Rosa Rubicondior: Refuting Creationism - Origins of the People of Papua New-Guinea

Male Huli tribe member in Tari area of Papua New Guinea in traditional clothes and face paint.

Image Credit: By Amy Nichole Harris / Shutterstock

New AI Study Clarifies the Origins of Papua New Guineans | University of Tartu

A team of researchers led by Dr. Mayukh Mondal of the Centre for Genomics, Evolution & Medicine, Institute of Genomics, University of Tartu, Estonia, have used AI-powered demographic modelling to estimate the genetic ancestry of the people of Papua New Guinea (PNG), whose origins have long been debated.

Papua New Guineans have physical features that differ noticeably from many Asian populations, and some superficial similarities to sub-Saharan Africans have led to speculation that they might descend from a very early migration out of Africa, predating most other non-African Homo sapiens. This new study strongly challenges that hypothesis: it attributes PNG’s genetic distinctiveness instead to a substantial Denisovan admixture followed by a prolonged period of isolation, a severe population bottleneck, and slower population growth.

According to the creationist mythologies, all human beings alive today descend from Adam and Eve—or, in some versions, from Noah and his family after a global flood. If that were literally true, then all living humans would share a very narrow genetic base: mitochondrial DNA (passed via the maternal line) would be limited to a very small number of variants, and all males would share essentially the same Y-chromosome (barring mutation) tracing back to the same male ancestor.

However, the observable facts are that human genetic diversity is much richer than those narratives predict. The mitochondrial DNA lineages in living people trace back to multiple distinct haplogroups with divergence times of tens to hundreds of thousands of years within Africa and beyond into archaic ancestors; similarly, Y-chromosome diversity indicates many lineages. Our human genome tells a far more complex story: long periods of evolution in isolation, multiple migrations, re-mixing, and interbreeding with related hominin species.

The same applies to other species which creationists mythology insists are the descendants of a small number of survivors of the same genocidal flood. Few living species show evidence of such a narrow genetic bottleneck, which would probably have resulted in far too much inbreeding resulting in extinction for most of them.

All non-African humans today are descended from the major “Out-of-Africa” (OOA) migration(s) of Homo sapiens. As populations moved into Eurasia, they interbred first with Neanderthals, then with Denisovans. Underlying all this, there is also the possibility of genetic contributions from even earlier human migrations (e.g. H. erectus) into the ancestors of Neanderthals, Denisovans, or earlier modern humans. Given the evidence that hominin populations often interbred when they came into contact, it would be surprising if there were no admixture between H. erectus (or similar early lineages) and the predecessors of Neanderthals and Denisovans (often thought to include H. heidelbergensis or H. antecessor).

How AI Helped Trace Papua New Guinean Ancestry. The University of Tartu team used artificial neural networks — AI models inspired by the brain—to test competing scenarios of Papua New Guinean origins.

The Question
Were Papuans descended from a separate, very early migration out of Africa, or from the same later migration as other non-Africans?
The Data
The researchers analysed whole-genome sequences from Papuan, East Asian, and African populations.
The Challenge
Traditional methods like the Relative Cross-Coalescent Rate (RCCR) sometimes suggest Papuans diverged earlier—but those signals can also be produced by bottlenecks or slow population growth.
The AI Approach

Millions of simulated genomes were generated under different models of human history.
A deep neural network was trained to recognise the subtle genetic patterns each model produced.
The AI was then given the real Papuan data to see which scenario best matched.

The Result
The AI showed Papuans are a sister group to East Asians, not an ancient separate lineage. Their distinctive signals arise from:

a severe bottleneck (population shrinking to thousands, not just a handful),
long periods of slow growth and isolation, and
admixture with Denisovans around 31,000 years ago.

Why This Isn’t Noah’s Flood
Scientists use the term bottleneck for reductions to thousands of individuals, lasting many generations. Even then, the genetic diversity remains far richer than would result from the eight flood survivors in creationist mythology. If only one family had repopulated the Earth a few thousand years ago, all humans today would carry essentially the same Y-chromosome and only a handful of mitochondrial DNA lineages, and the odds would be stacked against survival for more than a few generations due to accumulated recessing genes.

Instead, we see a wide range of ancient lineages tracing back tens to hundreds of thousands of years within Africa — utterly inconsistent with a single, recent “Ark” origin.

The results of the University of Tartu study are published, open access, in a technical paper Nature Communications, and are explains in a less technical form in a University of Tartu news item.

New AI Study Clarifies the Origins of Papua New Guineans
Papua New Guineans are living proof of how isolation, ancient mixing, and survival in remote islands can preserve a unique piece of our shared human story.
A team of European researchers, including Institute of Genomics has shed new light on the genetic origins of Papua New Guineans. The team uses advanced Artificial Intelligence (AI) tools to demonstrate that Papua New Guineans are closely related to other Asian populations. They share a common ancestry from the same ‘Out of Africa’ event that also gave rise to other non-African groups.

Papua New Guineans look strikingly different from other Asian groups and share some features with Sub-Saharan African populations, which fueled theories that they might have descended separately from other non-African populations.

According to lead author Dr. Mayukh Mondal, the unique physical features of Papua New Guineans probably come from natural selection: “Perhaps adaptations to tropical climates that make them look more like Sub-Saharan African groups, even though their genetics clearly link them to other Asian populations. More studies are needed to uncover how evolution shaped this remarkable population.” Mondal is connected to Estonia through a postdoctoral study in the field of evolutionary and population genetics at the Estonian Biocentre and work at the Centre for Genomics, Evolution and Medicine until 2023.

The genetic origin remains unresolved

Scientists generally agree that modern humans left Africa about 50,000 to 70,000 years ago, spreading into Europe, Asia, and beyond. Early archaeological studies have suggested that the ancestors of Papua New Guineans came from a separate, earlier migration (also known as the ‘First Out of Africa’ hypothesis), taking a coastal route through India and Southeast Asia. Archaeological evidence confirms that some of the Papuan New Guineans' genetic ancestry could have come from this ‘First out of Africa’ event. This is because the earliest human site in Oceania dates back to around 50,000 - 60,000 years ago, older than Europe’s oldest sites.

In recent decades, advances in DNA sequencing have tested this ‘First out of Africa’ hypothesis. However, studies of maternal (mitochondrial) and paternal (Y-chromosome) DNA have found no clear evidence that the main ancestry of Papua New Guineans came from an earlier migration. Instead, analyses suggest that their lineages connect to other non-African populations. Still, we cannot rule out a trace number of ancient migrations from the ‘First out of Africa’ population.

Interestingly, the Papua New Guinean genome carries a significant percentage of Denisovan DNA — a ghostly relative of Neanderthals. This unique inheritance likely came from mixing with Denisovans in Southeast Asia or Oceania — another element that confirms the complexity of Papua New Guinean ancestry.

Despite these researches, the genetic origin of Papuan New Guineans remains unresolved. Did Papua New Guineans split off before Europeans and Asians? Or have similar populations contributed to their genome? Did they carry ancestry from the enigmatic ‘First out of Africa’ population? Or are they part of the same family tree as other Asians living in proximity?

The map illustrates the introgression of the ancestry of Papua New Guineans.

Unique demographic history

In this study, scientists used high-quality genomic data and AI-powered models to compare different demographic scenarios for the origin of the Papuan New Guineans' genetic diversity. Their results suggest that Papua New Guineans are a sister group to other Asian populations. Contribution from a ‘First Out of Africa’ migration might not be needed to explain their origins.

The researchers found that the ancestors of Papuan New Guineans went through a dramatic population bottleneck — most likely their numbers dropped sharply after reaching Papua New Guinea and stayed low for thousands of years. Unlike other non-African groups, they did not experience the farming-driven population boom that reshaped Europe and Asia. This unique demographic history left genetic signatures that, if misunderstood, could look like evidence of a contribution from an unknown population.

Publication:
Mondal, M., André, M., Pathak, A.K. et al.
Resolving out of Africa event for Papua New Guinean population using neural network.
Nat Commun 16, 6345 (2025). https://doi.org/10.1038/s41467-025-61661-w

Abstract
The demographic history of the Papua New Guinean (PNG) population is a subject of interest due to its early settlement in New Guinea, its relative isolation and substantial Denisovan ancestry. Previous research suggested an admixture with an early diverged out of African population. This study re-examines the PNG population using newly published samples. Our findings demonstrate that the observed shifts in Relative Cross Coalescent Rate (RCCR) curves are driven by strong bottleneck and slower population growth rate of the PNG population, rather than the contributions from an earlier out of Africa population. Although a small contribution from the early out of Africa population cannot be ruled out, it is no longer needed to explain the observed results. Our analysis positions them as a sister group to other East Asian populations. This study provides insights on the PNG population and highlights the impact of population-specific demography on interpreting RCCR curves.

Introduction
The Papua New Guinean (PNG) population is among the most fascinating in the world, owing to its unique demographic history. Following the Out Of Africa (OOA) event, modern humans populated New Guinea at a remarkably early date-at least 50 thousand years ago¹. Since then, the population has remained relatively isolated compared to other OOA populations (such as European and East Asian populations)^2,3,4,5 and has gone through a strong bottleneck⁶. The substantial Denisovan ancestry within the PNG population^7,8 and the strong correlation between Denisovan and Papuan ancestries⁹, contribute to the genetic distinctiveness of the PNG population. Researchers have suggested that the genomes of PNG populations contain evidence of admixture with a modern human population that might have diverged from African populations - around 120 thousand years ago—much earlier than the proclaimed primary divergence between African and OOA populations^4,10. However, the extent to which this early diverged population contributed to the genome of PNG populations remains a subject of ongoing debate^3,4,11,12. Interestingly, this early migration hypothesis is more widely accepted by archeologists^{13,14,15,16,17}. Pagani et al.⁴ supports this hypothesis, notably through Relative Cross-Coalescent Rate (RCCR) analysis. This RCCR analysis suggests that the PNG population diverged from African populations significantly earlier than other OOA populations. They argued that this earlier divergence indicated by the RCCR curve might reflect a contribution from an earlier OOA population specific to PNG. While this shift in the RCCR curve is well-documented^2,3,5, some researchers attribute it to technical artefacts such as low sample sizes and phasing errors rather than genuine demographic events. The origins of the primary lineage of the PNG population have also been contested. Some researchers propose that the PNG population is closely related to the Asia-Pacific populations and serves as a sister group to other Asian populations^11,12,18. Conversely, other researchers argue that the PNG population is an outgroup to both European and East Asian populations^3,9,19. Recent advancements in analytical methods may provide insights into these debates. For example, Approximate Bayesian Computation with Deep learning and sequential Monte Carlo (ABC-DLS) allows for the use of any summary statistics derived from simulations to train neural networks, which can then predict the most likely demographic models and parameters based on empirical data²⁰. Additionally, the Relate software²¹ enhances RCCR analysis by employing a modified version of the hidden Markov model, initially used in the Multiple Sequentially Markovian Coalescent (MSMC) method^22,23, allowing for the analysis of thousands of individuals with greater robustness. In this paper, we re-examine the demographic history of the PNG population using recently published samples²⁴ combined with data from the 1000 Genome Project^25,26 and cutting edge methods^20,21. This approach has enabled us to address these longstanding questions with greater precision. We first generate empirical RCCR curves and demonstrate that the previously observed shift is unlikely to be the result of low sample size or phasing errors. Through simulations, we further show that the PNG population is indeed a sister group to East Asian populations, and this shift is probably not due to contributions from an earlier OOA population. Instead, it is likely a consequence of a strong bottleneck and slower population growth in the PNG population.

Fig. 1: Relate results of relative cross coalescent rate (RCCR) curve on empirical data using 40 samples per population.

AFR = Yoruba, EUR = British from England and Scotland, ASN = Han Chinese, and PNG = Highlanders of Papua New Guinea. The x-axis is years ago from modern times with the log scale. The y-axis is RCCR values calculated by Relate. The shaded regions are the 95 percent (mean ± two standard deviation) confidence intervals created from 10 separate random sampling events. The line represents the mean values.

Fig. 2: Simplified schematic of demographic models tested in this Study.

AFR Africa, EUR European, ASN East Asian, PAP Papua New Guinean, Model A Papua New Guineans and East Asians are sister groups, Model O Papua New Guineans are an outgroup of Europeans and East Asians, Model M a mixture between model A and O, Model AX Early out of Africans contributed to Papua New Guineans who are a sister group to East Asians. Model OX Early out of Africans contributed to Papua New Guineans who are an outgroup of Europeans and East Asians. Red arrow represents the Neanderthal introgression for all out of Africa populations, and the green represents the Denisova introgression for Papua New Guinean.

Fig. 3: The schema of the Model A with the best fitted mean values of parameters.

AFR Africa, EUR European, ASN East Asian, PAP Papua New Guinean, NEAI introgressed Neanderthal, NEAS sequenced Altai Neanderthal, DENI introgressed Denisova, and DENS sequenced Denisova. The corresponding values are written with the name of the parameters. The graph is not according to the scale. The y-axis represents time events from a thousand years ago (kya) from now.

Mondal, M., André, M., Pathak, A.K. et al.
Resolving out of Africa event for Papua New Guinean population using neural network.
Nat Commun 16, 6345 (2025). https://doi.org/10.1038/s41467-025-61661-w

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 this latest study demonstrates once again is how modern science, using cutting-edge tools such as AI, is able to make sense of the complex evidence written into our DNA. The story it tells is not a simple one of a single founding couple, or of a world repopulated from a small boatload of flood survivors, but a rich, intricate narrative of migration, isolation, adaptation, and interbreeding stretching back tens of thousands of years.

The contrast could not be starker: where creationist mythology offers a crude, easily falsified tale with no supporting evidence, genomics reveals a detailed and testable history that connects us not only with our African origins but also with now-extinct relatives like the Neanderthals and Denisovans. Far from diminishing our story, this complexity adds depth to our understanding of what it means to be human.

Once again, science delivers evidence; creationism delivers myth. And the more we learn, the more obvious it becomes which of those deserves our trust.

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