Rosa Rubicondior: Refuting Creationism - How Modern Humans Benefitted from Meeting Denisovans

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Genomes from Oceania offer new clues to human evolution | Yale News

A paper recently published by a Yale University-led team in the journal Science shows how Denisovan genes in the people of Near Oceania have contributed especially to their immune systems, and so have continued to influence human evolution for tens of thousands of years.

Who would be a creationist? It must be galling to wait so eagerly for that great day when biologists finally announce the collapse of evolutionary theory and admit that a better explanation of the observable evidence is one involving unevidenced magic entities doing conjuring tricks with chemistry and physics. That would make biology the first science to abandon natural explanations, ignore Occam’s Razor, and adopt magic as a basic principle. Sadly for creationists, that long-promised day shows no sign of arriving, despite having been predicted any day now for more than half a century.

But then, what would creationism be without a dogged refusal to change its mind when the evidence demands it, and the childish belief that the evidence itself must be part of some vast conspiracy to test the strength of faith? That is not science; it is apologetics dressed up in a lab coat.

The problem, as always, is that reality refuses to conform. The universe continues to produce evidence contradicting creationism and confirming the complex evolution of humans over deep time: migration, isolation, adaptation, bottlenecks, and repeated remixing with genes from other archaic human lineages, themselves the products of long evolutionary histories.

The real-world evidence written into our genomes is that most non-African human populations carry remnants of Neanderthal DNA, while Denisovan ancestry is especially marked in Near Oceanians and in some Asian populations. There is also evidence that Neanderthals and Denisovans themselves met and interbred in central Asia. Human evolution was not a simple ladder, still less a single act of special creation, but a branching, merging, reticulated history of populations moving, separating, adapting and sometimes meeting again.

Some of these archaic genes appear to have mattered because they were useful. In particular, they are often associated with immune responses to pathogenic bacteria and viruses. This makes evolutionary sense: Denisovan-like populations had already adapted to environments outside Africa, including their local burden of pathogens. When the ancestors of present-day Near Oceanians inherited some of that genetic variation through introgression, beneficial variants could be retained by natural selection, even while many other archaic variants were gradually lost.

The Yale-led team filled an important gap in our understanding of human evolution by sequencing the genomes of 177 individuals from 12 distinct populations in different parts of Near Oceania — the southwestern Pacific region that includes Papua New Guinea, the Bismarck Archipelago, and the Solomon Islands — and analysing them alongside 1,284 previously published genomes from individuals worldwide.

They found evidence that the ancestors of Near Oceanian populations interbred with at least three distinct Denisovan-like groups. They also identified thousands of archaic variants that affect how genes are switched on or off, with a notable concentration in immune and antiviral pathways. In other words, Denisovan DNA is not merely a fossil remnant in the genome; in some populations, it is still helping to shape biology today.

Background^ Denisovan DNA and Adaptive Introgression. Denisovans were an extinct archaic human lineage, closely related to Neanderthals, but distinct from both them and modern Homo sapiens. They were first recognised not from a complete skeleton, but from DNA recovered from a small finger bone found in Denisova Cave in the Altai Mountains of Siberia. Since then, genetic and fossil evidence has shown that Denisovan-like populations were probably widespread across parts of Asia during the Late Pleistocene.

Their importance today lies not in the few fossil fragments so far identified, but in the DNA they left behind in living people. When modern humans expanded out of Africa and moved through Asia and into Oceania, they encountered and sometimes interbred with archaic human populations, including Denisovan-like groups. Some of that inherited DNA has survived in the genomes of their descendants.

This process is known as introgression: genes from one population enter another through interbreeding. When those genes are useful and are preserved by natural selection, the process is called adaptive introgression. In simple terms, a population can acquire beneficial genetic variants from another population rather than having to wait for the same mutations to arise independently.

That is especially relevant in the case of immunity. Denisovan-like populations had lived outside Africa for hundreds of thousands of years and had already been exposed to local pathogens. Some of their immune-related genetic variants may therefore have been useful to incoming Homo sapiens populations facing unfamiliar bacteria, viruses and parasites.

The new Yale-led study of Near Oceanian genomes found evidence that the ancestors of present-day populations in Papua New Guinea, the Bismarck Archipelago and the Solomon Islands inherited DNA from at least three Denisovan-like groups. Many of these inherited variants appear to affect how genes are switched on or off, with a particular concentration in immune and antiviral pathways.

This is evolution in action at the genomic level. Human history was not a simple story of one specially-created species moving unchanged through time. It was a complex, branching and sometimes merging history of populations migrating, adapting, becoming isolated, meeting again, interbreeding, and leaving traces of those encounters in the genomes of living people.

The paper in Science was accompanied by an item in Yale News by Mike Cummings:

Genomes from Oceania offer new clues to human evolution
A Yale-led study of genomes from Near Oceania reveals a complex population history and evidence that DNA inherited from extinct hominins continues to influence human biology today

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A new Yale-led study provides one of the most detailed and comprehensive analyses to date of genetic variation in human populations in Oceania, filling a major gap in representation in genomics research.

Despite harboring remarkable diversity, populations in this vast region in the South Pacific historically have been overlooked in global human genetic studies, which have often focused largely on peoples of European descent, researchers say.

The drastic underrepresentation of Oceanians limits our understanding of human evolution and could exacerbate health inequalities as genomic research is used to develop novel medical treatments. To fill that gap, my research team embarked on a large-scale project to expand what is known about human genetic variation, including genetic variants inherited from extinct hominins.

Assistant Professor Serena Tucci, senior author
Department of Anthropology
Yale University
New Haven, CT, USA.

The study, published on June 11 [2026] in the journal Science, shows how the genes that ancient humans acquired after mating with extinct hominins continue to shape the biology, health, and survival of our species today.

For the study, the research team sequenced the genomes of 177 individuals across 12 distinct populations in different parts of Near Oceania — the southwestern portion of the Pacific region that includes Papua New Guinea, the Bismarck Archipelago, and the Solomon Islands — and analyzed them alongside a massive dataset of 1,284 previously published genomes from individuals worldwide.

This DNA is not just a remnant of ancient liaisons; it continues to influence our biology today.

Assistant Professor Serena Tucci

By tracing the deep history of the Pacific’s earliest pioneers, who migrated to the region by at least 45,000 years ago, the researchers uncovered unprecedented insights into human evolutionary history and adaptation. For example, they discovered that ancestors of Near Oceanic populations mated with at least three distinct groups related to Denisovans — an enigmatic hominin group initially discovered from fossil fragments in Siberia.

Previous studies showed that DNA inherited from extinct hominins, such as Neanderthals and Denisovans, survives, scattered, in the genomes of present-day human populations. With this study we have moved beyond simply ‘resurrecting’ this DNA to showing how it actively turns genes on and off, which is game-changing. This DNA is not just a remnant of ancient liaisons; it continues to influence our biology today.

Assistant Professor Serena Tucci

Mating between ancient humans and Denisovans left a legacy of many genetic variants, including some that contribute to functions in present-day humans, the researcher said.

For the new study, the researchers used an advanced functional genomic technique known as a “massively parallel reporter assay” to physically test the functional consequences of these genetic variants and identified over 3,100 that alter gene expression. This analysis provided some of the largest-scale evidence for how specific, adaptive genetic variants inherited from Denisovans function inside humans today, the researchers say.

While Denisovans vanished from the Earth thousands of years ago, this research proves that our histories remain deeply intertwined.

Assistant Professor Serena Tucci

They found that a substantial proportion of these adaptive and functional variants affected the interferon-gamma signaling pathway, a vital component of the human immune system that defends against infectious pathogens.

DNA from extinct hominins — Denisovans and Neanderthals — helped facilitate human adaptation to diverse environments that people encountered as they migrated into this region of the world. Pathogens are one of the strongest selective pressures — environmental factors that affect our ability to survive — throughout human evolution. We find evidence that genes inherited from Denisovans bolstered immunity to viruses and bacteria ancient humans encountered in Near Oceania.

Patrick Reilly, first author.
Department of Anthropology
Yale University
New Haven, CT, USA.

The study also revealed that Denisovan DNA influences skeletal development. The researchers discovered adaptive variants inherited from Denisovans in a specific gene called TRPS1. This same gene has been under strong positive selection in central African rainforest hunter-gatherers and highland populations in Ecuador, showing how evolution can result in recurrent local adaptations in different regions of the world.

While Denisovans vanished from the Earth thousands of years ago, this research proves that our histories remain deeply intertwined.

Assistant Professor Serena Tucci

The study shows that archaic DNA is still actively shaping human biology, said Steven Reilly, assistant professor of genetics at Yale School of Medicine and co-author of the study.

We found thousands of archaic variants that tune genes up or down, concentrated in immune and antiviral pathways. Neanderthals and Denisovans had adapted to life outside Africa over hundreds of thousands of years, and we inherited some of those genetic programs and co-opted them. Tens of thousands of years later, this DNA may still shape how these populations fight viruses — or their risk for autoimmune disease.

Assistant Professor Steven Reilly, co-author.
New Haven, CT, USA.

Coauthors of the study include Daniela Tejada-Martinez, Samantha L. Miller, Audrey Tjahjadi, Chang Liu, and Alysa Pomer of the Yale Human Evolutionary Genomics Laboratory; Stephen Rong, Jared Akers, and Margaret E. Prentice of Yale School of Medicine; D. Andrew Merriwether of Binghamton University; Françoise R. Friedlaender and Jonathan S. Friedlaender of Temple University; and George Koki of Papua New Guinea Institute for Medical Research.

Publication:
Patrick F. Reilly et al.
Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.
Science 392, eadr6749 (2026).DOI:10.1126/science.adr6749

Structured Abstract

INTRODUCTION
Because of their different settlement histories, the Pacific Islands have been divided into Near and Remote Oceania. Near Oceania—the region consisting of New Guinea, the Bismarck Archipelago, and the main Solomon Islands—was settled ~42,000 years ago and thereafter remained largely isolated at the edge of human settlement. Not until ~5000 years ago, with the advent of new migration pressures from Asia, were the rest of the Pacific Islands inhabited—Remote Oceania, encompassing Vanuatu, New Caledonia, Fiji, Polynesia, and Micronesia. Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity, including the largest amounts of archaic introgression inherited from Neanderthals and Denisovans. However, they have been substantially underrepresented in whole-genome sequencing and functional genomic consortia to date.

RATIONALE
We sequenced 177 high-coverage genomes from 12 diverse Near Oceanic populations and analyzed them alongside 1284 genomes from worldwide populations. We investigated the demographic history of groups descended from early settlers of the Pacific and the extent and distribution of Neanderthal and Denisovan introgression in Near Oceanic genomes, including adaptive archaic variation, and performed a massively parallel reporter assay to identify the functional consequences of adaptive archaic introgressed variants.

RESULTS
Near Oceanians in our study fall along a gradient of genetic similarity from Papuan-speaking groups of New Guinea and the Baining of New Britain to the Polynesian outlier groups of the Solomon Islands, although we also observed signals of long-term isolation in Papuan-speaking groups. Furthermore, both the Baining and Polynesian outlier groups showed evidence of major population bottlenecks, emphasizing complex population structure and demographic history in this region. We reconstructed archaic introgressed sequence covering 70.7% of the callable archaic genome (1.897 billion base pairs) including 505 million base pairs (Mbp) of previously unidentified archaic sequence and three times more Denisovan sequence than previous studies (831.9 Mbp). We uncovered evidence for introgression from three Denisovan-like groups into the ancestors of Near Oceanians, revealing a new twist on our interactions with archaic hominins. We refined maps of archaic “deserts” and identified a strong novel signal of adaptive Denisovan introgression at TRPS1, a skeletal development gene previously found under selection in central African rainforest hunter-gatherers and highland Ecuadorians. Using a massively parallel reporter assay, we discovered 3127 high-frequency introgressed expression-modulating variants targeting 1422 genes and found an enrichment of high-frequency introgressed variants with protein-coding, splicing, and regulatory impacts on immune pathways. These include adaptive archaic variants affecting genes in the interferon-γ pathway, including JAK1, GBP2, and the COVID-19–associated OAS1 locus, where we functionally characterized a Denisovan haplotype unique to Oceanic populations. Although some of these adaptive introgression signals, such as TNFAIP3 and HLA-DRA, may be related to malaria susceptibility, few are widely shared across Near Oceania, suggesting multiple independent instances of local adaptation. Many of these immune-related genes are also pleiotropic, including TRPS1 and TANK.

CONCLUSION
We characterized the evolutionary, phenotypic, and functional consequences of archaic introgressed variants in Near Oceanians and identified putatively causal archaic variants contributing to parallel local adaptation of both the immune system and skeletal development.

The complex evolutionary history of Near Oceanians.
Map of Oceanic and other worldwide populations included in this study, along with models showing a strong bottleneck (narrow population bar) and three Denisovan introgression events (dashed arrows) into Oceanians, targets of adaptive introgression in Oceanians, and a diagram of the method used to detect functional effects of archaic variants. AFR, Africans; OOA, Out-of-Africa; EUR, Europeans; EAS, East Asians; OCN, Oceanians; NEA, Neanderthals; DEN, Denisovans; ARC, archaic hominins; cCRE, candidate cis-regulatory element; MPRA, massively parallel reporter assay; emVar, expression-modulating variant.

Abstract
Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity yet are drastically underrepresented in human genomics. We generated 177 high-coverage Near Oceanian whole genomes and analyzed them alongside 1284 worldwide genomes, revealing major distinctions among and within islands, including long-term isolation and strong population bottlenecks. We reconstructed 1.897 billion base pairs of the archaic genome, including 831.9 million base pairs of Denisovan sequence, and found evidence for introgression from three Denisovan-like groups in Near Oceanians and adaptive Denisovan introgression at TRPS1, a skeletal development gene also under selection in central African rainforest hunter-gatherers and highland Ecuadorians. We then performed a massively parallel reporter assay and discovered 3127 high-frequency introgressed expression-modulating variants, finding an enrichment of functional impacts on genes in the interferon-γ signaling pathway including JAK1, GBP2, and OAS1.

Patrick F. Reilly et al.
Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.
Science 392, eadr6749 (2026).DOI:10.1126/science.adr6749

© 2026 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So, once again, the evidence is not merely consistent with evolution; it is inexplicable without it. The genomes of living people in Near Oceania preserve the record of ancient migrations, encounters with other human lineages, interbreeding, selection, and adaptation to local environments. These are not theological abstractions or just-so stories. They are measurable genetic facts.

Creationism has no coherent explanation for any of this. It cannot explain why humans carry different amounts of Neanderthal and Denisovan DNA, why some of that DNA is concentrated in immune-related regions of the genome, or why these patterns map so clearly onto ancient geography, population history and natural selection. All creationism can do is deny, misrepresent, or wave the evidence away with the usual appeal to magic.

The Denisovan contribution to the immune systems of Near Oceanians is a particularly elegant example of evolution’s practical consequences. A useful variant inherited from another archaic human population could be favoured by natural selection because it helped its new carriers survive in a pathogen-rich environment. That is not “micro-evolution” in any trivial sense; it is population genetics shaping the biology of living humans across tens of thousands of years.

And that is why papers like this are so damaging to creationist dogma. Human beings were not specially created as a fixed, separate “kind”. We are the descendants of evolving populations, shaped by migration, isolation, interbreeding and selection, with the evidence written in every cell of our bodies. The more closely science looks, the more detailed that evolutionary history becomes — and the less room remains for the childish magic of creationism.

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