Around 9,000 B.C.E., small groups of hunters and foragers began doing something remarkable: they stopped moving through the high Andes and started staying. The cold, oxygen-thin highlands of western South America — rising above 4,000 meters in places — became home. And in doing so, these early Andean peoples set off one of the most striking examples of human adaptation in the archaeological and genetic record.
What the evidence shows
- Andean highland settlement: Archaeological evidence places permanent human habitation in Peru’s highlands at roughly 9,000 B.C.E., confirmed by ancient DNA analysis published in Science Advances in 2018 C.E.
- Genetic divergence: Whole-genome sequencing of ancient highland Peruvians and modern lowland Chileans reveals that Andean lowland and highland populations split from a common ancestor approximately 8,750 years ago — within a few centuries of permanent settlement.
- Convergent evolution: Highland Andeans developed gene variants linked to stronger hearts to cope with low oxygen — a biological solution distinct from the high-altitude adaptations seen in Tibetans, who evolved changes affecting how blood carries oxygen.
A last great migration finds its ceiling
Modern humans left Africa roughly 60,000 years ago and spread across six continents. The Americas were among the last regions reached. Genetic evidence suggests the ancestors of Native Americans split from Siberian populations around 25,000 years ago, crossed a land bridge into the Pacific Northwest somewhere between 17,000 and 14,000 years ago, and then moved rapidly southward.
The Andes represent a kind of endpoint in that long journey — the mountainous spine running the length of western South America. Getting there was one challenge. Staying was another.
The research, led by Emory University anthropologist John Lindo, sequenced whole genomes from seven individuals who lived in Peru’s highlands between roughly 1,600 and 6,100 years ago. These ancient genomes were compared with DNA from two modern Indigenous groups: the Aymara, who still live in Bolivia’s highlands, and the Huilliche-Pehuenche, a lowland coastal people of Chile. The comparison revealed a clear genetic split dating to around 8,750 B.C.E. — the moment highland and lowland branches began diverging from a shared ancestral population.
The body’s solution to thin air
High altitude is physiologically hostile. The air carries less oxygen. The cold is relentless. Bodies must work harder just to move, breathe, and reproduce. Over generations, the highland Andeans’ genomes show the marks of natural selection working on exactly these pressures.
One of the most striking findings involves the heart. The ancient and modern highland Aymara show an uptick in gene variants associated with stronger cardiac function — a different biological path than the one Tibetans took. Tibetan high-altitude adaptation centers on genes that change how hemoglobin binds and releases oxygen in the blood. The Andean solution appears to be building a more powerful pump instead.
“What we see is convergent evolution,” said Mark Aldenderfer, an archaeologist at the University of California, Merced, and a study coauthor. “Here’s an environmental challenge that people are confronted with in their genomes, and there appear to be multiple ways to solve that.”
This kind of parallel biological innovation — independent populations arriving at different solutions to the same survival problem — speaks to the deep adaptability of the human species. It also complicates any simple story about what “high-altitude adaptation” looks like across humanity.
A wider migration picture
The Andes study is one of three papers published simultaneously in 2018 C.E. that together reshuffled understanding of how the Americas were populated. The Cell study, led by Max Planck Institute geneticist Cosimo Posth, uncovered two previously unknown population movements into South America. One connects Andean peoples to ancient Native Americans from California’s Channel Islands. Another links ancient Brazilians and Chileans to Anzick-1, a child associated with the North American Clovis culture who lived in Montana around 12,800 years ago.
A third study found signs of a population dispersal from Mexico or Central America into South America and northward into the Great Plains around 8,700 years ago — adding yet another layer to what researchers once thought was a single, simple southward march.
“It’s easy to fall into the trap of oversimplifying what was probably an extremely complex process, depicting it as straight arrows southward,” said Jennifer Raff, a geneticist at the University of Kansas.
The people who settled the high Andes were not following a plan. They were living — hunting, foraging, sheltering, raising children — and over generations their bodies and communities adapted to conditions that would have tested any population on Earth. The fact that their descendants still live in those highlands today, carrying the genetic signatures of that adaptation, is one of the more quietly astonishing facts in human prehistory.
Lasting impact
The highland Andes became one of the cradles of complex civilization in the Americas. The Tiwanaku state, the Wari empire, and eventually the Inca Empire — the largest empire in pre-Columbian history — all grew from the high-altitude agricultural and pastoral traditions that trace back to these early settlers. Andean peoples developed sophisticated terrace farming systems, llama and alpaca domestication, and textile technologies that would shape South American life for millennia.
The genetic research also matters for contemporary medicine. Understanding how Andean populations evolved cardiac and respiratory adaptations has direct relevance to research on heart disease, altitude sickness, and the biology of oxygen use — fields with wide medical application. These ancient genomes are not just historical records; they are living data with practical implications.
Indigenous communities in the Andes are increasingly involved in discussions about how their ancestors’ remains and DNA are studied and used. Several research teams working in this field have emphasized the importance of community consent and collaboration — a standard that is still unevenly applied across the discipline.
Blindspots and limits
Ancient DNA studies depend on preservation conditions, which favor cold and dry environments — meaning the highland Andes yield better samples than many other regions of the Americas. This creates a sampling bias: lowland, tropical, and coastal populations are underrepresented, and the picture of early South American migration remains incomplete. The genetic record also cannot capture the full complexity of how languages, cultures, and knowledge systems moved and changed alongside populations. What the DNA shows is movement and relatedness — it cannot tell us what these people believed, how they organized themselves, or what names they gave to the mountains they chose to call home.
Read more
For more on this story, see: National Geographic
For more from Good News for Humankind, see:
- Indigenous communities secure landmark land rights recognition at COP30
- Ghana establishes marine protected area at Cape Three Points
- The Good News for Humankind archive on prehistory
About this article
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