Ancient DNA from Sardinia reveals the genetic footprints of changing connectivity across the Mediterranean over six thousand years

Analysis of ancient DNA details the population history of the Italian island, providing new insight into its unique history and ancestral connections to other peoples of the Mediterranean

Joint release with the University of Chicago

The research, published in Nature Communications, analyzed genome-wide DNA data for 70 individuals from more than 20 Sardinian archaeological sites spanning roughly 6,000 years from the Middle Neolithic through the Medieval period.  No previous study has used genome-wide DNA extracted from ancient remains to look at the population history of Sardinia.  

“Geneticists have been studying the people of Sardinia for a long time, but we haven’t known much about their past,” said the University of Chicago’s John Novembre, PhD, a leading computational biologist who studies genetic diversity in natural populations. “There have been clues that Sardinia has a particularly interesting genetic history, and that understanding this history could also have relevance to larger questions about the peopling of the Mediterranean.”

The people of Sardinia have long been understood by geneticists as useful to study to understand human health. The island has one of the highest rates of people who live to 100 years or more, and its people have higher than average rates of autoimmune diseases and disorders such as beta-thalassemia and G6PD deficiency.  Many villages in Sardinia also have high levels of relatedness, which makes uncovering the genetics of traits simpler. Across the island, the frequencies of genetic variants often differ from mainland Europe.  These factors have made Sardinia a useful place to study genetic variants that may be linked to disease and aging.

Sardinia also has a unique archaeological, linguistic, and cultural heritage, and has been part of Mediterranean trade networks since the Neolithic age. How much the population’s genetic ancestry has changed through these times, however, has been unknown.  

To generate a new perspective on the genetic history of Sardinia, Francesco Cucca, a geneticist from the Università di Sassari, Italy, and Novembre brought together an interdisciplinary group with archaeologists and ancient DNA experts. The team, led by Johannes Krause at the Max Planck Institute for the Science of Human History in Jena and the University of Tübingen, helped coordinate the sampling and carried out the DNA sequencing and authentication.  The teams led by Novembre and Cucca then analyzed the data and shared the results with the whole group for an interdisciplinary interpretation.

“We were thrilled to be able to generate such a dataset spanning six thousand years because the retrieval of ancient DNA from skeletal remains from Sardinia is very challenging,” shared Cosimo Posth, an archaeogeneticist at the Max Planck Institute and co-first author of the study.  

Sampling DNA from ancient remains allows scientists to get a snapshot of people living at a specific time and place, instead of using modern DNA and inferring the past based on assumptions and mathematical models.  When the team compared the DNA of 70 ancient individuals collected from Sardinia to the DNA of other ancient and modern individuals, they uncovered two major patterns.

First, they saw that individuals in the Middle Neolithic period (4100-3500 BCE) were closely related to people from mainland Europe of the time.  Afterwards, genetic ancestry remained relatively stable on the island through at least the end of the “Nuragic” period (~900 BCE). This pattern differs from other regions of mainland Europe which experienced new ancestries entering from people moving across the continent in the Bronze Age.  

The results show the development of Sardinia’s distinctive nuraghe stone towers and culture (after which the Nuragic period is named) did not coincide with any detection of new genetic ancestry arriving to the island.  

“We found striking stability in ancestry from the Middle Neolithic through the end of the Nuragic period in Sardinia” said Joe Marcus, a PhD student in the Department of Human Genetics at the University of Chicago and a co-first author on the paper.  

Second, the team found evidence of the arrival of ancestry from different populations across the Mediterranean, first with Phoenicians originating from the Levant (modern-day Lebanon) and Punics, whose culture centered in Carthage (modern-day Tunisia).  Then, new ancestry continues being observed in the Roman period and further in the Medieval period as Sardinia becomes historically influenced by migration of people from modern-day Italy and Spain.

“We observed clear signals of dynamic periods of contact linking the island to the rest of the Mediterranean, appearing first in individuals from two Phoenician and Punic sites as early as 500 BCE, and then in individuals from the Roman and Medieval periods” said Harald Ringbauer, PhD, a postdoctoral researcher involved in the computational data analysis at the University of Chicago and a co-first author on the paper.

The group’s results help explain similarities with DNA from mainland European individuals of the Neolithic and Copper Age, such as “Ötzi the Iceman”, an almost perfectly preserved, 5,300-year-old human discovered in alpine ice in northern Italy in 1991. Specifically, among modern Europeans, Ötzi’s DNA is most similar to modern-day Sardinians.  The new study supports the theory that this similarity remains because Sardinia had less turnover of genetic ancestry over time than mainland Europe which experienced large-scale migrations in the Bronze Age.

This model of Sardinia’s population history—establishment followed by relative isolation and then the arrival of new sources of diversity—provides a new framework for understanding how genetic variants linked to disease risk and aging-related traits arose and spread.  Besides providing new insight into mysteries of the past, studying ancient DNA also has implications for the well-being of present-day humans.  

“For future studies, we want to look more precisely at mutations that we think are involved in disease and track their changes through time to understand how and why they changed in frequency,” Novembre said. “That will help us understand the history of these diseases, and in turn gain a richer view of human health and the factors shaping it.”

The study, “Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia,” was published February 24, 2020 in Nature Communications.  An independent study in Nature Ecology and Evolution also published February 24, 2020 comes to similar conclusions using different samples.