The Holocene Alien Years

Fst between ancient European populations
  Ba_MN Be_LN Ben_LN Cor_LN EHG LBK_EN Mo_HG Sp_EN Sp_MN Sw_NHG Un_EBA WHG
Baalberge_MN                        
Bell_Beaker_LN 0.020                      
BenzigeroH_LN 0.021 0.004                    
CordedW_LN 0.032 0.008 0.007                  
EHG 0.082 0.041 0.038 0.034                
LBK_EN 0.009 0.021 0.025 0.035 0.084              
Motala_HG 0.083 0.057 0.053 0.060 0.048 0.093            
Spain_EN 0.021 0.028 0.035 0.044 0.092 0.015 0.099          
Spain_MN 0.014 0.022 0.026 0.035 0.077 0.016 0.081 0.009        
SwedSk_NHG 0.066 0.050 0.048 0.054 0.058 0.078 0.034 0.084 0.074      
Unetice_EBA 0.016 0.002 0.003 0.005 0.034 0.022 0.051 0.030 0.023 0.043    
WHG 0.073 0.055 0.056 0.070 0.078 0.091 0.053 0.092 0.070 0.050 0.057  
Yamnaya 0.054 0.016 0.013 0.011 0.028 0.052 0.063 0.060 0.053 0.062 0.012 0.076

It is often said that the meeting of Europeans and Amerindians in the 15th century is our best taste of what it would be like to meet aliens. The analogy is rather straightforward, as Amerindians were not part of the broad interactions between societies over the Holocene, as they had removed themselves from the scene of action ~15,000 years ago. The interaction resulted in conflict and synthesis. A new people in Latin America arose who were biologically, and to a lesser extent culturally, a compound between two very distinct antecedents. In North America the dynamic was more of replacement and marginalization, often due to organized collective action on the part of white settlers and their political systems.

41ZlHlsdYXL._SY344_BO1,204,203,200_Above I have again placed a selection of Fst statistics from the preprint Massive migration from the steppe is a source for Indo-European languages in Europe. One must be careful about not over-interpreting these statistics. But, they give a good sense of genetic divergence between two populations, on average (I have uploaded all Fst values in an Excel file). In particular above I’ve focused on the ancient populations in the data set. EN is Early Neolithic, while MN is Middle, and LN is Late. HG is Hunter-Gatherer. I’ve bolded Fst values > 0.05, because to me that’s a pretty high threshold for serious genetic divergence. The LBK brought agriculture to vast swaths of Central Europe. These were the people who encountered the hunter-gatherers who had occupied the continent since the end of the last Ice Age. The genetic distance between these two groups is incredibly high. Between the generic “Western Hunter-Gatherer” population and the LBK the Fst value is 0.091. What does that mean? The Mala are a Dalit (outside the caste system) group from Southern India. The Fst between this group and WHG is 0.11. In other words, not that much greater than between WHG and LBK. The Fst between the Mala and the LBK, two populations separated by a continent and 7,000 years is 0.077, less than between WHG and LBK. The genetic distance between the Mala and the French is 0.051. Considerably less than between the WHG and LBK. The get a sense of how small the values between modern European groups are, the genetic distance between Lithuanians and Sardinians is 0.021. The genetic distance between Belarussians and the English is 0.004, or about 4% of the distance between WHG and LBK. My claim that the contact between the first farmers and the hunter-gatherers of early Europe was one of intercontinental scale interaction is justified by the fact that the genetic distance between Han Chinese and Europeans is about ~0.10, only marginally greater than between WHG and LBK.

These sorts of genetic distances on the ancient European landscape could only be due to massive cultural revolutions which produced demographic shifts which can in no way be modeled as continuous diffusion processes. The Bantu expansion is probably a good analogy for what happened in ancient Europe, it took a little over 1,000 years to traverse the whole continent of Africa, a much larger geographic zone than Europe. But a second issue that we must also focus on are the genetic distances between European hunter-gatherers. One could chalk up 0.078 between EHG and WHG to the fact that EHG has admixture from “Ancestral North Eurasians” (ANE) at a clip of ~40 percent. But even the distance between the Motala hunter-gatherers, who are only 15% ANE, and WHG is 0.053. The uniparental markers are strongly suggestive of a relatively small group expanding to fill Europe after the last Ice Age, they are overwhelmingly haplogroup I for Y chromosomes, and haplogroup U5 for females. So what gives with the high Fst values? This is far higher than any modern intra-European distances. One hypothesis that I think might be viable is that small effective population cranked up the genetic drift in these groups, whose marriage networks were sharply delimited by cultural fractionation as well as ecological constraints which reduced population density outside of narrow specially favored areas (e.g., marine environments). One consequence of excess drift is elevated Fst values, beyond what you might think would be plausible. I’m not specialist in cultural evolution, but my intuition tells me that hunter-gatherer groups can engage in fission rather rapidly, and these divisions may have enforced greater barriers to gene flow to relatively recently diverged groups than is the norm in modern agricultural and post-agricultural societies.

Another issue that comes to mind are future analyses of ancestry tracts and linkage disequilibrium in these populations. The reason I bring this up is the fact that we need to distinguish between genetic differences due to standard workaday isolation by distance, and those produced by pulse admixture events (see Gideon Bradburd’s preprint for more elucidation of this issue). For various reasons outlined in the preprint above I’m convinced that a group like EHG, and later the hunter-gatherers of Scandinavia, did undergo admixture with a very different population during the early Holocene, after their expansion from the Ice Age refugia. But ultimately looking at patterns of this ancestry in the chromosomes as well as estimating a time since admixture would nail the coffin on this likelihood.

Finally, there’s the issue of “Nazi optics.” When word of these results started to percolate last spring a friend who is a prominent human geneticist blurted out “it sounds like the Nazis were right!” By this, he meant that this story of migrations, and demographic turnover, would be much more in place in Europe before World War 2. But there’s an immediate refutation of any attempt to Nazify these results: the Fst statistics made it clear that long term result of the clash of peoples in the early to mid Holocene has been amalgamation. The Bronze Age people of Europe, who gave rise to the historic nations, are the heirs of both the hunter-gatherers long indigenous to the continent, and disparate aliens, who arrived as strangers thousands of years ago.

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