Replacement or continuity?

 

Inuit meat cache, Kazan River (source: Library and Archives Canada / PA-101294). Because of their high meat diet, hunters produce more body heat than farmers do. Natural selection has thus favored certain mtDNA sequences over others in humans with this profile of heat production. A change in selection pressure may therefore explain, at least in part, the genetic divide between late hunter-gatherers and early farmers in Europe.

 

Who were the ancestors of present-day Europeans? The hunter-gatherers of the Paleolithic and the Mesolithic? Or the Neolithic farmers who began to spread out of the Middle East some 10,000 years ago?

This debate has teetered back and forth for the past thirty years. On the basis of various genetic polymorphisms, L.L. Cavalli-Sforza and his students argued that Europeans are largely descended from Middle Eastern farmers (Ammerman and Cavalli-Sforza, 1984; Cavalli-Sforza et al., 1994). On the basis of mtDNA and Y chromosomal data, two other research teams, one led by Martin Richards and the other by Ornella Semino, maintained that the European gene pool is over 75% of native hunter-gatherer origin (Richards et al., 2000; Semino et al., 2000). If we look only at the present-day gene pool, Europeans seem far too differentiated to be the descendants of Neolithic farmers from the Middle East.

Over the last few years, new evidence has swung the debate back to the model of population replacement. By retrieving DNA from ancient skeletal remains, we can now compare the latest hunter-gatherers with the earliest farmers, and what we see is a sharp genetic divide between the two (Bramanti et al., 2009). The farmers seem to have been immigrants who replaced the hunter-gatherers. This is direct evidence, so what more is there to say? Facts are facts.

Yet there is always more to say. Facts may be illusory or, if real, wrongly interpreted. For one thing, wherever we have a fairly continuous time series of ancient DNA, the genetic divide no longer appears between the latest hunter-gatherers and the earliest farmers. It appears between the earliest farmers and somewhat later farmers. This is particularly so when we examine haplogroup U lineages, whose disappearance is widely seen as evidence for population replacement. According to a study of 92 Danish remains, these lineages remained common after the Neolithic and reached their current low prevalence only during the Early Iron Age (Melchior et al., 2010).

If this genetic divide is not solely due to population replacement, what else might be responsible? Mishmar et al. (2003) were the first to suggest natural selection:

Thus, extensive global population studies have shown that there are striking differences in the nature of the mtDNAs found in different geographic regions. Previously, these marked differences in mtDNA haplogroup distribution were attributed to founder effects, specifically the colonizing of new geographic regions by only a few immigrants that contributed a limited number of mtDNAs. However, this model is difficult to reconcile with the fact that northeastern Africa harbors all of the African-specific mtDNA lineages as well as the progenitors of the Eurasia radiation, yet only two mtDNA lineages (macrohaplogroups M and N) left northeastern Africa to colonize all of Eurasia (1, 2) and also that there is a striking discontinuity in the frequency of haplogroups A, C, D, and G between central Asia and Siberia, regions that are contiguous over thousands of kilometers. Rather than Eurasia and Siberia being colonized by a limited number of founders, it seems more likely that environmental factors enriched for certain mtDNA lineages as humans moved to the more northern latitudes.

[...] We now hypothesize that natural selection may have influenced the regional differences between mtDNA lineages. This hypothesis is supported by our demonstration of striking differences in the ratio of nonsynonymous (nsyn)/synonymous (syn) nucleotide changes in mtDNA genes between geographic regions in different latitudes. We speculate that these differences may reflect the ancient adaptation of our ancestors to increasingly colder climates as Homo sapiens migrated out of Africa and into Europe and northeastern Asia.

This hypothesis has since received support from Balloux et al. (2009):

We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the ND₃ and ATP6 genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans.

Humans have to adapt to two sources of warmth: climate and internal body heat, which in turn varies with lifestyle and diet. Diet in particular results in different patterns of body heat production between hunter-gatherers and farmers, as explained by Speth (1983):

One aspect of protein metabolism relevant to this issue concerns the high "specific dynamic action" (SDA) of protein ingestion. The SDA of food refers to the rise in metabolism or heat production (diet-induced thermogenesis) resulting from the ingestion of food [...] The SDA of a diet consisting largely of fat is about 6- 14%, while that of a diet high in carbohydrates is about 6%. In striking contrast, the SDA of a diet consisting almost entirely of protein may be as high as 30%; or, in other words, for every 100 calories of protein ingested, up to 30 calories are needed to compensate for the increase in metabolism. Thus, persons whose diets are high in protein experience higher metabolic rates than those whose diets are composed largely of carbohydrate. For example, members of Eskimo populations, at least 90% of whose caloric needs were traditionally met by meat and fat (cf. Draper 1980:263; Hoygaard 1941), had basal metabolic rates 13 to 33% above the DuBois standard, which is based on the metabolic rates of populations consuming western diets (Itoh 1980:285).

Conclusion

Before ancient DNA became available, the prehistory of populations had to be inferred. The age of a genetic lineage was inferred from the degree of differentiation divided by the mutation rate. Since both variables could be known only approximately, the time depths of Europe's genetic lineages were likewise known only approximately.

Ancient DNA seems to promise a clearer picture because the only source of uncertainty is the age of the skeletal material. Unfortunately, this new method is more sensitive to uncertainty from another source: natural selection. Late hunter-gatherers and early farmers had to adapt to different environments. There certainly was a genetic divide between the two, but did it result from differences in origin or from differences in natural selection?

Natural selection distorts the picture if either method is used, since both assume that mtDNA is selectively neutral. The distortion is more serious, however, with the new method, which assumes selective neutrality across the genetic divide between late hunter-gatherers and early farmers—the very moment in prehistory when this assumption is most likely to fail. The old method assumes selective neutrality throughout the entire time depth of Europe’s genetic lineages—an assumption that may indeed be true over most of that time.

Even if the lineage has no selective value in and of itself, natural selection can still distort the picture. This is especially so for mtDNA:

Selection can change allele frequency even at a locus not responsible for fitness differences. Because there is little or no recombination in mitochondrial DNA, selection at one nucleotide affects the frequencies of all other variable nucleotides for the whole molecule. Selection on the nuclear genome, particularly nuclear-encoded proteins that are imported into the mitochondrion and X-linked markers that can have a high effective linkage to mtDNA, can also cause changes in the frequencies of mtDNA haplotypes. Equally importantly, selection on any other cytoplasmically inherited traits will directly affect the frequencies of mtDNA. (Ballard and Whitlock, 2004)

This is less of a problem with nuclear DNA because of recombination, but the problem remains if the presumably neutral gene is close to another gene of high selective value.

In raising these points, I am not trying to argue that Middle Eastern farmers made no contribution to the European gene pool. There is good archaeological evidence of these farmers pushing up the Danube and into central Europe. Elsewhere, however, the evidence for population replacement becomes weaker and the evidence for continuity correspondingly stronger. This is the conclusion that Zvelebil and Dolukhanov (1991) make with respect to northern and eastern Europe:

The transition to farming occurred very slowly and took a long time to complete, the whole process lasting 1500-4000 years. In the far north and northeast of Europe, the process was never completed. [...] Local hunter-gatherer societies played a significant role in the transition. There is strong evidence for continuity in material culture in most regions throughout the transition. Although this neither proves nor disproves the case for population movement associated with the transition (small groups of people could have migrated, leaving little or no trace in the archaeological record), such evidence does not support the colonization model for the transition to farming and it does indicate that local hunter-gatherer traditions were passed on from generation to generation during the long period of the adoption of farming.

And yet the advent of farming brought massive genetic change to northern and eastern Europe, including widespread decline of haplogroup U—the sort of change that is supposed to mean massive population replacement. Since farming began to spread to this region only 6,000 years ago, even later among the Finnish and Baltic peoples, there is only a very narrow time frame in which northern and eastern Europeans could have evolved their characteristic physical appearance, assuming of course that population replacement had actually happened.

Even in central Europe, where population replacement is well documented, we are still unsure whether it was permanent or temporary. Indeed, we see evidence of the replacers being later replaced, perhaps by natives who had never disappeared from the vicinity of the farming settlements (Haak et al., 2005; Rowley-Conwy, 2011).

 

References

Ammerman, A.J. and L.L. Cavalli-Sforza. (1984). The Neolithic Transition and the Genetics of Populations in Europe, New Jersey: Princeton University Press.

Ballard, J.W.O. and M.C. Whitlock. (2004). The incomplete natural history of mitochondria, Molecular Ecology, 13, 729-744.

http://dna.ac/filogeografia/PDFs/Ballard%26Whitlock_04_MTrev.pdf

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. Biological Sciences, 276 (1672), 3447-55.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817182/?tool=pmcentrez

Bramanti, B., M. G. Thomas, W. Haak, M. Unterlaender, P. Jores, K. Tambets, I. Antanaitis-Jacobs, M.N. Haidle, R. Jankauskas, C.-J. Kind, F. Lueth, T. Terberger, J. Hiller, S. Matsumura, P. Forster, and J. Burger. (2009). Genetic discontinuity between local hunter-gatherers and Central Europe's first farmers, Science, 326 (5949), 137-140.

http://jsarf.free.fr/palanthsci/Europe's%20First%20Farmers%20Were%20Immigrants.pdf

Cavalli-Sforza, L.L., P. Menozzi, and A. Piazza. (1994). The History and Geography of Human Genes, New Jersey: Princeton University Press.

Haak, W., P. Forster, B. Bramanti, S. Matsumura, G. Brandt, M. Tänzer, R. Villems, C. Renfrew, D. Gronenborn, K.W. Alt, and J. Burger. (2005). Ancient DNA from the first European farmers in 7500-year-old Neolithic sites, Science, 310 (5750), 1016-1018.

http://www.sciencemag.org/content/310/5750/1016.short

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

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011898#pone-0011898-g002

Mishmar, D., E. Ruiz-Pesini, P. Golik, V. Macaulay, A.G. Clark, S. Hosseini, M. Brandon, K. Easley, E. Chen, M.D. Brown, R.I. Sukernik, A. Olckers, and D.C. Wallace. (2003). Natural selection shaped regional mtDNA variation in humans, Proceedings of the National Academy of Sciences (USA), 100 (1), 171-176.

http://www.pnas.org/content/100/1/171.full

Richards, M., V. Macaulay, E. Hickey, E. Vega, B. Sykes, et al. (2000). Tracing European founder lineages in the Near Eastern mtDNA pool, American Journal of Human Genetics, 67, 1251-1276.

http://www.sciencedirect.com/science/article/pii/S0002929707629541

Rowley-Conwy, P. (2011). Westward ho! The spread of agriculturalism from Central Europe to the Atlantic, Current Anthropology, 52 (S4), S431-S451.

http://arkeobotanika.pbworks.com/w/file/fetch/48307263/Rowley-Conwy%2011%20CA%20Farming%20westward.pdf

Semino, O., G. Passarino, P.J. Oefner, A.A. Lin, S. Arbuzova, et al. (2000). The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective, Science, 290, 1155-1159.

http://fboekelo.tripod.com/boekelo/GP/semino.pdf

Speth, J.D. (1983). Energy source, protein metabolism, and hunter-gatherer subsistence strategies, Journal of Anthropological Archaeology, 2, 1-31.

http://faculty.ksu.edu.sa/archaeology/Publications/Hearths/Energy%20source,%20protein%20metabolism,%20and%20hunter-gatherer%20subsistence%20strategies.pdf

Zvelebil, M. and P. Dolukhanov. (1991). The transition to farming in Eastern and Northern Europe, Journal of World Prehistory, 5, 233-278.

http://link.springer.com/article/10.1007/BF00974991