Rosa Rubicondior: Refuting Creationism - Ecuadorian Human Genome Refutes The Biblical Creation Myth

Ancient Ecuadorian genomes | EurekAlert!

Ancient DNA is giving the people of South America something biblical mythology never provided: a history reconstructed from evidence. That history involves regional ancestry, movement, cultural change and communities persisting through environmental upheaval. A new study of ancient genomes from coastal Ecuador adds another piece to this picture, while also revealing a much darker aspect of life there: tuberculosis affecting an infant long before European contact.

In a paper published in PNAS Nexus, John Lindo and colleagues report four ancient human genomes from Salango, spanning approximately 2,300 to 740 years ago. Their genetic similarities suggest substantial local continuity over more than 1,500 years, despite volcanic disruption and major cultural transformations. Changing customs and social organisation need not mean that one population replaced another: communities can change their ways of life while retaining much of their ancestry.

The chronological challenge to young-Earth creationism requires a distinction. These burials are younger than the supposed biblical Flood, so their ages alone do not demonstrate survival across it. However, the researchers’ demographic modelling places the divergence of the coastal Ecuadorian lineage from other Southern Native American lineages at approximately 9,800 years ago. That estimate is model-dependent, rather than a direct date for a skeleton, but it points to population history extending beyond the entire conventional young-Earth chronology.

Claiming that the descendants of Noah migrated to the America during the last few thousand years, forgot all about the god who had caused the flood and the name of the man who had saved humanity and invented a language unrelated to that of their ancestors, while a divine trickster manipulated their genomes to make it look like they diversified thousands of years earlier, raises uncomfortable questions of anthropology and theology for creationists. Four genomes cannot settle every demographic question; they nevertheless add evidence to a history that cannot reasonably be compressed into recent dispersal from Noah’s family.

The infant provides a second, sobering finding. Alongside skeletal lesions consistent with tuberculosis, the researchers recovered ancient DNA belonging to the Mycobacterium tuberculosis complex. Limited pathogen coverage prevents a detailed evolutionary placement, but the combined evidence supports infection around 2,300 years ago. For advocates of a benevolent intelligent designer, an infant afflicted by tuberculosis poses an uncomfortable question: what benevolent purpose is served by a pathogen capable of causing such suffering?

These remains preserve traces of both ancestry and disease. Recovering those traces, comparing competing explanations and acknowledging uncertainty is how science reconstructs the past. The resulting history owes its shape to the evidence, rather than to a requirement that the evidence conform to an ancient creation story.

How DNA Reveals Population Continuity—and Dates Deeper Ancestry. Ancient DNA can help answer two different questions: did people living in the same place at different times share a similar ancestry? And how far back does the history of that ancestry extend? These questions require different analyses, and their answers should not be confused.

What does “genetic continuity” mean?

A population exhibits genetic continuity when much of its ancestry persists across successive generations. This does not mean that everyone has identical DNA, that nobody moves into the area, or that the population remains genetically unchanged. Mutations, genetic drift and intermarriage continue to alter the distribution of genetic variants.

Continuity is therefore compatible with contact and migration. A community can retain a substantial contribution from its earlier inhabitants while also acquiring ancestry from neighbouring populations.

How can researchers recognise continuity?

Researchers compare genetic variants across ancient individuals, then examine how those individuals relate to other ancient and present-day populations. Shared patterns across many positions in the genome can reveal common ancestry and help assess whether successive inhabitants belonged to broadly similar ancestral populations.

At Salango, the four sampled individuals span approximately 2,300 to 740 years ago. Their genetic similarities support substantial local ancestry continuity over more than 1,500 years. Their relationships with other South American populations also place them within a wider history of regional connections.

Cultural change is not necessarily population replacement

Archaeologists often distinguish cultural periods by changes in pottery, architecture, burial practices or economic organisation. These categories describe material culture; they do not automatically identify separate biological populations.

People can adopt new technologies, religious practices or political arrangements without being replaced by newcomers. Conversely, migrants can adopt local customs. Combining archaeology with ancient DNA helps researchers investigate which processes best explain a particular transition.

Two different clocks: burial age and ancestry

The age of a burial concerns when a particular person lived. Depending on the evidence available, it may be established through radiocarbon dating or inferred from the archaeological context. A date assigned from associated pottery or a cultural phase is not the same as a direct radiocarbon date on the individual.

A population-divergence estimate concerns a much earlier stage in the ancestry of those people. Researchers use demographic models to investigate how observed genetic differences could have accumulated as ancestral populations became differentiated, sometimes with subsequent gene flow between them.

The Salango study’s estimate of approximately 9,800 years concerns this deeper population history. It does not mean that the sampled skeletons are 9,800 years old, that Salango itself was necessarily occupied then, or that an ancestral population became completely isolated on a particular date.

Why are these estimates qualified?

Demographic estimates depend on assumptions about mutation rates, generation lengths, population sizes, migration and the relationships among the populations included. Statistical uncertainty within a model does not capture every possible uncertainty about the model itself.

Likewise, four ancient genomes provide a valuable but limited sample. They cannot establish that every community in coastal Ecuador had the same history, or exclude migration and episodes of population change between the sampled periods.

The distinction to remember: the sampled genomes support continuity across approximately 1,500 years; modelling investigates ancestral relationships extending much further into the past. These are complementary findings, but they are not interchangeable dates.

Source: Lindo and colleagues, Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America, PNAS Nexus (2026).

The paper in PNAS Nexus was accompanied by a research report released through EurekAlert!:

Ancient Ecuadorian genomes
Ancient genomes from coastal Ecuador reveal 1,500 years of genetic continuity in an understudied part of the ancient world. John Lindo and colleagues sequenced four genomes from individuals excavated at Salango on Ecuador’s central coast, from around 2,300 years ago, 1,900 years ago, and 740 years ago. The four genomes cluster with ancient and present-day populations from Ecuador, Colombia, and Peru, consistent with shared ancestry within a northwestern South American genetic continuum.

Skeletal elements from an infant buried in Salango, Ecuador. (A) Showing lesions (red); grey bones were not recovered. (B) Petrous portion with lytic lesions and new bone formation. (C) Left clavicle and (D) right humerus with new bone plaques. (E) Ribs with lytic lesions and (F) right ilium with a large lytic defect.
Credit: Lindo et al. (2026)

The Salango population likely diverged from other Southern Native Americans around 9,800 years ago. All four individuals showed genetic similarities, suggesting population continuity at Salango despite major cultural and environmental changes, including the aftermath of the Pululahua volcanic eruption around 2,360 years ago, the rise of chiefdoms, and the development of maritime and overland trade. In addition, one individual, an infant, exhibited skeletal lesions consistent with tuberculosis. The researchers recovered DNA from the Mycobacterium tuberculosis complex and reconstructed a pathogen genome, providing rare genetic evidence of tuberculosis in the pre-contact Americas. According to the authors, the study opens new opportunities to trace both population history and infectious disease along South America’s Pacific coast.

Publication:
John Lindo, Daniel Rivas Alava, Sara Juengst, Yemko Pryor, Sophie K Joseph, Juan J Ortiz Aguilu, Richard Lunniss
Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America PNAS Nexus 5(10), 2026, pgag323, https://doi.org/10.1093/pnasnexus/pgag323

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Significance Statement.
Ancient genomes from Salango provide the first genomic evidence from Ecuador's Pacific coast, revealing over 1,500 years of genetic continuity despite major environmental and cultural transformations. These findings indicate coastal Ecuador as an important component of early Southern Native American population history and highlight long-term connections between coastal and Andean populations. We also recovered authentic Mycobacterium tuberculosis complex DNA from an infant with skeletal lesions consistent with tuberculosis, providing rare molecular evidence of infectious disease in pre-contact Ecuador. Together, these results offer new insights into the demographic and biological history of the Pacific coast of South America.

Abstract
The demographic history of pre-Columbian South American populations remains poorly understood, particularly along the Pacific coast where ancient genomic data are scarce. Here, we present the first whole genomes from ancient individuals buried at Salango, Ecuador, spanning ∼2,300 to ∼740 years before present and representing 3 distinct cultural phases. Despite major environmental disruption following the Pululahua volcanic eruption and substantial sociopolitical change, these individuals exhibit remarkable genetic continuity across nearly 2 millennia. Population genetic analyses consistently support long-term continuity at Salango, while demographic modeling suggests that the Ecuadorian coastal lineage diverged from other Southern Native American (SNA) lineages approximately 9,800 years ago (95% CI: 9.6–10.1 ka). Together, these findings are consistent with coastal Ecuador representing a long-standing component of early South American population structure while maintaining connections with neighboring Andean populations through time. In addition, we recovered authentic Mycobacterium tuberculosis complex (MTBC) DNA from an infant dated to ∼2,300 BP with skeletal lesions consistent with tuberculosis, providing molecular evidence for one of the earliest documented cases of MTBC infection in pre-contact South America. Although the moderate pathogen genome coverage precludes detailed phylogenetic interpretation, the combined osteological and molecular evidence expands the record of tuberculosis in ancient South America. Overall, our study provides the first ancient genomic data from Ecuador, establishing an important geographic reference for investigating the demographic and biological history of the Pacific coast of South America.

Figure 4
Demographic model and estimated divergence times for the Salango genomes within a continental framework. The best-fitting fastsimcoal2 model was inferred from the joint site-frequency spectrum of ancient and present-day Indigenous populations from North and South America. Gray nodes indicate fixed divergence times (Siberia–Americas, ∼23 ka; Northern Native American–Southern Native American, ∼16 ka), whereas colored nodes indicate median divergence-time estimates from 100 parametric bootstrap estimations. The Salango lineage diverged from Rio Uncallane at 9.30 ka (95% bootstrap interval: 9.18–9.38 ka) and from the inferred ancestral Southern Native American lineage at 9.80 ka (9.63–10.10 ka). The estimated divergences of the Patagonia, Brazil/Sumidouro, and Colombia lineages were 11.33 ka (11.20–11.33 ka), 11.83 ka (11.73–11.88 ka), and 12.30 ka (12.18–12.30 ka), respectively. These intervals are conditional on the specified model topology, fixed deep divergence times, and archaeological calibration.

John Lindo, Daniel Rivas Alava, Sara Juengst, Yemko Pryor, Sophie K Joseph, Juan J Ortiz Aguilu, Richard Lunniss
Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America
PNAS Nexus 5(10), 2026, pgag323, https://doi.org/10.1093/pnasnexus/pgag323

Copyright: © 2026 The authors.
Published by Oxford University Press on behalf of The National Academy of Science. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The Salango genomes add another piece to the history of Indigenous South Americans: communities whose ancestry persisted through cultural change and whose connections extended beyond their immediate locality. Four individuals cannot tell the whole story, but they provide evidence against which explanations can be tested. As further genomes become available, that history will become more detailed, and some interpretations may change. That is how a reconstruction grounded in evidence improves.

For young-Earth creationism, the difficulty lies in the deeper population history inferred from these genetic relationships. The sampled burials themselves post-date the supposed Flood, but the demographic analysis places an ancestral divergence approximately 9,800 years ago—well before the conventional biblical date of creation. That estimate remains conditional on the model and its assumptions; acknowledging those conditions does not make a recent dispersal from Noah’s family an equally credible explanation. Such an alternative would need to account for the genetic evidence and produce testable predictions of its own.

The infant with evidence of tuberculosis adds a more personal dimension. Behind the population statistics was a child afflicted by a destructive infection long before Europeans reached these shores. This finding does not, by itself, resolve the evolutionary history of the pathogen, but it presents advocates of benevolent intelligent design with the familiar problem of suffering built into the natural world. Invoking a designer supplies neither a biological explanation for the infection nor a convincing moral justification for it.

Science can recover something of this child’s experience and the ancestry of the community to which it belonged because the past leaves evidence that can be examined. Creationism begins with a prescribed history and requires the evidence to fit. At Salango, as elsewhere, it is the evidence that deserves the final word.

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