Refuting Creationism - No Ancestral Couple, Not Even An Ancestral Species - All Modern Humans Are Hybrids

Reconstruction of a Neanderthal woman.

‘A history of contact’: Princeton geneticists are rewriting the narrative of Neanderthals and other ancient humans

Our understanding of our relationship with contemporaneous archaic hominins such as Neanderthals has changed over the past 25 years or so. It was once believed that, as separate species, there would have been no successful interbreeding, despite a few fossils suggesting a mixture of both Neanderthal and Homo sapiens feature, then Nobel Prize-winning Svante Pääbo's group at the Max Plank Institute analysed a Neanderthal genome and showed that modern Eurasia Homo sapiens have 2-3% Neanderthal DNA, so interbreeding must have taken place.

Since then, the same team has discovered a second extinct hominin, the Denisovans, and shown that they too interbred with Neanderthals in Eurasia and Homo sapiens in East and Southeast Asia, especially.

And now we know that Africans' too carry evidence of Neanderthal genetic ingression.

In other words, ever since Homo sapiens left Africa and moved into the territory of at least two archaic hominins, the descendants of an earlier migration out of Africa, probably Homo erectus, have behaved much like a ring species of incompletely speciated geographical subspecies where barriers to hybridization had not fully evolved.

What information do you have on Neanderthals and Denisovans and their interactions with Homo sapiens? Neanderthals and Denisovans are two distinct groups of archaic humans that coexisted and interacted with Homo sapiens during the late Pleistocene epoch. Here's an overview of each group and their interactions with modern humans:

Neanderthals

Who they were:

• Neanderthals (Homo neanderthalensis) lived in Europe and western Asia from around 400,000 to 40,000 years ago.
• They were adapted to cold climates, with robust bodies, large noses, and strong limbs.
• They had sophisticated tools, engaged in symbolic behavior, and possibly had language.

Interactions with Homo sapiens:

• Neanderthals interbred with early modern humans, contributing about 1-2% of the genome in non-African populations today.
• Evidence of this interbreeding comes from both fossil records and genetic studies.
• The interactions included both peaceful exchanges and competition for resources, with Neanderthals eventually going extinct around 40,000 years ago, shortly after the arrival of modern humans in Europe.

Denisovans

Who they were:

• Denisovans (Homo sapiens denisova) are known from a limited number of fossils found in the Denisova Cave in Siberia, dating back to around 100,000 to 40,000 years ago.
• Their physical characteristics are less well understood due to the scarcity of remains, but genetic evidence suggests they were a distinct group from both Neanderthals and modern humans.

Interactions with Homo sapiens:

• Denisovans also interbred with early modern humans, particularly with populations in Asia and Oceania.
• Genetic evidence indicates that some modern human populations, especially Melanesians and Aboriginal Australians, have up to 5% Denisovan DNA.
• Denisovan genes have been linked to adaptations in modern humans, such as high-altitude adaptation in Tibetans.

Shared Characteristics and Differences

Commonalities:

• Both Neanderthals and Denisovans shared a common ancestor with modern humans, likely around 500,000 to 700,000 years ago.
• Both groups used tools and had complex social structures.
• Genetic evidence shows that Neanderthals and Denisovans also interbred with each other.

Differences:

• Neanderthals were primarily located in Europe and western Asia, whereas Denisovans were located in Asia.
• The extent of cultural and technological differences between the groups is still under research, but their adaptations to different environments suggest some variation in lifestyle and skills.

Legacy and Impact

The interactions between these groups have left a lasting legacy in the genetic makeup of modern humans. The interbreeding events have contributed to the diversity of the human genome and have provided insights into the evolutionary history of our species. Understanding these interactions helps scientists learn more about the movement, adaptation, and survival of early human populations.

Research and Discoveries

Ongoing research continues to reveal new insights about Neanderthals and Denisovans:

• Advanced DNA sequencing techniques are uncovering more details about their genetic contributions to modern humans.
• New fossil discoveries are providing additional information about their physical characteristics and behaviors.
• Interdisciplinary studies, combining archaeology, genetics, and anthropology, are helping to create a more comprehensive picture of these archaic humans and their interactions with Homo sapiens.

Why are they regarded as distinct species and not subspecies or geographical variants?

Neanderthals and Denisovans are regarded as distinct species rather than subspecies or geographical variants of Homo sapiens due to several key factors:

1. Morphological Differences
   
   Neanderthals:
   • Neanderthals exhibited distinct skeletal features that differentiate them from modern humans, including a more robust build, prominent brow ridges, larger noses, and a different cranial shape.
   • These differences are consistent and significant across numerous Neanderthal fossils found in Europe and western Asia.
   Denisovans:
   • Although fewer Denisovan fossils have been discovered, the available evidence suggests they had distinct physical traits, notably in dental morphology. Their teeth and bones differ enough from both Neanderthals and modern humans to warrant classification as a separate species.
2. Genetic Evidence
   
   • Neanderthals and Denisovans: Genomic studies show that Neanderthals and Denisovans were genetically distinct from each other and from Homo sapiens. While they interbred with modern humans and with each other, the genetic differences are significant enough to classify them as separate species.
   • Genetic Divergence: The degree of genetic divergence between these groups and modern humans supports their classification as separate species. For example, Neanderthals and modern humans diverged approximately 500,000 to 700,000 years ago, which is a substantial time period allowing for significant genetic differentiation.
3. Evolutionary History and Ancestry
   
   • Common Ancestors: Neanderthals, Denisovans, and modern humans shared a common ancestor, but they evolved separately for hundreds of thousands of years. This long period of separate evolution allowed each group to develop unique adaptations to their environments.
   • Distinct Evolutionary Paths: The distinct evolutionary paths taken by these groups led to the development of unique physical and genetic traits. These differences are consistent with the definition of distinct species, which typically involves separate evolutionary lineages with unique adaptations.
4. Reproductive Isolation
   
   • Interbreeding Evidence: While there is evidence of interbreeding between Neanderthals, Denisovans, and Homo sapiens, it was not extensive enough to merge the populations into a single species. The gene flow was limited, and the hybrid offspring likely faced challenges in survival and reproduction.
   • Speciation Criteria: The limited gene flow and the distinct adaptations and evolutionary trajectories meet the criteria for speciation. Species are often defined as groups of organisms that are reproductively isolated and follow distinct evolutionary paths.
5. Behavioral and Cultural Differences
   
   • Archaeological Evidence: Archaeological findings suggest that Neanderthals and Denisovans had different tool-making techniques, social structures, and possibly even cognitive abilities compared to early modern humans. These differences in behavior and culture further support their classification as separate species.

Conclusion

The classification of Neanderthals and Denisovans as distinct species from Homo sapiens is supported by a combination of morphological, genetic, evolutionary, and behavioral evidence. These differences are significant and consistent enough to differentiate them from being merely subspecies or geographical variants. Understanding these distinctions helps scientists trace the complex evolutionary history of the human lineage and the interactions between different human species.

The evidence for this is the fact that no Neanderthal Y-chromosomes have ever been found in Homo sapiens, not have Neanderthal X-chromosomes. This probably indicates that only female children of a Neanderthal father and a H. sapiens mother were viable and fertile; male children were either non-viable or sterile.

However, this picture may be misleading since it was shown in 2020 that Neanderthals had acquired Y-chromosomes from both H. sapiens and Denisovans, so it is possible that the Neanderthals that later bred with H. sapiens had H. sapiens Y-Chromosomes.

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. They have found evidence historical genetic exchange that suggests a more close relationship between these ancient hominins and H. sapiens, than was previously thought, with several waves of H. sapiens and Neanderthal admixture.

The team has found that modern humans and Neanderthals shared a common ancestor about 600,000 years ago and that by about 250,000 years ago, modern humans had acquired their modern characteristics. From then on, for about 200,000 years until Neanderthals disappeared about 40,000 years ago, modern humans and Neanderthals had interacted frequently.

Their findings are the subject of a paper in Science and are explained in a Princeton University press release:

‘A history of contact’: Princeton geneticists are rewriting the narrative of Neanderthals and other ancient humans

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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.

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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
The Lewis-Sigler Institute for Integrative Genomics
Princeton University, Princeton, NJ, USA.

We now know that for the vast majority of human history, we’ve had a history of contact between modern humans and Neanderthals.

Professor Joshua Akey, co-author
The Lewis-Sigler Institute for Integrative Genomics
Princeton University, Princeton, NJ, USA.

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 Akey.

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 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.

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 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.

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.

I don’t like to say ‘extinction,’ because I think Neanderthals were largely absorbed

Professor Joshua Akey.

His 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.

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 Akey.

“Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years,” by Liming Li, Troy J. Comi, Rob F. Bierma, and Joshua M. Akey, appears in the July 13 issue of the journal Science (DOI: 10.1126/science.adi1768). This research was supported by the National Institutes of Health (grant R01GM110068 to JMA).

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 Homgenome, 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 (N_e) 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 et al. ,
Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years.
Science 385, eadi1768 (2024). DOI:10.1126/science.adi1768.

Copyright © 2024 The Authors, published by American Association for the Advancement of Science. reprinted with kind permission under licence #5827201142176.

Rather than exterminating the Neanderthals, the evidence is that we simply absorbed the small and declining population into our larger and growing population. Of course there is no way we can know what relationship we had with them - as equals, as an underclass or even as a slave race, but the result is that there is more Neanderthal DNA in the world today than there ever was when the last wave of modern human migrants absorbed them.

Contrary to the childish fairy tale in the Bible of all humanity originating from a single, magically-created couple, who then 'sinned' and causes 'The Fall', the reality is that modern humans didn't even originate from a single species, but from a mixture of at least three distinct species that had diversified from a common ancestor a few hundred thousand years earlier. And of course that leaves in tatters the notion of original sin - the device the priesthood have used for centuries to tell us we need them to provide the cure for our inherited 'defect', otherwise an unimaginably horrible fate awaits us when we die because God hates us the way he designed us (when we can't ask for our money (and life) back).

Curiously, that daft notion of original sin by a founder couple, which is the entire basis of Christianity, even those flavours of it that claim to accept evolution on an old earth, and purport to see no conflict between their religion and science, and even claim science supports them, is nonetheless believed in by those same supposedly enlightened churches.

But which priest, preacher or theologian is going to have the integrity to stand up and say the entire reason for their existence, and the source of their livelihood - selling phony 'cures' for an imaginary illness - is nonsensical, immoral and unsupported by the facts?

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