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Genomes, Migrations, and Culture in the Early Civilizations of the Middle East

John Novembre Professor, Department of Human Genetics and Department of Ecology & Evolution
Maanasa Raghavan Neubauer Family Assistant Professor, Department of Human Genetics
David Schloen Professor of Near Eastern Archaeology, Oriental Institute and Department of Near Eastern Languages and Civilizations; Director, Program in Digital Studies of Language, Culture, and History
James Osborne Assistant Professor of Near Eastern Archaeology, Oriental Institute and Department of Near Eastern Languages and Civilizations
Hannah Moots Postdoctoral Fellow, Oriental Institute, University of Chicago; Ph.D. (2021) Anthropology, Stanford University

With support from the Neubauer Collegium for Culture and Society, the Stevanovich Institute on the Formation of Knowledge, and the Department of Human Genetics of the University of Chicago.


In the past forty years, DNA analysis has emerged as a powerful method for understanding genetic variation in modern human populations and for “fingerprinting” individuals. But there was little success in analyzing the skeletal remains of ancient populations due to the degradation of the DNA over time and the fact that ancient DNA samples are very easily contaminated by modern DNA. In just the last five years, however, new laboratory methods have been developed for extracting and sequencing DNA from skeletal remains many thousands of years old. These methods are coupled with innovative statistical and computational techniques for comparing DNA sequences to fill in the gaps and correct for modern contamination. This has enabled the reconstruction of thousands of complete genomes from ancient specimens found in a wide range of geographical and chronological contexts. A brilliant light has suddenly been shed on genetic variation within past human populations around the world, which can now be compared to variation found in present-day populations in the same regions. Historical events can plausibly be inferred to account for the observed variation, answering questions of who moved where and interbred with whom, and when did they do it—and raising the more complicated question of how these population movements and resultant genetic mixing are related to the ethnolinguistic groups known in historical sources and in our world today.

The reconstruction of entire genomes from the distant past has caused an “ancient DNA revolution” that is having a dramatic impact on archaeology and ancient history worldwide—as dramatic as the “radiocarbon revolution” that followed the invention of radiocarbon dating in 1949 by Willard Libby at the University of Chicago. Ancient DNA is overturning firmly entrenched ideas about the migrations and mixing of ancient peoples and re-igniting old debates about the causes of cultural change. Archaeologists today quite rightly resist the crude biological reductionism that animated earlier models of cultural change in the nineteenth and early twentieth centuries. These old models were conceived in terms of sweeping invasions by warlike elites and the domination of one essentialized “people” by another, in many cases with the racist implication that the dominant group were genetically superior to those they conquered and so naturally imposed their culture upon them. It is therefore understandable that recent decades have witnessed an aversion to migration models of cultural change and a preference for models that emphasize endogenous change due to the slow diffusion of ideas. Diffusion models allow for complex social interactions and the possibility that cultural influences are disseminated from the bottom up as well as from the top down within a socio-political hierarchy.

However, it must be admitted that the archaeological evidence is often ambiguous: a change in architectural and material styles in a particular region might have been caused endogenously by diffusion or exogenously by a population migration, or by some combination of the two. And no one denies that population migrations do happen and can have a major cultural impact, so this explanation cannot be ruled out a priori. Nonetheless, an anti-migration mentality took root among archaeologists due to the excesses of previous migration models, the ambiguity of the archaeological evidence, and the absence of direct biological evidence for population migrations.

Now, however, migration models of cultural change are being revived by ancient-DNA studies. In a number of cases where migrations were once doubted we have clear genetic evidence of a striking coincidence between major cultural changes and relatively rapid and large-scale movements of people from one geographical region to another. For example, ancient DNA studies show that there was a major migration from Central Asia into the Indian subcontinent around 2000 BCE that seems to lend credence to older notions of conquest by warlike “Indo-Aryans” with their horses and chariots. These findings have sometimes led geneticists, who are not trained in cultural or historical studies, to speak rather simplistically about the relationship between genetic variation and ethnic identity, in a way that raises red flags for archaeologists and historians. The clash of perspectives between archaeologists and geneticists has caused mutual misunderstanding and unhelpful polemics on the part of some archaeologists, who resist what they see as the implicit racism and positivism of scientific work in human genetics. Most geneticists would reply, however, that when they speak of genetic variation they are by no means endorsing a monolithic concept of “race”— a term they avoid—and they point out that notions of racial purity are in fact undermined by the new data, which show constant movement and mixing of people in the past. (See the discussion of this issue in the popular book published in 2018 by a leading ancient-DNA researcher, David Reich of Harvard University, entitled Who We Are and How We Got Here: The New Science of the Human Past.)

Ancient Human Genomes Map

A map showing all published ancient human genomes from the region dating between 3500 BCE and 500 CE. This 4000-year date range was chosen to span the dates of inhabitation at Kish. The data shown are from a number of publications, compiled and curated by Dr. David Reich’s lab as part of the Allen Ancient DNA Resource (AADR 2021).

We at the University of Chicago are poised to join these debates and make a major impact in this discussion via a collaborative, interdisciplinary approach that fosters mutual understanding across disciplinary boundaries. The co-PIs of this project are very much aware of and sensitive to the complex questions concerning race and identity that arise when we discuss human genetic variation at the level of populations. Unfortunately, there has frequently been a lack of understanding among archaeologists of the methods and interpretive frameworks used by geneticists, and vice versa. The way to avoid a truculent and uncomprehending stalemate is for each side to acquire a deeper knowledge of the methodology and mode of argumentation of the other side in the course of actual research on topics of mutual interest, with a structured series of discussions to lay bare points of disagreement and reach an interpretive consensus. This is what we hope to accomplish in the proposed project.

We are particularly well placed to do this on our campus because UChicago has long been a world leader in archaeology—especially the archaeological investigation of the foundational civilizations of the Middle East via the Oriental Institute, which was established in 1919 and has six archaeologists on its faculty. Within the UChicago faculty as a whole there are fifteen archaeologists in five different departments who specialize in a wide range of regions and periods. More recently, UChicago has become a leader in ancient-DNA research, culminating in the establishment last year by project co-PI Maanasa Raghavan of a state-of-the-art lab for extracting and analyzing DNA from ancient specimens recovered from archaeological contexts (https://www.genscapelab.com/). This ancient-DNA “wet” lab complements the computationally oriented population genetics lab of project co-PI John Novembre (http://jnpopgen.org), which develops statistical methods for extracting information from large-scale genomic data to improve understanding of (1) basic genomic biology, (2) the biology of heritable disease traits, (3) the genetic basis of evolutionary processes, and (4) the history and evolution of various species, especially humans.

Genomes Lab

GenScape lab member, Esha Bandyopadhyay, preparing a sample for DNA extraction.

Meanwhile, co-PIs James Osborne and David Schloen in the Oriental Institute have increasingly engaged with the exciting new data and debates surrounding ancient DNA in the course of their archaeological fieldwork in the Middle East. We are now ready to join forces in collaborative efforts that span the Humanities Division and the Biological Sciences Division, both to pursue groundbreaking research and to develop a curriculum in archaeogenetics that will train UChicago archaeology students in this new specialty, as is already being done at peer institutions such as Stanford.

Middle Eastern Case Studies

The proposed project will focus on three case studies from the Bronze Age of the Middle East (ca. 3000 to 1000 BCE) that raise the question of endogenous cultural change versus exogenous changes due to population migrations. The world’s earliest literate civilizations emerged in the Middle East in this period along the Tigris and Euphrates Rivers in southern Iraq (Sumer) and in the Nile Valley of Egypt. The surrounding regions in Greater Mesopotamia, Anatolia (in presentday Turkey), and the Levant (Syria and Israel/Palestine) were part of this civilizational interaction sphere of the “Ancient Near East” (to use the current scholarly designation). Thus, we have textual records from the third and second millennia BCE, along with copious archaeological data, that have been used to construct historical narratives for the whole of the Ancient Near East in terms of political states and the ethnic and linguistic groups attested in the texts. As in other branches of ancient studies, an early fondness for migration models of exogenous cultural change and a tendency to essentialize ethnolinguistic groups as enduring monolithic entities moving in lockstep around the map have given way in recent decades to a preference for more complex models of social interaction that emphasize the endogenous diffusion of cultural traits. The Middle East therefore presents an excellent opportunity to assess the impact of ancient-DNA research on current historical narratives, which have eschewed what scholars see as overly simplistic migration models but may have been overly skeptical of such models.

Indeed, a major contribution of our project will be to augment significantly the ancient genomic data from the “cradle of civilization” in the Middle East. There has been relatively little ancient DNA analysis of Middle Eastern specimens, in comparison to Europe and other geographical regions, in part because DNA is not as well preserved in the Middle Eastern climate. Techniques for recovering DNA from such specimens have steadily improved, giving us reason to think we will succeed. This is one reason why the proposed project needs a postdoctoral researcher with prior laboratory experience (see below), because such a person can cope with the methodological challenges posed by the poor state of preservation of the DNA.

More specifically, we will analyze the DNA from human remains excavated at the following Bronze Age sites dating to the third and second millennia BCE:

  1. Alishar in central Turkey, a walled city that was excavated by the Oriental Institute from 1927 to 1932 and whose changing population and culture have a bearing on longstanding debates concerning the geographic origin and migration of the “Indo-Europeans,” in light of the fact that the languages of Turkey documented in texts of the second and first millennia BCE are linguistically classified as Indo-European, with vestiges of earlier nonIndo-European languages that were spoken in the area appearing in names found in later texts. The rulers of the Hittite Empire that emerged in central Turkey around 1650 BCE spoke an Indo-European language (Hittite) which is the earliest language of this family.
  2. Kish in southern Iraq, near Baghdad, which was excavated by Chicago’s Field Museum of Natural History from 1923 to 1933. Kish was a massive mudbrick city of the Sumerians of great political and cultural significance. In the course of the third millennium BCE, the Sumerians (whose language is a linguistic isolate unrelated to any known language) came into contact with Semitic speakers called “Akkadians,” who eventually became politically dominant, with the eventual disappearance of Sumerian as a spoken language. There are many unanswered questions about the Akkadian “invasion” (if such it was) and the degree of intermarriage and intermingling of Sumerians and Akkadians in Mesopotamian society. Kish has a long history of occupation and DNA analysis of the human remains recovered from different archaeological levels of this site (primarily crania) will shed light on these questions.
  3. Nahal Tabor in the Northern Jordan Valley in Israel, which was excavated by the Oriental Institute in the 1960s. This is an ancient cemetery that was in use for a long period during the Bronze Age and contains human remains that we will use to test the hypothesis of a major migration from Turkey and Syria into the Southern Levant around 2900 BCE, which has been proposed on archaeological grounds based on pottery styles and other aspects of material culture. If the migration hypothesis is borne out, we want to determine the degree of intermarriage between the indigenous population and the newcomers.

Over the course of the project, we will analyze approximately 80 samples from these three sites. The samples will be taken from inside teeth and from the petrous bone of the inner ear, which are the skeletal locations in which DNA is most likely to be preserved. The human remains from Alishar and Nahal Tabor are currently housed in the Oriental Institute and the Field Museum has agreed to make the crania recovered from Kish available to us for analysis.

DNA Processing Flowchart

DNA extraction, library preparation, and sequencing flow chart. Adapted from image created by Susanna Sawyer