary advantage in context of Pacific islands.

tac foley · 29-11-2018 10:37pm

So, too, do Peruvians. Genetically optimised to live at great altitudes, their blood has more oxygen-carrying capacity, their lungs have great volume and many other 'modifications', to enable them to 'linve long and prosper' above 10,000 feet.

Wibbs · 29-11-2018 11:50pm

Yep as you say Tac Peruvians have a similar suite of genes from the Denisovans as the Tibetan and Nepalese. Funny enough, of the populations so far sampled Peruvians show the most Denisovan and Neandertal genes and with longer sequences to boot of all. They're the most genetically distinct from African populations. They also show much less admixture with colonising peoples from Europe compared to other Native South American populations. They look like the "purest" population most related to the first settlers in the Americas. Which might explain the archaic levels going on. Their ancestors would have been close to, or even had the oul dance with no pants with archaics in their original homeland. But because their ancestors made it to Peru and were then much more isolated from other Native Americans, held onto more of their archaic genes.

dubhthach · 07-01-2019 2:45pm

Relevant video. It's just over an hour long:
Ancient DNA and the New Science of the Human Past -- November 2018 at Havard

he covers European population dynamics from 32m in, he gets to population turnover in Britain and Iberia around 48m+ (references various papers)

Poor Uncle Tom · 07-01-2019 8:58pm

Brilliant, I'd love to see an overlay of archaeological events and would like to see if there are any other large migratory events.

dubhthach · 08-01-2019 11:10am

Poor Uncle Tom wrote: »

Brilliant, I'd love to see an overlay of archaeological events and would like to see if there are any other large migratory events.

Well it would seem the transition to Bronze age was the last time there was major population turnover in Europe. After that it's probably a case that various peoples moving around are actually very alike. After all there isn't a huge amount of difference between various Europeans.

There was a recent paper about Germanic migration in post-Roman period, what will be interesting is when we start seeing samples from say the Balkans covering the post-Roman period given the large scale Slavic migrations that are known both from history and linguistically (some would argue that mainland Greeks are shifted towards Poles for example due to this)

From an Irish point of view we are still waiting on paper with regards to 50+ genomes covering Mesolithic, Neolithic, Bronze and Iron ages. It would seem the PhD attached to it was awarded, but thesis is embargoed until 2020 probably until scientific papers are published

http://www.tara.tcd.ie/handle/2262/82960
A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory

Abstract:
This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH). Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time.

Poor Uncle Tom · 08-01-2019 1:15pm

No longer the case of looking for the 'missing link' it's now a case of uncovering the hidden chain.

The fantastic irony, that it's taken until very recently (10 - 12 years ago) to prove interbreeding between modern humans and Neanderthals actually happened and to see the evolving theories being proven / disproven so quickly since.

That Neanderthal question.

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