Creationism in Crisis - Dinosaurs Evolved Warm-Bloodedness 180 Million Years Before 'Creation Week'

Artist’s impression of a dromaeosaur, a type of feathered theropod, in the snow. This raptor was a relative of Velociraptor.

Davide Bonadonna/Universidade

First ‘warm-blooded’ dinosaurs may have emerged 180 million years ago | UCL News - UCL – University College London

Of all the different orders of living organisms' only mammals and birds today are warm-blooded, i.e., they are able to maintain a body temperature, within a certain range of ambient temperatures, by either producing heat or losing it, as necessary.

It might be thought that this indicates that the ability evolved in a common ancestor but of the ancestors of birds, the evidence suggests that many dinosaurs were cold-blooded like today's reptiles, and mammals are descendants of an earlier, pre-dinosaurian reptiles, so these similar processes for maintaining the body temperature may be more a matter of convergence than common ancestry.

Do mammals and birds use the same method to maintain their body temperature, and if not, how do they differ? Mammals and birds both maintain their body temperatures through endothermy, meaning they generate and regulate heat internally to keep their body temperatures stable. However, there are differences in how they achieve this due to variations in their physiology and behaviors. Here’s an overview of the similarities and differences:

Similarities in Temperature Regulation

1. Metabolic Heat Production:
   • Both mammals and birds generate heat through metabolic processes. This involves breaking down food to produce energy, with heat being a byproduct.
2. Insulation:
   • Both groups have evolved insulating layers to retain heat. Mammals have fur or hair, while birds have feathers. These layers trap air and provide a barrier against the cold.
3. Shivering Thermogenesis:
   • Both can generate additional heat through shivering, which involves rapid muscle contractions that produce heat.
4. Behavioral Adjustments:
   • Both mammals and birds engage in behaviors to manage their temperature, such as seeking shade or shelter, sunning themselves, or altering their activity levels based on the ambient temperature.

Differences in Temperature Regulation

1. Physiological Mechanisms:
   • Sweating and Panting: Mammals often use sweating and panting to cool down. Sweat glands secrete moisture that evaporates, taking heat away from the body. Dogs, for instance, pant to evaporate moisture from their respiratory tract. Birds, on the other hand, do not sweat. Instead, they often rely on a behavior called gular fluttering, where they rapidly move the skin in their throat to increase evaporation and cool down.
   • Brown Adipose Tissue (BAT): Many mammals, especially small ones and those living in cold environments, have brown adipose tissue that generates heat through non-shivering thermogenesis. Birds lack this type of tissue.
2. Heat Exchange Systems:
   • Countercurrent Heat Exchange: Birds have highly efficient countercurrent heat exchange systems in their legs and feet, which minimize heat loss. Blood vessels are arranged such that warm arterial blood warms the cooler venous blood returning to the body, conserving heat. While some mammals also use countercurrent heat exchange (such as in extremities), the systems are particularly pronounced and crucial in birds.
3. Basal Metabolic Rate:
   • Birds generally have higher basal metabolic rates compared to mammals of similar size, which means they produce more heat relative to their body size. This higher metabolic rate is partly due to the high energy demands of flight.
4. Hibernation and Torpor:
   • Many mammals can enter states of torpor or hibernation to conserve energy and reduce body temperature during periods of cold or food scarcity. While some birds also enter torpor, true hibernation is rare in birds. Instead, some birds migrate to warmer regions to avoid cold weather.

Behavioral Differences

1. Migration:
   • Migration is a key strategy for many birds to avoid extreme temperatures. While some mammals also migrate, it is far more common and pronounced in birds.
2. Nesting and Roosting:
   • Birds often build insulated nests or seek out warm roosting spots to maintain body temperature, especially during breeding seasons or cold nights. Mammals, on the other hand, may use burrows, dens, or other insulated shelters.

In summary, while both mammals and birds use endothermic processes to maintain their body temperatures, the specific physiological and behavioral strategies they employ can differ significantly due to their distinct evolutionary paths and physical characteristics.

A team of researchers led by University College London (UCL) and Universidade de Vigo, Spain, scientists has concluded that dinosaurs may have evolved warm-bloodedness as long ago as 180 million years ago, some 50 million years after the first dinosaurs evolved.

They concluded this after relating the evolutionary tree of the dinosaurs throughout the Mesozoic era to climate and geographical changes over the same time period and examining 1000 dinosaur fossils.

Their findings are the subject of an open access paper in the Cell Press journal, Current Biology. Their work is also explained in a UCL news release:

The ability to regulate body temperature, a trait all mammals and birds have today, may have evolved among some dinosaurs early in the Jurassic period about 180 million years ago, suggests a new study led by UCL and University of Vigo researchers.

In the early 20^th century, dinosaurs were considered slow-moving, “cold-blooded” animals like modern-day reptiles, relying on heat from the sun to regulate their temperature. Newer discoveries indicate some dinosaur types were likely capable of generating their own body heat but when this adaptation occurred is unknown.

The new study, published in the journal Current Biology, looked at the spread of dinosaurs across different climates on Earth throughout the Mesozoic Era (the dinosaur era lasting from 230 to 66 million years ago), drawing on 1,000 fossils, climate models and the geography of the period, and dinosaurs’ evolutionary trees.

The research team found that two of the three main groupings of dinosaurs, theropods (such as T. rex and Velociraptor) and ornithischians (including relatives of the plant eaters Stegosaurus and Triceratops), moved to colder climates during the Early Jurassic, suggesting they may have developed endothermy (the ability to internally generate heat) at this time. In contrast, sauropods, the other main grouping which includes the Brontosaurus and the Diplodocus, kept to warmer areas of the planet.

Previous research has found traits linked to warm-bloodedness among ornithischians and theropods, with some known to have had feathers or proto-feathers, insulating internal heat.

Our analyses show that different climate preferences emerged among the main dinosaur groups around the time of the Jenkyns event 183 million years ago, when intense volcanic activity led to global warming and extinction of plant groups. At this time, many new dinosaur groups emerged. The adoption of endothermy, perhaps a result of this environmental crisis, may have enabled theropods and ornithischians to thrive in colder environments, allowing them to be highly active and sustain activity over longer periods, to develop and grow faster and produce more offspring.

Dr Alfio Alessandro Chiarenza, first author
Centro de Investigación Mariña
Departamento de Ecoloxía e Bioloxía Animal
Universidade de Vigo, Vigo, Spain

And Department of Earth Sciences
University College London, London, UK.

Theropods also include birds and our study suggests that birds’ unique temperature regulation may have had its origin in this Early Jurassic epoch. Sauropods, on the other hand, which stayed in warmer climates, grew to a gigantic size at around this time – another possible adaptation due to environmental pressure. Their smaller surface area to volume ratio would have meant these larger creatures would lose heat at a reduced rate, allowing them to stay active for longer.

Dr Sara Varela, Co-author
Centro de Investigación Mariña
Departamento de Ecoloxía e Bioloxía Animal
Universidade de Vigo, Vigo, Spain.

In the paper, the researchers also investigated if sauropods might have stayed at lower latitudes to eat richer foliage unavailable in colder polar regions. Instead, they found sauropods seemed to thrive in arid, savannah-like environments, supporting the idea that their restriction to warmer climates was more related to higher temperature and then to a more cold-blooded physiology. During that time, polar regions were warmer, with abundant vegetation. The Jenkyns event occurred after lava and volcanic gasses erupted from long fissures in the Earth’s surface, covering large areas of the planet.

This research suggests a close connection between climate and how dinosaurs evolved. It sheds new light on how birds might have inherited a unique biological trait from dinosaur ancestors and the different ways dinosaurs adapted to complex and long-term environmental changes.

Dr Juan L. Cantalapiedra, co-author
Departamento de Paleobiología
Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain.

The study involved researchers from UCL, University of Vigo, the University of Bristol and the Museo Nacional de Ciencias Naturales in Madrid, and received funding from the European Research Council, the Spanish Ministry of Research, the Natural Environment Research Council and the Royal Society.

Highlights

• Warm-blooded dinosaurs flourished in varied climates.
• Dinosaur groups adapted differently to climate, suggesting diverse thermophysiologies.
• Endothermy in theropods and possibly ornithischians evolved by the Early Jurassic
• Sauropod niche conservatism suggests higher thermal sensitivity and poikilothermy.

Graphical Abstract

Summary

A fundamental question in dinosaur evolution is how they adapted to long-term climatic shifts during the Mesozoic and when they developed environmentally independent, avian-style acclimatization, becoming endothermic.^1,2 The ability of warm-blooded dinosaurs to flourish in harsher environments, including cold, high-latitude regions,^3,4 raises intriguing questions about the origins of key innovations shared with modern birds,^5,6 indicating that the development of homeothermy (keeping constant body temperature) and endothermy (generating body heat) played a crucial role in their ecological diversification.⁷ Despite substantial evidence across scientific disciplines (anatomy,⁸ reproduction,⁹ energetics,¹⁰ biomechanics,¹⁰ osteohistology,¹¹ palaeobiogeography,¹² geochemistry,^13,14 and soft tissues^15,16,17), a consensus on dinosaur thermophysiology remains elusive.^{1,12,15,17,18,19} Differential thermophysiological strategies among terrestrial tetrapods allow endotherms (birds and mammals) to expand their latitudinal range (from the tropics to polar regions), owing to their reduced reliance on environmental temperature.²⁰ By contrast, most reptilian lineages (squamates, turtles, and crocodilians) and amphibians are predominantly constrained by temperature in regions closer to the tropics.²¹ Determining when this macroecological pattern emerged in the avian lineage relies heavily on identifying the origin of these key physiological traits. Combining fossils with macroevolutionary and palaeoclimatic models, we unveil distinct evolutionary pathways in the main dinosaur lineages: ornithischians and theropods diversified across broader climatic landscapes, trending toward cooler niches. An Early Jurassic shift to colder climates in Theropoda suggests an early adoption of endothermy. Conversely, sauropodomorphs exhibited prolonged climatic conservatism associated with higher thermal conditions, emphasizing temperature, rather than plant productivity, as the primary driver of this pattern, suggesting poikilothermy with a stronger dependence on higher temperatures in sauropods.

Chiarenza, Alfio Alessandro; Cantalapiedra, Juan L.; Jones, Lewis A.; Gamboa, Sara; Galván, Sofía; Farnsworth, Alexander J.; Valdes, Paul J.; Sotelo, Graciela; Varela, Sara
Early Jurassic origin of avian endothermy and thermophysiological diversity in dinosaurs Current Biology (2024) DOI: 10.1016/j.cub.2024.04.051

Copyright: © 2024 The authors.
Published by Elsevier. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Dinosaurs have always been a problem for creationists because their existence betrays the fact that the age of Earth as calculated from the Bible geneaolgies is wildly inaccurate by several orders of magnitude, but this paper piles on the agony by showign a clear evolutionary pathway from poikilothermy (cold-bloodedness) to homeothermy (warm-bloodedness) supported by geological, geographical and climatological evidence sometime around 180 million years before the biblical 'Creation Week'.

And it goes without saying that, being biologists, the authors of the paper show no sign of abandoning the TOE in favour of the childish notion of magic creation by an unproven supernatural entity. Indeed, they could scarcely be considered scientists if they included magic and superstition in their explanation for natural phenomena like creationists pseud-scientists are obliged to for contractual reasons.

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Creationism in Crisis - Earth's Magnetic Field 3.5 Billion Years Before 'Creation Week'.

Illustration of the dynamo mechanism that generates the Earth's magnetic field: convection currents of fluid metal in the Earth's outer core, driven by heat flow from the inner core, organized into rolls by the Coriolis force, generate circulating electric currents, which supports the magnetic field.

Andrew Z. Colvin via Wikimedia (CC BY-SA 4.0)

Researchers find oldest undisputed evidence of Earth’s magnetic field | University of Oxford

The problem with trying to sustain a belief that Earth is just a few thousand years old, is that scientists keep finding evidence that it is very much older. Here, for example, is a recent paper by Oxford University and Massachusetts Institute of Technology scientists that shows not only the Earth had a magnetic field 3.5 billion years ago, but that it was not hugely dissimilar in strength to the present magnetic field.

To add insult to injury, Earth's magnetic field, and the way it deflects harmful solar radiation away from the surface if often cited by creationists as evidence for their absurd claim that Earth is fine tuned for life, so a god must have fine-tuned it. If that were true, it was fine tuned for life almost 3.5 billion years before creationists believe there was any, and before there was even a universe, let alone solar radiation and Earth.

But then what did the primitive Bronze Age hill farmers who described the universe as a small, flat planet with a dome over it centred on the Middle East in the Bible, know about solar radiation, magnetic fields or the history of the planet? Well, nothing at all, obviously!

Creationism in Crisis - Evolving Horses Trample All Over Creationism

Top: Eohippus
Bottom: Hipparion

Modern Arabian Horse

Top: Miohippus
Bottom: Merychippus

Feral modern horses, Ogden, Utah, USA.

Kelly Lambright via Getty Images

Horses lived in the Americas for millions of years – new research helps paleontologists understand the fossils we’ve found and those that are missing from the record

Those few creationists who understand the science hate the record of horse evolution found in the fossil record because it runs counter to their dogma. It shows progressive change over millions of years from a small five-toed herbivore the size of a dog, through increasing size and a progressive reduction in toes to give the modern horse which walks on the tips if a single digit on each foot.

It is a fossil record which gives the lie to creationist assertions that there are no transitional fossils since each stage is clearly intermediate between its ancestors and its descendants. Moreover, most of the evolutionary history of the horse takes place in the very long period of Earth's history from before 'Creation Week' when creationists dogma says Earth was magicked out of nothing by a magic man made of nothing who then magicked all the animals out of dirt, exactly as they are today without ancestors.

And there is more embarrassment for those creationists who like to imagine Stephen J Gould and Nilse Eldredge somehow refuted Darwinian evolution with 'punctuated equilibrium' because the evolution of the horse in North America is a perfect illustration of how Darwinian evolution can produce a local fossil record that looks like a period of 'equilibrium' followed by rapid, even sudden, change in form.

Horses originally evolved in North America before crossing over the land bridge between Alaska and Siberia into Asia where they underwent allopatric speciation and then became extinct in North America during the last Ice Age. The domesticated descendants of the Asian horse were then reintroduced to North America by European colonists during the Middle Ages and subsequently became feral. Any examination of the fossil record will now show what appears to have been a sudden change from the Pliocene horse to the modern horse around 800 years ago because the Darwinian evolution occurred not locally but in Asia, where the fossil record will show what appears to have been the sudden appearance of a Pliocene horse without ancestors and no clear relationship to anything in the local fauna.

Creationism in Crisis - A Dinosaur Fossil In The 'Wrong' Place - But Not What Creationists Hoped For

Ajnabia odysseus

Artist's impression

Duckbill dinosaur discovery in Morocco – expert unpacks the mystery of how they got there

Here's something to excite creationists!

It's a fossil out of place!

Sadly though, it's not out of place in the geological column - which would falsify evolution - but out of place geographically. It's the fossil of a duck-billed dinosaur in Morocco, North Africa, but it's closest relatives appear to be from Europe, which was a long sea voyage away at the time and no obvious island chain for them to island hop on.

And to add to the mystery, the European duck-billed dinosaurs didn't evolve in Europe, but in North America, so they must have got to Europe somehow.

When the news from science is relentless in its refutation of creationism, it would have been nice to find something to give the poor beleaguered fools a few crumbs of comfort, but it was not to be. This one is just as relentless s all the others.

Creationism in Crisis - 4,000 Year-Old Human Teeth From Ireland Show No Signs Of The legendary Biblical Flood - But Every Sign of Evolution

The scientists extracted the information from teeth like the one pictured here.

Image credit: Dr Lara Cassidy.

Killuragh Cave, County Limerick, Ireland.

Photo: Sam Moore; Owner: Marion Dowd.

Genetic secrets from 4,000-year-old teeth to illuminate the impact of changing human diets over the centuries - News & Events | Trinity College Dublin

What can you tell from two, 4000-year-old human teeth found in a limestone cave in Ireland?

Firstly, you can tell a great deal about the food their owner ate and what state their oral hygiene was in.

Secondly, you can tell how the microbiome of the human mouth has evolved over the last 4000 years.

Thirdly, you can tell that, wherever creationism's global flood took place, it missed this cave in Ireland, because had the cave been flooded, the remains of bacterial DNA in the plaque on the teeth would have been washed off, even in the unlikely event of the skeletal remains staying in the cave.

And lastly, you can tell the cave is very much older than the 10,000 years creationists believe Earth has existed for because limestone caves form slowly over millions of years due to the action of water on limestone deposits that themselves take millions of years to accumulate and be compressed into limestone.

But then the ignorant goat-herders who invented the mythical global flood knew nothing of limestone cave formation, Ireland, the people who lived there, the state of their oral hygiene, or micro-organisms for that matter, so what did you expect? Miracles?

The two teeth, from the same individual, were part of a large skeletal assemblage excavated from Killuragh Cave, County Limerick, by the late Peter Woodman of University College Cork. They have been used by researchers from Trinity College, Dublin to recover a remarkably well-preserved microbiome which shows major changes in the oral microenvironment from the Bronze Age to today.

The researchers, led by Dr Lara Cassidy, an assistant professor in Trinity’s School of Genetics and Microbiology and including scientists from the Atlantic Technological University and University of Edinburgh, have published their findings, open access in the journal Molecular Biology and Evolution and describe them in a Trinity College News release:

Researchers from Trinity have recovered remarkably preserved microbiomes from two teeth dating back 4,000 years, found in an Irish limestone cave. Genetic analyses of these microbiomes reveal major changes in the oral microenvironment from the Bronze Age to today.

The teeth both belonged to the same male individual and also provided a snapshot of his oral health.

The study, carried out in collaboration with archaeologists from the Atlantic Technological University and University of Edinburgh, was published today in leading journal Molecular Biology and Evolution.

The authors identified several bacteria linked to gum disease and provided the first high-quality ancient genome of Streptococcus mutans, the major culprit behind tooth decay.

While S. mutans is very common in modern mouths, it is exceptionally rare in the ancient genomic record. One reason for this may be the acid-producing nature of the species. This acid decays the tooth, but also destroys DNA and stops plaque from fossilising. While most ancient oral microbiomes are retrieved from fossilised plaque, this study targeted the tooth directly.

Another reason for the scarcity of S. mutans in ancient mouths may be the lack of favorable habitats for this sugar-loving species. An uptick of dental cavities is seen in the archaeological record after the adoption of cereal agriculture thousands of years ago, but a far more dramatic increase has occurred only in the past few hundred years when sugary foods were introduced to the masses.

The sampled teeth were part of a larger skeletal assemblage excavated from Killuragh Cave, County Limerick, by the late Peter Woodman of University College Cork.

While other teeth in the cave showed advanced dental decay, no cavities were visible on the sampled teeth. However, one tooth produced an unprecedented amount of S. mutansDNA, a sign of an extreme imbalance in the oral microbial community.

We were very surprised to see such a large abundance of S. mutans in this 4,000-year-old tooth. It is a remarkably rare find and suggests this man was at a high risk of developing cavities right before his death.

Dr Lara Cassidy, senior author.
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.

The researchers also found that other streptococcal species were virtually absent from the tooth. This indicates the natural balance of the oral biofilm had been upset – mutans had outcompeted the other streptococci leading to the pre-disease state.

The team also found evidence to support the "disappearing microbiome" hypothesis, which proposes modern microbiomes are less diverse than those of our ancestors. This is cause for concern, as biodiversity loss can impact human health. The two Bronze Age teeth produced highly divergent strains of Tannerella forsythia, a bacteria implicated in gum disease.

These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite the modern samples deriving from Europe, Japan and the USA. This represents a major loss in diversity and one that we need to understand better.

Iseult Jackson, first author.
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.

Very few full genomes from oral bacteria have been recovered prior to the Medieval era. By characterising prehistoric diversity, the authors were able to reveal dramatic changes in the oral microenvironment that have happened since.

Over the last 750 years, a single lineage of T. forsythia has become dominant worldwide. This is the tell-tale sign of natural selection, where one strain rises rapidly in frequency due to some genetic advantage it holds over the others. T. forsythia strains from the industrial era onwards contain many new genes that help the bacteria colonise the mouth and cause disease.

S. mutans has also undergone recent lineage expansions and changes in gene content related to pathogenicity. These coincide with humanity’s mass consumption of sugar, although we did find that modern S. mutans populations have remained more diverse, with deep splits in the S. mutans evolutionary tree pre-dating the Killuragh genome.

Dr Lara Cassidy.

The scientists believe this is driven by differences in the evolutionary mechanisms that shape genome diversity in these species.

S. mutans is very adept at swapping genetic material between strains. This means an advantageous innovation can be spread across S. mutans lineages like a new piece of tech. This ability to easily share innovations may explain why this species retains many diverse lineages without one becoming dominant and replacing all the others.

Dr Lara Cassidy.

In effect, both these disease-causing bacteria have changed dramatically from the Bronze Age to today, but it appears that very recent cultural transitions in the industrial era have had an inordinate impact.

Technical details and background to the research is given in the team's open access paper in Molecular Biology and Evolution:

Abstract

Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.

Introduction

The oral cavity is the most well-studied aspect of the ancient human microbiome, mainly due to the excellent preservation of DNA in calculus (fossilized dental plaque). However, three quarters of published ancient oral metagenomes date to within the last 2,500 years, with few full genomes available from prior to the medieval period (Fellows Yates et al. 2022). While a small number of much older preagricultural genomes have yielded important insights (Fellows Yates et al. 2021), prehistoric diversity and the impact of Holocene dietary transitions are not well characterized. Common oral taxa identified in these metagenomes include the “red complex” bacteria Tannerella forsythia, Treponema denticola, and Porphyromonas gingivalis, which are important in the development of periodontitis, a highly polymicrobial disease (Socransky et al. 1998). However, another species with a major impact on public health, Streptococcus mutans, is not preserved in calculus (Velsko et al. 2019), and has no published ancient genomes.

Streptococcus mutans is the primary cause of dental caries (Lemos et al. 2019.1), and is common in modern oral microbiomes (Achtman and Zhou 2020). Its lack of preservation in ancient microbiomes may be largely due to its acidogenic nature; acid degrades DNA and prevents plaque mineralization, which is the main substrate used for sampling (Velsko et al. 2019). Its absence may also reflect less favorable habitats for S. mutans across most of human history. Indeed, metagenomic surveys of ancient and modern microbiomes suggest that the species only became a dominant member of the oral microbiota after the medieval period due to major dietary changes, such as the popularization of sugar (Adler et al. 2013; Achtman and Zhou 2020). However, another study of modern genomes has placed more emphasis on the Neolithic transition as a driver of S. mutans proliferation (Cornejo et al. 2013.1). Caries are observed more frequently in the archaeological record after the adoption of cereal agriculture, but rise in incidence through time with a sharp increase in the Early Modern period (Bertilsson et al. 2022.1).

The relative importance of prehistoric and recent dietary transitions in the evolution of red complex bacteria is also poorly characterized. Tannerella forsythia is one of the better studied species (Warinner et al. 2014; Bravo-Lopez et al. 2020.1; Philips et al. 2020.2; Honap et al. 2023), with 55 genomes currently available (supplementary table S1, Supplementary Material online). Surveys of preagricultural (Fellows Yates et al. 2021) and European medieval diversity (Warinner et al. 2014; Philips et al. 2020.2) have shown no clear temporal trends in T. forsythia phylogenetic structure, although functional differences between ancient and modern genomes have been observed (Warinner et al. 2014; Philips et al. 2020.2). However, these data have not been coanalyzed. Here, we shed light on prehistoric oral pathobiont diversity, as well as recent changes in these species’ demography and functional repertoire, by retrieving the first ancient S. mutans genome and two distinct strains of T. forsythia from a single Early Bronze Age individual.

[…]

Conclusion

Adding a temporal dimension to pathogen genomics allows us to better estimate the timing of key evolutionary changes, as well as to capture extinct diversity. In this study, we have reconstructed ancient genomes for T. forsythia and S. mutans, which demonstrate dramatic changes in oral pathobiont population dynamics and functional composition in the last 750 years. For both species, there is a distinction between postindustrial and earlier genomes in terms of virulence factors. This is clearest in T. forsythia, where there is a temporal transect of ancient genomes: here, preindustrial genomes have a stark difference in functional repertoire compared to industrial and modern genomes. Both the host immune response and interactions with other oral microbes would be impacted by these changes. Although there is only 1 ancient S. mutans genome (KGH2-B) of sufficient quality to compare with the modern dataset, analysis in tandem with phylogenetic information implies that the modern mutacin repertoire is also a relatively recent acquisition.

Concurrent population expansions were inferred in both S. mutans and T. forsythia phylogenies in the postmedieval period, but extant S. mutans populations harbor much deeper diversity compared to T. forsythia. We hypothesize that this is related to the species’ different susceptibilities to genome-wide selective sweeps, which are more likely to occur when within-population recombination is low (Bendall et al. 2016). Streptococcus mutans is a highly recombining species (Cornejo et al. 2013.1), allowing advantageous variation to be exchanged between population members and resulting in gene-specific sweeps. In T. forsythia, genome structure is relatively stable and small-scale mutation appears to be the major driving force of diversification (Endo et al. 2015). This could lead to repeated purges in genetic heterogeneity in the population. These purges may have intensified in the past several centuries, as evidenced by the loss of diversity in modern and industrial populations, relative to prehistoric strains from the same Early Bronze Age individual. In general terms, higher biodiversity in ecosystems makes them more resilient to perturbations from environmental stressors (e.g. dietary changes and colonization by pathogenic bacteria in the case of the oral microbiome). The reduction in T. forsythia diversity over time coincides with a general loss of oral biodiversity discussed in Adler et al. (2013).

Going forward, denser sampling of ancient microbial populations may provide new insights into the evolutionary mechanisms that underlie bacterial taxon formation, adaptation and maintenance of diversity, which can vary depending on species and environment. Some species will be more amenable to dense temporal sampling than others. In particular, low levels of S. mutans preservation in the ancient DNA record may pose a significant challenge. Targeted capture of genes of interest (e.g. mutacins) as well as the core genome may provide a solution, but risks losing pangenomic diversity. In the case of T. forsythia, which is more abundant in the archaeological record, ancient metagenomic assemblies in the future may allow for the identification of hitherto unknown virulence factors in earlier strains; our analysis here is limited to the genomic content of modern T. forsythia samples, as all the ancient genomes are reference-aligned.

Overall, our findings demonstrate the utility of ancient genomes in characterizing different modes of pathobiont evolution. Temporal resolution of virulence genes can provide further insight into the shifting selection regimes of pathobionts in the human oral microbiome. In addition, these results highlight that recent cultural transitions, such as the popularization of sugar, are most relevant to understanding the shaping of present-day oral pathobiont diversity.

Iseult Jackson, Peter Woodman, Marion Dowd, Linda Fibiger, Lara M Cassidy
Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae017, https://doi.org/10.1093/molbev/msae017

Copyright: © 2024 The authors/Society for Molecular Biology and Evolution.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

There is a lot there for creationists to try to ignore or lie about, either to themselves or to the fools they are trying to recruit into their money-making scam.

1. There is the geological evidence of a limestone cave which takes millions of years to form.
2. There is the evidence for evolution in the differences between the genomes of the micro-organisms found on the plaque on the surface of the teeth.
3. There is the absence of any evidence for a global flood in the fact that the contents of the cave have not been submerged in water and have none of the inevitable deposits on them that would have resulted from such a flood.
4. There is the evidence that there were people living in Ireland 4,000 years ago when creationists legend says they should all have been drowned in a global flood (which apparently never reached County Limerick).
5. There is the evidence for evolution in both the micro-organisms themselves and also in the biodiversity of the human oral microbiome which have changed significantly as the main sources of food have changed, showing how the environment drives evolutionary change.

All in all, a great deal of cognitive dissonance for which creationists will need to employ their usual coping mechanisms.

---

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Creationism in Crisis - Now It's An Ancestral Amphibian from 270 Million Years Before 'Creation Week' - And Another Gap Closes

Fossil skull of Kermitops gratus

Brittany M. Hance, Smithsonian.

Fossil skull of Kermitops gratus

Brittany M. Hance, Smithsonian.

Researchers Name Prehistoric Amphibian Ancestor Discovered in Smithsonian Collection After Kermit the Frog | Smithsonian Institution

Once upon a time, about 10,000 years ago, a magic man made of nothing appeared from nowhere and decided to create a universe that looked like a small flat planet with a dome over it, or so some ignorant Bronze Age pastoralists told their children.

Of course, they were doing their best with what little knowledge they had of the world they lived in and its history, so they filled the gaps in their knowledge and understanding with stories, and of course got it almost entirely and spectacularly wrong.

We know this because, unlike the story-tellers from the fearful infancy of our species, we now have the knowledge and understanding that centuries of careful science has revealed to us - at least those of us with the capacity to learn and understand the science know it. This is why those still unable to believe their mummy and daddy could be wrong about the superstitions they were taught as children but have since learned some science, are increasingly calling the creation stories in the Bible allegorical or metaphorical, while those who have a more objective view dismiss then as the work of ignorant people who knew no better.

Of course, despite herculean mental efforts, none of the creation myth can be forced into an allegory or metaphor for the existence of early proto-amphibians 270 million years before the little domed universe was magicked up out of nothing, and the existence of just such an animal was shown to be a fact of history when it was examined by palaeontologists from George Washington University who examines a fossil in the collection of the Smithsonian’s National Museum of Natural History and found to be 270-million-year-old fossil of a previously unknown proto-amphibian, which they have named Kermitops gratus after Kermit the Frog.

The three scientists who made this discovery, led by Calvin So, a doctoral student at the Department of Biological Sciences, George Washington University, Washington, DC, USA, have pubished their finding open access in the Zoological Journal of the Linnean Society and explained it in a Smithsonian Museum news release:

Creationism in Crisis - An Ancestral Croccodile from 215 Million Years Before 'Creation Week'

An artist’s interpretation of the newly identified aetosaur Garzapelta muelleri.

Márcio L. Castro.

An artist’s interpretation of the newly identified aetosaur Garzapelta muelleri

Márcio L. Castro.

Tanks of the Triassic: New Crocodile Ancestor Identified | Jackson School of Geosciences | The University of Texas at Austin

In that very long period of Earth's history, long before creationism's god decided to create a small flat planet with a dome over it, and before even the dinosaurs rose to pre-eminence, another group of reptiles had evolved into armour-plated tank-like creatures with thick body-plates and fringes of curved spikes to deter predators. Some of these were later to evolve into the modern crocodiles.

Now three researchers from the University of Texas at Austin have identified a new species that lived 215 million years ago in the Triassic. The newly-identified species was found on a museum shelf where it had been since its discovery in Garza County in northwest Texas, some 30 years ago by the palaeontologist, Bill Mueller. The researchers have named the new species in his honor, as Garzapelta muelleri (Pelta = plate).

Creationism in Crisis - Rice Paddy Snakes In Thailand Diversified About 2.5 Million Years Before 'Creation Week'

Hypsiscopus plumbeus

Photo: Bryan L. Stuart

Hypsiscopus murphyi sensu

Photo: Bryan Stuart

Rice paddy snake diversification was driven by geological and environmental factors in Thailand, molecular data suggests | KU News

In one of those far-away places that the simple-minded authors of the story in Genesis about a small flat Earth with a dome over it being magicked up out of nothing in the Middle East, 10,000 years ago, could never have guessed existed, and some 2.5 million years before they though Earth existed, major environmental changes were driving the diversification of a species of snake into several descendant species, just as the Theory of Evolution predicts.

If those simple-minded Bronze Age pastoralists had known about it and understood its significance in terms of the history of life on Earth and the dynamic geology of the planet, just imagine how different their imaginative tale would have been! As it was, they had to do their best with what little knowledge and understanding they had.

The snake in question was the Rice Paddy snake, otherwise known as a mud snake, and the far-away place was Thailand where the rise of the Khorat Plateau caused environmental changes that resulted in the evolutionary diversification of the Hypsiscopus genus.

The team of researchers from various American and Southeast Asian Universities, who have shown this link between environmental change and evolutionary radiation in a genus was led by Dr. Justin Bernstein, of the University of Kansas Center for Genomics. Their findings are published open access in Scientific Reports and are explained in a Kansas University news release: