Rosa Rubicondior: Creationism Refuted - New Understanding of Modern Human And Neanderthal Interbreeding

Princeton geneticists are rewriting the narrative of Neanderthals and other ancient humans

The picture of modern human (Homo sapiens) interactions with Neanderthals (H. neanderthalensis) has just become significantly richer. New evidence reveals not just a single episode of contact within the last 50,000 years, but several waves of interaction spanning much of our species’ 200,000-year history.

It was previously believed that after our last common ancestor with Neanderthals and Denisovans split into separate populations around 600,000 years ago, one lineage remained in Africa and eventually evolved into H. sapiens by about 200,000 years ago. The other migrated into Eurasia and gradually diverged into Neanderthals in the west and Denisovans in the east, with limited contact between them. According to this model, modern humans left Africa around 60,000 years ago, encountered Neanderthals in Eurasia, and interbred with them shortly afterwards—about 40,000 to 50,000 years ago.

However, a new genomic analysis provides evidence for at least three distinct episodes of interbreeding. One occurred around 200,000 to 250,000 years ago—very early in the history of H. sapiens. Another took place about 100,000 to 120,000 years ago, long before the final major migration out of Africa, and the last around 40,000 years ago, as previously believed.

These findings suggest that there may have been multiple early migrations of H. sapiens into Eurasia, followed in some cases by return migrations back into Africa, before the final, successful dispersal around 60,000 years ago.

Some of the team’s evidence comes from detecting H. sapiens DNA in the Neanderthal genome, so these ingressions could have come from earlier migrations that then failed, leaving only their DNA in the Neanderthal population.

There are still unresolve questions about which species migrated out of Africa, when, and whether some, such as H. rhodesiensis, had a wide distribution across African and Eurasia with regional variants, so it is entirely possible that the earliest interactions with Neanderthals could have been between, say H. rhodesiensis which brought Neanderthal genes back into Africa and then interbred with diverging H. sapiens.

See the right-hand panel for an explanation of this so-called 'muddle in the middle'.

The study, led by researchers at Harvard University and Princeton University under the direction of Professor Joshua Akey of Princeton’s Lewis-Sigler Institute for Integrative Genomics, also supports the view that Neanderthals did not simply go extinct. Instead, their dwindling populations were gradually absorbed into expanding populations of modern humans.

Can you shed some light on the so-called 'muddle in the middle' of the human evolutionary tree where some species remained in Africa while others migrated into Eurasia to become ancestral to Neanderthals and Denisovans? Certainly. The so-called “muddle in the middle” refers to a particularly complex and poorly resolved period in human evolution, roughly between 800,000 and 300,000 years ago. During this time, several hominin species and populations were evolving, migrating, and interbreeding across Africa and Eurasia. The fossil and genetic evidence is fragmentary, often ambiguous, and frequently reinterpreted as new discoveries emerge. Here’s a breakdown of the key issues and players involved:

What is the “muddle in the middle”?

The term was popularised by palaeoanthropologists to describe the lack of consensus about how different Middle Pleistocene hominins are related, especially those leading up to Homo sapiens, Homo neanderthalensis, and Denisovans. It highlights:

Unclear taxonomy (What species are we looking at?)
Uncertain migration patterns
Frequent hybridisation
Sparse and morphologically variable fossils
Disagreement over whether some fossils represent separate species or transitional populations

Geographic and Evolutionary Context

Africa: This is where modern humans (Homo sapiens) eventually arose. Several archaic species existed here during the Middle Pleistocene.
Eurasia: Populations that had left Africa earlier continued evolving, giving rise to Neanderthals in Europe and Denisovans in Asia.

Key Hominin Candidates

Homo heidelbergensis

Lived: ~700,000–300,000 years ago
Range: Europe, Africa, possibly Asia
Significance:

Often considered a common ancestor of both Neanderthals and modern humans.
European populations likely evolved into Neanderthals.
African populations may have evolved into Homo sapiens.

Issues:

Some researchers view African specimens as distinct enough to warrant a different species name (see below).

Homo rhodesiensis

Lived: ~300,000–125,000 years ago
Range: Africa (e.g. Kabwe skull, Zambia)
Significance:

Sometimes considered the African counterpart of H. heidelbergensis.
Possibly more directly ancestral to Homo sapiens.

Issues:

Its species status is debated. Some scholars fold it into H. heidelbergensis, others treat it as a separate lineage.

Homo antecessor

Lived: ~1.2 million – 800,000 years ago
Range: Western Europe (e.g. Atapuerca, Spain)
Significance:

One of the earliest known hominins in Europe.
Some propose it as a common ancestor to both Neanderthals and modern humans, via H. heidelbergensis.

Issues:

Very fragmentary evidence.
Still controversial as a distinct species.

Interbreeding and Genetic Evidence

Recent genomic studies have shown that:

There were multiple episodes of interbreeding among different archaic humans (including H. sapiens, Neanderthals, Denisovans, and possibly other unknown groups).
The lineages were not neatly separated. Instead, evolution was reticulate (branching and reconnecting), not a cleanly splitting tree.
Some Eurasian fossils (e.g. the Sima de los Huesos hominins in Spain, ~430,000 years old) show early Neanderthal traits but are also genetically linked to Denisovans, suggesting a shared common ancestor still unresolved.

Why it’s still a muddle

The fossil record is sparse and often damaged.
Species boundaries are blurred by gene flow.
Many hominin fossils show a mosaic of traits, making classification difficult.
Different researchers favour different classification schemes (e.g. lumpers vs splitters).

Summary

The “muddle in the middle” reflects a genuine complexity in our evolutionary past:

Between 800,000 and 300,000 years ago, multiple hominin populations were diverging, migrating, and interbreeding.
Taxa like H. heidelbergensis, H. rhodesiensis, and H. antecessor may represent regional variants, transitional forms, or separate species.
The boundaries between them are fluid, and it’s likely that many of these hominins could interbreed, which further blurs the lines.

The research has just been published in Science. It is also the subject of a Princeton University news article by Liz Fuller-Wright.

Princeton geneticists are rewriting the narrative of Neanderthals and other ancient humans
Ever since the first Neanderthal bones were discovered, people have wondered about these ancient hominins. How are they different from us? How much are they like us? Did our ancestors get along with them? Fight them? Love them? The recent discovery of a group called Denisovans, a Neanderthal-like group who populated Asia and Oceania, added its own set of questions.
Now, an international team of geneticists and AI experts are adding whole new chapters to our shared hominin history. Under the leadership of Joshua Akey, a professor in Princeton’s Lewis-Sigler Institute for Integrative Genomics, the researchers have found a history of genetic intermingling and exchange that suggests a much more intimate connection between these early human groups than previously believed.

This is the first time that geneticists have identified multiple waves of modern human-Neanderthal admixture.

Professor Liming Li, first author
Department of Medical Genetics and Developmental Biology
School of Medicine
The Key Laboratory of Developmental Genes and Human Diseases,
Southeast University
Nanjing, China.

We now know that for the vast majority of human history, we’ve had a history of contact between modern humans and Neanderthals. The hominins who are our most direct ancestors split from the Neanderthal family tree about 600,000 years ago, then evolved our modern physical characteristics about 250,000 years ago. From then until the Neanderthals disappeared — that is, for about 200,000 years — modern humans have been interacting with Neanderthal populations.

Professor Joshua M. Akey, senior author
The Lewis-Sigler Institute for Integrative Genomics.
Princeton University, Princeton, NJ, USA.
The results of their work appear in the current issue of the journal Science.

Neanderthals, once stereotyped as slow-moving and dim-witted, are now seen as skilled hunters and tool makers who treated each other’s injuries with sophisticated techniques and were well adapted to thrive in the cold European weather.

(Note: All of these hominin groups are humans, but to avoid saying “Neanderthal humans,” “Denisovan humans,” and “ancient-versions-of-our-own-kind-of-humans,” most archaeologists and anthropologists use the shorthand Neanderthals, Denisovans, and modern humans.)

Mapping the gene flow

Using genomes from 2,000 living humans as well as three Neanderthals and one Denisovan, Akey and his team mapped the gene flow between the hominin groups over the past quarter-million years.

The researchers used a genetic tool they designed a few years ago called IBDmix, which uses machine learning techniques to decode the genome. Previous researchers depended on comparing human genomes against a “reference population” of modern humans believed to have little or no Neanderthal or Denisovan DNA.

Akey’s team has established that even those referenced groups, who live thousands of miles south of the Neanderthal caves, have trace amounts of Neanderthal DNA, probably carried south by voyagers (or their descendants).

With IBDmix, Akey’s team identified a first wave of contact about 200-250,000 years ago, another wave 100-120,000 years ago, and the largest one about 50-60,000 years ago.

That contrasts sharply with previous genetic data.

To date, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, stayed put for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago and go on to people the rest of the world. Our models show that there wasn’t a long period of stasis, but that shortly after modern humans arose, we’ve been migrating out of Africa and coming back to Africa, too. To me, this story is about dispersal, that modern humans have been moving around and encountering Neanderthals and Denisovans much more than we previously recognized.

Professor Joshua M. Akey.

That vision of humanity on the move coincides with the archaeological and paleoanthropological research suggesting cultural and tool exchange between the hominin groups.

A DNA insight

Li and Akey’s key insight was to look for modern-human DNA in the genomes of the Neanderthals, instead of the other way around.

The vast majority of genetic work over the last decade has really focused on how mating with Neanderthals impacted modern human phenotypes and our evolutionary history — but these questions are relevant and interesting in the reverse case, too.

Professor Joshua M. Akey.

They realized that the offspring of those first waves of Neanderthal-modern matings must have stayed with the Neanderthals, therefore leaving no record in living humans.

Because we can now incorporate the Neanderthal component into our genetic studies, we are seeing these earlier dispersals in ways that we weren’t able to before.

Professor Joshua M. Akey.

The final piece of the puzzle was discovering that the Neanderthal population was even smaller than previously believed.
Genetic modeling has traditionally used variation — diversity — as a proxy for population size. The more diverse the genes, the larger the population. But using IBDmix, Akey’s team showed that a significant amount of that apparent diversity came from DNA sequences that had been lifted from modern humans, with their much larger population.

As a result, the effective population of Neanderthals was revised down from about 3,400 breeding individuals down to about 2,400.

How Neanderthals vanished

Put together, the new findings paint a picture of how the Neanderthals vanished from the record, some 30,000 years ago.

[Professor Key's] idea is that Neanderthal populations slowly shrank until the last survivors were folded into modern human communities. This “assimilation model” was first articulated by Fred Smith, an anthropology professor at Illinois State University, in 1989.

I don’t like to say ‘extinction,’ because I think Neanderthals were largely absorbed. Our results provide strong genetic data consistent with Fred’s hypothesis, and I think that’s really interesting. Neanderthals were teetering on the edge of extinction, probably for a very long time. If you reduce their numbers by 10 or 20%, which our estimates do, that’s a substantial reduction to an already at-risk population. Modern humans were essentially like waves crashing on a beach, slowly but steadily eroding the beach away. Eventually we just demographically overwhelmed Neanderthals and incorporated them into modern human populations.

Professor Joshua M. Akey.

Publication:
Liming Li, Troy J. Comi, Rob F. Bierma, and Joshua M. Akey
Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 385, eadi1768 (2024). DOI:10.1126/science.adi17

Structured Abstract

INTRODUCTION
For much of modern human history, we were only one of several different groups of hominins that existed. Studies of ancient and modern DNA have shown that admixture occurred multiple times among different hominin lineages, including between the ancestors of modern humans and Neanderthals. A number of methods have been developed to identify Neanderthal-introgressed sequences in the DNA of modern humans, which have provided insight into how admixture with Neanderthals shaped the biology and evolution of modern human genomes. Although gene flow from an early modern human population to Neanderthals has been described, the consequences of admixture on the Neanderthal genome have received comparatively less attention.

RATIONALE
A better understanding of how admixture with modern humans influenced patterns of Neanderthal genomic variation may provide insights into hominin evolutionary history. For example, DNA sequences inherited from modern human ancestors in Neanderthals can be used to test hypotheses on the frequency, magnitude, and timing of admixture and the population genetics characteristics of Neanderthals. Introgressed modern human sequences in Neanderthals can also be used to refine estimates of Neanderthal ancestry in contemporary individuals. We developed a simple framework to investigate introgressed human sequences in Neanderthals that is predicated on the expectation that sequences inherited from modern human ancestors would be, on average, more genetically diverse and would result in local increases in heterozygosity across the Neanderthal genome.

RESULTS
We first used a method referred to as IBDmix to identify introgressed Neanderthal sequences in 2000 modern humans sequenced by the 1000 Genomes Project. We found that sequences identified by IBDmix as Neanderthal in African individuals from the 1000 Genomes Project are significantly enriched in regions of high heterozygosity in the Neanderthal genome, whereas no such enrichment is observed with sequences detected as introgressed in non-African individuals. We show that these patterns are caused by gene flow from modern humans to Neanderthals and estimate that the Vindija and Altai Neanderthal genomes have 53.9 Mb (2.5%) and 80.0 Mb (3.7%) of human-introgressed sequences, respectively. We leverage human-introgressed sequences in Neanderthals to revise estimates of the amount of Neanderthal-introgressed sequences in modern humans. Additionally, we show that human-introgressed sequences cause Neanderthal population size to be overestimated and that accounting for their effects decrease estimates of Neanderthal population size by ~20%. Finally, we found evidence for two distinct epochs of human gene flow into Neanderthals.

CONCLUSION
Our results provide insights into the history of admixture between modern humans and Neanderthals, show that gene flow had substantial impacts on patterns of modern human and Neanderthal genomic variation, and show that accounting for human-introgressed sequences in Neanderthals enables more-accurate inferences of admixture and its consequences in both Neanderthals and modern humans. More generally, the smaller estimated population size and inferred admixture dynamics are consistent with a Neanderthal population that was decreasing in size over time and was ultimately being absorbed into the modern human gene pool.

Detecting modern human–to-Neanderthal gene flow (H→N) and its consequences.
Modern human–to-Neanderthal admixture causes a local increase in heterozygosity in the Neanderthal genome, a characteristic that enabled approaches to quantify and detect introgressed sequences. We leveraged modern human–introgressed sequences in the Neanderthal genome to refine estimates of Neanderthal ancestry in contemporary humans by decomposing IBDmix-detected segments into those attributable to human-to-Neanderthal (H→N) versus Neanderthal-to-human (N→H) gene flow in 2000 modern human individuals. We also used modern human–introgressed sequences to discover that Neanderthals had a smaller effective population size (Ne) than previously estimated and that a second wave of modern human–to-Neanderthal gene flow occurred ~100 to 120 thousand years ago (ka). bps, base pairs.

Abstract
Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.

Liming Li, Troy J. Comi, Rob F. Bierma, and Joshua M. Akey
Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 385, eadi1768 (2024). DOI:10.1126/science.adi17

© 2024 The American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

The discovery of multiple waves of interbreeding between *Homo sapiens* and Neanderthals over a period of nearly 200,000 years presents a major challenge to creationist narratives, especially those grounded in young-Earth or literalist interpretations of scripture. These findings reaffirm the complex, branching, and interwoven nature of human evolution, rooted in deep time and documented through both fossils and genomics. For creationists, who typically argue that all humans descend from a single pair (e.g., Adam and Eve) created a few thousand years ago, such evidence must either be ignored, misrepresented, or outright denied to preserve their worldview.

Firstly, the notion that anatomically modern humans existed and interbred with closely related hominins like Neanderthals as far back as 200,000–250,000 years ago starkly contradicts the creationist timescale, which limits the age of the Earth to about 6,000 to 10,000 years. The existence of multiple migrations out of Africa, long before the so-called "final" dispersal around 60,000 years ago, is irreconcilable with any model that denies deep geological and evolutionary time. The only recourse for creationists is to deny the dating methods entirely—methods that are independently corroborated across disciplines including palaeontology, genetics, geology, and archaeology.

Secondly, the genetic evidence shows that modern non-African humans carry Neanderthal DNA, and that this genetic legacy stems from several separate periods of interbreeding. This demolishes the idea of a biologically distinct and divinely created human “kind.” The creationist strategy has often been to argue that Neanderthals were just ‘degenerate’ humans post-Flood, or alternatively, non-human animals incapable of interbreeding with “true” humans. The science shows both positions to be false: Neanderthals were a sister species, fully capable of producing fertile offspring with modern humans, and part of the broader human family tree that includes a number of now-extinct relatives.

Finally, the idea that Neanderthals were "absorbed" into *Homo sapiens* populations rather than being wiped out outright further undercuts simplistic, binary thinking in creationist ideology. Evolutionary theory predicts such population dynamics: extinction by absorption is a well-documented process in nature. For creationists, however, the implications are theologically awkward. The evidence shows humanity as a messy, branching, reticulated process—one far removed from the linear, tidy special creation model.

In summary, this new evidence forces creationists into an increasingly untenable position. They must reject not just isolated findings, but entire scientific disciplines working in harmony. As the data become clearer, the only tools left to defend creationism are misrepresentation, cherry-picking, and denialism—all tactics that reveal the fragility of their position in the face of overwhelming evidence.

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