Evolution isn’t a straight line: Modern humans come from 2 ancient lineages

“Two souls, alas, dwell in my breast.” Like Goethe’s Doctor Faust, we all have an inner duality. Recent discoveries about the deep past of human evolution reveal that for more than a million years, humanity was divided into two distinct branches. About 300,000 years ago, those estranged cousins reunited. Every one of us carries within our genes the results of that split, and the reunion of those two mystery populations.

The discovery represents a major reversal of the prevailing theory of human evolution, which suggested that modern humans descended from a single ancestral lineage in Africa.

A more detailed family tree for humanity

Studying human evolution is like trying to solve a four-dimensional puzzle, with just a few pieces scattered across the entire world, and across millions of years. The findings, published in Nature Genetics by a team of researchers from the University of Cambridge, are based on a new method called coalescent-based reconstruction of ancient admixture (“cobraa” for short).

Imagine cobraa as a mathematical detective, examining full-genome sequences of modern human DNA to determine how populations intermixed and evolved over time. Astonishingly, simply by analyzing genetic clues from modern humans (rather than by examining any ancient DNA), cobraa can build a more detailed family tree for humanity than ever before — and can do so for other species too, by the way.

Here’s the big takeaway for Homo sapiens: About 1.5 million years ago, our distant ancestors split into two distinct groups, labelled A and B on this graph. Soon after the separation, group A experienced an evolutionary bottleneck: its population shrank radically. This may have been due to climate change, food scarcity, or some other challenge, but at this point, nobody really knows.

Group A eventually recovered and generated evolutionary offshoots; Neanderthals and Denisovans were genetically distinct human populations that evolved from this separate strand of humanity. (Neanderthals were genetically distinct enough to be considered a separate species. Due to a lack of fossils, the jury is still out on the Denisovans.)

That was well before around 300,000 years ago, when Groups A and B reintegrated with each other. However, it is also possible to say that Group A absorbed Group B, as the genetic legacy of Group A in our shared ancestry is approximately 80%, while that of Group B is only about 20%.

Group B genes may have been important

The research suggests that some of the genes contributed by Group B, the minority population, particularly those related to brain function and neural processing, may have played a crucial role in human evolution.

The study also found that genes inherited from Group B were often located away from regions of the genome associated with gene functions, suggesting that they may have been less compatible with the majority of the genetic background. This hints at a process known as purifying selection, where natural selection removes harmful mutations over time.

Sometime before 100,000 years ago, the Khoisan emerged as a distinct population within our species. The Khoisan are the indigenous, pre-Bantu peoples of Southern Africa, composed of two groups: the pastoralist Khoikhoi and the San, hunter-gatherers otherwise known as the Bushmen. About 22,000 years ago, they constituted the bulk of humanity. Today, they number only about 100,000 individuals, and their ancient languages and lifestyles are under threat of extinction.

Over the millennia, genetic exchange between the Khoisan and non-Khoisan populations in Africa has continued. Around 50,000 years ago, humanity sprouted another branch when a small population left Africa. They went on to populate the rest of the world and, in a re-do of the previous merger, they absorbed what remained of the Neanderthal and Denisovan populations, who, according to this graph, contributed about 2% of the DNA of non-African populations.

Applying the cobraa method to chimpanzees, gorillas, dolphins, and bats, the researchers found these species exhibit similar patterns of genetic exchange and reintegration, supporting the idea that few, if any, species evolve in isolated, distinct lineages, and that genetic exchange and reintegration may be the norm rather than the exception.

The researchers hope to refine their methods to account for more gradual genetic exchanges than the sharp splits and reunions suggested by their current model. They also want to relate their findings to discoveries in anthropology, which suggest that early humans may have been more diverse than previously thought.

For more, see the entire article: Trevor Cousins, Aylwyn Scally, Richard Durbin: A structured coalescent model reveals deep ancestral structure shared by all modern humans, in Nature Genetics, 18 March 2025.

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