Introduction & Methods
The demographic history of the human species has always fascinated us. It is known that the ancestral human lineage appeared in East Africa, and that it subsequently migrated out of Africa towards Eurasia, separating into distinct lineages through time. Although many studies have focused on human demographic history, some aspects remain unknown, partly due to the difficulty in finding ancient samples from wide geographic and temporal scales. Particularly, the specific origins of certain populations at more local scales, remains uncertain.
For example, it is known that early European farmers originated at least in part from the Near-East, which was one of the centers of the development of agriculture, and that hunter-gatherers were already present in Europe when early farmers arrived. However, as Lazaridis et al (2014) mention, modeling present-day Europeans as a mixture of only these two ancestral populations does not account for all present genetic diversity. Their main goal was therefore to clarify the prehistory of present-day Europeans.
To address this question, the authors sequenced the genomes of nine ancient Europeans: seven from Sweden and one from Luxembourg (hunter-gatherers), as well as one farmer from Stuttgart, Germany, a member of the first widespread farming culture in central Europe.
They compare these ancient genomes with those of other ancient and contemporary humans in order to investigate from which ancestral groups modern European groups derive. They first perform a PCA analysis of all genomes, then calculate test statistics for admixture between populations in order to investigate the ancestry of present-day European populations, and finally model the deep relationships between populations.
Main Findings
Figure 2 of the paper shows a PCA allowing us to get a sense of the similarity between all ancient and modern populations. I always find it interesting to see geographic patterns in PCAs using genetic data. Looking at Figure 2 we see that there is a West/East pattern from left to right on the graph – present-day Near-Easterners cluster to the right, whereas present-day Westerners cluster more to the left.
An ancient West hunter-gatherer group clusters even further to the left, while an early European farmer cluster, including the farmer individual newly sequenced for this paper, falls between the ancient West hunter-gatherer group and the present-day Near-Easterners. There is also a cluster corresponding to what the authors call an “ancient North Eurasian” population.
Drawing from these observations as well as the test statistics and the admixture model, some of the main findings of the paper are:
1) The Stuttgart farmer’s ancestors were likely of Near-Eastern origin, consistent with the assumption that European farmers originated from the Near-East.
2) Early European farmers had some ancestry from West hunter-gatherers, meaning that early farmers originated from the Near-East but mixed with hunter-gatherers after their arrival to Europe.
3) Modern Europeans derive from at least three ancestral populations: West hunter-gatherers, early European farmers, and the ancient North Eurasian population. Ancient North Eurasian ancestry has increased in the European population since the time of early farmers.
Further Personal Comments
Although this article addresses a novel and interesting question, I thought it was poorly written and hard to follow. The authors jump from one subject to another and the text lacks a pleasant reading flow.
Many methodological aspects are therefore difficult to grasp, and some remain unclear – for example, on the PCA in Fig. 2, it is unclear why the ancient genomes are “projected” onto the principal component space. Understanding the test statistics calculated is also difficult, and almost impossible without referring to the supplementary information.
I thought it would have been interesting to have more than one ancient farmer sample, but considering the difficulty in finding such ancient genomes the small sample size isn’t’ surprising. It may however be a bit of a stretch to interpret observations such as the copy number of salivary amylase genes or the presence of skin-lightening alleles from so few individuals. I thought these points seemed to be superfluous and were mentioned only to entice readers with the mention of putatively adaptive diversity.
Nevertheless, it is an interesting topic and shows that human demographic history is quite complex, consisting of many migration and admixture events. This paper brings us a small step closer towards understanding this complexity – at least in a European context.
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P., Schraiber, J., Castellano, S., Lipson, M., Berger, B., Economou, C., Bollongino, R., Fu, Q., Bos, K., Nordenfelt, S., Li, H., de Filippo, C., Prüfer, K., Sawyer, S., Posth, C., Haak, W., Hallgren, F., Fornander, E., Rohland, N., Delsate, D., Francken, M., Guinet, J., Wahl, J., Ayodo, G., Babiker, H., Bailliet, G., Balanovska, E., Balanovsky, O., Barrantes, R., Bedoya, G., Ben-Ami, H., Bene, J., Berrada, F., Bravi, C., Brisighelli, F., Busby, G., Cali, F., Churnosov, M., Cole, D., Corach, D., Damba, L., van Driem, G., Dryomov, S., Dugoujon, J., Fedorova, S., Gallego Romero, I., Gubina, M., Hammer, M., Henn, B., Hervig, T., Hodoglugil, U., Jha, A., Karachanak-Yankova, S., Khusainova, R., Khusnutdinova, E., Kittles, R., Kivisild, T., Klitz, W., Ku?inskas, V., Kushniarevich, A., Laredj, L., Litvinov, S., Loukidis, T., Mahley, R., Melegh, B., Metspalu, E., Molina, J., Mountain, J., Näkkäläjärvi, K., Nesheva, D., Nyambo, T., Osipova, L., Parik, J., Platonov, F., Posukh, O., Romano, V., Rothhammer, F., Rudan, I., Ruizbakiev, R., Sahakyan, H., Sajantila, A., Salas, A., Starikovskaya, E., Tarekegn, A., Toncheva, D., Turdikulova, S., Uktveryte, I., Utevska, O., Vasquez, R., Villena, M., Voevoda, M., Winkler, C., Yepiskoposyan, L., Zalloua, P., Zemunik, T., Cooper, A., Capelli, C., Thomas, M., Ruiz-Linares, A., Tishkoff, S., Singh, L., Thangaraj, K., Villems, R., Comas, D., Sukernik, R., Metspalu, M., Meyer, M., Eichler, E., Burger, J., Slatkin, M., Pääbo, S., Kelso, J., Reich, D., & Krause, J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans Nature, 513 (7518), 409-413 DOI: 10.1038/nature13673