An important advancement in human evolution studies has been achieved after scientists retrieved one of the oldest human genetic data set from an 800.000-year-old tooth belonging to the hominin species Homo antecessor.

The findings by scientists from the University of Copenhagen (Denmark), in collaboration with colleagues from the CENIEH (National Research Center on Human Evolution) in Burgos, Spain, and other institutions including the Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra) in Barcelona are published today April 1, 2020 in Nature.

“Ancient protein analysis provides evidence for a close relationship between Homo antecessor, us (Homo sapiens), Neanderthals, and Denisovans. Our results support the idea that Homo antecessor was a sister group to the group containing Homo sapiens, Neanderthals, and Denisovans, although we have to assume that the phylogenetic trees we have obtained are a good descriptor of the overall population relationships among these hominin groups.” says Frido Welker, Postdoctoral Research Fellow at the Globe Institute, University of Copenhagen, and first author on the paper. 

A research team led by the University of Copenhagen (Denmark) and the National Center for Research on Human Evolution (CENIEH-ICTS) in Burgos and with the participation of the Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra) in Barcelona has recovered one of the oldest human genetic data sets obtained to date. The achievement has been obtained after analyzing a tooth of 800,000 years old, belonging to the Homo antecessor species.

Reconstructing the human family tree

By using a technique called mass spectrometry, researchers sequenced ancient proteins from dental enamel, and confidently determined the position of Homo antecessor in the human family tree.

The new molecular method developed by researchers at the Faculty of Health and Medical Sciences, University of Copenhagen, enables scientists to retrieve molecular evidence to accurately reconstruct human evolution from further back in time than ever before. 

The human and the chimpanzee lineages split from each other about 9-7 million years ago. Scientists have relentlessly aimed to better understand the evolutionary relations between our species and the others, all now extinct, in the human lineage.

“Much of what we know so far is based either on the results of ancient DNA analysis, or on observations of the shape and the physical structure of fossils. Because of the chemical degradation of DNA over time, the oldest human DNA retrieved so far is dated at no more than approximately 400.000 years”, says Enrico Cappellini, Associate Professor at the Globe Institute, University of Copenhagen, and leading author on the paper.

The new paleoproteomic technique allows scientists to retrieve molecular evidence to accurately reconstruct human evolution from times that were not yet accessible.

“Now, the analysis of ancient proteins with mass spectrometry, an approach commonly known as palaeoproteomics, allow us to overcome these limits”, he adds.
 

Theories on human evolution

The fossils analyzed by the researchers were found by palaeoanthropologist José María Bermúdez de Castro and his team in 1994 in stratigraphic level TD6 from the Gran Dolina cave site, one of the archaeological and paleontological sites of the Sierra de Atapuerca, Spain.

Initial observations led to conclude that Homo antecessor was the last common ancestor to modern humans and Neanderthals, a conclusion based on the physical shape and appearance of the fossils. In the following years, the exact relation between Homo antecessor and other human groups, like Neanderthals and ourselves, has been discussed intensely among anthropologists.

Although the hypothesis that Homo antecessor could be the common ancestor of Neanderthals and modern humans is very difficult to fit into the evolutionary scenario of the genus Homo, new findings in TD6 and subsequent studies revealed several characters shared among the human species found in Atapuerca and the Neanderthals. In addition, new studies confirmed that the facial features of Homo antecessor are very similar to those of Homo sapiens and very different from those of the Neanderthals and their more recent ancestors.

“I am happy that the protein study provides evidence that the Homo antecessor species may be closely related to the last common ancestor of Homo sapiens, Neanderthals, and Denisovans. The features shared by Homo antecessor with these hominins clearly appeared much earlier than previously thought. Homo antecessor would therefore be a basal species of the emerging humanity formed by Neanderthals, Denisovans, and modern humans”, adds José María Bermúdez de Castro, Scientific Co-director of the excavations in Atapuerca and co-corresponding author on the paper.

The protein study of the analyzed fossils of Homo antecessor, which were found in 1994 at the TD6 stratigraphic level of the Gran Dolina site (Sierra de Atapuerca), provides evidence of a possible close relationship between Homo antecessor, the common ancestor of the Neanderthals, modern humans, and Denisovans.

World class-expertise

Findings like these are made possible through an extensive collaboration between different research fields: from paleoanthropology to biochemistry, proteomics and population genomics.

Retrieval of ancient genetic material from the rarest fossil specimens requires top quality expertise and equipment. This is the reason behind the now ten-years-long strategic collaboration between Enrico Cappellini and Jesper Velgaard Olsen, Professor at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen and co-author on the paper.

“This study is an exciting milestone in palaeoproteomics. Using state of the art mass spectrometry, we determine the sequence of amino acids within protein remains from Homo antecessor dental enamel. We can then compare the ancient protein sequences we ‘read’ to those of other hominins, for example Neanderthals and Homo sapiens, to determine how they are genetically related”, says Jesper Velgaard Olsen. “I really look forward to seeing what palaeoproteomics will reveal in the future”, concludes Enrico Cappellini.

The study of human evolution by palaeoproteomics will continue in the next years through the recently established EU-funded “Palaeoproteomics to Unleash Studies on Human History (PUSHH)” Marie S. Curie European Training Network (ETN), led by Enrico Cappellini, and involving many of the co-authors on the paper.

"The recovery of molecular samples from very old fossils combined with new computational techniques has brought about a revolution in the way we understand the relationship of species that are no longer among us. Many researchers in this study are involved in a European network of evolutionary work, and the coming years promise to be fascinating, "says Tomàs Marquès-Bonet, director of the Institute for Evolutionary Biology (IBE, CSIC-Pompeu Fabra University) with a dual appointment at the Centro Nacional de Análisis Genómico (CNAG-CRG) of the Centre for Genomic Regulation (CRG) and co-author of the article.

"The recovery of molecular samples from very old fossils combined with new computational techniques has brought about a revolution in the way of understanding the relationship of species that are no longer among us. The coming years promise to be fascinating", says Tomàs Marquès-Bonet, director of the Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra) and co-author of the article.

"In 1997, the Atapuerca team opened a huge scientific debate on the role of Homo antecessor and now we have closed it from where it was not possible to dream at the time, from paleoproteomics. We hope that the same technique will close many more debates in the future "adds Carles Lalueza-Fox, IBE principal investigator and co-author of the article.

"In 1997, the Atapuerca researchers opened a huge scientific debate on the role of Homo antecessor and now we have closed it from where one could not dream at the time, from paleoproteomics. We hope that the same technique will close many more debates in the future"adds Carles Lalueza-Fox, IBE principal investigator and co-author of the article.

The research is mainly funded by VILLUM FONDEN, the Novo Nordisk Foundation, "la Caixa" and the Marie Sklowowska-Curie Actions Individual Fellowship and International Training Network programmes. Excavations and research of the Sierra de Atapuerca sites, in Spain, are funded by the Spanish “Ministerio de Ciencia, Innovación y Universidades”, “Consejería de Cultura” of the the “Junta de Castilla y León”, and the “Fundación Atapuerca”.

Reference article: F. Welker et.al.  The dental proteome of Homo antecessor. Nature; April 2020. DOI: https://doi.org/10.1038/s41586-020-2153-8