Interwoven Human ancestry
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Using genealogical relationships in DNA, UC Berkeley researchers have uncovered hidden contributions from extinct human populations that left no sequenced genomes.
Meaghan Marohn
The evolutionary ancestry of modern Homo sapiens is far more complex than anything the authors of the Bible’s absurdly simplistic origin myths could have imagined. We already know that populations of our species migrating out of Africa interbred with Neanderthals and Denisovans, and that these two archaic lineages also exchanged genes with one another. Consequently, most people with ancestry outside Africa carry some Neanderthal DNA, while many Asian and especially Oceanian populations also carry Denisovan DNA.
Now, according to a paper just published in Science, our ancestry is even more complicated. A team led by researchers at the University of California, Berkeley, with colleagues at Johns Hopkins University and 54Gene, has identified genetic material inherited from two previously unknown archaic hominin lineages. These are described as “ghost” lineages because no sequenced genome from either population is available: their existence must be inferred from the traces they left in the genomes of living people.
The researchers developed a computational method called TRACE — TRacking Archaic Contributions via ARG Estimation — which reconstructs genealogical relationships among segments of DNA. By identifying regions whose ancestry extends unusually far back in time, TRACE can detect contributions from extinct populations without requiring DNA recovered from their bones.
One of these ghost populations interbred directly with H. sapiens in Africa more than 50,000 years ago, before the principal expansion of modern humans into Eurasia. This unknown lineage appears to have separated from the ancestors of modern humans about 800,000 years ago, around the time that the lineage ancestral to Neanderthals and Denisovans also became distinct from ours.
Because the interbreeding occurred before the major migration out of Africa, its genetic legacy is now present in both African and non-African populations. The researchers estimate that each living person has inherited approximately 0.5–1 per cent of their genome from this ghost lineage — an amount comparable with the Neanderthal contribution found in many non-African genomes.
The second population was even more ancient. This “super-archaic” lineage had separated from other hominins approximately 1.8 million years ago and apparently interbred with Denisovans in Eurasia more than 200,000 years ago. Denisovans later interbred with H. sapiens, thereby passing a small quantity of this much older DNA into modern human populations. Its signal is clearest in Oceanian genomes, which contain the highest proportions of Denisovan ancestry.
The identities of these ghost populations remain unknown. Their estimated ages overlap with those of Middle Pleistocene Homo populations in Africa and Homo erectus in Eurasia, but the genetic evidence does not yet justify assigning either lineage to a named fossil species.
The picture emerging from modern genetics is therefore not a simple family tree in which one human species replaced another in an orderly succession. It is a tangled web of populations that separated, migrated, met again and exchanged genes repeatedly across Africa and Eurasia. Several genetically differentiated hominin populations existed at overlapping times and remained sufficiently closely related to produce fertile offspring.
That is vastly different from the tale invented by the authors of Genesis. Their mythology reduces the origin of humanity to a recently manufactured couple, followed a few generations later by the extermination of almost everyone alive and a second population bottleneck consisting of Noah’s household. Had the entire human population passed through two such extreme bottlenecks only a few thousand years ago, our genomes would contain an unmistakable signature of very recent common ancestry and a catastrophic loss of genetic diversity. No such signature exists.
Instead, our DNA records population divisions, migrations and repeated episodes of interbreeding extending across hundreds of thousands of years — and, through this super-archaic contribution, back into lineages more than a million years old. The authors of Genesis did not merely overlook a few incidental details: they got the timescale, geography, population history and fundamental shape of human ancestry wrong.
It is understandable therefore that creationist cult leaders, whose livelihood depends on it, feed their followers on a diet of deliberate disinformation while discouraging scientific enquiry and encouraging instead the view that science is unreliable and scientists are untrustworthy, so the best test of reality is 'faith' and dependence on a book which they declare to be the inerrant word of a creator god, with no more substantive evidence than the claim in the same book.
How TRACE Detects DNA from Unknown Ancestors. TRACE stands for TRacking Archaic Contributions via ARG Estimation. It is a computational method for finding pieces of DNA inherited from archaic hominins—even when no DNA from those hominins has ever been recovered.The paper in Science was accompanied by an article in UC Berkeley News, written by Robert Sanders:
A genome contains many different family trees
Because chromosomes exchange sections during the production of eggs and sperm, each person’s genome is a mosaic assembled from many ancestors. Consequently, different sections of a chromosome can have different genealogical histories.
An ancestral recombination graph, or ARG, is a computational reconstruction that joins these local genetic family trees together while allowing for the recombination events that occurred between them.
Looking for unusually deep branches
In an ordinary section of the genome, copies of that DNA carried by living people eventually converge, or coalesce, upon a relatively recent common ancestor.
DNA inherited from an archaic population behaves differently. That population may have separated from the ancestors of modern humans hundreds of thousands of years earlier. When it later interbred with Homo sapiens, it introduced DNA belonging to this much older branch of the human family tree.
Within an ARG, such DNA appears as an unusually long, isolated branch that does not join the other modern human lineages until much farther back in time. While that branch remains separate, numerous other human DNA lineages may already have coalesced with one another.
TRACE therefore examines two principal features:
- how long a particular DNA lineage remains separate before joining the others; and
- how many other lineages coalesce during the same period.
The combination helps distinguish DNA introduced by an archaic population from genetic variation produced by the normal history of a single population.
No archaic reference genome is required
Earlier methods often identified archaic DNA by comparing modern genomes with sequenced Neanderthal or Denisovan genomes. That approach cannot identify ancestry from a population whose DNA has never been recovered.
TRACE instead reconstructs relationships using present-day human genomes alone. Once it has located candidate archaic segments, researchers can compare them with known Neanderthal and Denisovan DNA. Segments that match can be classified accordingly; deeply divergent segments that match neither provide evidence of an otherwise unknown “ghost” population.
The researchers tested TRACE using computer simulations and showed that it could recover known Neanderthal and Denisovan contributions. Its ability to rediscover these independently identified sequences provided an important check that it was detecting genuine archaic ancestry rather than random genetic variation.
What TRACE cannot tell us
TRACE can reveal that a deeply separated population contributed DNA, estimate when its lineage diverged and identify the parts of modern genomes that it affected. It cannot, by itself, tell us what those hominins looked like or assign them confidently to a named fossil species. Connecting a ghost lineage with Homo erectus or another known hominin would require additional fossil, protein or ancient-DNA evidence.
New technique pinpoints human DNA inherited from ‘ghost’ ancestors
Neanderthals and Denisovans interbred with modern human ancestors, leaving behind telltale DNA in our genomes. Now we have evidence of modern human interbreeding with two much older but unknown ancestors.
July 30, 2026
Two mysterious human relatives left their genetic footprints in the modern human genome alongside the DNA of Neanderthals and Denisovans, underscoring the fact that our ancestors interbred with many groups of hominins they encountered over millions of years of evolution.
While previous research found hints that modern humans had interbred with ancient hominins in addition to now-extinct Neanderthals and Denisovans, a new study by UC Berkeley researchers pinpoints areas of the genome inherited from these unknown ancestors and establishes a timeline. This was possible using a new technique the researchers developed that leverages hundreds of genomes from modern-day humans to find ancient genealogical relationships.
One of the unknown ancestors, which the researchers refer to as a ghost ancestor, interbred with modern humans in Africa prior to 50,000 years ago, before the most recent migration of Homo sapiens out of Africa into Europe and Asia. These genes comprise around 1% of the genomes of modern humans, comparable to the amount of Neanderthal DNA in the human genome. That unknown hominin lineage actually split off from the modern human lineage around the same time that Neanderthals and Denisovans diverged around 800,000 years ago, though they interbred with modern humans earlier.
Previous publications suggested that there might be ghost ancestry — ancestry from unknown archaic lineages in modern humans — but they hadn’t concluded whether this unknown ancestry is present only in Africans or not, and when this introgression event happened. We were actually able to find and map genomic locations in modern humans that are from this ghost lineage and show that this ghost ancestry is in all modern humans, not only in Africans.
Yulin Zhang, co-first author.
Center for Computational Biology
University of California Berkeley
Berkeley, CA, USA.
The other mysterious ancestor — what the researchers call a super-archaic ancestor — was a hominin descended from a 1.8 million-year-old lineage that interbred with Denisovans in Eurasia, likely more than 200,000 years ago. Denisovans later shared some of the super-archaic DNA with modern humans through interbreeding with Homo sapiens.
The super-archaic finding is particularly exciting because it reveals genetic contributions from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population.
DR. Arjun Biddanda, co-first author.
Department of Biology
Johns Hopkins University
Baltimore, MD, USA.
The findings highlight the fact that early modern humans not only lived side-by-side with numerous related hominin groups in Africa and Eurasia over the past million years, but that they were close enough genetically to interbreed with many of them.
With ancient DNA from Neanderthals and Denisovans and with these new genealogical methods, we are learning that mixture among human populations has been very pervasive across time, and that this is also likely to be true at ancient time scales. We often think of human evolution as a branching tree, but new genomic data and analytical methods reveal a much more interconnected history — more like a complex web of populations connected by repeated episodes of migration and mixing.
Associate Priya Moorjani, co-corresponding author.
Center for Computational Biology
University of California Berkeley
Berkeley, CA, USA.
Though it’s unclear who these ghost and super-archaic ancestors were, the inferred divergence time overlaps with the existence of Middle Pleistocene Homo groups in Africa 800,000 years ago and Homo erectus in Eurasia 1.8 million years ago, respectively.
Zhang, Biddanda, Moorjani and their colleagues published their findings online July 30 in the journal Science.
Tracing archaic DNA
When modern humans first moved out of Africa some 50,000 years ago, they interbred with two much older hominin lineages in Eurasia, the Neanderthals and Denisovans. While those older lineages went extinct, they left some of their DNA in the modern human genome — a discovery made possible by the extraction and sequencing of ancient DNA from Neanderthal and Denisovan fossils.
But researchers also saw hints in the human genome of much earlier interbreeding. Because we have no DNA from other extinct hominins, however, it was challenging to identify their contributions.
A timeline showing four separate instances (colored arrows) of archaic hominins interbreeding with early Homo sapiens. The dates were inferred from a genealogical analysis of present-day human genomes using TRACE, a technique developed at UC Berkeley.Yulin Zhang and Priya Moorjani/UC Berkeley
Moorjani’s team developed a technique called TRACE (TRacking Archaic Contributions via ARG Estimation) that locates these regions by analyzing complete genomes from present-day humans only. Using genome data from modern individuals from around the world, the team reconstructed genealogical relationships — what’s called an ancestral recombination graph (ARG) –– across the genome, creating a detailed map of how DNA segments are related through shared ancestry over time.
Genealogies preserve a record of our evolutionary past. TRACE reconstructs those histories across the genome. By identifying regions whose ancestry extends unusually far back in time, we can uncover genetic contributions from extinct human populations, even in the absence of ancient DNA.
Associate Priya Moorjani.
Some of the regions with the oldest ancestry matched DNA from sequenced Neanderthal genome, which makes up about 1% of the human genome. Looking exclusively at genomes from people in Asia and Oceania, the only populations having substantial Denisovan DNA, they also correctly identified known regions of Denisovan introgression.
But many of the ancient regions contained neither Neanderthal nor Denisovan DNA. The researchers determined that these stretches of DNA came from two distinct lineages, with different introgression times. The ghost lineage was found in all humans, non-Africans and Africans, indicating that the gene flow occurred before modern humans made their final excursion out of Africa and spread rapidly throughout the world.
We discovered that about 2% of the modern human genome is from archaic hominins. In the case of the ghost lineage, modern-day Africans and non-African populations both inherited similar amounts of ghost ancestry. Each individual has about 0.5 to 1% of their genome inherited from this ghost lineage.
Yulin Zhang.
The researchers recovered the other lineage by analyzing only genomes from populations in Oceania — peoples living in the island nations of the Pacific Ocean — which have been shown to have higher proportions of Denisovan DNA, sometimes up to 4%. The super-archaic ancestry popped up in regions of Denisovan DNA, suggesting that this DNA came via gene flow through Denisovans into modern humans. Since Denisovans harbor between 3% and 5% super-archaic DNA, only a small fraction of that is inherited by modern humans, Moorjani said.
TRACE allowed us to contextualize how the ancestry segments from these previously uncharacterized hominins are distributed throughout the human genome. We found that these contributions are widespread throughout the genome, and ghost ancestry is detected even in regions previously thought to be intolerant of Neanderthal and Denisovan ancestry.
DR. Arjun Biddanda.
Many archaic segments are enriched in regions associated with immunity and metabolic function, according to Moorjani.This pattern is not entirely surprising. Adaptation to new pathogens and food sources has been one of the strongest selective pressures in human evolution. Interbreeding with other human groups introduced new genetic variation, providing additional raw material for natural selection. Beneficial variants could then be retained and spread over many generations. I think these new computational methods that allow us to reconstruct genealogical relationships are really the next frontier in this field because they are allowing us to uncover hidden episodes from our past without requiring ancient DNA,
Associate Priya Moorjani.
Moorjani hopes to detect faint signals of additional lineages in human DNA as the world’s genome databases become more diverse, sampling a broader variety of humanity. The discovery of more Denisovan genomes — currently only one has been published — would also help. Protein sequences recently obtained from Homo erectus fossils could even help identify who the super-archaic ancestor was.
Moorjani noted that TRACE should also work with other species, “allowing us to also uncover really different patterns across the tree of life.” Other co-authors of the paper are Sarah Johnson of Berkeley’s Center for Computational Biology and Colm O’Dushlaine of 54Gene, Inc., in Washington, D.C. The work was funded by the National Science Foundation.
Publication:
This study adds another layer of complexity to the already intricate history preserved in the human genome. Far from presenting a problem for evolutionary theory, the findings are precisely the sort of evidence that an evolutionary framework can accommodate: populations separate and diverge, migrate into new regions, encounter one another again and exchange genes. Human evolution was not a simple procession of one species replacing another, but a shifting network of related populations connected by repeated episodes of interbreeding.
The researchers had no difficulty explaining their results through known evolutionary processes. They did not need to insert an act of special creation whenever a new lineage appeared, nor invoke supernatural intervention to explain how DNA passed between populations. Genetic divergence, migration, recombination, natural selection and ordinary reproduction were sufficient. Indeed, TRACE works because those processes leave detectable and mathematically predictable signatures in living genomes.
Creationism, by contrast, predicts none of this. It offers no reason why every living person should carry DNA from an unidentified African hominin lineage, why some people should possess Denisovan DNA containing an even older super-archaic contribution, or why those genetic fragments should occur in identifiable regions with genealogies extending hundreds of thousands of years into the past. Such findings can only be accommodated by creationism after the event, through vague appeals to unspecified “created kinds” and conveniently unobservable miracles.
Our genomes therefore contain something Genesis conspicuously lacks: an evidential record of our real ancestry. Humanity did not begin with a recently manufactured couple, pass through a second bottleneck aboard a wooden boat and then diversify magically within a few generations. We emerged from ancient, geographically dispersed and repeatedly interconnected populations whose history reaches back far beyond the few thousand years allowed by biblical mythology. Evolution explains that history; creationism merely denies that it happened.
So, it looks like creationists must continue to cling to the forlorn expectation that biologists are about to abandon 'Darwinism' and adopt evidence-free superstitious creationism instead - amongst the more childish and demonstrably false beliefs that have sustained creationism for more than half a century as the evidence against it continues to pile up.
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