South America represented the final landmass to be settled by humans, a process many researchers once envisioned as being quite straightforward. The prevailing theory held that early populations, stemming from a largely homogenous ancestral group, traversed the continent around 15,000 years ago—a relatively recent event in the grand sweep of human history. These pioneers purportedly adapted to the continent’s diverse environments, ranging from dense rainforests to windswept high-altitude plateaus, and subsequently remained relatively stationary.
However, a recent publication in the journal Nature reveals that these migratory events were far from simple. By examining ancient and contemporary genomes collected across South America and external populations, the research team uncovered evidence indicating that genetically distinct groups populated the continent in at least three separate waves. Furthermore, some individuals or communities carried genetic variants potentially beneficial, acquired from very early ancestry linked to Australasian populations.
“Much of the pre-colonial genetic diversity has been lost,” making it difficult for scientists to piece together the complex demographic history of South America, notes Cosimo Post, an archaeogeneticist at the University of Tübingen, who was not involved in the Nature study. Consequently, efforts to recover even fragments of this diversity are “an extremely important undertaking.” His own team published supplementary findings today in Current Biology, identifying traces of unexpected genetic variation and previously unseen movements within 52 ancient genomes from Argentina and Uruguay.
For the Nature study, Tabita Hünemeier, a geneticist at the University of São Paulo and the Institute of Evolutionary Biology, collaborated with researchers and Indigenous communities across Latin America to sequence 128 complete genomes from living individuals stretching from northern Mexico down to southern Argentina. The team then analyzed these new sequences alongside established genetic databases and previously published ancient DNA.
Earlier research had established the first two major colonization pulses into South America, the earliest involving people genetically related to the Anzick child, buried in Montana 12,700 years ago. A second wave of movement followed around 9,000 years ago, ultimately contributing the largest proportion of ancestry to the genomes of most ancient and modern South Americans, including those studied by Post.
Hünemeier and her colleagues identified evidence of a third migratory influx, whose genetic signature first appears in their dataset approximately 1,300 years ago before spreading widely across the continent and even reaching the Caribbean. These newcomers show genetic links to Mesoamerican individuals from Mexico and Central America, although the researchers are currently uncertain about their exact point of origin or their closest relatives. “Without the source population and more direct evidence [of this third pulse] from ancient DNA, it is tough to understand” when and how this third migration occurred, Post comments.
The study also delves back into a persistent genetic puzzle in the American story that has been debated for over a decade: how did signals of Australasian ancestry appear in some ancient and contemporary South American genomes? The genetic variants from this lineage constitute only about 2% of the total ancestry in carriers, yet this proportion has remained remarkably stable over the last 10,000 years. “This signal keeps showing up,” states Post. “It must mean something.”
Hünemeier hypothesizes that the individuals carrying this ancestry belonged to several distinct groups that inhabited Beringia—the now-submerged landmass connecting Eastern Siberia and Alaska—over millennia, from which this lineage eventually dispersed southward into the Americas. (This particular Australasian ancestry, sometimes referenced as Population Y or the Ypykuéra signal, after the Tupi word for “ancestor,” is distinct from the genetic overlap some Polynesian populations share with South Americans. Scientists continue to debate the origins of that later gene exchange—for instance, whether Polynesian navigators might have reached western South America around 800 years ago—but the findings from the Nature publication do not directly pertain to that separate enigma.)
Hünemeier’s team also made the first attempt to ascertain whether the genes inherited from these ancient Australasian ancestors conferred any adaptive advantages. The researchers discovered that at least some of these genes are associated with fertility and immune response and appear to have been targets of positive natural selection. This suggests they might have provided an evolutionary edge under specific environmental conditions. If true, this could explain their persistence across such a vast timescale, Hünemeier suggests, although she cautions that this hypothesis requires further rigorous testing.
“This is a step forward,” remarks Post, “even if it’s not the final chapter of the story.”
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