Thursday, June 30, 2022

Extreme founder events among ancestral Europeans



Expansion of steppe pastoralists (Narasimhan et al. 2019)


How much of the present-day European gene pool comes from the indigenous hunter-gatherers? How much from Neolithic farmers of Anatolian origin? And how much from steppe pastoralists of the Don-Volga area? There is no easy answer.



A “founder event” results when a few people split off from their original population and found a new one. The fewer they are, the likelier they will differ genetically, on average, from the original population. The founder event is a “bottleneck” through which only a small fraction of the original genetic diversity can pass into the new population.


A founder event is one of three reasons why adjacent populations may differ from each other genetically. The other two are:


Natural selection – The boundary between two adjacent populations often corresponds to a change in the natural environment (vegetation, climate, etc.) or the cultural environment (diet, way of life, rules and prohibitions, sexual division of labor, etc.). The two populations are thus subjected to different regimes of natural selection.


Population admixture or replacement – One of the two adjacent populations has admixed with or been replaced by a population that has moved into the area.


In practice, a founder event overlaps with differences in natural selection. When pioneers move into a new area, they tend to be better suited to the local conditions than the people they left behind. The less suited are less likely to go, and if they do go they are more likely to go back … or die. So, from the outset, there already is some selection.


A new study of ancient DNA has shown that founder effects have been more frequent and more “extreme” than previously thought: “In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy” (Tournebize et al. 2022, p. 1)


Contrary to popular belief, Ashkenazi Jews are not the outcome of a particularly extreme founder event:


Across worldwide populations, we identified 53 groups that have experienced more extreme founder events (with significantly higher founder intensity) than AJs [Ashkenazi Jews], who have high rates of recessive diseases due to their history of founder events (Tournebize et al. 2022, p. 7)


Perhaps those recessive diseases are not due to a founder event. Perhaps they are a side-effect of selection for an adaptive trait. If a founder effect had been the cause, those diseases would be distributed randomly over different metabolic pathways. Actually, they are all associated with excessive storage of sphingolipids, a key component of neural tissue (Cochran et al. 2006; Diamond 1994).


Founder events seem to have been frequent among ancestral Europeans, regardless of whether they were hunter-gatherers, farmers, or pastoralists. But those events seem to have been more “intense” among European hunter-gatherers. In other words, founder groups were smaller and spent more time passing through the population bottleneck.


Recent analysis has shown that present-day Europeans are a mixture of three major ancestry groups related to ancient European hunter-gatherers, Anatolian farmers, and Eurasian Steppe pastoralists. […] Across the three groups, we found that the frequency of founder events was similar, ranging between 90–100%. However, the average founder intensity was significantly higher in European hunter-gatherers […] compared to the Near Eastern farmers […] or the Steppe pastoralists. (Tournebize et al. 2022, p. 11)


Hunter-gatherers had more intense founder events because they had a lower population density. Founder groups were thus smaller and less representative of the original population from which they came.


… we found local hunter-gatherer groups had more extreme founder events than the Neolithic farmers or Bronze Age individuals. This suggests that population sizes in Europe have increased over time, coupled with changes in ancestry and transitions in lifestyle. Our results are consistent with a recent study that measured short runs of homozygosity in ancient Europeans and found a similar increase in population size during the Neolithic period. Our results are also in agreement with archeological evidence for increased population size during the Neolithic transition. (Tournebize et al. 2022, p. 14)


This takes us back to the previous quote: Europeans are a mix of indigenous hunter-gatherers, Anatolian farmers, and steppe pastoralists. These three groups, and their roles in European prehistory, can be summarized as follows:


·         Farmers began to move into Europe from present-day Turkey about 10,000 years ago. Initially, they advanced rapidly through territory inhabited by small nomadic bands.

·         About 7,000 years ago, the wave of advance stalled along a line running from the Low Countries to the Black Sea. To the north, along the North Sea and the Baltic, were large semi-sedentary communities of hunter-fisher-gatherers who could less easily be replaced because they were so numerous.

·         About a thousand years later, farming resumed its northward advance, although the advance was now much more a matter of people adopting farming rather than being replaced by farmers.

·         Meanwhile, around 5,400 years ago, some hunter-gatherers in the Don-Volga area adopted pastoralism and began to expand westward into Europe and southeastward into the Middle East, Central Asia, and South Asia. They may have been ancestral Indo-Europeans.


How much did each of the three groups contribute to the European gene pool? Which group contributed the most and which the least? The question is hard to answer, for three reasons:


Double counting


The hunter-gatherers of Mesolithic Europe contributed to the present European gene pool both directly and indirectly. The steppe pastoralists were themselves indigenous hunter-gatherers who had adopted pastoralism, plus an admixture of up to 18% from Anatolian farmers. As the Anatolian farmers pushed into Europe, they became gradually “Europeanized” through intermixture with local hunter-gatherers. It is also possible that the Anatolian farmers were themselves the product of an earlier expansion of European hunter-gatherers into the Middle East (Frost 2014).


Founder events


We measure population replacement by measuring the degree of genetic difference between the original group and the one that replaced it. Is that a valid method? Let’s take the replacement of hunter-gatherers by farmers, and let’s assume that all of the farmers were descended from hunter-gatherers who had adopted farming. The two groups would still be genetically different. The farmers would have been the product of a founder event—a small and genetically unrepresentative group of hunter-gatherers who had decided to take up farming.


Differences in natural selection


Population replacement is hard to measure for another reason: hunter-gatherers and farmers lived under different regimes of natural selection. They were selected for their ability to adapt to different diets, types of shelter, and means of subsistence. To go from one way of life to the other required not only cultural change but also genetic change.


For instance, the population frequency of haplogroup U shows a sharp break at the time boundary between late hunter-gatherers and early farmers (Bramanti et al. 2009). That break strongly suggests that the original Europeans were largely replaced by farmers spreading into Europe from the Middle East. Yet haplogroup U would persist in Denmark at high frequencies long after the transition to farming (Melchior et al. 2010). In Latvia and Ukraine it would persist into Neolithic times (Jones et al. 2017). Haplogroup U probably disappeared from the European gene pool because it ceased to be adaptive. It has been shown to shift the energy balance away from ATP synthesis and toward production of body heat, a useful adaptation if you sleep in makeshift shelters and pursue game in all kinds of weather (Balloux et al. 2009; Montiel-Sosa et al. 2006). It’s less useful if you sleep in a warmer environment and can plan your outdoor activities.




Whenever I make this argument, the counter-argument is that founder events and natural selection could not possibly explain all of the genetic difference we see between late hunter-gatherers and early farmers in Europe. I agree. I’m just saying that the magnitude of the demographic replacement has been overestimated.




Balloux F., L.J. Handley, T. Jombart, H. Liu, and A. Manica. (2009). Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proceedings of the Royal Society B. Biological Sciences 276: 3447-3455.


Bramanti, B., M.G. Thomas, W. Haak, M. Unterlaender, P. Jores, K. Tambets, I. Antanaitis-Jacobs, M.N. Haidle, R. Jankauskas, C.J. Kind, et al. (2009). Genetic discontinuity between local hunter-gatherers and Central Europe's first farmers. Science 326: 137-140.


Cochran, G., J. Hardy, and H. Harpending. (2006). Natural history of Ashkenazi intelligence. Journal of Biosocial Science 38(5): 659-693.


Diamond, J.M. (1994). Jewish Lysosomes. Nature 368: 291-292.


Frost, P. (2014). The new European phenotype: expansion into the Middle East. Evo and Proud, January 25.


Jones, E.R., G. Zarina, V. Moiseyev, E. Lightfoot, P.R. Nigst, A. Manica, et al. (2017). The Neolithic transition in the Baltic was not driven by admixture with early European farmers, Current Biology 27(4): 576-582.


Melchior, L., N. Lynnerup, H.R. Siegismund, T. Kivisild, and J. Dissing. (2010). Genetic diversity among ancient Nordic populations. PLoS One 5(7): e11898


Montiel-Sosa, F., E. Ruiz-Pesini, J.A. Enriquez, A. Marcuello, C. Diez-Sanchez, J. Montoya, D.J. Wallace, and M.J. López-Pérez, (2006). Differences of sperm motility in mitochondrial DNA haplogroup U sublineages. Gene 368: 21-27.


Narasimhan, V.M., N. Patterson, P. Moorjani, N. Rohland, R. Bernardos, S. Mallick, I. Lazaridis, et al. (2019). The formation of human populations in South and Central Asia. Science 6: 365(6457): eaat7487.  


Tournebize, R., G. Chu, and P. Moorjani. (2022). Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet 18(6): e1010243.

Thursday, June 23, 2022

Ancestral East Asians and adaptation to coronaviruses


Early farming village in China (Wikicommons – Xinyang City Museum, Gary Todd)


Respiratory viruses began to propagate more easily when hunting and gathering gave way to farming and as settlements grew larger. Humans may have then evolved to use coronaviruses as a natural vaccine against deadlier respiratory diseases, like tuberculosis and pneumonia.



A new genomic study has found that East Asians had to adapt to epidemics of coronaviruses some 25,000 years ago. The authors looked at gene variants for proteins that interact with coronaviruses in five East Asian populations: Han Chinese (Beijing); Han Chinese (South China); Dai (Yunnan, China); Japanese; and Vietnamese. There were three main findings:


·         Ancestral East Asians had to adapt to coronavirus epidemics around 25,000 years ago

·         They adapted by acquiring mutations that are close to genes that regulate the development of lung tissue and other tissues affected by COVID-19

·         Those mutations either promote or block infection by coronaviruses (Souilmi et al. 2021, p. 3505).


The last finding is puzzling. Did those ancestral East Asians become more vulnerable or less vulnerable to coronaviruses? The authors simply say that half of those mutations from 25,000 years ago have “anti- or proviral effects” versus 29% of all proteins that interact with coronaviruses (Souilmi et al. 2021, p. 3509). Fine. But how many of those mutations were antiviral and how many proviral?


It might seem strange that natural selection would actually make people more susceptible to coronavirus infections. Yet such susceptibility could be beneficial. A viral infection can boost immunity to other pathogens, including deadly ones that cause tuberculosis, pneumonia, or pneumonic plague. Until recently, coronaviruses were typically mild in their effects, producing what we call the “common cold.” They may thus act as a natural vaccine against deadlier respiratory diseases (Frost 2020).


Respiratory diseases are believed to have become serious for humans when hunting and gathering gave way to farming. People became sedentary and their settlements grew larger with time, thus providing respiratory viruses with better conditions for propagation (Comas et al. 2013). This theoretical model is in conflict, however, with the above finding that ancestral East Asians began adapting to coronaviruses some 25,000 years ago, long before they adopted farming and became sedentary. We’re thus left with the unlikely conclusion that coronavirus epidemics began among scattered bands of hunter-gatherers.


The estimate of 25,000 years ago is probably wrong. The authors arrived at that figure by calculating the latest date when the ancestors of the four East Asian groups were still a single population. But East Asians are not descended from a single population. Their origins are best described by the "Two-Layer" (TL) hypothesis:


·         Modern humans spread into East Asia through a northern route and a southern route.

·         The southerners were then replaced to varying degrees by northerners who spread out of northeast Asia and successively occupied northern China, southern China, and Southeast Asia (Oxenham and Buckley 2016; Xu et al. 2006).

·         Thus, as you go farther south in East Asia, the population has a greater admixture from the earlier southern “layer”—from hunter-gatherers who closely resemble the relic groups that still exist in parts of Southeast Asia, i.e., the Andaman Islanders, the Aeta of the Philippines and the Maniq and Semang of the Malayan Peninsula.


Admixture from that older southern substrate pushes back in time the latest common ancestors, who never existed. Adaptation to coronaviruses therefore happened at a later date, probably when the “northerners” pushed into what is now northern China and adopted farming. They then grew in population, pushed farther south, and intermixed with the hunter-gatherers who lived there. 





Comas, I., M. Coscolla, T. Luo, et al. (2013). Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics 45: 1176–1182.


Frost, P. (2020). Does a commensal relationship exist between coronaviruses and some human populations? Journal of Molecular Genetics 3(2): 1-2.


Frost, P. (2022). A natural vaccine. Evo and Proud, February 21


Oxenham, M., and H.R. Buckley. (2016). The population history of mainland and island Southeast Asia, in M. Oxenham and H.R. Buckley (eds) The Routledge Handbook of Bioarchaeology in Southeast Asia and the Pacific Islands. Routledge.


Souilmi, Y., M.E. Lauterbur, R. Tobler, C.D. Huber, A.S. Johar, S.V. Moradi, W.A. Johnston, N.J. Krogan, K. Alexandrov, and D. Enard. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Current Biology 31(16), 3504–3514.e9.


Xue, Y., T. Zerjal, W. Bao, S. Zhu, Q. Shu, J. Xu, R. Du, S. Fu., P. Li, M.E. Hurles, H. Yang, C. Tyler-Smith. (2006). Male demography in East Asia: A north-south contrast in human population expansion times. Genetics 172: 2431-2439,

Monday, June 13, 2022

Humans and the olfactory environment


Perfume burner, Egypt, c. 700-900 (Wikicommons, Musée du Louvre, Marie-Lan Nguyen)


We have sought to remake our environment in ever more appealing ways, including its smell. But the change hasn’t been one-way. By remaking our olfactory environment, we’ve ended up remaking ourselves.



I’ve published a new paper in Psych. When I wrote it, I had three aims:


·         Explain the concept of gene-culture coevolution

·         Provide a concrete example, i.e., how we have coevolved with the odors around us, not only in our ability to emit and sense them but also in our ability to represent them mentally

·         Develop the theoretical basis of gene-culture coevolution


Please feel free to comment. The following is the abstract:



As hunter-gatherers, humans used their sense of smell to identify plants and animals, to find their way within a foraging area, or to distinguish each other by gender, age, kinship, or social dominance. Because women gathered while men hunted, the sexes evolved different sensitivities to plant and animal odors. They also ended up emitting different odors. Male odors served to intimidate rival males or assert dominance. With the rise of farming and sedentism, humans no longer needed their sense of smell to find elusive food sources or to orient themselves within a large area. Odors now came from a narrower range of plants and animals. Meanwhile, body odor was removed through bathing to facilitate interactions in enclosed spaces. This new phenotype became the template for the evolution of a new genotype: less sensitivity to odors of wild plants and animals, lower emissions of male odors, and a more negative response to them. Further change came with the development of fragrances to reodorize the body and the home. This new olfactory environment coevolved with the ability to represent odors in the mind, notably for storage in memory, for vicarious re-experiencing, or for sharing with other people through speech and writing.





Frost, P. (2022). Humans and the olfactory environment: a case of gene-culture coevolution? Psych 4(2): 301-317.  


Monday, June 6, 2022

Recent cognitive evolution in Europe: a new study of ancient DNA


Polygenic scores for alleles associated with educational attainment - Europeans of different time periods (Kuijpers et al. 2022)


According to a new study of ancient European DNA, cognitive evolution stagnated after the last ice age and then speeded up with the rise of farming. It stagnated again during Antiquity and then speeded up again sometime between then and now.



In my last post, I mentioned an ancient DNA study of 99 genomes from sites across Europe and Central Asia. It showed an apparent increase in mean cognitive ability between 4,560 and 1,210 years ago, as measured by alleles associated with educational attainment (Woodley et al. 2017).


That finding has been partially replicated by a new study of 827 genomes from ancient European remains and 250 genomes from modern Europeans. It looks like cognitive evolution stagnated after the last ice age and then speeded up with the rise of farming. It stagnated again during Antiquity and then speeded up again sometime between then and now:


Interestingly, while the period between the Early Upper Paleolithic and the Neolithic is characterized by stagnation or slight decrease in PRS related to intelligence, the genetic data show a clear increase in the scores for educational attainment, intelligence, and fluid intelligence from the Neolithic onwards, while the traits related with unipolar depression tend to decrease from that era on. The most significant differences can be observed comparing the pre-Neolithic and Neolithic groups, as well as the post-Neolithic and modern groups, whereas the period between the Neolithic and post-Neolithic shows a very constant distribution of PRS scores. (Kuijpers et al. 2022).


The authors define the time periods as follows:


Early Upper Paleolithic era – before 28,000 years BC

Late Upper Paleolithic era – 28,000 to 11,000 BC

Mesolithic - 11,000 to 5500 BC

Neolithic - 8,500 to 3900 BC

Post-Neolithic - 5000 BC and more recent ages (no end date given)

Modern – circa 1950 AD


The Mesolithic, the Neolithic, and the Post-Neolithic overlap a lot with each other. This is because their boundaries are defined by cultural changes that came to different parts of Europe at different times. The Neolithic began when hunting and gathering gave way to farming, which came later to northern Europe. Similarly, the post-Neolithic began with the advent of metallurgy, which likewise came later to northern Europe.


Such overlap is problematic for three reasons:


·         In some cases, there is uncertainty as to whether the ancient DNA came from the remains of hunter-gatherers or those of farmers.

·         “Hunter-gatherer” is not a homogeneous category. It includes not only small nomadic groups but also the hunter-fisher-gatherers of the Baltic and North Sea, who attained a degree of sedentism, population growth, and social complexity that we normally associate with farmers (Price 1991).

·         The Post-Neolithic is too long to be meaningful. It covers all of recorded history, and then some.


The study’s authors could have divided the Post-Neolithic into smaller time periods to give us a better look at changes during historical times. In particular, did cognitive evolution regress during Classical Antiquity? That was the preliminary finding of a team led by Michael Woodley of Menie (2019) in a study of ancient DNA from Greece. They found that mean cognitive ability increased from the Neolithic to the Mycenaean period and then decreased sometime between the latter and the present day. That study was never published, perhaps because the geographic area and the time periods were too small to provide robust results.


To get more robust results, we could look at ancient DNA from the entire Greco-Roman world, perhaps divided into three time periods: 5000 to 1000 BC; 1000 to 0 BC; and 0 to 500 AD. Was there a large increase in mean cognitive ability followed by an equally large decrease? Or was there simply a long period of stagnant evolution?


In a previous post, I argued that the culture of Classical Antiquity, particularly in its later stages, caused cognitive evolution to regress (Frost 2022). There were several reasons:


·         A decline in fertility and family formation, particularly among the upper classes;

·         A corresponding increase in female hypergamy, often by freed slaves, which reduced the reproductive importance of upper-class women;

·         An increase in the foreign slave population, which disrupted cognitive evolution within the local population. Even if there had been demographic overflow from the upper classes, that overflow could not have replaced the lower classes, since those classes were being replaced from external sources.


We need a clearer picture. According to the current data, it looks like cognitive evolution simply stagnated during the Post-Neolithic, but I suspect that time period is so broadly defined that it conceals a regression during the centuries before the fifth century collapse and the centuries immediately after.




Frost, P. (2022). When did Europe pull ahead? Evo and Proud, May 16.


Kuijpers, Y., J. Domínguez-Andrés, O.B. Bakker, M.K. Gupta, M. Grasshoff, C.J. Xu, Joosten LAB, J. Bertranpetit, M.G. Netea, and Y. Li. (2022). Evolutionary Trajectories of Complex Traits in European Populations of Modern Humans. Frontiers in Genetics 13: 833190.


Price, T.D. (1991). The Mesolithic of Northern Europe. Annual Review of Anthropology, 20, 211-233. Price, T. D. (1983). The European Mesolithic. American Antiquity 48(4), 761–778.  


Woodley, M.A., S. Younuskunju, B. Balan, and D. Piffer. (2017). Holocene selection for variants associated with general cognitive ability: comparing ancient and modern genomes. Twin Research and Human Genetics 20: 271-280.


Woodley of Menie, M.A., J. Delhez, M. Peñaherrera-Aguirre, and E.O.W. Kirkegaard. (2019). Cognitive archeogenetics of ancient and modern Greeks. London Conference on Intelligence