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Ancient Tooth Proteomes Clarify Hominin Relationships, Evolutionary History

NEW YORK – A paleoproteomic analysis of tooth samples from ancient hominins in Spain and Georgia suggests that a species called Homo antecessor belongs to a deep hominin lineage adjacent to that containing humans and related archaic hominins.

"Our results support the idea that Homo antecessor was a sister group to the group containing Homo sapiens, Neanderthals, and Denisovans," co-first author Frido Welker, a postdoctoral researcher in evolutionary genomics at the University of Copenhagen's Globe Institute, said in a statement. He and his colleagues published their findings in Nature on Wednesday.

Recognizing the rampant DNA degradation that can occur in very old samples, Welker and colleagues from the University of Copenhagen, the Max Planck Institute of Biochemistry, and elsewhere used mass spectrometry to analyze proteins in dental enamel samples from an 800,000-year-old H. antecessor representative (estimated at between 772,000 and 949,000 years old) from a site in Sierra de Atapuerca, Spain, along with a 1.78 million-year-old molar sample from a Homo erectus sample from Dmanisi, Georgia.

"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," co-senior author Enrico Cappellini, an evolutionary genomics researcher at the University of Copenhagen, said in a statement, noting that "the analysis of ancient proteins with mass spectrometry, an approach commonly known as palaeoproteomics, allows us to overcome these limits."

With these newly assessed enamel proteomes, and data from more recent human tooth samples, the team performed a protein-based phylogenetic analysis that pointed to a split between the H. antecessor lineage and the lineage leading to modern humans, Neanderthals, and Denisovans.

"Our dataset provides a unique molecular resource of hominin biomolecular sequences from Early and Middle Pleistocene hominins, and represents — to our knowledge — the oldest ancient hominin proteomes presented to date," the authors wrote, noting that their current results suggest "H. antecessor represents a hominin taxon closely related to the last common ancestor of H. sapiens, Neanderthals, and Denisovans."

Because available H. antecessor samples suggest that the ancient hominin shared some facial features with modern humans that are not found in archaic hominins such as Neanderthals or Denisovans, meanwhile, the investigators suggested that these facial features may have "considerably deep ancestry in the genus Homo." That, in turn, indicates that characteristic Neanderthal-like facial features represent a derived, rather than ancestral, cranial morphology.

"The features shared by Homo antecessor with these hominins clearly appeared much earlier than previously thought," co-corresponding author José María Bermúdez de Castro, scientific co-director of excavations at an archaeological and paleontological site at Sierra de Atapuerca in Spain, said in a statement. "Homo antecessor would therefore be a basal species of the emerging humanity formed by Neanderthals, Denisovans, and modern humans."