In the study, scientists performed a genetic analysis on the bones of 133 human individuals from late Neolithic megalithic graves near Warburg in North Rhine-Westphalia. The team discovered the genome of the bacterium Yersinia pestis in the bone samples of two independent individuals. Additionally, previously published genomic data from a bone sample of a Neolithic dog found in Ajvide (Sweden) suggested a potential infection route.
© Carsten Reckweg, CRC 1266/Uni Kiel
What was creationism's divine malevolence up to with one of its most successful pathogens with which if killed hundreds of millions and changes society - the Yersinia pestis bacterium which caused the waves of black death and plague that regularly spread across the world?
It seems to have been experimenting, possibly trying to either perfect its virulence or work out the best delivery system to ensure it got to and killed as many people as possible. Sometimes, entire villages were wiped out. Not far from where I currently live are a couple of former villages that disappeared during the black death - the village of Woodperry near Oxford is an example, surviving now only in the name 'Woodperry Road' and a farmhouse later built on the site.
But 5000 years ago, Y. pestis doesn't seem to have been anything like a virulent as it became in the 12th Century. According to a recent discovery, it was capable of killing the occasional neolithic farmer but not of becoming a major pandemic able to kill hundreds of thousands and depopulate vast areas.
So, what changed, and more to the point, which explanation would a creationist prefer; the one which blames their god or the one which attributes it to evolution, climate change and cultural changes in human society? One thing we can be sure of though is the Michael J. Behe's biologically nonsensical religious apologetic of 'genetic entropy', causing the bacterium to 'devolve' away from an assumed created perfection (as though that were remotely possible), can be ruled out, because whatever the changes were, it led to a massive increase in the number of Y. pestis organisms, so was indisputably beneficial to it - in other words, in classical terms, it evolved.
Scientists have recently found Yersinia pestis in the bones of Neolithic Europeans* How does this fit with what we understood to be the Asian origins of the Black Death? The discovery of Yersinia pestis (the bacterium that causes plague) in the bones of Neolithic Europeans significantly changes our understanding of the pathogen’s history and origins. Historically, the Black Death (which devastated Europe in the 14th century) was believed to have originated in Asia, particularly in the region of modern-day China or Central Asia, and spread to Europe through trade routes like the Silk Road.This discovery, and what it means for our understanding of the evolution (for creationists, read, redesign) of Y. pestis was made by researchers from Kiel, Münster, Schleswig and Hamburg in Germany who have reported their findings, open access, in Communications Biology.
Key Points on the New Discovery
In Summary
- Older Presence in Europe: The finding of Y. pestis in Neolithic European remains, dating back several thousand years before the Black Death, suggests that the bacterium may have been present in Europe long before the Middle Ages. This implies a more complex geographic history for the pathogen than previously thought.
- Diversity of Strains: Ancient DNA studies show that the strains of Y. pestis found in these Neolithic remains are genetically distinct from those associated with the Black Death. This suggests that multiple strains of Y. pestis existed, circulating in different regions across a longer timeframe than initially understood.
- Multiple Origins and Evolution: The findings support the idea that Y. pestis may have evolved in multiple locations, or at least spread across Eurasia much earlier than previously recognized. This challenges the simplistic view of a single origin in Asia. Instead, Y. pestis may have been circulating widely among human and animal populations, with different strains emerging and evolving independently.
- Potential Early Pandemics: The discovery also raises the possibility that there were earlier plague outbreaks in human history that have not been well-documented or studied. These Neolithic strains could represent unknown or lesser-known pandemics that impacted prehistoric human populations.
- Revised Understanding of Spread: If Y. pestis was present in Europe thousands of years before the Black Death, it suggests that the bacterium's spread was influenced by different human migrations, trade, and interactions over a long period. It underscores the role of interconnectedness in human history and the movement of diseases across continents.
While the Black Death of the 14th century may still have links to Central Asia, the presence of Y. pestis in Neolithic Europe indicates that the bacterium’s history is far more ancient and geographically widespread than previously believed. It highlights a need to rethink the narrative of the plague's origin and spread, considering a more complex, multi-regional evolutionary history.
Neolithic plague bacterium did not cause mass mortality
Study by the Collaborative Research Centre 1266 ‘Scales of Transformation‘ shows possible infection paths of Yersinia pestis 5000 years ago.
Since the catastrophic pandemics of the Middle Ages, one disease has almost proverbially symbolised contagion and death: the plague. It is now known that the plague bacterium Yersinia pestis has been present in Central and Northern Europe for more than 5000 years. However, it is still uncertain whether it also led to pandemics and mass deaths in its early forms.
Researchers from Kiel, Münster, Schleswig and Hamburg have now analysed bones from late Neolithic farmers within the framework of the Collaborative Research Centre 1266 ‘Scales of Transformation’ at Kiel University (CAU). ‘Our analyses indicate isolated infections rather than epidemics,’ said Prof. Dr Ben Krause-Kyora, a specialist in ancient DNA (aDNA) at the Institute of Clinical Molecular Biology at Kiel University and lead author of the study recently published in the international journal Communications Biology.
For the study, the team genetically analysed the bones of 133 human individuals from late Neolithic megalithic graves near Warburg in North Rhine-Westphalia. The graves belong to the so-called Wartberg culture, which dates from around 5500 to 4800 years before the present.
The team identified the genome of the plague-causing bacterium, Yersinia pestis, in the bone samples of two individuals. The bacteria belonged to different strains. The infected individuals were not related, lived in different times, and were interred in separate megalithic tombs. This suggests that the infections were independent incidents, with no direct transmission between the two people.
Overall, we see a high diversity of Yersinia pestis during the Neolithic period. This could indicate a low specialisation of the bacterium at this early stage of its evolution. This may have facilitated its survival in different environments and animals.
Ben Krause-Kyora, corresponding author
Institute of Clinical Molecular Biology
Kiel University, Kiel, Germany
This and the low number of plague cases among the 133 examined individuals show that the megalithic structures do not represent collective burials of victims of a massive plague outbreak. Whether the early forms of Yersinia pestis caused symptoms as severe as those in the Middle Ages is still unknown.
But how did Neolithic people become infected in the first place? Unlike the medieval strains of the bacterium, the Neolithic ones could not be spread by fleas.
Deforestation changed the landscapes of central and northern Europe in the Neolithic period. This attracted new rodent species from steppe areas to the east and south. They could have been natural reservoirs for Yersinia pestis.
Previously published genomic data from the bone sample of a Neolithic dog from Sweden indicated a possible infection pathway. When the Kiel team re-analysed the data, they found that the dog was also infected with the plague bacterium at the time of its death.
‘However, we don't know how often people came into contact with these animals or their carcasses. This is the first record of Yersinia pestis in a Neolithic dog. Since dogs are often found in human settlements at that time, they could have played a role in individual infections. Overall, the results of our study suggest that the plague pathogen was already frequently present in or near human settlements, but that it led to isolated infections rather than large-scale disease outbreaks.
These results are also crucial for the ROOTS Cluster of Excellence, in which we are investigating how changes in climate, land use and diet may have influenced the spread of pathogens, especially Yersinia pestis.
Ben Krause-Kyora.
AbstractThe discussion makes interesting reading, though it'll probably make uncomfortable reading for creationists, as it's all about how a more virulent strain evolved and says nothing about magic designers or even 'genetic entropy', as though neither of those are ideas worthy of consideration by serious, mainstream biologists:
Yersinia pestis has been infecting humans since the Late Neolithic (LN). Whether those early infections were isolated zoonoses or initiators of a pandemic remains unclear. We report Y. pestis infections in two individuals (of 133) from the LN necropolis at Warburg (Germany, 5300–4900 cal BP). Our analyses show that the two genomes belong to distinct strains and reflect independent infection events. All LN genomes known today (n = 4) are basal in the phylogeny and represent separate lineages that probably originated in different animal hosts. In the LN, an opening of the landscape resulted in the introduction of new rodent species, which may have acted as Y. pestis reservoirs. Coincidentally, the number of dogs increased, possibly leading to Y. pestis infections in canines. Indeed, we detect Y. pestis in an LN dog. Collectively, our data suggest that Y. pestis frequently entered human settlements at the time without causing significant outbreaks.
Introduction
Plague is considered one of the most notorious scourges of humanity and was responsible for at least three pandemics in historical times1. Its causative agent, Yersinia pestis, has been infecting humans for more than 5000 years. The oldest Y. pestis genomes so far have been detected in remains of a hunter-gatherer from Riņņukalns, Latvia (RV2039; 5300–5050 cal BP)2 and a farmer from Gökhem, Sweden (Gökhem_2; 5040–4867 cal BP)3 (Fig. 1A), here referred to as Late Neolithic (LN). The two LN genomes represent strains in the early stages of Y. pestis evolution and were shown to be ancestral to a phylogenetically distinct lineage termed Late Neolithic and Bronze Age (LNBA; 4800–2500 cal BP), which was present throughout Eurasia until at least the third millennium BP4. Both LN strains lacked the virulence factors and mutations observed in much later forms that were required for efficient transmission from rodents to humans via fleas2,3,4,5. However, it remains unclear whether the Y. pestis infections detected in the LN skeletal remains were due to isolated zoonoses or marked the beginning of a long-lasting pandemic across Eurasia sustained by human-to-human contact2,3,4,6. Another question centers on what may have facilitated the transmission of Y. pestis to humans before adaptations to the flea evolved. Various as yet unknown rodent species could have acted as primary hosts for Y. pestis at that time. Human exposure to these rodents and possibly Y. pestis might have been increased through domesticated carnivores, i.e. dogs, which hunted these animals. This could also have led to Y. pestis infections in the canines themselves. In this study, we extend our understanding of Y. pestis evolution during the LN by presenting two new genomes from human individuals and providing evidence of a Y. pestis infection in a dog.Fig. 1: Map of LN sites.
Location of archaeological sites in which LN Y. pestis was identified in human (Warburg, Riņņukalns, Gökhem) and canine remains (Ajvide) (A). Warburg necropolis with the gallery graves I, III-V and building II (B).
Fig. 2: Phylogeny of ancient and modern Y. pestis genomes.
Maximum likelihood phylogenetic tree based on the SNP alignment (10,743 positions) of 226 modern genomes, 62 published ancient genomes, the novel genomes Warburg_1 and Warburg_2 (red) and the outgroup Y. pseudotuberculosis. LN strains are highlighted in green and LNBA strains in yellow. Dating of the ancient strains is given as calibrated years before the present (cal BP). Country abbreviation is given in brackets (CH = Switzerland, CG = Congo, CN = China, CZ = Czech Republic, DE = Germany, EE = Estonia, ES = Spain, FR = France, FSU = Former Soviet Union, HR = Croatia, IN = India, IR = Iran, KG = Kyrgyzstan, KZ = Kazakhstan, LT = Lithuania, LV = Latvia, MG = Madagascar, MM = Myanmar, MN = Mongolia, NP = Nepal, PL = Poland, RU = Russia, SE = Sweden, UA = Ukraine, UG = Uganda, UK = United Kingdom, US = United States). Unique positions to the outgroup were excluded to facilitate the visualisation. Bootstrap values were calculated for 1000 replicates and nodes with a support above 90 are marked with an asterisk. The scale corresponds to substitutions per site. Genomes included in the phylogeny are listed in Supplementary Data 5.
Fig. 3: Molecular dating of early Y. pestis.
Maximum clade credibility tree based on 42 modern and ancient Y. pestis genomes and the two genomes from Warburg (red). All dates are given as calibrated years before the present (cal BP). Country abbreviation is provided in brackets as described in Fig. 2. Genomes included in the molecular dating analysis are listed in Supplementary Data 6.
DiscussionSo, not only evidence of Yersinia pestis being around in Neolithic Europe some 5000 or more years ago - before the mythical biblical flood which would have obliterated the evidence along with the bacterium, if it had really happened, but evidence that the bacterium had diversified into several different strains, one of which was later to give rise to one of the most lethal pandemics ever experience with about 25% of the population dying from it.
In this study, we identified Y. pestis in two individuals from the LN necropolis at Warburg in Germany. Our results suggest that the two Y. pestis genomes (Warburg_1 and Warburg_2) belonged to distinct strains. They differed in 82 positions (Supplementary Fig. 7). Due to this genetic distance, it can be assumed that the two genomes did not directly evolve from each other. This finding is also reflected in the typology of the phylogenetic tree indicating a divergence of the genomes long before the infections occurred (Fig. 3). In addition, the genomes were detected in unrelated individuals who were buried in different gallery graves. All evidence suggests that both infections represent independent events and thus appear not epidemiologically linked.
Interestingly, despite the screening of numerous specimens from each gallery grave (total n = 133), we found no further infections with Y. pestis or any other pathogen. In another collective WBC grave at the site of Niedertiefenbach (n = 42; present-day Germany), no signs of pathogens were detected either9. It must be acknowledged that pathogen-negative results do not necessarily mean absence of infection, as taphonomic processes may have degraded any microbial traces. In addition, both the Warburg and Niedertiefenbach samples consisted of petrous bones as well as teeth, the latter being the better source material for the detection of blood-borne viruses and bacteria16. These limitations notwithstanding, the arguments presented above (i.e., independent infection events at Warburg) and the overall small number of 2 positives among the 175 tested WBC individuals suggest that the collective graves were not used for the burial of victims of a plague outbreak or other epidemics, as previously suggested for the same period3. The few Y. pestis cases in the WBC are consistent with the results of other large-scale pathogen screenings that have so far revealed only single infections with human pathogens (Y. pestis, Salmonella enterica) or endemically occurring infections (hepatitis B virus, parvovirus B19, Helicobacter pylori) in Neolithic remains17. Also, the mortuary practice of single and multiple inhumations during that period does not indicate mass mortality, as would be expected in an epidemic. The findings from the Neolithic are thus in marked contrast to the short-term mass burials and the high pathogen load seen in the Middle Ages18,19.
The two Warburg genomes increase the number of Y. pestis genomes from the LN to four. All LN genomes were distinct from each other and represent lineages separated by an extended period of independent evolution (Figs. 2 and 3). The high diversity and the basal position of the LN Y. pestis lineages may reflect a low level of specialization at this early evolutionary stage. Such reduced specialization potentially facilitated their survival across diverse environments and a wide host range. According to the current phylogeny, the LN strains gave rise to two lineages, one from which the pathogens of the deadly Justinianic and medieval plagues emerged and another that led to the LNBAs (Fig. 2). The LNBA clade went extinct sometime in the third millennium BP4 (Figs. 2 and 3). For more than 2000 years, the LNBA strains were the dominant Y. pestis lineage in humans across Eurasia4. They may represent an adaptation to a very specialized Y. pestis ecology (e.g., host(s)), as reflected by the increasing pseudogenization of bacterial genes over time4. This process could have led to the evolutionary dead-end of the LNBA lineage and to a less severe, perhaps even chronic, manifestation of plague in humans that resembled an endemic rather than a pandemic disease2,4.
During the LN, woodland clearance increasingly created open landscapes in central and northern Europe20,21,22,23 that attracted a variety of new rodent species (e.g., European hamster Cricetus cricetus24) originally native to the steppe further east or south. Some of these species could have been natural reservoirs of Y. pestis1 and an infection in humans would have been feasible through close contact with a Y. pestis-positive wild animal or carcass25,26. However, we do not know how frequent such encounters were, especially when the animals in question were not normally hunted or touched by humans. Therefore, we propose the dog as facilitator which could have increased exposure of humans to Y. pestis from various wild animals, especially those with which humans did not come into regular contact. The archaeological record during the LN shows large numbers of dog remains, for instance, as material for ornamentation (pendants and jewellery made from dog teeth, e.g., 356 teeth [canines] in the grave Wewelsburg 118 in Altendorf)27. In addition, the animals were likely used for hunting and herding28,29. If dogs preyed on infected animals, this could have increased the probability of Y. pestis transmission from rodents to humans. Since modern dogs can develop pneumonic plague and infect humans directly without the need for flea adaptation1,26, the question arises whether this was also the case during the LN. Given instances of dog-to-human transmissions today1, it is possible that dogs themselves acted as a Y. pestis reservoir for humans at the time, or vice versa.
To the best of our knowledge, C90 is so far the only case of Y. pestis infection in a Neolithic dog. This small number may be explained by the innate resistance of dogs to Y. pestis which leads to rapid pathogen clearance and a low fatality rate1,30. If Neolithic dogs recovered from plague as frequently and quickly as their modern counterparts30, most that were ever infected would be Y. pestis-negative at the time of their death (and in the palaeogenomic pathogen screening). Thus, we might underestimate the actual number of infected dogs.
The presence of Y. pestis in a dog from present-day Sweden fits well with the geographical distribution pattern of the four infected human individuals (Fig. 1A). Surprisingly, all five Y. pestis findings from the LN occupy a relatively small geographical area in northwestern Europe. Overall, the results suggest a significant Y. pestis exposure in and around human settlements at the time, most likely leading to isolated infections rather than large-scale disease outbreaks.
Susat, J., Haller-Caskie, M., Bonczarowska, J.H. et al.
Neolithic Yersinia pestis infections in humans and a dog. Commun Biol 7, 1013 (2024). https://doi.org/10.1038/s42003-024-06676-7
Copyright: © 2024 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Or, for creationists who reject the idea of evolution and who insist that nothing happens unless their favourite god so wills it, one of the most successful attempts to kill as many people as possible and inflict massive suffering on the world, that their favourite pestilential malevolence has ever achieved.
The lesson of history is that because so many people subscribed to Bible-literalist creationism in the Middle Ages, the Black Death produced a fundamental change in attitudes towards the god whom they believed caused this suffering, and the beginnings of the rejection of the casual corruption, gluttony and debauchery the Christian Church had degenerated into and the beginnings of ideas that were eventually to lead to the Protestant Reformation and, in the more enlightened parts of the world, to the enlightenment and the rejection of religious superstition in favour of Humanism and scientific rationalism.
Clearly, some people in some parts of the world have never managed to achieve that degree of enlightenment.
The Malevolent Designer: Why Nature's God is Not Good
This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.
Illustrated by Catherine Webber-Hounslow.
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Illustrated by Catherine Webber-Hounslow.
The Unintelligent Designer: Refuting The Intelligent Design Hoax
ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.
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