Neanderthal DNA in the human population of Latin America

An investigation reveals the true extent of the genetic legacy of Neanderthals in the current human population of Latin America.

“We think of Neanderthals as being very different from us. From the discovery of the first Neanderthal fossils in Europe in the mid-19th century until relatively recently, there was a widespread idea that there was not much in common between them and humans. However, scientific research has made it possible to verify that modern humans have an important genetic contribution from Neanderthals. In other words, we have Neanderthal DNA in different proportions,” explains Miguel Delgado, a researcher at the National Council for Scientific and Technical Research (CONICET) in Argentina as well as a professor at the Faculty of Natural Sciences and Museum of the National University of La Plata (FCNyM, UNLP) in Argentina.

Delgado is a member of an international consortium that, based on information from more than six thousand current people, was able to determine a significant persistent Neanderthal genetic fingerprint in the genes responsible for face variation in various groups of the present-day Latin American population.

The comparison with fossil remains of more than a dozen Neanderthals corroborated the direction of the genetic effect found.

Rolando González-José, CONICET researcher at the Patagonian Institute of Social and Human Sciences (IPCSH, CONICET) and director of the Patagonian National Center (CENPAT, CONICET), and Virginia Ramallo, Council researcher at IPCSH also participated in the study.

Neanderthal skull, from the collection of the Museo de La Plata in Argentina, used for the study. (Photo: CONICET / R. Baridón)

The study is the work of almost 40 researchers, mostly anthropologists and geneticists, from Latin America and Europe who make up the Consortium for the Analysis of Diversity and Evolution in Latin America (CANDELA), oriented to the study of the genetic architecture of the physical variation of the populations that inhabit the continent. “Visible morphological features, such as the shape of the teeth, face and head, plus data at the genomic level, inform us about the diversity and biological evolution that has occurred in the American continent. Emerged in 2010, our consortium was the first to investigate these issues at a regional level”, says Delgado.

The research team, headed by Qing Li from Fudan University in China, based its work on the analysis of the faces of almost 6,500 Latin Americans/as –a large and diverse sample– based on photographs processed in two dimensions using automatic software that It yields coordinates or points of interest that allow the identification and measurement of morphological features. “At the same time, we did different types of genomic analysis to relate the facial morphology of each individual to specific genes. Thus, we identify the regions of the face and the genes that are influencing morphological diversity”, she comments.

The Latin American samples were compared with those of more than 19,000 people from Europe (10,115), Asia (5,298) and Africa (3,631) to see the morphological and genetic relationship with the most recent Latin American ancestors; with data from previous studies; and they were also compared with fossil records of 12 Neanderthals who inhabited much of Europe and Asia between 500,000 and 40,000 years ago, and Denisovans, another population of archaic humans who lived in Asia between 500,000 and 30,000 years ago. “The fossil record of the latter is very scarce, there are only a few dental pieces, skull fragments and a few remains of limbs. In a previous work by our team, we were able to identify a Denisovan haplotype (set of genetic markers) that influences the lower part of the face in current Latin Americans”, Delgado points out, adding: “Likewise, the shape of the nose in the Latin American sample it is also influenced by the Neanderthal heritage.”

According to Delgado, these works show that, in current Latin American populations, different morphological traits –especially in the mid facial region– are directly related to the genetic inheritance of archaic humans as a result of their interbreeding with anatomically modern humans millennia ago.

“This type of study is an example of how the constitution of biobanks that store human diversity enhances all types of research that help us better understand the genetic and non-genetic basis of complex phenotypes. Its implementation is strategic not only for the case of the physical traits studied in this research, but also for specific biomedical traits of the Argentine population, the main argument for the creation of the PoblAr Program,” says González-José.

Delgado postulates that, sometime between 200,000 and 40,000 years ago, the Neanderthal and Denisovan populations interbred with anatomically modern humans at various times, and the gene pool continued from there. Subsequently, that heritage was transmitted to the ancestors of the current Native Americans and Europeans, the latter being the ancestors of the current Latin Americans.

“The Denisovan heritage in present-day Latin Americans came through the Native Americans, while the Neanderthal did through the European component. However, it is still difficult to know the exact moment in which these genetic exchanges occurred, although it is very possible that they have occurred in the last 50,000 years,” Delgado points out, adding: “This genetic inheritance has given us advantages and disadvantages at evolutionary level. The Denisovans, for example, developed in a very complicated environmental context in the Siberian region. The Denisovan component, then, allowed our ancestors to have the ability to adapt to very cold and dry environments. On the other hand, there is evidence of the important relationship of the Neanderthal component in relation to certain diseases”.

A notable aspect of the work is that it was replicated in other current human populations and even in other species (for example, mice), and in all cases many of the genes that influence facial variation were found. “This gives us the pattern that, in reality, the genetic influence is much broader: basically, in vertebrates, but above all for species genetically close to humans such as great apes, that is, chimpanzees, orangutans and gorillas, and archaic hominins”.

For Delgado, this type of study has additional importance on a social level: “They are very useful for overturning xenophobic or racist discourse. Our differences as a species are morphological, not genetic. Structural racism that stigmatizes the other has no genetic basis.

For his part, Ramallo concludes: “It is always interesting to follow the repercussion of studies like this, beyond the conclusions and new research that can be carried out later. I highlight the value of working together, because the construction of knowledge is always a common task. In 2010, when the calls for volunteers began in Mexico, Colombia, Chile, Peru and Brazil, we did not think that we could end up observing the past of our genus Homo. In order to develop more studies in the future, we must commit ourselves solidly and ethically to the projects today. DNA banks and associated information, such as the CANDELA Consortium, allow us to study the variability of our populations and understand the processes that gave rise to it. We have to celebrate that diversity.”

The study is entitled “Automatic landmarking identifies new loci associated with face morphology and involves Neanderthal introgression in human nasal shape”. It has been published in the academic journal Communications Biology, from the Nature group. (Source: Marcelo Gisande / CONICET. CC BY 2.5 AR)