Saturday, November 8, 2014

A look at an early European


 
Kostenki Man, reconstructed by Mikhail Gerasimov (1907-1970). An early European who was not yet phenotypically European.

 

Who were the first Europeans? We now have a better idea, thanks to a new paper about DNA from a man who lived some 38,700 to 36,200 years ago. His remains were found at Kostenki, a well-known Upper Paleolithic site in central European Russia (Seguin-Orlando et al., 2014).

Kostenki Man tells us several things about the first Europeans and, more broadly, the first non-African humans:

The Neanderthal encounter

Modern humans received their Neanderthal admixture when they were just spreading out of Africa some 54,000 years ago. At that time, they had not yet encountered the Neanderthals and were entering the territory of the Skhul/Qafzeh hominids, a semi-archaic people of the Middle East. So we may have got our Neanderthal admixture indirectly. The Skhul/Qafzeh hominids had probably interbred with their Neanderthal neighbors to the north, and our ancestors may have then picked up this admixture while in the Middle East. 

When our ancestors spread farther north into Europe, some 45,000 to 42,000 years ago, they could have interbred directly with Neanderthals, but they didn't. Perhaps the two groups were just too different. They seem to have intermixed only via a third party that was neither fully modern nor fully archaic.


A strange detour ... and then another!

There was initially a large continuous population across northern Eurasia, perhaps composed of nomads who pursued wandering herds of reindeer across the European Plain and its eastward extension into central and northern Asia.

Not long before the time of Kostenki Man, these Northern Eurasians began to split into three regional groups: Western Eurasians, Eastern Eurasians, and the ancestors of Middle Eastern farmers. The degree of reproductive isolation is unclear, however, and gene flow may have continued between all three groups until the onset of the last ice age some 25,000 years ago. This may be why Kostenki Man does not fit perfectly into any of the three groups, although he is genetically closest to Western Eurasians.

Yes, Northern Eurasians were ancestral to the early farming peoples of the Middle East. It seems that early modern humans had to head north, learn to hunt reindeer, and then head south again before they could start farming. Sounds like a strange detour. Wouldn't it have been easier to stay put and do it locally? You know, Middle-Eastern hunter-gatherers becoming Middle Eastern farmers? Apparently not.

It gets even more convoluted. After some of those Northern Eurasians had gone south to the Middle East, some of their farming descendants "returned" to Europe and partially replaced its hunter-gatherers, particularly in southern and central Europe. This second detour has been greeted with disbelief. Dienekes (2014), for instance, has written: "I don't think many archaeologists would derive European farmers from Russia (Russia is actually one of the last places in Europe that became agricultural)."

True, but farming requires a mindset that may have come from those northern hunters (Frost, 2014). When Piffer (2013) looked at human variation in alleles at COMT, a gene linked to executive function, working memory, and intelligence, he found that northern hunting peoples had more in common with farming peoples than with other hunter-gatherers, "possibly due to the higher pressure on technological skills and planning abilities posed by the adverse climatic conditions."

That mindset made farming possible, but the first steps toward farming could not be taken in a cold climate. They had to be taken in a place with a long growing season and a wide variety of domesticable plants and animals, such as in the Middle East. Once farming had developed there, it could move back north, while taking along its technologies, its food crops, and its livestock species. 

Farming can develop in the tropics with a "tropical" mindset, but it looks very different. The farming that arose in West Africa is overwhelmingly women's work and seems to have wholly developed out of female plant gathering. The guinea fowl is the only animal that has been domesticated for food consumption in sub-Saharan Africa.


The Ice Age was not so bad 

The Upper Paleolithic humans of northern and eastern Europe did not die out during the last ice age, as was commonly thought. They survived the glacial maximum intact.


The European phenotype came later

Kostenki Man was dark-skinned, dark-eyed, and rather short. These details, curiously enough, appear not in the paper but in a review of the paper, published by the same journal, as well as in an interview with one of the authors (Associated Press, 2014; Gibbons, 2014). 

So we now have an upper bound for the emergence of the European phenotype, i.e., light skin and a diverse palette of hair and eye colors. The lower bound has been set by the remains of a Swedish hunter-gatherer, dated to 8,000 years ago, who had the "European" allele for light skin at the gene SLC24A5 (Skoglund et al., 2014).


Conclusion

My main criticism centers on the dating to 38,700 - 36,200 years ago. At the Kostenki site, the radiocarbon dating used to be some 10,000 years younger. It was then recalibrated to an older range of dates when a layer of volcanic ash at the site was attributed to a volcano that had erupted in southern Italy some 39,000 years ago. This recalibration was initially controversial, but the controversy has since subsided (Sinitsyn and Hoffecker, 2006). I would not rule out a subsequent re-recalibration.

By retrieving ancient DNA from an early modern human, we have made a key advance in human paleogenetics, perhaps more so than by sequencing the Neanderthal genome. We again see that evolution did not slow down with the emergence of anatomically and behaviorally modern humans some 60,000 years ago. It actually began to speed up, as humans began to enter not only new natural environments but also new cultural environments of their own making.
 

References 

Associated Press (2014). DNA study dates Eurasian split from East Asians, The Columbus Dispatch, November 6
http://hosted2.ap.org/OHCOL/07e34bb59e064cedb7e2776e8db4b4f7/Article_2014-11-06-EU--Eurasian%20Split/id-ae36fa368c634c7383d807942bd5fe67 

Dienekes (2014). Genome of Kostenki-14, an Upper Paleolithic European (Seguin-Orlando, Korneliussen, Sikora, et al. 2014), Dienekes' Anthropology Blog, November 7
http://dienekes.blogspot.ca/2014/11/genome-of-kostenki-14-upper-paleolithic.html  

Frost, P. (2014). The first industrial revolution, Evo and Proud, January 18
http://evoandproud.blogspot.ca/2014/01/the-first-industrial-revolution.html 

Gibbons, A. (2014). European genetic identity may stretch back 36,000 years, Science, News, November 6
http://news.sciencemag.org/archaeology/2014/11/european-genetic-identity-may-stretch-back-36000-years 

Piffer, D. (2013). Correlation of the COMT Val158Met polymorphism with latitude and a hunter-gather lifestyle suggests culture-gene coevolution and selective pressure on cognition genes due to climate, Anthropological Science, 121, 161-171.
https://lesacreduprintemps19.files.wordpress.com/2014/01/correlation-of-the-comt-val158met-polymorphism-with-latitude-and-a-hunter-gather-lifestyle-suggests-culturee28093gene-coevolution-and-selective-pressure-on-cognition-genes-due-to-climate.pdf 

Seguin-Orlando, A., T.S. Korneliussen, M. Sikora, A.-S. Malaspinas, A. Manica, I. Moltke, A. Albrechtsen, A. Ko, A. Margaryan, V. Moiseyev, T. Goebel, M. Westaway, D. Lambert, V. Khartanovich, J.D. Wall, P.R. Nigst, R.A. Foley, M.M. Lahr, R. Nielsen, L. Orlando, and E. Willerslev. (2014). Genomic structure in Europeans dating back at least 36,200 years, Science, Published online 6 November 2014
http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114
http://www2.zoo.cam.ac.uk/manica/ms/2014_Seguin_Orlando_et_al_Science.pdf  

Sinitsyn, A.A., and J.F. Hoffecker. (2006). Radiocarbon dating and chronology of the Early Upper Paleolithic at Kostenki, Quaternary International, 152-153, 164-174.
http://www.sciencedirect.com/science/article/pii/S1040618206000206 

Skoglund, P., H. Malmstrom, A. Omrak, M. Raghavan, C. Valdiosera, T. Gunther, P. Hall, K. Tambets, J. Parik, K-G. Sjogren, J. Apel, E. Willersley, J. Stora, A. Gotherstrom, and M. Jakobsson. (2014). Genomic diversity and admixture differs for stone-age Scandinavian foragers and farmers, Science, 344 (6185), 747-750.
http://www.sciencemag.org/content/344/6185/747.short
 

17 comments:

Sean said...

He had a excess of Neanderthal genes, which must have been slowly purged from the modern human genome. The hair colour genes from Neanderthals would have been lying around unused in the genome in most people and only come through to expression in a few to confer the advantage that got them selected.

Photos of the skull show he had a massive jaw and large though well spaced teeth. Magdalenian girl from southern France at least 13,000 years ago, had the first known occurrence of an impacted wisdom tooth. In 2012 Belezal et al said selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started within the last 11,000-19,000 years. A lot of changes in that time, maybe they were adaptations for chasing reindeer!

------------------
Re. the variant COMT Met allel and how it may do what it does.

"When Piffer (2013) looked at human variation in alleles at COMT, a gene linked to executive function, working memory, and intelligence, he found that northern hunting peoples had more in common with farming peoples than with other hunter-gatherers, "possibly due to the higher pressure on technological skills and planning abilities posed by the adverse climatic conditions."

Piffer goes into how the other Val allele makes the Pygmies good dads. The Inuit and COMT study Piffer references was really about the Inuit's Met varient being worse at clearing polutants. Pollutants are basically xenoestrogens, hence the same team's interest in breast cancer in Inuit women (see here). So as I read it the COMT Met allele is for a suit ofr 'Men are from Mars' traits rather that warm 'Venus' emotions, and it seems to do that by clearing estrogens.

Christopher Badcock has a theory "that we possess two parallel cognitive systems: one adapted to the real world of objects (mechanistic cognition), and one to the mental world of other people and their minds (mentalistic cognition); that the two systems are “anti-correlated” and vary inversely by way of mutual inhibition, producing a see-saw, either/or effect comparable to the way a Necker cube switches perspective (here)."

Anonymous said...

The Gerasimov reconstruction looks strikingly like the face of an Australian Aborigine, or perhaps like some of the "Veddoid" tribal peoples of southern India. Something like this was probably the default phenotype across Eurasia prior to the evolution of the classically "Caucasoid" and "Mongoloid" traits.

One of the more curious findings in this study is that Kostenki Man possessed some "Basal Eurasian" ancestry, which is absent in other Late Pleistocene North Eurasians. One hears more and more about these "Basal Eurasians" in genetic studies on prehistoric populations. Is there any way of ascertaining which modern populations retain this genetic component to the highest degree? I wonder if it might have some connection to the "Veddoid" element that some early 20th century anthropologists claimed to identify among the more isolated tribes of the southern Arabian Peninsula.

SD said...

Re. that reconstruction, he looks exactly like a guy I know from India! However, how old was he? Why is he clean shaven? As if the first thing palaeolithic men did after they woke up in the morning was to have a dump and then shave. The La Brana reconstruction at least had that bit right.

Anonymous said...

I'm confused - the man above doesn't look as if he could have come from the skull shown on Dienekes.

There's another reconstruction of KOSTENKI XIV by Mikhail Gerasimov on this page* and it looks more like the skeleton shown at Dienekes - broad jaw and wide eyes.

http://www.kunstkamera.ru/images/g/09_04.jpg

*www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=15;t=005669

Sean said...

"KOSTENKI XIV by Mikhail Gerasimov" link is to a site with malware.

Anonymous said...

Sean, have a look at the egypt search page, it's about the work of the artist, seems reputable, both photos are on the page (the malware link is the 'copy image location' and the same thing happens with the other photo too)

Sean said...

K14 was a bit odd, it had a much lower cranial capacity that the general run of the Kostenki Man type. See here.

Anonymous said...

You keep defending this theory of yours after everything we now know...?

I will have a chuckle and congratulate you if it's ever 'confirmed' but let's just say I won't be holding my breath. Both Dienekes and Cochran have posited a much simpler and more convincing (so far) explanation.

barakobama said...

Peter,

I can tell before you read the supp. info or if you payed the money the real paper, you were looking for this very early European to be something exotic, non-western, totally differnt from modern ones, etc., which distorted your reasoning.

"This may be why Kostenki Man does not fit perfectly into any of the three groups, although he is genetically closest to Western Eurasians."

He's closer to native americans than to middle easterns(not counting Caucasus). Overall he is by far closest to modern Europeans, specifically northern Europeans and Basque(high WHG), and even more specially northeast Europeans. Next he is closest to southern Europeans, then to Caucasus, then to native Americans, then middle easterns, and south-central Asians.

Basically WHG-ANE ancestry correlates to his closest relatives. This is why native Americans(~44% ANE) are so close to him, and why Lithuanians(<80% WHG-ANE) are his closest modern relatives. Most middle easterns may have around as much WHG-ANE as native americans, but their majority basal Eurasian which is more distant to WHG-ANE than east Asian.

I don't think we should use such clean cut distinctions such as south Asia, west Asia, and Europe when talking about people who lived some 36,000 years ago. His people are very important to the ancestry of native Americans, Siberians, south-central Asians, middle easterns, and Europeans.

"An early European who was not yet phenotypically European."

Obviously the typical mainland European appearance(mostly pigmentation), came from admixed population going through selection during the Neolithic and bronze age. I suspect EEF was similar to modern near easterns and Sardinians, and WHG-ANE were deep-brown like native Americans and south-Asians.

It's interesting to think what ancient people looked like. In the stone age it would have probably been harder to make a clean cut distinction between Europeans, middle easterns, and south Asians.

Anonymous said...

"You keep defending this theory of yours after everything we now know...?"

I don't know what I think about the main idea but what we "know" is changing with each genome.

Anonymous said...

@barak

"Basically WHG-ANE ancestry correlates to his closest relatives. This is why native Americans(~44% ANE) are so close to him, and why Lithuanians(<80% WHG-ANE) are his closest modern relatives."

Isn't that the point though? Is the EEF in places like Lithuania EEF or is it something similar that spread earlier?

Anonymous said...

Sean, thanks, my main confusion remains - how can the skull at Dienekes be the head above?

EEF etc are derived from Principal Compenents analysis aren't they? Isn't this the danger of statistics, ie theory based on aggregations is only going to be as accurate as the aggregations were in the first place? Maybe it would be less open to error to follow the spread of specific genes without trying to match genes to derived groupings?

Michael said...

"Maybe it would be less open to error to follow the spread of specific genes without trying to match genes to derived groupings?"

This is actually less informative, but nonetheless useful. Y chromosome and mtDNA haplogroups behave as single genes. The problem/advantage is that single genes only tell you if two populations interacted a single time. If the gene was very advantageous, like lactose tolerance for a farmer/herder, then it would spread leaving few other signs of its original context. Whole genome averages show which entire populations were mixing. Random genomic noise doesn't have to be advantageous to remain after a few generations.

Anonymous said...

Thanks Michael,

I think what i'm understanding is that averages,SNPs?, deal with chemical formations (of the DNA) without reference to expression. ? This is what group A is; but that says nothing about what group A does.

Sean said...

Re, photo:- Who said it was?; the post is about genes.

Anon."Random genomic noise doesn't have to be advantageous to remain after a few generations. This is what group A is; but that says nothing about what group A does."

I think the finding that "Genes once thought to have arrived with the first farmers, for instance, now seem to have been around much earlier. “Until now, it seemed clear this was something that came into Europe during the Neolithic,” says Pontus Skoglund, a geneticist at Harvard Medical School." is relevant to the idea that separate populations were coming in and adding things.

Only for a few out of tens of thousands of genes is there thought to be a certain (though very small) effect on intelligence, Variation in alleles at COMT for example.

Peter Fros_ said...

Sean,

Kostenki has a bit more Neanderthal ancestry than we do: 2.4% versus less than 2%. The decline might be the cumulative effect of natural selection against maladaptive Neanderthal alleles. Or it might not even be a real difference, i.e., sampling error.

Piffer cites studies showing the association between COMT and human cognition:

"Stable and flexible cognition depend in part on different alleles of the COMT gene. Carriers of the Met allele are disadvantaged in tasks requiring cognitive flexibility, due to the
opposite effects of dopamine levels on WM and cognitive flexibility (Witte and Flöel, 2012). Whilst Met carriers show better performance on the Wisconsin Card Sorting Test(WCST) and other tasks of WM or executive functions(Egan et al., 2001; Bruder et al., 2005; Caldù et al., 2007; Enoch et al., 2009), they also show larger switching costs when performing a task-switching paradigm (Colzato et al., 2010). Conversely, Val carriers are better at expressing their emotions in verbal form(Swart et al., 2011) and show lower switching costs, which translate into a higher index of cognitive flexibility (Colzato et al., 2010). In a recent study, the
COMT gene locus explained 5.8% of the variance in donation behaviour, with Val carriers donating about twice as much money as individuals without a Val allele. This suggests that the Val allele favors prosocial/altruistic behavior"

Anon, SD,

Soviet journals describe the Kostenki XIV skull as of "Negroid type." I'm still looking for a more detailed description.

Anon,

It's not so much my dumb idea as the dumb idea of this paper's authors. They see West Eurasians, East Eurasians, and basal Eurasians as having a common ancestry outside Africa. This ancestral Eurasian population postdates the split in the Middle East between the ancestors of Australo-Melanesians and other non-Africans. Given the rapidity with which modern humans colonized Europe, this subsequent split would have been somewhere in northern Eurasia.

Barak,

You don't have to pay for a copy of the paper. You can access it via a link in my references.

Try clicking here:

http://www2.zoo.cam.ac.uk/manica/ms/2014_Seguin_Orlando_et_al_Science.pdf

Beyond Anon said...

The visage on that bust reminds me of Aboriginal Australians for some reason.