Category Archives: Genetic

The spread of steppe and Iranian-related ancestry in the islands of the Western Mediterranean

IPHES researchers Beatriz Gamarra and Marina Lozano, from the Paleoanthropology department, have collaborated in this research

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The Mediterranean Sea has been a major route for maritime migrations as well as frequent trade during prehistory, yet the genetic history of the Mediterranean islands is not well documented despite recent developments in the study of ancient DNA.

An international team led by Researchers from the University of Vienna, Harvard University and University of Florence, Italy, is filling in the gaps with the largest study to date of the genetic history of ancient populations of Sicily, Sardinia and the Balearic Islands, increasing the number of individuals with reported data from 5 to 66.

The results reveal a complex pattern of immigration from Africa, Asia and Europe which varied in direction and timing for each of these islands. IPHES researchers Beatriz Gamarra and Marina Lozano, from the Paleoanthropology unit, have collaborated in this research. Beatriz Gamarra, now postdoctoral fellow Beatriu de Pinós at IPHES, during her previous period at University College of Dublin (UCD, Ireland), prepared some of the bone samples that were later analyzed by the leading authors of this research in the ancient DNA laboratories of UCD, University of Vienna and Harvard University. Marina Lozano, IPHES researcher and Associate Professor at URV, analyzed the human remains of Cave 127 (Formentera) providing the samples of these individuals and the anthropological context of this site.

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Beatriz Gamarra (left) with Marina Lozano, IPHES researchers

Some of the paper’s most striking findings concern the island of Sardinia. Despite contacts and trade with other Mediterranean populations, ancient Sardinians retained a mostly local Neolithic ancestry profile until the end of the Bronze Age.

However, during the second half of the 3rd millennium BC, one of the studied individuals was of entirely of North African ancestry. Together with two Iberians reported in 2019, this new more than 1% of studied individuals from southern Europe from the Copper and Bronze Ages were part of immigrant families from North Africa.

“Our results show that maritime migrations from North Africa were widespread and important long before the era of the eastern Mediterranean seafaring civilizations and moreover were occurring in multiple parts of the Mediterranean”, says Ron Pinhasi, a co-senior author of the department of Evolutionary Anthropology, University of Vienna.

During the Iron Age expansion and establishment of Greek and Phoenician colonies, the Sardinian individuals analyzed from that period had little, if any, ancestry from the previous long-established populations.

“Despite these population fluxes, modern Sardinians retained 56-62% of ancestry from the first Neolithic farmers that arrived in Europe around 8000 years ago”, says David Caramelli a co-senior author, and Director of Department of Biology at the University of Florence.

The team’s results on Sardinia are fully consistent with the findings of another paper on ancient Sardinian genetics published on the same day in the journal Nature Communication and led by John Novembre, Johannes Krause and colleagues.

The paper also goes beyond Sardinia to understand population changes in other central and western Mediterranean islands.

“One of the most striking findings concerns the arrival of ancestry that ultimately came from the Russian Steppe. While the ultimate origin of this ancestry was Eastern Europe, in the Mediterranean islands much of it arrived from the west, and in fact we can pinpoint Iberia as its specific source”, says David Reich, a co-senior author at Harvard University, who is also an Investigator of the Howard Hughes Medical Institute and at the Broad Institute of MIT and Harvard. “This was likely also the case for the Balearic Islands, in which some early residents probably derived at least part of their ancestry from Iberia”, says first author Daniel Fernandes, of the department of Evolutionary Anthropology, University of Vienna.

Sicily was also impacted from the east by a different movement. People with ancestry related to ancient Greek “Mycenaeans” reached Sicily at a time overlapping the period of Mycenaean trade connections to the island. An important direction for future ancient DNA work will be to determine whether it was Greek migrants, or people from further east in the Mediterranean, who carried this ancestry to Sicily.

Reference

Fernandes, D.M., and alter 2020. “The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean”. Nature Ecology and Evolution.

Genetic data from 1.7 million years ago identified, the oldest recorded to date

The journal Nature has reported the finding of a rhinoceros tooth at the site in Dmanisi, Georgia, where members of IPHES and the URV are working

Molar found in Dmanisi and which has provided the genetic information discussed in the article

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A recent finding has paved the way to a revolution in the study of evolution after an international team working in Dmanisi (Georgia) has acquired genetic data from a 1.7-million-year-old rhinoceros tooth, the oldest to have been identified to date. The data acquired is a full set of proteins – a proteome – identified in the animal’s dental enamel and is 1 million years older than the oldest DNA sequenced from a horse and which dates back 700,000 years.

The finding was announced in an article published in the journal Nature, which was authored by leading scientists from the University of Copenhagen and Saint John’s College (University of Cambridge). However, the project also counted on the participation of 48 other researchers, two of whom were ICREA (Catalan Institute of Research and Advanced Studies) researchers from IPHES (Catalan Institute of Human Palaeoecology and Social Evolution) and the URV (Universitat Rovira i Virgili): Bienvenido Martínez-Navarro, who studies the large carnivores at Dmanisi (bears, hyenas and sabre-toothed tigers), and Jordi Agustí, who analyses the small mammals from the same site, which has become one of the main sources of information on the first humans.

Molar found in Dmanisi and which has provided the genetic information discussed in the article. Credits: Natural History Museum of Denmark

The finding reported in Nature is a major advance in the field of biomolecular studies into ancient fossil remains and may provide an answer to some of the mysteries of animal and human biology, enabling scientists to accurately reconstruct evolution over time, now from much further back in the past.

In the last 20 years, ancient DNA has been used to tackle a variety of questions about the evolution of extinct species, adaptation and human migration, but it has its limits. The new genetic information will make it possible to reconstruct molecular evolution beyond the habitual time limits of the preservation of DNA, so the analysis of ancient protein from dental enamel is the start of an exciting new chapter in the analysis of molecular evolution, as the scientists participating in the study have been quick to point out.

The DNA data that genetically track human evolution only cover the last 400,000 years. But the lineages that led to modern humans and chimpanzees – the living species that is genetically closest to humans – separated some 6 or 7 million years ago, which means that the scientific community currently has no genetic information for 90% of the evolutionary path that has led to modern humans.

Neither does the scientific community know how we are genetically linked to extinct species such as Homo erectus – the oldest species known of the genus Homo with human body proportions similar to those of Homo sapiens. Everything known about Homo erectus at the moment is almost exclusively based on anatomic, not genetic, information.

Stephonorhinus rhinoceros skeleton. Credits: Natural History Museum of Denmark.

The researchers used ancient sequencing technology (based on the innovative technology known as mass spectrometry) to retrieve genetic information from the tooth of a 1.7-million-year-old Stephanorhinus, an extinct species of rhinoceros that lived throughout Mediterranean Europe and in western Asia. They managed to sequence the ancient protein and retrieved genetic information that had been impossible to obtain with DNA sequencing.

Tooth enamel is extremely hard, abundant and long-lasting. It is found in mammals and provides more genetic information than collagen, the only other protein that has been retrieved from fossils more than a million years old. As a result, applying mass spectrometry to this material opens up a wide range of possibilities for a more advanced evolutionary study in both humans and mammals, and it will revolutionise research methods based on molecular markers.

Molecular phylogenetic analyses show that the Stephanorhinus rhinoceros comes from a group related to the woolly rhinoceros (Coelodonta antiquitatis). This shows that Coelodonta evolved from a primitive representative of Stephanorhinus which, therefore, has at least two evolutionary lines.

This rearrangement of the evolutionary lineage of a single species may seem like a mere small adjustment, but the identification of changes in numerous extinct mammals and humans may lead to a new understanding of how the world has evolved. The discovery may enable scientists from all over the world to collect genetic data  from ancient fossils and construct a larger, more accurate picture of the evolution of hundreds of species, including our own.

Bibliographic reference. Cappellini et al., “Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny”, Nature  (2019).