Rosa Rubicondior: Refuting Creationism - Our Ancestry In Africa Was More Complex Than We Thought

Thursday, 20 March 2025

Refuting Creationism

Our Ancestry In Africa Was More Complex Than We Thought

Early Homo sapiens in Africa

AI-generated image (ChatGPT4.5)

Plaster reconstructions of the skulls of human ancestors

Jose A. Bernat Bacete via Getty Images

Genetic study reveals hidden chapter in human evolution | University of Cambridge

Traditionally, creationists have been fascinated by complexity, wrongly assuming that intricate biological systems are definitive evidence of intelligent design. In reality, simplicity is typically a hallmark of efficient, intelligent design, whereas complexity often emerges from evolutionary processes that accumulate layers of adaptation, frequently to compensate for earlier suboptimal features.

However, one particular form of complexity is likely to provoke considerable confusion among creationists: the evolutionary history of our own species in Africa. Once imagined as a straightforward, linear progression - from Australopithecines through transitional species like Homo erectus, which then migrated out of Africa into Eurasia - the true narrative has proven far more intricate. Homo sapiens evolved within Africa, and subsequently some populations ventured into Eurasia, encountering and interbreeding with the descendants of earlier migrations, notably Neanderthals and Denisovans, who had evolved independently from Homo erectus.

Given our species' propensity to interbreed with closely related hominins - likely facilitated by sexual activity serving recreational and social bonding purposes alongside procreation, a trait possibly shared by our ancestral and cousin species - recent research indicates a highly complex evolutionary pattern. Rather than a simple linear progression, the evolution of humans involved multiple episodes of diversification, genetic isolation, subsequent renewed contact, and interbreeding within Africa's vast landscapes, creating a rich mosaic of genetic heritage.

What is the current consensus regarding the evolution of Homo sapiens up to the point of migration into Eurasia?

The current consensus regarding the evolution of Homo sapiens up to the migration out of Africa emphasizes a complex, branching evolutionary process rather than a simple linear progression. Key points of this consensus include:

Multiregional Evolution within Africa:
Homo sapiens emerged approximately 300,000 years ago, with evidence from fossils in sites such as Jebel Irhoud (Morocco), Omo Kibish (Ethiopia), and Florisbad (South Africa), suggesting a geographically widespread and genetically diverse early population rather than a single localized origin.
Diverse Lineages and Interbreeding:
Africa hosted several contemporary hominin species and populations, which periodically diverged, evolved independently, and later came back into contact, exchanging genetic material through interbreeding events. This complex process created the mosaic genetic pattern observed today.
Multiple Waves of Migration and Interbreeding:
It is now recognized that early migrations out of Africa were not singular events. Instead, multiple dispersals occurred between approximately 120,000 and 50,000 years ago. Modern Homo sapiens populations migrating into Eurasia encountered and interbred with earlier populations, notably Neanderthals and Denisovans, thus incorporating some of their DNA into the genomes of modern humans outside Africa.
Genomic Evidence:
Advances in ancient DNA analysis have confirmed extensive gene flow and admixture, showing that contemporary human populations carry genetic evidence from these early interbreeding events, which has significantly revised earlier views of human evolution as a neat, linear pathway.
In essence, the consensus is now characterized by a dynamic, interconnected network of evolutionary paths, emphasizing continuous genetic exchange and regional differentiation, culminating in the global dispersal and diversity of modern humans.

ChatGPT4.5 [Response to user request]
Retrieved from https://chatgpt.com/

Information Continually updated

The recent research by Trevor Cousins, Aylwyn Scally & Richard Durbin of Cambridge University, UK is published, open access, in the journal Nature Genetics and explained in a University of Cambridge news release. It shows that we are descended not from one but from at least two and probably more ancestral species, even before those of us from Eurasia met and interbred with Neanderthals and Denisovans. If we were dogs, we would be a truly mongrel variety.

Genetic study reveals hidden chapter in human evolution
Modern humans descended from not one, but at least two ancestral populations that drifted apart and later reconnected, long before modern humans spread across the globe.
Using advanced analysis based on full genome sequences, researchers from the University of Cambridge have found evidence that modern humans are the result of a genetic mixing event between two ancient populations that diverged around 1.5 million years ago. About 300,000 years ago, these groups came back together, with one group contributing 80% of the genetic makeup of modern humans and the other contributing 20%.

For the last two decades, the prevailing view in human evolutionary genetics has been that Homo sapiens first appeared in Africa around 200,000 to 300,000 years ago, and descended from a single lineage. However, these latest results, reported in the journal Nature Genetics, suggest a more complex story.

The question of where we come from is one that has fascinated humans for centuries. For a long time, it’s been assumed that we evolved from a single continuous ancestral lineage, but the exact details of our origins are uncertain.

Dr Trevor Cousins, first author
Department of Genetics
University of Cambridge, Cambridge, UK.

Our research shows clear signs that our evolutionary origins are more complex, involving different groups that developed separately for more than a million years, then came back to form the modern human species.

Professor Richard Durbin, co-author
Department of Genetics
University of Cambridge, Cambridge, UK.

While earlier research has already shown that Neanderthals and Denisovans – two now-extinct human relatives – interbred with Homo sapiens around 50,000 years ago, this new research suggests that long before those interactions – around 300,000 years ago – a much more substantial genetic mixing took place. Unlike Neanderthal DNA, which makes up roughly 2% of the genome of non-African modern humans, this ancient mixing event contributed as much as 10 times that amount and is found in all modern humans.

The team’s method relied on analysing modern human DNA, rather than extracting genetic material from ancient bones, and enabled them to infer the presence of ancestral populations that may have otherwise left no physical trace. The data used in the study is from the 1000 Genomes Project, a global initiative that sequenced DNA from populations across Africa, Asia, Europe, and the Americas.

The team developed a computational algorithm called cobraa that models how ancient human populations split apart and later merged back together. They tested the algorithm using simulated data and applied it to real human genetic data from the 1000 Genomes Project.

While the researchers were able to identify these two ancestral populations, they also identified some striking changes that happened after the two populations initially broke apart.

Immediately after the two ancestral populations split, we see a severe bottleneck in one of them—suggesting it shrank to a very small size before slowly growing over a period of one million years. This population would later contribute about 80% of the genetic material of modern humans, and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged.

Professor Aylwyn Scally, co-author
Department of Genetics
University of Cambridge, Cambridge, UK.

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

However, some of the genes from the population which contributed a minority of our genetic material, particularly those related to brain function and neural processing, may have played a crucial role in human evolution.

Dr Trevor Cousins.
Beyond human ancestry, the researchers say their method could help to transform how scientists study the evolution of other species. In addition to their analysis of human evolutionary history, they applied the cobraa model to genetic data from bats, dolphins, chimpanzees, and gorillas, finding evidence of ancestral population structure in some but not all of these.

What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic. Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.

>Dr Trevor Cousins.
So who were our mysterious human ancestors? Fossil evidence suggests that species such as Homo erectus and Homo heidelbergensis lived both in Africa and other regions during this period, making them potential candidates for these ancestral populations, although more research (and perhaps more evidence) will be needed to identify which genetic ancestors corresponded to which fossil group.

Looking ahead, the team hopes to refine their model to account for more gradual genetic exchanges between populations, rather than sharp splits and reunions. They also plan to explore how their findings relate to other discoveries in anthropology, such as fossil evidence from Africa that suggests early humans may have been far more diverse than previously thought.

The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing. And it tells us that our history is far richer and more complex than we imagined.

Professor Aylwyn Scally.

Abstract
Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.

Main
Improvements in the technology to extract ancient DNA have enabled an increasingly detailed picture of human evolutionary genetics in the late Pleistocene and Holocene¹, which overwhelmingly suggests that in the last tens of thousands of years, there has been repeated separation and subsequent remixing, or admixture, of populations. Further back in time, high-coverage genomes from Neanderthals and Denisovans strongly indicate gene flow from these archaic humans into non-Africans^2,3,4,5, and more ancient gene flow from the ancestors of modern humans into the ancestors of Neanderthals^6,7,8. Moreover, researchers have demonstrated that models that incorporate a contribution of ancestry within the last ~100 thousand years from an unknown archaic population better explain patterns of polymorphism in African populations than a model without such a contribution^{9,10,11,12,13,14,15,16}. However, the presence of more ancient admixture events is less clear¹⁷.

The history of effective population size changes is another important quantity in understanding evolutionary genetics¹⁸. The pairwise sequentially Markovian coalescent (PSMC)¹⁹ was introduced to infer changes over time in the coalescence rate, the inverse of which can be interpreted as the history of effective population sizes. PSMC assumes that a population evolved under panmixia, with random mating in the ancestral population at all times. In light of the repeated evidence for ancestral population structure and admixture summarized above, PSMC’s assumption of an unstructured evolutionary history is questionable. Moreover, theoretical analysis shows that for any panmictic model with changes in the effective population size, there necessarily exists a structured model that can generate exactly the same pairwise coalescence rate profile without changes in population sizes^20,21.

Here we address whether the use of additional information can restore identifiability. We demonstrate that the transition matrix of the PSMC hidden Markov model (HMM) has information that can distinguish a structured model from a panmictic model, even if they have matching coalescence rate profiles. We parameterize a model of ancestral population structure that leverages this information and introduce this in an HMM called cobraa. This approach can be applied to diploid sequence data from any species, and we show a variety of different inferred histories in various mammals including humans. Applying cobraa to data from the 1000 Genomes Project (1000GP)^{22,23,24,25,26} and the Human Genome Diversity Project (HGDP)^27,28, we show that a model of deep population structure, where modern humans are a result of two populations that diverged ~1.5 million years ago (Ma) admixing together ~300 thousand years ago (ka) in a ratio of ~80:20%, better explains the data than does a continuously panmictic model. We use posterior decoding to infer regions of the modern human genome that are derived from each population and find evidence for selection against the material from the population contributing the minority of ancestry. Moreover, we find a strong association between regions derived from the major ancestral population and human–Neanderthal or human–Denisovan divergence, suggesting that the majority population was the primary ancestral population to Neanderthals and Denisovans.
Cousins, T., Scally, A. & Durbin, R. A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02117-1

Copyright: © 2025 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What wonderful and inspiring stories emerge from the rich complexity of our evolutionary history on the African savannah. Groups of hominins diverged, became isolated, then met again and interbred, merging their lineages into what ultimately became our single species. One lineage, emerging through a genetic bottleneck, played a central role, not only giving rise to modern Homo sapiens but also ancestral Eurasian groups such as Neanderthals and Denisovans.

The resulting species - a hybrid with enhanced genetic diversity and vigour - developed the extraordinary ability to think abstractly, weave narratives from minimal clues, and communicate complex ideas. This remarkable brain and adaptability were shaped purely by natural selection in an environment full of challenges, continuously filtering each generation for traits favourable for survival and reproduction.

We owe everything to these early humans, whose resilience and adaptability paved the way for our species' success.

How much richer and more fulfilling this evidence-based narrative is compared to the simplistic, unsupported idea of a magical creator fashioning a man from dirt and a woman from his rib, as imagined by Bronze-Age storytellers in the Bible. Indeed, our capacity to craft imaginative stories from limited evidence stems from our African ancestry - but this innate creativity is vastly enhanced when combined with the power of careful observation, rigorous analysis, and scientific inquiry.

Science reveals the genuine stories of our past, infinitely more compelling and authentic than any mythological tale.

Advertisement

Amazon