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Wednesday, September 21, 2016

Two pronged AMH colonization of Eurasia. Or not


A robust but healthy debate by proxy between three teams of population geneticists over at Nature today. Emphasis is mine:

Absract: High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations (2, 3, 4, 5) or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history (7, 8, 9) and refuelled the debate on the mutation rate in humans (10). Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record (11), and admixture between AMHs and Neanderthals predating the main Eurasian expansion (12), our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Pagani et al., Genomic analyses inform on migration events during the peopling of Eurasia, Nature, Published online 21 September 2016, doi:10.1038/nature19792

...

Abstract: Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Mallick et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations, Nature, Published online 21 September 2016, doi:10.1038/nature18964

...

Abstract: The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Malaspinas et al., A genomic history of Aboriginal Australia, Nature, Published online 21 September 2016, doi:10.1038/nature18299

46 comments:

Poise n Pen said...

Aside from a couple genes for malaria resistance, not a single eurasian gene is proven to come from africa and not a single african hominid has a higher brain capacity than contemporaneous eurasian hominids.

All we have to do to prove multiregionalism is find a dozen archaic introgressions of 2-3%. From there we can assume a similar amount of genes common to people today have those hominids as their source especially when they are localized to the same ranges. And that's it, we're done.

And we are already halfway there if not more. But people are easily propagandized unfortunately.

Davidski said...

How many bottles of wine have you had tonight? Be honest.

Poise n Pen said...

On a Wednesday evening? None. I don't drink very often anyway.

I'm guessing that's not the case in the Davidski household, or do you have a list of genes that have been proven African in origin by sequencing ancient African remains and finding them there long before they are found in Eurasia? Yeah, didn't think so.

It's just ironic you make fun of Dienekes when you are even more clueless than he is, even Genetiker is much more rational than you are. No one comes to these blogs for your opinions, they just come because they are grateful someone has the time on their hands to repost this stuff so we don't have to click refresh 10 times a day ourselves.

Grey said...

"We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa."

"We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans."

"We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations."

I wonder if a back migration might square the circle with instead of Papuans, Aborigines, Andamanese being relics of the original OoA wave they were part of the back migration also but have more of the original wave than others cos it suited their environment.

Onur said...

Here is a Nature review of the three Nature papers:

http://www.nature.com/articles/nature19472.epdf?referrer_access_token=P5ZuMuU3hn-i93nGnnt7cNRgN0jAjWel9jnR3ZoTv0ML7dYwCLLpnSW3wDC4QFcgpM-K9D0-ftY45S22EestXcP0LYhMKzjdkxQ838hNNLQxOPIi3Oi7XVNmg5TN1r_HLbKVaIYk-l3RXVT203JyS_7iS1MOKgG4F0zBgeQ6hUJ8JpQ-8sdQ77Fn_8IWrkx-ourp6166xoBfYV1ZAmYgCx1m2YdVQPpO0282oDjKtPh8KqzesBpw6The9YxlDg3u&tracking_referrer=www.nytimes.com

MomOfZoha said...

@Davidski:

Is there any population that has a Papuan component WITHOUT Ancestral South Indian (ASI) component -- aside from Papuans themselves? Preferably, is there any such population that might have any relevance to (Anatolian or non-Anatolian) Turks and/or Near Easterners?

I need to know since my dad has non-negligible Papuan contribution with zero accompanying ASI (his other zero is sub-Saharan), and lack of aforementioned population in spreadsheet screws my analytical admixture analysis (giving too high distance). These are from Gedrosia Near East Neolithic K13 project of GEDmatch, whose accompanying spreadsheet did not have any population matching constraints in my original question.

I put "this stuff" aside for months but since you mention Papuans now, it suits my present procrastinations... Thanks.

Davidski said...

I can't comment about results from other projects, because I'm usually not very familiar with their tests.

So what are you seeing for your dad using the Eurogenes calcs?

MomOfZoha said...

@Davidski:
*This* is my father's results from Eurogenes K13 project that I had previously recorded:
1 West_Asian 29.06
2 East_Med 26.69
3 West_Med 14.86
4 Red_Sea 7.59
5 North_Atlantic 7.58
6 Baltic 5.23
7 Siberian 4.65
8 South_Asian 2.13
9 Oceanian 1.06

And *his* top min-distance 4-way admixture results from same project have too high distances:
1 Georgian + Nogay + Samaritan + South_Italian @ 3.267398
2 Algerian_Jewish + Georgian + Nogay + Syrian @ 3.401815
3 Georgian + Nogay + Samaritan + Sephardic_Jewish @ 3.491206
4 Georgian + Nogay + Sephardic_Jewish + Syrian @ 3.542657
5 East_Sicilian + Georgian + Nogay + Samaritan @ 3.544914

Davidski said...

A lot of people get some Oceanian noise, usually less than 1%, but sometimes a bit over. This is probably just archaic or really ancient ancestry that doesn't fit well into any of the other clusters.

I'd say the inflated distances in those models are mostly caused by a bit too much Siberian for someone from the Near East. But again, I can't see anything really out of the ordinary there.

postneo said...

@grey
"I can't speak to any vedic or sanskrit connection but they probably get the general idea from stuff like this.
https://en.wikipedia.org/wiki/Norse_funeral#Ibn_Fadlan_account"

interesting, thanks, this is a medieval post islamic account. Humans tend to do similar things over time, we cannot always lump them as common culture. Moreover these are 2500-3000 years removed from andronovo.

In india also there was sati probably starting 550 AD where wife joins husband for cremation. These are not vedic by any stretch. In fact brahmins seemed to have frowned on such holier than thou "high honor" practices before doing it themselves later on.

there was also the practice of Jauhar later in india which had some shades of ritual suicide Seppuku/ hara-kiri part of medieval Japanese bushido. During islamic invasions there are accounts of all males in a kingdom fighting to their death while the female population jumps in bonfires. These are highly eulogized events..

The more important point though ....kurgan or Egyptian type burials of rulers with chariots and grave goods is anti-vedic so to speak. Only people who have renounced wealth and family ever got buried. It is a high honour ritual, but with no grave goods.


There is a cottage industry of spurious andronovo and vedic links.

MomOfZoha said...

@Davisdki:

"A lot of people get some Oceanian noise, usually less than 1%, but sometimes a bit over. This is probably just archaic or really ancient ancestry that doesn't fit well into any of the other clusters.

I'd say the inflated distances in those models are mostly caused by a bit too much Siberian for someone from the Near East. But again, I can't see anything really out of the ordinary there."

BTW, my Dad's Papuan was 2.6% in the Gedrosia Near East Neolithic K13, and his Polar was higher than his Siberian (yours looks like the summation of Polar+Siberian). Interestingly, my Mom has even more Siberian (6.35%) than my Dad from your project, as well as a little bit "Amerindian" (1.24%) -- though you might not tell "phenotypically". Of course, Turks are expected to have more Siberian than their non-Turk Near Eastern neighbors. I don't know if my family has more Siberian than the average Anatolian Turk, though being from Central Anatolian villages it is possible. Yet, *none* of their haplogroups are particularly "Altaic" BTW...

I get what you are saying though. Being around (for example) 12.5% "Altaic" in an otherwise Near Eastern area would totally screw with a 4-way admixture oracle that requires equal 25% contributions. Probably also the reason why some other (totally unexpected btw) components are arising in compensation. Not that I have a problem with those if we really are "so Levantine", if you know what I mean. I wouldn't mind being a good Samaritan.

Davidski said...

Yeah, you'd need population samples from across Turkey to get more coherent models for your parents. Because, as you probably know, there are huge differences between some Turkish regions, particularly in the types and levels of Central Asian ancestry.

Onur said...

@Davidski

there are huge differences between some Turkish regions, particularly in the types and levels of Central Asian ancestry.

That is because the Central Asian genetic contribution is the most recent notable genetic contribution to the genepool of the area of modern-day Turkey, so it has had less time and opportunity to attain a uniform distribution level within the genepool than the other notable genetic contributions to the genepool.

Karl_K said...

It could be that the Denisovans admixture of the population in question was actually from a population of Denisovans that had hybridized with an early wave Out Of Africa population of 'modern humans'.

We know that African-like modern humans admixed into the Altai Neanderthal population. We know that Altai-like Neanderthals admixed into the Altai-Denisovan population. So it isn't a stretch that there would be groups of Denisovans with 30% early wave Out Of Africa admixture.

This could cause the confusion. What one group lumps completely into Denisovan, another divides into pieces.

Both could be correct.

Awale Abdi said...

Kind of a hilarious coincidence given my most recent post. I'd say the whole "earlier dispersal" idea is dead. These guys are clearly part of the "Eurasian-bottle-neck" and then some... But, it is possible that they draw just a bit of their ancestry from very early migrants to the region who weren't part of the E-bottle-neck.

@ Onur

This is off-topic but; could you link me to a very large variant of your avatar? That looks like a nice picture.

Kurd Dgk said...

To clarify, they are suggesting a 2% genetic contribution to Papuans from a group basal to African Pygmies, W Africans, and E Africans, that left Africa as early as 120 kya. This in addition to contributions from Denisova and Neanderthal, making Papuans the most exotic modern group.

Karl_K said...

@Kurd

There js no doubt that they are the people with the most 'exotic' ancestry of people alive today. This has been clear for quite a while.

The point of the post is whether or not they have 'early out of africa' ancestry.

If you read the papers, even the ones that dismiss it say things like, "we obtain an upper bound of a few per cent for the possible contribution to Australians and New Guineans".

And that is exactly what was the conclusion of the paper that went with it as well.

So. After reading all the papers and supplements, it looks like there could be a chance that these populations have a tiny bit of early out of africa ancestry.

The main problem is that we have no genetic data from direct ancestral groups. This makes it very hard to interpret.

epoch2013 said...

A number of news articles appeared over this, most describing a single event creating our DNA. However, the BBC has a surprisingly balanced article: http://www.bbc.com/news/science-environment-37408014

In it David Reich answers:

"In our paper, we exclude more than about 2% ancestry in Australians, Papuans, and New Guineans from an early dispersal population, and our best estimate is 0%.

"I am a bit concerned that poorly modelled features of the methods used by Pagani and colleagues may have contributed to a false-positive signal of early dispersal ancestry in them. However, an alternative possibility is that the truth is around 2%, and this might just be consistent with all three studies."

Grey said...

postneo

"interesting, thanks, this is a medieval post islamic account. Humans tend to do similar things over time, we cannot always lump them as common culture. Moreover these are 2500-3000 years removed from andronovo."

yeah, not arguing the connection - just that at first sight those theories seem like someone's weird sexual fantasy but there's an apparent basis for them

MomOfZoha said...

@Davidski:
"Yeah, you'd need population samples from across Turkey to get more coherent models for your parents. Because, as you probably know, there are huge differences between some Turkish regions, particularly in the types and levels of Central Asian ancestry."

Oh, the differences are so huge that I'd need specific villages in the vicinity of their villages and so forth. Konya province is diverse enough, we don't need to confuse things further by considering Black Sea peoples, Aegeans, Balkan migrants, and so forth... My dad is from a specific village that is likeliest a combination of some Turkmen (not Nogay, who we never heard of before) with existing Anatolian groups specific to that village-region (it was capital of "Isaura Nova", and its people called "Isaurian mountaineers" by a visiting English archaeologist in 1909).

Anyway, I wrote here because his "2.6% Papuan" coming up on the Gedrosia Near East Neolithic was strange, especially in lieu of any ASI. I don't think 2.6% is negligible, and -- on the subject of Papuans -- was just wondering how the heck that shows up (even if just "archaically") in an Anatolian Turk.

BTW, he had very little Neanderthal (lowest in my family certainly, and also much lower than the general 23andme present-day database). I wish we could also test "Denisovan"ness (or number of Denisovan invariants, etc.)....

Oinkselot said...

Well, one thing is certain - we don't come here for YOUR useless and redundant, racialy motivated conspiracy theory opinions.

Onur said...

@Awale Abdi

This is off-topic but; could you link me to a very large variant of your avatar? That looks like a nice picture.

Thank you. You can find a much larger version of my avatar on my Facebook profile: https://www.facebook.com/onur.dincer.3994

jparada said...

not a single african hominid has a higher brain capacity than contemporaneous eurasian hominids.

How is this supposed to be relevant? Unless you can show fossil evidence pointing otherwise, the most sensible guess is that Homo itself evolved in Africa and spread from there to the rest of the world.

terryt said...

This is definitely relevant regarding the settlement of Australia and New Guinea. Interestingly the video shows the Philippines as being settled long after Australia/New Guinea. That is pretty much what the haploid evidence indicates, but it eliminates the Philippines as being the place Wallace's Line was first breached. It also shows Sulawesi settled earlier than I would have thought but the original crossing may have been from Borneo to there. The video opens the possibility that Y-DNAs C1b and K2b crossed the line at roughly the same time: C1b via Timor to Australia and K2b via Sulawesi to New Guinea:

https://archaeologynewsnetwork.blogspot.co.nz/2016/09/past-climate-change-swings-orchestrated.html#DqfxtIiGqtWxvUxh.97

Onur said...

@terryt

The link you gave is about the recent Timmermann & Friedrich paper. The results of that paper are based on computer simulations of climate change whereas the results of the papers covered in this thread are based on genetics. In addition, the Timmermann & Friedrich paper not only ignores genetics but also the extinctions and absorptions (by archaics) of early out-of-Africa Homo sapiens groups and the competition from the archaic Homo species like Neanderthals.

terryt said...

I knew I'd seen a still from the video before. Thanks for the information. Although it's not based on genetics it is still quite interesting.

Kurd Dgk said...

M O Zoha

The calculator you refer to is based on a supervised run, which generally have a higher margin of error and a greater calculator effect than unsupervised runs. We use supervised runs when we gave specific goals in mind, which are not readily achieved using an unsupervised runs. I would defer to unsupervised calculators for minor admixture.

capra internetensis said...

@Onur

According to a newspaper article the authors plan to include archaic competition in later research. (It sounds tricky though since it's not like we really know how they differed from modern humans in behaviour and subsistence.) They also specified that back-migration was part of the modeled movement.

The authors mentioned that the reason that modern humans didn't actually occupy Europe at the time indicated by the model could be the Neanderthals. It does make the whole thing kind of useless though - except to show when the bridges between Africa and Eurasia were most easily crossed.


postneo said...

Even if they find a few more archaics besides Neanderthal and Denisova their contributions will be even smaller.

The only N and D that contributed to us are those that were quick to interbreed with AMH. The holdouts were washed out by AMH and hybrids. Some positive selection of archaic traits must have occurred long after these events.

Similar to the saga of wolves vs domestic dogs. Only the gregarious(to humans) wolves/archaics made it and holdouts dwindled.

Is it possible to determine fertility in N and D vs AMH through DNA? Other primates have slightly longer estrus than humans. But Inter birth interval is probably the differentiator. In gorillas its 4 years and even longer in Orangutans.

epoch2013 said...

Another interesting thing about the fact that this admixture is only found east of the Wallace line is that this brings the Toba eruption back into focus. The eruption's plume went westward.

epoch2013 said...

So, thinking of Toba as a trigger event: What if the OoA wasn't exterminating or outcompeting other humans, but basically expanded in (partially) emptied area's?

Karl_K said...

@epoch2013

"So, thinking of Toba as a trigger event: What if the OoA wasn't exterminating or outcompeting other humans, but basically expanded in (partially) emptied area's?"

Then why couldn't other archaics expand into those same areas. It still sounds like outcompeting.

capra internetensis said...

MHs being tropically adapted could have had an advantage in the areas hardest hit - Mainland Southeast Asia and India. But still had to outcompete Neanderthals in Europe and so forth anyway.

Matt said...

I don't really have much to add but Sapiens outcompeting Neanderthals seems different to me when we have a genetic sample now of the El Miron ("Aurignacian") group being replaced at like 75:25 at most in Europe by their Villabruna ("Mesolithic") relatives. Before that it looks like the Vestonice went totally extinct. That could have been outcompetition as well, but how much due to a genetic / developmental factor?

Outcompetition still seems likely for Neanderthals vs Sapiens, but when multiple paleolithic Sapiens clades seem to be totally replaced, I wonder if it actually needs a very large relative advantage to explain the Neanderthal v Sapiens case.

epoch2013 said...

@Karl_K

Neanderthals did, didn't they? After Shkul and Qafzeh AMH came Neanderthals.

epoch2013 said...

@Matt

Take the Magdalenians. They most likely followed reindeers. That means they kept going further north (we have an idea which cultures, such as Ahrensburg). However, WHG managed to use *all* the space freed by ice and thus grew larger. 75/25 actually looks likes good survival for both.

I would like to know if there might be a possibility to model Villabruna as Vestonice plus an unknown HG and a tad ANE. Is there a way to check that?

epoch2013 said...

@Matt

Or maybe the Laacher See eruption was involved, 12900 BC?

Onur said...

@capra

According to a newspaper article the authors plan to include archaic competition in later research.

I am already aware of that plan and the newpaper article. Would be nice to see their new results published.

The authors mentioned that the reason that modern humans didn't actually occupy Europe at the time indicated by the model could be the Neanderthals. It does make the whole thing kind of useless though - except to show when the bridges between Africa and Eurasia were most easily crossed.

Exactly. Rather than making sensationalist but unsupported interpretations that make it to the headlines, they should have sticked to what their climate simulations show and keep their study as academic as possible, even if that would make it more boring and less attractive for the popular press and the public.

Ryan said...

"So, thinking of Toba as a trigger event: What if the OoA wasn't exterminating or out-competing other humans, but basically expanded in (partially) emptied area's?"

I wonder if Toba devastating human populations in South Asia with could create the appearance of two waves of migration.

How do we explain the absence of mtdna Haplogroup M in modern western Eurasian populations? Some sort of bottleneck in the Middle East... or two migrations... or...?

Onur said...

@Ryan

How do we explain the absence of mtdna Haplogroup M in modern western Eurasian populations? Some sort of bottleneck in the Middle East... or two migrations... or...?

mtDNA haplogroup M existed in Western Eurasia (at least in the European part) beginning from the early times of the modern human presence in Europe during the early Upper Paleolithic at the latest until the LGM bottleneck tens of thousands of years later according to the ancient DNA results of the Fu et al. 2016 paper (see Extended Data Table 1).

Onur said...

Extended Data Table 1: http://www.nature.com/nature/journal/v534/n7606/fig_tab/nature17993_ST1.html

jparada said...

mtDNA haplogroup M existed in Western Eurasia (at least in the European part)

And.....a branch of this haplogroup exists today in Africa and the Middle East, among populations of predominantly West Eurasian ancestry.

Ryan said...

@Onur - I'm aware, but the populations that replaced them lacked mtDNA haplogroup M. And those original populations aren't really anymore related to West Eurasians today than they are to East Eurasians. So how did the ancestors of modern West Eurasians lose haplogroup M? Or, if they never had M in significant numbers, how did N and M become so intertwined in East/South Eurasia?

@jparada - Those seem to all be backmigrations as far as we can tell. Some more recent than others.

Shaikorth said...

@Ryan

If you look at fig 4 of Fu et al, mtDNA M Aurignacians like Goyet Q116 were early West Eurasian. IBS map of that sample's affinity to moderns also demonstrates this: http://oi66.tinypic.com/2d6uth.jpg

For comparison Vestonice 16, a later Gravettian with mtDNA U. Even though they didn't descend from Aurignacians they were another early West Eurasian branch:
http://oi64.tinypic.com/2hwp9y1.jpg

terryt said...

"if they never had M in significant numbers, how did N and M become so intertwined in East/South Eurasia?"

I think this option is more likely than the ancestors of modern West Eurasians losing haplogroup M. That would raise a problem with the survival of N. As to the matter of the lines becoming so mixed in South and, especially, East Asia I think the most likely explanation is that the main migration route from the ancient Middle East into Eurasia was north of the Tibetan Plateau. Basal N is not present in South Asia at all, and even M seems most likely to have entered South Asia from the east. I would think that extinction in much of SW and Central Asia was the result of increased aridity and climate deterioration. Humans were easily able to survive in the east even with the Toba eruption. The early M found in the west is a remnant of that first movement towards the north.

Onur said...

@Ryan

I'm aware, but the populations that replaced them lacked mtDNA haplogroup M. And those original populations aren't really anymore related to West Eurasians today than they are to East Eurasians. So how did the ancestors of modern West Eurasians lose haplogroup M? Or, if they never had M in significant numbers, how did N and M become so intertwined in East/South Eurasia?

Those tested mtDNA haplogroup M-carrying Paleolithic Europeans (all of whom are pre-LGM samples) are genetically closer to modern West Eurasians than they are to modern East Eurasians, they had no apparent East Eurasian genetic connection, the Fu et al. paper is full of ample demonstration of this. So the loss of mtDNA haplogroup M in Europe is best explained by the LGM bottleneck.

The sample size and spatiotemporal scope of the tested Paleolithic Europeans are not sufficient to say with any degree of confidence that mtDNA haplogroup M was a rare haplogroup in pre-LGM Europe, it may well have been the dominant mtDNA haplogroup in some parts of Europe during some periods of pre-LGM Europe.

In many parts of East/South Eurasia the LGM had softer effects than in Europe, this likely explains the better preservation of the pre-LGM haplogroup structure there than in Europe.