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Neanderthal Gene Influences Modern Human Nose Shape

Modern human and archaic Neanderthal skulls side by side.
Modern human and archaic Neanderthal skulls side by side, showing difference in nasal height. Credit: Dr. Kaustubh Adhikari, UCL.
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A new study from University College London (UCL) and collaborators finds that genetic material inherited from Neanderthals can affect the nose shape of modern humans. The research is published in Communications Biology.

Linking ancient DNA to modern facial features

In 2010 the first Neanderthal genome was sequenced, an achievement that saw Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, win the 2022 Nobel Prize for Physiology or Medicine. The field of paleogenomics has continued to advance over the last 13 years, with the sequencing of a variety of ancient samples revealing novel insights into the history of our ancient ancestors. “Since the Neanderthal genome has been sequenced, we have been able to learn that our own ancestors apparently interbred with Neanderthals, leaving us with little bits of their DNA,” says Dr. Kaustubh Adhikari, a statistical geneticist in the Stern lab at UCL. We know that these “little bits” of Neanderthal DNA can confer an increased susceptibility to diseases, such as severe COVID-19, while the same gene variants may provide protection against HIV infection.

A collaborative team of researchers, including Adhikari, published a new genome-wide association study (GWAS) that explores genetic markers associated with specific human facial features in over 6,000 Latin Americans. The team identified one specific genome region associated with nose shape that carries genetic material inherited from the Neanderthals. It is the second piece of research that links DNA from ancient humans to modern human facial features; in 2021, the same team identified a gene inherited from ancient Denisovans that influences lip shape.

What is a GWAS study?

A GWAS is a commonly adopted approach in genetics research for identifying genomic variants associated with specific phenotypes, which could include facial features as per this study, or a disease, for example. Participants involved in a GWAS study have their DNA “scanned” to identify variants that occur frequently in individuals that express a phenotype, in which case the variant would be classed as being “associated” with that phenotype. It’s important to note that GWAS cannot prove causation, only correlation.

Neanderthal gene associated with increased nasal height

A common critique of ancient DNA analysis is that the field has predominantly focused on the genetics of European individuals, Dr. Andres Ruiz-Linares, professor of human genetics at UCL and chair of CANDELA (Consortium for the Analysis of the Diversity and Evolution of Latin America), explains: “Most genetic studies of human diversity have investigated the genes of Europeans; our study’s diverse sample of Latin American participants broadens the reach of genetic study findings, helping us to better understand the genetics of all humans.” Ruiz-Linares is a co-corresponding author on the new paper.

The research team collected 2D photographs from over 6,000 volunteers involved in the CANDELA study, all of whom have been previously studied in GWASs exploring physical traits. These individuals were of mixed European, Native American and African ancestry and were recruited from Colombia, Chile, Mexico, Peru and Brazil. Several computer platforms were used to place “landmarks” onto the 2D photographs, which were then compared to the participants’ genetic information. The researchers focused particularly on distance points on the individuals’ faces, such as the space between the tip of the nose or the edge of the lips.

“We detected significant associations at 42 genome regions, 9 of which have been previously reported,” the researchers write. “In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans or Africans, and one mouse homologous region influences craniofacial morphology in mice.”

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In people with Native American ancestry (in addition to east Asian ancestry in a separate cohort), one genome region – ATF3 – contained genetic material inherited from Neanderthals. This genetic material was associated with an increased nasal height. “It has long been speculated that the shape of our noses is determined by natural selection; as our noses can help us to regulate the temperature and humidity of the air we breathe in, different shaped noses may be better suited to different climates that our ancestors lived in,” says Dr. Qing Li from Fudan University, the study’s first author. “The gene we have identified here may have been inherited from Neanderthals to help humans adapt to colder climates as our ancestors moved out of Africa.”

Li and colleagues are confident that the automated approach used in this study could be widely adopted, given the ease-of-access researchers have to 2D photographs. “The study of larger and more diverse study samples should enable a fuller assessment of the genetic architecture of facial variation in the global human population and of the evolutionary forces that have shaped this variation across the world,” the scientists conclude.

Reference: Li Q, Chen J, Faux P, et al. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape. Commun Biol. 2023;6(1):481. doi: 10.1038/s42003-023-04838-7


This article is a rework of a press release issued by University College London. Material has been edited for length and content.