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When indigenous people occupied Lagoa Santa

Ancient DNA reveals rapid human colonization of South America 14,000 years ago

When the girl who would later become known as Luzia lived in a cave in what is now the town of Lagoa Santa, Minas Gerais, some 11,000 years ago, she could never have imagined that in the twenty-first century, her appearance and ancestry would be the source of intrigue and debate among scientists (see article). Genetic sequencing of her compatriots and contemporaries—but not Luzia herself—suggests that the large lips and broad nose, features typically associated with the humans that first occupied the Americas, probably do not represent reality. “Luzia was a native American, she was not African,” says geneticist Tábita Hünemeier, from the Institute of Biosciences at the University of São Paulo (IB-USP). “The genetic data shows that the ancestry of the people in Lagoa Santa is 100% Amerindian, with the possible exception of one individual, 3% of whose genome originates from another population,” says archaeologist André Strauss, from the Museum of Archaeology and Ethnology at USP. He and Hünemeier are coauthors of a study published in the journal Cell and he is named on another in Science, both published on November 8, which establish a new chapter in the story of how the Americas were colonized. The people of Lagoa Santa have a great deal of information to share.

The findings surprised Brazilian archaeologists, since Luzia’s people were the basis for the popular theory proposed 30 years ago by bioanthropologist Walter Neves, recently retired from IB-USP, on how the Americas were settled (see Pesquisa FAPESP issue no. 195). Neves measured skulls collected in the region, observing that they were different from those found elsewhere. He proposed that the population was descended from a first wave of migrants with physical characteristics similar to current Australians and Africans, and that they left no descendants of their own. Based on this interpretation, British forensic expert Richard Neave, from the University of Manchester, UK, reconstructed Luzia’s face in the 1990s. The indigenous peoples who later became typical of the continent, meanwhile, descended from a later migratory wave, more East Asian in appearance: with straight, dark hair and narrow eyes. According to Brazilian anthropologist Mark Hubbe, from Ohio State University, USA, and one of the authors of the Cell paper, this theory is not necessarily disputed by the new studies. “The Lagoa Santa morphology is not highly specific—it is similar to late Pleistocene groups and continues in populations of African origin,” he says. “Although the settlement of North America resulted from a single demographic expansion, Neves’s model is still applicable in South America, which has undergone a more complex process.”

But this complexity has nuances, now revealed by scientists who have used ancient DNA to sequence the complete genome of these peoples, allowing them to reconstruct their history in more detail. In 2012, while studying his PhD at the Max Planck Institute in Germany, Strauss began studying the DNA of bones found in Lapa do Santo, a cave in the Lagoa Santa region (see Pesquisa FAPESP issue no. 247). The sequencing was performed by German biochemist Johannes Krause, who is also a coauthor of the Cell article and currently directs the Max Planck Institute for the Science of Human History. “At first, we didn’t have much success,” recalls Strauss. But then other researchers demonstrated that the petrous bone, from near the ear, was a better source of DNA. The problem is that removing this dense piece of bone is a destructive process and any damage to an important specimen like Luzia would be unacceptable. Strauss’s group minimized the risk by generating high-definition three-dimensional images. The study examined the ancient DNA of 49 individuals from 16 locations in Central and South America (seven from Lapa do Santo and eight from three other locations in Brazil) and proposes a change to the Neves model.

In 2015, American statistician and bioinformatics researcher David Reich, from Harvard University, contacted geneticists Francisco Salzano (1928–2018) and Maria Cátira Bortolini, from the Federal University of Rio Grande do Sul (UFRGS). He had conducted an exploratory analysis of DNA from the Amazonian Surui and Karitiana peoples using in vitro cell cultures, but lacked the knowledge of these indigenous populations needed to interpret the data. “The two populations are highly comparable, with very similar members,” explains Hünemeier. A broader sample indicated that peoples from Australia and Melanesia contributed to the settlement of South America, arriving via the Bering Strait, which linked Siberia to Alaska at the time. A later wave of descendants of natives from Oceania and Asia became known as population Y (see Pesquisa FAPESP issue no. 234). Its existence, however, is questioned in the study published in Cell this month—coordinated by Reich.

The article suggests that Luzia’s people were similar to the Clovis culture, which lived in present-day North America. The research involved analysis of 12,800-year-old bones found at the Anzick archaeological site in the USA. This line of ancestry has also been identified in the earliest skulls examined in Belize, in Central America, and Los Rieles, in Chile. Between 9,000 years ago and now, the picture changes. “The lineage was completely replaced by another migratory wave that quickly spread, with the Luzia branch disappearing completely,” says Hünemeier (see map).

The similarity is genetic, but it has not been possible to estimate what the Clovis people looked like. “We only have the skullcap of one young man from Anzick,” says IB-USP archaeologist Mercedes Okumura, who did not participate in the studies and is the current coordinator of the laboratory set up by Walter Neves. More skulls and skeletons are needed to get a solid idea of what the Clovis population looked like, but for the people of Lagoa Santa, British forensic reconstruction specialist Caroline Wilkinson, from Liverpool John Moores University, UK, has proposed a new physiognomy in partnership with Strauss, based on the scanned skull and the newly discovered absence of Australo-Melanesian ancestry.

A very similar story regarding the colonization of South America is described in a paper published in the journal Science, written by geneticist Eske Willerslev, from the University of Copenhagen. Based on DNA extracted from 15 skeletons found in locations ranging from Alaska to Patagonia, six of which are over 10,000 years old, it is clear that human populations spread rapidly throughout South America as soon as they passed the glacial areas of North America more than 14,000 years ago. The speed of their dispersal is evident thanks to DNA from five skeletons collected in Lagoa Santa by Danish scientist Peter Lund in the nineteenth century. The bones were found in the Sumidouro cave and kept in the Natural History Museum of Denmark—the same collection that Neves examined and which inspired his model. The genome of these skeletons is very similar to that of the mummy from Spirit Cave, in the USA, a contemporary of the oldest Lagoa Santa specimen.

“The two articles agree on the rapid expansion and likely second wave of migration to South America,” summarizes Mexican geneticist Víctor Moreno-Mayar, a postdoctoral fellow at the Center for Geogenetics in Copenhagen, and lead author of the study. “A population established in Mesoamerica, probably in Mexico, also contributed by moving both north and south around 8,000 years ago,” he adds, noting that the outcome is different to that seen with the other group. He explains that the classic model describes a movement from north to south, where people colonized each location and then stayed there. But the reality seems to have been less straightforward. “This occupation process probably took place along the Pacific coast, giving rise to both the people who occupied Monte Verde [archaeological site in Chile] and the people of Lagoa Santa,” says geneticist Fabrício Santos, from the Federal University of Minas Gerais, coauthor of the study. “They were settling a continent with no human competitors.”

Caroline Wilkinson / John Moores University

Santos emphasizes the historical importance of analyzing the material collected by Lund. “Today we know that all these ancient peoples in the Americas, prior to about 8,000 years ago, shared very similar morphologies with few Mongolian traits,” he says. Despite this, all the analyzed Paleoamericans—the term used for the oldest inhabitants of the continent, which had a distinct appearance from subsequent peoples—are genetically more similar to present-day indigenous populations than any other past or present human group. The DNA of one of the individuals from the Sumidouro cave contained segments similar to those found in populations of Australia and Asia—the population Y described by Reich in 2015. It is still unclear what the finding means, since nothing similar was identified in the samples from North America, through which the populations would have migrated. Not even in Spirit Cave. “In any case, there is no link between the cranial morphology of Luzia’s people and population Y,” says Strauss.

An important aspect in both studies was the combined use of statistics, genetics, archaeology, and bioanthropology—traditionally incongruous areas. Mercedes Okumura reinforces the importance of an interdisciplinary approach: “Genomic analysis of ancient DNA opens a window to something that was purely science fiction just 20 years ago, but the results need to be interpreted in light of what we already know, such as archaeology and morphology studies.” According to Okumura, it is normal for different sources to provide sometimes discordant evidence. The challenge is to discover how the pieces fit together in order to elucidate the full history of these peoples.

Scientific articles
POSTH, C. et al. Reconstructing the deep population history of Central and South America. Cell. On-line. 8 nov. 2018.
MORENO-MAYAR, J. V. et al. Early human dispersals within the Americas. Science. On-line. 8 nov. 2018.