Wednesday, 27 November 2024

Mallevolent Design - How Salmonella Sneaks Past Our Defences To Make Us Sick


Intestinal lumen
New study shows how salmonella tricks gut defenses to cause infection

There is a simple paradox at the heart of creationism that I have never even seen an attempt to resolve. It all comes from two beliefs: there is only one designer god capable of designing living organisms and that designer god designed us complete with our immune system with which we can attempt to resist attack by pathogens, and that pathogens are not the work of this design, but are the result of 'genetic entropy' and 'devolution' since Adam & Eve let 'sin' into the world. The fact that Michael J. Behe, who invented that excuse, has let slip that ID Creationism is Bible literalism in a lab coat seems to be lost on his followers who still dutifully insist that it is a scientific alternative to evolution and should be taught in school science class (presumably now with the tale of Adam & Eve taught as real history and 'sin' as a real force in science).

The paradox is, did the designer god give Adam & Eve an immune system, or did it design an upgrade when 'sin' allowed pathogens to exist? If the former, it was anticipating and planning for the so-called 'fall'; if the latter, it lacked foresight so is not omniscient.

But however creationists resolve this paradox they still have to explain why the 'intelligently designed' immune system doesn't work very well and why whatever is designing pathogens seems to be able to overcome it.

The nonsense about 'sin', 'the fall', etc., is trivially easy to refute because any improvement in a parasite's ability to parasitise its host can't possibly be regarded as a devolution from some assumed initial perfection because an improvement can't be worse that what it's an improvement on. The whole nonsense of 'devolution' is biological gobbledygook, intelligently designed to appeal to scientifically illiterate simpletons who want to fit the Bible superstition somewhere in the reasoning without bothering too much about the logic or the biology.

So, the paradox boils down to why an intelligent designer would be having an arms race with itself so the parasites it creates can continue to parasitise the victims it creates complete with their immune system it created to stop them. Creationists normally flee in terror at the mere mention of arms races, which is why you'll never see them discussed in the cult literature apart from where pathogens are waved aside as 'caused by sin', blah, blah, blah...
So, it would be refreshing indeed to see a genuine attempt by an intelligent design creationist try to give some rational explanation, and hopefully without giving away the fact that ID creationism is merely Christian fundamentalism in disguise, for the discovery by a new UC Davis Health study that shows how the Salmonella bacteria, a major cause of food poisoning, can invade the gut even when protective bacteria are present.

As an added embarrassment for creationists, Salmonella is closely related to Escherichia coli (E.coli) that they usually cite Michael J. Behe as 'proving' it must have been designed by their god because its flagellum is 'irreducibly complex'.

First a little AI background information about Salmonella, where it came from and what it does to us:
Tell me all about Salmonella, please. Salmonella is a genus of bacteria that is commonly associated with foodborne illnesses in humans and animals. These bacteria are known for causing a range of conditions, from mild gastroenteritis to more severe diseases like typhoid fever. Here's an overview of Salmonella:
  1. What is Salmonella?
    Salmonella are rod-shaped, Gram-negative bacteria belonging to the family Enterobacteriaceae. They are facultative anaerobes, meaning they can grow in both oxygen-rich and oxygen-poor environments.
  2. Types of Salmonella
    Salmonella is classified into two broad categories based on the diseases they cause:

    1. Non-typhoidal Salmonella (NTS):
      • Causes salmonellosis, a common form of food poisoning.
      • Found in many animals, including poultry, cattle, reptiles, and amphibians.
      • Symptoms include diarrhea, fever, abdominal cramps, and vomiting.
    2. Typhoidal Salmonella:
      • Includes Salmonella Typhi and Salmonella Paratyphi, which cause typhoid and paratyphoid fever, respectively.
      • These infections are severe, systemic diseases primarily transmitted through contaminated water or food.
  3. How is Salmonella Transmitted?
    • Foodborne: Consuming undercooked or contaminated meat (especially poultry), eggs, or dairy products.
    • Waterborne: Drinking contaminated water.
    • Contact: Handling animals or surfaces contaminated with Salmonella, such as pet reptiles or farm animals.
    • Person-to-Person: Rare but possible in cases of poor hygiene, especially among caregivers.
  4. Symptoms of Salmonella Infection
    The symptoms vary based on the type:
    • Salmonellosis (non-typhoidal): Appears 6-72 hours after exposure; lasts 4-7 days.
      • Diarrhea
      • Fever
      • Abdominal cramps
      • Nausea and vomiting
    • Typhoid Fever: Develops gradually over 1-2 weeks.
      • High fever
      • Weakness
      • Abdominal pain
      • Rose-colored spots on the skin
      • Constipation or diarrhea
  5. Risk Groups
    • Infants, young children, and the elderly.
    • People with weakened immune systems, such as those with HIV or undergoing chemotherapy.
    • Travelers to regions with poor sanitation.
  6. Diagnosis
    • Laboratory Testing: Stool, blood, or urine samples are tested for the presence of Salmonella.
    • Serotyping: Identifies specific Salmonella strains, useful for outbreaks and epidemiological studies.
  7. Treatment
    • Non-typhoidal Salmonella: Often self-limiting; hydration is crucial. Antibiotics are usually unnecessary unless the infection spreads beyond the intestines.
    • Typhoidal Salmonella: Requires prompt antibiotic treatment, such as ciprofloxacin or azithromycin. Severe cases may require hospitalization.
  8. Prevention
    1. Food Safety:
      • Cook meat and eggs thoroughly.
      • Avoid cross-contamination between raw and cooked foods.
      • Wash fruits and vegetables well.
      • Store food at proper temperatures.
    2. Hygiene:
      • Wash hands frequently, especially after handling animals or raw foods.
      • Sanitize surfaces and utensils.
    3. Vaccination:
      • Vaccines are available for Salmonella Typhi for travelers to high-risk areas.
    4. Pet Precautions:
      • Avoid contact with reptiles or amphibians, especially for children under five.
  9. Global Impact
    • Non-typhoidal Salmonella: A leading cause of foodborne illnesses worldwide.
    • Typhoid Fever: Endemic in many developing countries, with poor sanitation contributing to its prevalence.
Interesting Facts
  • Salmonella is named after American scientist Daniel Elmer Salmon, though it was first discovered by Theobald Smith in 1885.
  • These bacteria can survive on dry surfaces for weeks and in water for months.


What is known about the evolutionary origins of the genus and their relationship to other genera?

The genus Salmonella has a fascinating evolutionary history that reflects its adaptation to a wide range of hosts and ecological niches. Here's an overview of what is known about its evolutionary origins and relationships with other genera:
  1. Evolutionary Origins
    • Family and Order:
      • Salmonella belongs to the family Enterobacteriaceae and the order Enterobacterales. This group includes other genera such as Escherichia, Klebsiella, Yersinia, and Shigella.
      • These bacteria are believed to have a common ancestor that lived in the intestinal tracts of primitive animals hundreds of millions of years ago.
    • Divergence from Common Ancestor:
      • Genomic analyses suggest that Salmonella diverged from its closest relative, Escherichia coli, approximately 100–150 million years ago. This divergence was likely driven by adaptation to different ecological niches and hosts.
      • Salmonella has specialized in both intestinal and systemic infections, while E. coli primarily remained a commensal organism with occasional pathogenic strains.
  2. Genomic Evolution
    • Horizontal Gene Transfer (HGT):
      • A significant driver of Salmonella's evolution has been the acquisition of genes through horizontal gene transfer. This process introduced:
        • Virulence genes (e.g., pathogenicity islands).
        • Antibiotic resistance genes.
      • These acquisitions allowed Salmonella to colonize new hosts and environments.
    • Pathogenicity Islands:
      • The genome of Salmonella contains specialized regions called Salmonella Pathogenicity Islands (SPIs) that encode genes crucial for infection.
      • SPIs are thought to have been acquired from other bacteria through HGT and are absent in its close relatives, such as E. coli.
    • Adaptive Evolution:
      • Salmonella has developed mechanisms to survive harsh conditions, such as the acidic environment of the stomach or macrophage phagosomes. Genes encoding acid resistance and intracellular survival are key to this adaptation.
  3. Speciation and Lineage Divergence
    • The genus Salmonella is divided into two main species:
      1. Salmonella enterica: The most diverse and widespread species, with six subspecies and over 2,500 serovars.
      2. Salmonella bongori: Found primarily in cold-blooded animals, such as reptiles.
    • Host Adaptation:
      • Salmonella enterica has evolved to infect a wide range of warm-blooded and cold-blooded hosts, whereas S. bongori remains restricted to reptiles.
      • Within S. enterica, specific serovars have adapted to particular hosts (e.g., S. Typhi for humans and S. Dublin for cattle).
  4. Relationship to Other Genera
    • Closest Relatives:
      • Escherichia coli: Shares a common ancestor with Salmonella. The two genera are highly similar at the genomic level but differ significantly in pathogenicity and host adaptation.
      • Shigella: Genetically very similar to E. coli but evolved independently to cause invasive infections.
    • Phylogenetic Placement:
      • Within Enterobacteriaceae, Salmonella is part of a subgroup that includes pathogens like Shigella and Yersinia.
      • Comparative genomics shows that Salmonella diverged from E. coli after acquiring genes enabling systemic infection and survival in macrophages.
  5. Ecological and Evolutionary Pressures
    • Host-Pathogen Interactions:
      • The evolutionary success of Salmonella is linked to its ability to exploit host defenses. For example, genes enabling intracellular survival have allowed it to persist within macrophages.
    • Environmental Reservoirs:
      • While primarily associated with animals, Salmonella can survive in environmental reservoirs like water and soil. This versatility has helped it spread globally.
  6. Evolutionary Insights from Genomics
    • Advances in genomic sequencing have clarified Salmonella's evolutionary trajectory:
    • Core Genome: Highly conserved genes related to metabolism and cell structure.
    • Accessory Genome: Includes mobile genetic elements like plasmids, transposons, and bacteriophages that contribute to virulence and antibiotic resistance.
  7. Molecular Clock Studies:
    • Analysis of mutation rates suggests that Salmonella continues to evolve rapidly, especially in response to human interventions like antibiotics.
Key Takeaways:
  • Salmonella evolved from a common ancestor with E. coli but adapted to systemic infections through gene acquisition and environmental pressures.
  • Its genomic flexibility and ability to colonize diverse hosts have been critical to its evolutionary success.
  • Relationships with other genera, like Escherichia and Shigella, reveal a shared evolutionary history with divergence driven by ecological specialization.


Is there much evidence of host-specificity?

Yes, there is considerable evidence of host specificity in Salmonella, with some serovars adapting to infect specific hosts more effectively than others. However, the extent of host specificity varies among Salmonella serovars and is influenced by their evolutionary adaptations and ecological niches. Here's a breakdown:
  1. Host-Specific vs. Broad-Host-Range Serovars
    • Host-Specific Serovars:
      • These serovars are restricted to specific hosts and often cause severe, systemic infections in their target species.
        • Salmonella Typhi: Human-specific, causing typhoid fever.
        • Salmonella Paratyphi: Human-specific, causing paratyphoid fever.
        • Salmonella Dublin: Primarily infects cattle but can occasionally infect humans, usually causing severe disease.
        • Salmonella Choleraesuis: Adapted to pigs and can cause systemic infections in swine.
    • Broad-Host-Range Serovars:
      • These serovars infect a wide range of hosts and typically cause gastroenteritis.
        • Salmonella Enteritidis: A leading cause of foodborne illness in humans, associated with poultry and eggs but can infect other animals.
        • Salmonella Typhimurium: Infects a wide variety of mammals, birds, and reptiles, and is a common cause of foodborne illness.
  2. Mechanisms of Host Specificity
    The host specificity of Salmonella serovars is influenced by several genetic and molecular factors:
    • Pathogenicity Islands (SPIs):
      • Salmonella Pathogenicity Islands (SPIs) encode virulence factors like Type III Secretion Systems (T3SSs) that allow the bacteria to invade and survive in host cells.
      • Differences in SPI genes contribute to host specificity. For instance:
        • S. Typhi and S. Paratyphi have unique virulence factors (e.g., Vi antigen) that help evade the human immune system.
        • S. Dublin has genes that enhance its ability to persist in cattle.
    • Adhesins and Surface Proteins:
      • Host specificity is often mediated by adhesins, which enable the bacteria to bind to specific host tissues.
      • For example, S. Typhi expresses fimbriae and adhesins that preferentially bind to receptors found in human intestinal epithelial cells.
    • Immune Evasion:
      • Host-specific serovars have evolved mechanisms to evade or modulate the immune responses of their target hosts.
        • S. Typhi produces proteins that suppress human immune responses, facilitating systemic infection.
    • Metabolic Adaptations:
      • Host-specific serovars often exhibit metabolic pathways tailored to the nutrient environment of their host. For example, some serovars can utilize host-specific compounds as energy sources.
  3. Evidence from Genomic Studies
    Genomic studies have revealed key differences between host-specific and broad-host-range serovars:
    • Unique Genes:
      • Host-specific serovars often have genes not found in broad-host-range strains. These genes may encode virulence factors, metabolic enzymes, or regulatory proteins specific to their host environment.
    • Pseudogenes:
      • Host-restricted serovars like S. Typhi often have many pseudogenes—nonfunctional remnants of genes. This suggests they have lost functions unnecessary for survival in their specific host, leading to a narrowing of their ecological niche.
    • Phylogenetic Insights:
      • Phylogenetic analysis shows that host-restricted serovars tend to form distinct clades, reflecting their adaptation to specific hosts.
  4. Experimental Evidence
    • Animal Models:
      • Studies using animal models have demonstrated the inability of host-specific serovars to infect non-native hosts effectively.
        • S. Typhi does not cause disease in mice or cattle without genetic modification.
        • S. Dublin causes systemic disease in cattle but only sporadic, severe infections in humans.
    • Natural Observations:
      • Epidemiological data show strong associations between certain serovars and specific hosts. For example:
        • S. gallinarum and S. pullorum are highly adapted to poultry, causing fowl typhoid and pullorum disease, respectively.
  5. Exceptions and Spillover Events

    While some Salmonella serovars are highly host-specific, spillover events can occur:
    • Broad-host-range serovars like S. Typhimurium can infect a wide variety of species, often leading to zoonotic transmission to humans.
    • Host-specific serovars can occasionally infect non-native hosts, sometimes leading to severe disease. For instance:
      • S. Dublin can cause life-threatening bacteremia in humans, particularly in immunocompromised individuals.
  6. Implications for Public Health and Veterinary Medicine

    Understanding host specificity is crucial for controlling Salmonella infections:
    • Zoonotic Risks: Broad-host-range serovars pose significant zoonotic threats, especially in foodborne outbreaks.
    • Vaccination and Control Strategies: Vaccines and interventions can be tailored to target specific serovars in their primary hosts (e.g., poultry vaccines against S. Enteritidis).
Conclusion
Host specificity in Salmonella reflects a complex interplay of genetic, molecular, and ecological factors. While some serovars are highly specialized, others maintain the flexibility to infect a broad range of hosts, contributing to their global prevalence and significance as pathogens.
What the UC Davis Health study, led by Professor Andreas Bäumler of the Department of Medical Microbiology and Immunology found is the subject of a paper in Proceeding of The National Academy of Science (PNAS) and a UC Davis press release by Nadine A Yehya:
New study shows how salmonella tricks gut defenses to cause infection
(SACRAMENTO) A new UC Davis Health study has uncovered how Salmonella bacteria, a major cause of food poisoning, can invade the gut even when protective bacteria are present. The research, published in the Proceedings of the National Academy of Sciences, explains how the pathogen tricks the gut environment to escape the body's natural defenses.
The digestive system is home to trillions of bacteria, many of which produce short-chain fatty acids (SCFAs) that help fight harmful pathogens. But Salmonella manages to grow and spread in the gut, even though these protective compounds are present. The study asks: How does Salmonella get around this defense?

We knew that Salmonella invades the small intestine, although it is not its primary site of replication. The colon is.

Professor Andreas Bäumler, lead author
Department of Medical Microbiology and Immunology
School of Medicine
University of California at Davis, Davis, CA, USA.

Bäumler and his team discovered that the answer lies in how the pathogen changes the gut’s nutrient balance. When Salmonella enters the small intestine, it causes inflammation in the gut lining and disrupts the normal absorption of amino acids from food. This creates an imbalance in nutrients in the gut.

The imbalance gives Salmonella the resources it needs to survive and multiply in the large intestine (colon), where beneficial bacteria usually curb its growth. The study showed that salmonella causes inflammation in the small intestine in order to derive nutrients that fuel its replication in the colon.

Salmonella alters gut nutrient environment to survive

Using a mouse model, the team looked closely at how Salmonella changed the chemical makeup of the gut. They traced amino acid absorption in the small and large intestines.

They found that in mice that were infected with Salmonella, there was less absorption of amino acids into the blood. In fact, two amino acids, lysine and ornithine, became more abundant in the gut after infection. These amino acids helped Salmonella survive by preventing the growth-inhibiting effects of SCFAs. They did this by restoring Salmonella’s acidity (pH) balance, allowing the pathogen to bypass the microbiota’s defenses.

Our findings show that Salmonella has a clever way of changing the gut’s nutrient environment to its advantage. By making it harder for the body to absorb amino acids in the ileum, Salmonella creates a more favorable environment for itself in the large intestine.

Professor Andreas Bäumler.

In the study, the team showed that Salmonella uses its own virulence factors (disease causing molecules) to activate enzymes that break down key amino acids like lysine. This helps the pathogen avoid the SCFAs’ protective effects and grow more easily in the gut.

New insights could lead to better gut infection treatments

The new insights potentially explain how the gut environment changes during inflammatory bowel disorders , such as Crohn's disease and ulcerative colitis, and could lead to better treatments for gut infections. By understanding how Salmonella changes the gut environment, researchers hope to develop new ways to protect the gut microbiota and prevent these infections.

This research uses a more holistic approach to studying gut health. It not only gives us a better understanding of how Salmonella works, but also highlights the importance of maintaining a healthy gut microbiota. Our findings could lead to new treatments that help support the microbiota during infection. By learning how a pathogen manipulates the host’s system, we can uncover ways to boost the host’s natural defenses.

Dr. Lauren Radlinski, first author.
Department of Medical Microbiology and Immunology
School of Medicine
University of California at Davis, Davis, CA, USA.

The study’s results could inspire future treatments, including probiotics or dietary plans designed to strengthen the body’s natural defenses against harmful pathogens.

Coauthors of the study are Andrew Rogers, Lalita Bechtold, Hugo Masson, Henry Nguyen, Anaïs B. Larabi, Connor Tiffany, Thaynara Parente de Carvalho and Renée Tsolis of UC Davis.
Significance
The microbiota protects the host from microorganisms that cause disease in unprotected or immunocompromised individuals. Enteric pathogens such as Salmonella enterica serovar (S.) Typhimurium are adept at circumventing and weakening these protections and in doing so render the host susceptible to infection. Here, we identify a strategy by which S. Typhimurium uses its virulence factors to manipulate the host environment in the small intestine to trigger downstream changes in the environment of the large intestine that enable the pathogen to overcome microbiota-mediated defenses. The more general implications of our work are that ileitis-induced malabsorption causes downstream changes in microbial growth conditions in the large intestine, which can trigger compositional changes.

Abstract
The gut microbiota produces high concentrations of antimicrobial short-chain fatty acids (SCFAs) that restrict the growth of invading microorganisms. The enteric pathogen Salmonella enterica serovar (S.) Typhimurium triggers inflammation in the large intestine to ultimately reduce microbiota density and bloom, but it is unclear how the pathogen gains a foothold in the homeostatic gut when SCFA-producing commensals are abundant. Here, we show that S. Typhimurium invasion of the ileal mucosa triggers malabsorption of dietary amino acids to produce downstream changes in nutrient availability in the large intestine. In gnotobiotic mice engrafted with a community of 17 human Clostridia isolates, S. Typhimurium virulence factors triggered marked changes in the cecal metabolome, including an elevated abundance of amino acids. In an ex vivo fecal culture model, we found that two of these amino acids, lysine and ornithine, countered SCFA-mediated growth inhibition by restoring S. Typhimurium pH homeostasis through the inducible amino acid decarboxylases CadA and SpeF, respectively. In a mouse model of gastrointestinal infection, S. Typhimurium CadA activity depleted dietary lysine to promote cecal ecosystem invasion in the presence of an intact microbiota. From these findings, we conclude that virulence factor–induced malabsorption of dietary amino acids in the small intestine changes the nutritional environment of the large intestine to provide S. Typhimurium with resources needed to counter growth inhibition by microbiota-derived SCFAs.


The gut microbiota is a critical frontline barrier that precludes the expansion of invading microorganisms through the production of antimicrobial compounds and the depletion of essential nutrients (1). During homeostasis, obligately anaerobic bacteria dominate the microbiota of the large intestine and ferment unabsorbed carbohydrates to produce high luminal concentrations of the short-chain fatty acids (SCFAs) acetate, propionate, and butyrate. These SCFAs are weak acids that become protonated in mildly acidic environments (HAc), such as the lumen of the colon (pH 5.7 to 6.2) (2), as the pH approaches the respective negative base-10 logarithm of the acid dissociation constant (pKa) for each molecule (~pH 4.7). Protonated SCFA are membrane permeable, but exposure to a more neutral pH in the cytosol (pH 7.2 to 7.8) (35) results in their dissociation into the salt and a proton (Ac + H+). The consequent acidification of the bacterial cytosol results in growth inhibition and serves as a canonical, nonspecific defense mechanism against invading enteric pathogens such as Salmonella enterica serovar Typhimurium (S. Typhimurium) (3, 68).

S. Typhimurium uses its virulence factors, two type III secretion systems (T3SS-1 and T3SS-2) (9, 10) encoded by Salmonella pathogenicity island (SPI)1 and SPI2 (11, 12), respectively, to break colonization resistance through mechanisms that are not fully resolved (13, 14). T3SS-1 and T3SS-2 trigger intestinal inflammation (1517), which boosts growth of S. Typhimurium by increasing the availability of host-derived respiratory electron acceptors, including tetrathionate (18), nitrate (19, 20), and oxygen (21). In addition, aspartate is liberated when phagocyte-derived reactive oxygen species lyse luminal bacteria (22), which fuels growth of S. Typhimurium through fumarate respiration (23). Tetrathionate respiration has been shown to promote growth of S. Typhimurium in the lumen of the murine cecum by utilizing ethanolamine (24), which is generated when taurine liberated during deconjugation of bile acids is used as an electron acceptor by Deltaproteobacteria. Oxygen and nitrate enable the pathogen to utilize host-derived lactate (25) or 1,2-propanediol (26), a microbiota-derived fermentation product of pentoses. However, growth during in vitro culture under conditions that mimic the cecal environment suggests that high concentrations of SCFAs and the acidic environment of the cecum counter the competitive edge that oxygen and nitrate respiration confer upon the pathogen (27). These data suggest that S. Typhimurium virulence factors act on the host to generate yet unidentified resources that enable the pathogen to overcome growth inhibition by SCFAs in the lumen of the large intestine.

Here, we used untargeted metabolomics to identify resources generated by S. Typhimurium virulence factor activity during gastrointestinal infection and investigated their role in countering SCFA-mediated intracellular acidification.

I wonder if a creationist would be brave enough to attempt to explain these advantageous abilities of Salmonella, which enable it to survive and overcome our natural defences in our intestines in terms of 'devolution' from an initially designed perfection, or, if not, explain why, if the E.coli's flagellum is proof of their designer god, as devotees of Michael J. Behe insist, it isn't also proof of their designer god's work in Salmonella.

Alternatively, perhaps they could talk us through the process by which 'sin' is able to redesign a pathological bacterium to make it better at making us sick and increasing the suffering in the world, and even tailor-making some serovars so they target specific species, one of which is human.

Tuesday, 26 November 2024

Transitional Form News - Precambrian Common Ancestor of Insects, Arachnids, and Nematode Worms


Researchers Scott Evans (left) and Ian Hughes examine a fossil bed at Nilpena Ediacara National Park.
Droser Lab/UCR.
Tiny worm makes for big evolutionary discovery | UCR News | UC Riverside

The refutation of creationism continues today with news of another one of those 'non-existent' transitional species that turn up with monotonous regularity only to be dismissed by creationists as 'not transitional but fully formed' with now two gaps in the record where there was originally one, or by simply dismissing the dating method as unreliable and coincidentally wrong by an order of magnitude sufficient to make 6-10,000 years look like x-million years.
Another big disappointment for creationists is the fact that this one is from before the Cambrian when their traditional disinformation claims lots of species popped into existence without ancestors by magic in a single event called the 'Cambrian explosion'. The Cambrian 'explosion' was of course a period of some 6-10 million years during which many of the basic body plans of multicellular organisms evolved.

This fossil however was before then and was clearly the ancestral stem species from which a whole range of Cambrian organism, collectively known as Ecdysozoa evolved. These are a group of organisms with an outer cuticle which is shed periodically as the organism grows. The vast group includes nematode worms and arthropods such as insects, spiders, crustaceans like crabs, shrimps, lobsters, and the horseshow crab. So, this discovery, which the palaeontologists have named Uncus dzaugisi sits at the base of this branch of the evolutionary tree. It resembled a nematode worm.

Tell me all about the Ecdysozoa, please. Ecdysozoa is a major clade of animals within the larger group known as Protostomia, distinguished by their unique mode of growth, which involves periodic moulting of an external cuticle. The term "ecdysozoa" comes from the Greek word ecdysis, meaning "to strip off" or "to shed," referring to this moulting process.

Characteristics of Ecdysozoa
  1. Moulting (Ecdysis):
    • The defining feature of Ecdysozoans is the shedding of their cuticle—a tough, non-living outer layer made of proteins, polysaccharides (like chitin), or collagen. This process allows them to grow, as the rigid cuticle limits continuous size increase.
    • After moulting, a new, larger cuticle is secreted, which hardens over time.
  2. Body Structure:
    • Many have a hydrostatic skeleton, relying on fluid pressure in their body cavity for movement and structure.
    • Most lack cilia or flagella in their adult form, distinguishing them from other protostomes.
  3. Diversity:
    • The group includes some of the most diverse and abundant organisms on Earth, ranging from microscopic species to large, visible ones.
  4. Nervous System:
    • Typically, they have a ventral nerve cord and a dorsal brain, with varied sensory adaptations.

Major Groups Within Ecdysozoa
Ecdysozoa includes eight phyla, with two of the most well-known being Arthropoda and Nematoda:
  1. Arthropoda
    • The largest and most diverse group of animals, including insects, arachnids, crustaceans, and myriapods.
    • They have segmented bodies, jointed appendages, and a hard exoskeleton.
    • Examples: Butterflies, crabs, spiders, centipedes.
  2. Nematoda (Roundworms)
    • Microscopic to macroscopic worms with a cylindrical, unsegmented body.
    • Found in nearly every habitat on Earth, often as parasites in plants and animals.
    • Examples: Caenorhabditis elegans (a model organism), Ascaris (a human intestinal parasite).
  3. Tardigrada (Water Bears)
    • Microscopic, water-dwelling animals known for their extreme resilience to harsh environments.
    • They can survive desiccation, radiation, and even the vacuum of space.
  4. Onychophora (Velvet Worms)
    • Segmented, soft-bodied terrestrial animals with slime glands used for capturing prey.
  5. Priapulida
    • Marine worms with a tubular body, often found burrowing in sediment.
  6. Kinorhyncha
    • Tiny, segmented marine animals often referred to as "mud dragons."
  7. Loricifera
    • Microscopic animals inhabiting marine sediment, with a complex, retractable body.
  8. Nematomorpha (Horsehair Worms)
    • Parasites as larvae, often controlling the behaviour of their insect hosts.

Evolution and Phylogeny
  • Ecdysozoa was proposed as a clade in 1997, based on molecular evidence (notably studies of ribosomal RNA).
  • They share a common ancestor with other protostomes but diverged early to adopt their unique moulting strategy.
  • Their evolutionary success is evident in their sheer numbers and adaptability, especially in arthropods.

Ecological and Economic Importance
  1. Ecological Roles:
    • Many ecdysozoans are key components of ecosystems as decomposers, predators, prey, and parasites.
    • Insects, a subgroup of arthropods, are critical for pollination and nutrient cycling.
  2. Economic Impact:
    • Beneficial: Insects (e.g., bees) aid in agriculture, while nematodes play a role in soil health.
    • Harmful: Some ecdysozoans are pests or parasites causing diseases in humans, animals, and crops.

Fun Facts
  • Tardigrades can enter a state called cryptobiosis, surviving for decades without water or food.
  • Arthropods are the most successful phylum, with over a million described species, and likely many more undiscovered.
  • Nematodes may account for about 80% of individual animals on Earth.
The discovery was made by a team from University of California, Riverside (UCR), led by Professor Mary Droser a distinguished professor of geology. The have explained their findings in the journal, Current Biology, and in a UCR press release:
Tiny worm makes for big evolutionary discovery
UC Riverside scientists have described ‘Uncus,’ the oldest ecdysozoan and the first from the Precambrian period
Everyone has a past. That includes the millions of species of insects, arachnids, and nematode worms that make up a major animal group called the Ecdysozoa. Until recently, details about this group’s most distant past have been elusive. But a UC Riverside-led team has now identified the oldest known ecdysozoan in the fossil record and the only one from the Precambrian period. Their discovery of Uncus dzaugisi, a worm-like creature rarely over a few centimeters in length, is described in a paper published today in Current Biology.

Scientists have hypothesized for decades that this group must be older than the Cambrian, but until now its origins have remained enigmatic. This discovery reconciles a major gap between predictions based on molecular data and the lack of described ecdysozoans prior to the rich Cambrian fossils record and adds to our understanding of the evolution of animal life.

Mary L. Droser, co-author Earth and Planetary Sciences University of California, Riverside
Riverside, CA , USA.


The ecdysozoans are the largest and most species-rich animal group on Earth, encompassing more than half of all animals. Characterized by their cuticle — a tough external skeleton that is periodically shed — the group comprises three subgroups: nematodes, which are microscopic worms; arthropods, which include insects, spiders, and crustaceans; and scalidophora, an eclectic group of small, scaly marine creatures.

Like many modern-day animal groups, ecdysozoans were prevalent in the Cambrian fossil record and we can see evidence of all three subgroups right at the beginning of this period, about 540 million years ago. We know they didn’t just appear out of nowhere, and so the ancestors of all ecdysozoans must have been present during the preceding Ediacaran period.

Ian V. Hughes, first author
Organismic and Evolutionary Biology
Harvard University, Cambridge, MA, USA.


DNA-based analyses, used to predict the age of animal groups by comparing them with their closest living relatives, have corroborated this hypothesis. Yet ecdysozoan fossil animals have remained hidden among scores of animal fossils paleontologists have discovered from the Ediacaran Period.

Top: Uncus fossil from Nilpena Ediacara National Park. The numbers correspond to the coordinates of this fossil on the fossil bed surface. Bottom: 3D laser scans enable the researchers to study the fossils’ shape and curvature.
Droser Lab/UCR.
Ediacaran animals, which lived 635-538 million years ago, were ocean dwellers; their remains preserved as cast-like impressions on the seabed that later hardened to rock. Hughes said uncovering them is a labor-intensive, delicate process that involves peeling back rock layers, flipping them over, dusting them off, and piecing them back together to get “a really nice snapshot of the sea floor.”

This excavation process has only been done at Nilpena Ediacara National Park in South Australia, a site Droser and her team have been working at for 25 years that is known for its beautifully preserved Ediacaran fossils.

Nilpena is perhaps the best fossil site for understanding early animal evolution in the world because the fossils occur during a period of heightened diversity and we are able to excavate extensive layers of rock that preserve these snapshots. The layer where we found Uncus is particularly exciting because the sediment grains are so small that we really see all the details of the fossils preserved there.

Assistant Professor Scott Evans, co-author
Earth, Ocean, and Atmospheric Sciences
Florida State University, Tallahassee, FL, USA.


While the team didn’t set out to find an early ecdysozoan during their 2018 excavation, they were drawn to a mysterious worm-like impression that they dubbed “fishhook.”

Sometimes we make dramatic discoveries and sometimes we excavate an entire bed and say ‘hmmm, I’ve been looking at that thing, what do you think?’ That’s what happened here. We had all sort of noticed this fishhook squiggle on the rock. It was pretty prominent because it was really, really deep.

Because it was deep, we knew it wasn’t smooshed easily so it must have had a pretty rigid body. At this point we knew this was a new fossil animal and it belong to the Ecdysozoa.

Ian V. Hughes


After seeing more of the worm-like squiggles the team paid closer attention, taking note of fishhook’s characteristics. Other defining characteristics include its distinct curvature and the fact that it could move around — seen by trace fossils in the surrounding area. Paul De Ley, an associate professor of nematology at UCR, confirmed its fit as an early nematode and ruled out other worm types.

The team called the new animal Uncus, which means “hook” in Latin, noting in the paper its similarities to modern-day nematodes. Hughes said the team was excited to find evidence of what scientists had long predicted; that ecdysozoans existed in the Ediacaran Period.

It’s also really important for our understanding of what these early animal groups would have looked like and their lifestyle, especially as the ecdysozoans would really come to dominate the marine ecosystem in the Cambrian.

Ian V. Hughes

The paper is titled “An Ediacaran bilateran with an ecdysozoan affinity from South Australia.” Funding for the research came from NASA.
Highlights
  • A new, motile bilaterian is described from the Ediacaran of South Australia
  • Features including morphology and movement suggest an ecdysozoan affinity
  • This discovery firmly places ecdysozoans in the Precambrian

Summary
Molecular clocks and Cambrian-derived metazoans strongly suggest a Neoproterozoic origin of many animal clades.1,2,3,4 However, fossil bilaterians are rare in the Ediacaran, and no definitive ecdysozoan body fossils are known from the Precambrian. Notably, the base of the Cambrian is characterized by an abundance of trace fossils attributed to priapulid worms,5,6 suggesting that major divisions among ecdysozoan groups occurred prior to this time. This is supported by ichnofossils from the latest Ediacaran or early Cambrian left by a plausible nematoid,7,8,9 although definitively attributing this inferred behavior to crown-Nematoida remains contentious in the absence of body fossils.10 Given the high probability of the evolution of Ecdysozoa in the Proterozoic, the otherwise prolific fossil record of the Ecdysozoa, and the identification of more than 100 distinct Ediacaran genera, it is striking that no Ediacaran body fossils have been confidently assigned to this group. Here, we describe Uncus dzaugisi gen. et. sp. nov. from the Ediacara Member (South Australia), a smooth, vermiform organism with distinct curvature and anterior-posterior differentiation. The depth of relief of Uncus is unique among Ediacara fossils and consistent with a rigid outer cuticle. Ecological relationships and associated trace fossils demonstrate that Uncus was motile. Body morphology and the inferred style of movement are consistent with Nematoida, providing strong evidence for at least an ecdysozoan affinity. This validates the Precambrian origin of Ecdysozoa, reconciling a major gap between predicted patterns of animal evolution and the fossil record.4

I think my favourite quote from one of the scientists is "We know they didn’t just appear out of nowhere, and so the ancestors of all ecdysozoans must have been present during the preceding Ediacaran period", which just about describes the difference between someone who knows the Theory of Evolution is correct because he understands the evidence for it, and a creationists who believes in fully formed living organisms made from nothing, magically popping into existence from nowhere, with magic spells cast by an unproven supernatural deity their mummy and daddy told them about.

The ancestral form, the transitional species, was in exactly for rock formation of exactly the right age which the theory of evolutionary decent with modifiction from a common ancester predicted.

And in case a creationist is tempted to try the 'radiometric dating is flawed/wrong/faked fallacy. The Ediacaran rock formation these fossils were found in was independently dated several different ways that all converged on a 98-million-year span from 635 to 538 million years ago known as the Ediacaran. The Most important being the Uranium-Lead (U-Pb) dating of zircons found in the layers of volcanic ash sandwiched within the rocks. To compress 600 million years of radioactive decay into less than 6-10,000 years would have caused Earth's rocks to melt and the seas to boil away. And the weak nuclear force would have been so weak that atoms could not have formed, let alone life, and there would have been no planet and no universe to fine tune for it either.
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Common Ancestry - Ancient Choanoflagellates Genes Used To Make A Mouse


Choanoflagellates, singly and as a colony.
Scientists recreate mouse from gene older than animal life - Queen Mary University of London

If there is one thing designed to get creationists chanting 'Common Designer!' it's evidence of the same gene doing the same thing in lots of different organisms, no matter how distantly related they are.

But when that gene is needed because of a basic design blunder long ago in the evolution of multicellular organisms, that chant looks increasingly forlorn.

For example, scientists have just shown how SOX and POU genes isolated from a single-celled choanoflagellate can be used to convert a mouse cell to function as the stem cell to clone another mouse. The reason this works is because something needs to reset the epigenetic setting in specialised cells. In a multicellular organism like a mouse, this effectively means any cell produced after the first few cell divisions of the fertilised zygote.

But why would a single-celled organism like a choanoflagellate need to do that? The answer it that epigenetics originally evolved to make an organism more able to respond to environmental changes and stresses.

Sunday, 24 November 2024

Refuting Creationism - How Pterosaurs Evolved


AI-generated image.
New fossil discovery reveals key step in the evolution of flying reptiles - Queen Mary University of London

Although creationists insist dinosaurs coexisted with humans before their god launched his genocidal flood, and even twist words like 'behemoth' in the Bible to try to show how the authors of genesis were familiar with dinosaurs (as though there was only one species) what they never explain is why the same authors said nothing at all about the pterodactyls that were contemporaneous with dinosaurs.

The real reason is of course that pterodactyls and dinosaurs lived in that vast expanse of time before 'Creation Week' when 99.9975% of everything that happened on Earth happened.

The evidence for this can be found in any palaeontological article that deals with the evolution of these first flying vertebrates, like this one about the discovery of a new species, Skiphosoura bavarica, which is also helping to understand how these reptiles evolved. It was identified by a team led by Dr David Hone, a palaeontologist from Queen Mary University of London. Early pterosaurs had a wingspan of about 2 meters (6 feet) but they evolved into massive creatures with wing spans up to 10 meters (30 feet). On the ground, some of them may have been at tall as a giraffe!

Pterosaurs, their evolution, and their relationship to dinosaurs. Pterosaurs were a group of flying reptiles that lived during the Mesozoic Era, from the late Triassic (about 228 million years ago) to the end of the Cretaceous (66 million years ago). They were the first vertebrates to achieve powered flight and were remarkable for their diversity in size, morphology, and ecological niches. Here's a detailed overview of pterosaurs, their evolution, and their relationship to dinosaurs:


  1. Evolutionary Origins
    • Pterosaurs belonged to the clade Pterosauria, which is part of the larger group Archosauria, making them close relatives of dinosaurs and crocodilians.
    • Their exact evolutionary origins are debated, but they likely evolved from small, ground-dwelling or arboreal reptiles within the clade Avemetatarsalia, which also includes dinosaurs and birds.
    • Early pterosaurs, such as Eudimorphodon and Dimorphodon, appeared in the late Triassic and already exhibited the characteristic wing structure.
  2. Anatomy and Adaptations for Flight
    • Pterosaurs' wings were formed by a membrane of skin, muscle, and other tissues stretched along an elongated fourth finger, which supported the main wing structure.
    • Other adaptations included:
      • Lightweight skeletons with hollow bones to reduce weight.
      • Keel-like breastbones to anchor powerful flight muscles.
      • Complex cranial crests in some species, possibly for display or aerodynamic purposes.
      • Unique respiratory adaptations with air sacs similar to those in modern birds.
  3. Relationship to Dinosaurs
    • Pterosaurs and dinosaurs share a common ancestor, but they are distinct groups within Archosauria. Pterosaurs are not considered dinosaurs.
    • The distinction lies in their lineage: dinosaurs belong to the clade Dinosauria, while pterosaurs form their own separate clade.
  4. Diversity and Evolutionary Trends
    • Pterosaurs diversified into two main groups:
      1. Rhamphorhynchoids (Early Pterosaurs):
        • Typically small to medium-sized.
        • Long tails with a vane or rudder-like structure at the tip.
        • Examples: Rhamphorhynchus, Dimorphodon.
        • Lived during the Triassic and Jurassic periods.
      2. Pterodactyloids (Advanced Pterosaurs):
        • Larger body sizes, including giants like Quetzalcoatlus with wingspans exceeding 10 meters.
        • Short tails or no tails.
        • Adapted to various ecological roles, such as fish-eating, filter-feeding, and scavenging.
        • Examples: Pteranodon, Istiodactylus, Quetzalcoatlus.
        • Dominated the skies during the Jurassic and Cretaceous periods.
  5. Ecological Roles
    • Pterosaurs occupied diverse ecological niches:
      • Some were piscivores, using long, pointed jaws to catch fish.
      • Others were filter feeders, like Pterodaustro, which had bristle-like teeth.
      • Large pterosaurs may have been scavengers or predators of small terrestrial animals.
      • Their crests may have been used for sexual selection, thermoregulation, or species recognition.
  6. Extinction
    • Pterosaurs went extinct at the end of the Cretaceous period during the mass extinction event 66 million years ago, likely caused by the asteroid impact and subsequent environmental changes.
    • Birds, which evolved from theropod dinosaurs, survived and continued to dominate the skies, taking over many of the ecological niches once held by pterosaurs.
  7. Fossil Evidence
    • Pterosaur fossils are relatively rare due to their fragile skeletons, but significant discoveries have been made worldwide, revealing exquisite details of their anatomy and even soft tissues like wing membranes and pycnofibers (hair-like structures covering their bodies).



Key Distinctions from Dinosaurs
  • Dinosaurs were primarily terrestrial, with a diverse range of locomotion and body plans, whereas pterosaurs were adapted for flight.
  • Birds are considered modern-day dinosaurs (descendants of theropods), but they are not descended from pterosaurs.



Pterosaurs are an incredible example of evolutionary innovation, showcasing how vertebrates conquered the skies long before birds. Their fossils continue to provide insights into the complexity of prehistoric life and the adaptive potential of ancient reptiles.
Dr Hone's team have published their findings in the journal Current Biology and describe it in a Queen Mary University news release:
New fossil discovery reveals key step in the evolution of flying reptiles
A remarkable new fossil discovery is shedding light on how flying reptiles, known as pterosaurs, evolved from their early forms into the later giants that ruled prehistoric skies.
The new species, named Skiphosoura bavarica, was identified by a team led by Dr David Hone, a palaeontologist from Queen Mary University of London. Their findings were published today in the journal Current Biology.

The pterosaurs, close relatives of dinosaurs, were the first vertebrates to achieve powered flight. While early species typically had wingspans of about 2 metres, later pterosaurs evolved into enormous forms with wingspans reaching 10 metres. The discovery of Skiphosoura bavarica provides critical insights into how these transformations occurred.

Hailing from southern Germany, Skiphosoura boasts a rare, nearly complete skeleton preserved in three dimensions—a significant contrast to the often-flattened fossils of its relatives. Measuring about 2 metres in wingspan, the new species’ most striking feature is its short, stiff, sword-like tail, which inspired its name: “sword tail from Bavaria.”

This is an incredible find. It really helps us piece together how these amazing flying animals lived and evolved. Hopefully, this study will inspire more research into this important evolutionary transition.

Dr. David William Elliott Hone, lead author, School of Biological and Behavioural Sciences
Queen Mary University of London, UK.
For two centuries, scientists divided pterosaurs into two major groups: early non-pterodactyloids, characterised by short heads, long tails, and specific wing and toe structures, and the later pterodactyloids, which had larger heads, shorter tails, and other adaptations for efficient flight. Intermediate species, like the Darwinopterus discovered in the 2010s, showed how the head and neck evolved first. Skiphosoura represents a critical step beyond the Darwinopterus. Its head and neck resemble the more advanced pterodactyloids, while its wrist, tail, and foot show transitional features. These traits help trace the gradual adaptations that allowed later pterosaurs to grow to massive sizes. The study also reconstructed the evolutionary family tree of pterosaurs, placing Skiphosoura between Darwinopterus and true pterodactyloids. Additionally, a Scottish pterosaur named Dearc was identified as a key intermediate between early pterosaurs and Darwinopterus. Together, these findings form a near-complete evolutionary sequence for pterosaurs, detailing how their anatomy changed over time. The discovery was made possible through the efforts of an international team. Adam Fitch, from the University of Wisconsin-Madison, highlighted the significance of Skiphosoura:

Pterosaurs have long been symbols of the unique life of the past. Skiphosoura represents an important new form for working out pterosaur evolutionary relationships and how this lineage arose and changed.

Adam Fitch, co-author
University of Wisconsin-Madison UW Geology Museum, Madison, WI, USA.

Having worked on over 60 pterosaurs from the Solnhofen limestone, it became clear during preparation that this fossil displayed features from both major groups of pterosaurs, with the shortened tail being a crucial diagnostic trait.

Stefan Selzer, co-author
Grabenäcker 12, Hemhofen, Germany.

Bruce and René Lauer of the Lauer Foundation, who contributed to the project, underscored the importance of modern techniques such as UV photography in uncovering fine details of the specimen.

We are proud to bring this important specimen to science and further the understanding of pterosaur evolution.

Bruce Lauer, co-author
Lauer Foundation for Paleontology, Science and Education
Wheaton, IL, USA.

With its blend of cutting-edge research, meticulous preparation, and international collaboration, the study of Skiphosoura bavarica offers a significant leap forward in understanding the evolutionary journey of these extraordinary flying reptiles.
Highlights
  • A new pterosaur, Skiphosoura bavarica, is named from the Jurassic of Germany
  • The specimen is much larger than other known forms and is preserved in three dimensions
  • The Skiphosoura helps document the transition from early pterosaurs to the pterodactyloids
  • The tail is short but retains the supporting structures of earlier forms
Summary For over a century, there was a major gap in our understanding of the evolution of the flying Mesozoic reptiles, the pterosaurs, with a major morphological gap between the early forms and the derived pterodactyloids.1 Recent discoveries have found a cluster of intermediate forms that have the head and neck of the pterodactyloids but the body of the early grade,2 yet this still leaves fundamental gaps between these intermediates and both earlier and more derived pterosaurs. Here, we describe a new and large Jurassic pterosaur, Skiphosoura bavarica gen. et sp. nov., preserved in three dimensions, that helps bridge the gap between current intermediate pterosaurs and the pterodactyloids. A new phylogeny shows that there is a general progression of key characteristics of increasing head size, increasing length of neck and wing metacarpal, modification to the fifth toe that supports the rear wing membrane, and gradual reduction in tail length and complexity from earlier pterosaurs into the first pterodactyloids. This also shows a clear evolution of the increasing terrestrial competence of derived pterosaurs. Furthermore, this closes gaps between the intermediates and their ancestors and descendants, and it firmly marks the rhamphorhynchines and ctenochasmatid clades as, respectively, being the closest earliest and latest groups to this succession of transitional forms.
Figure 1 Key elements of Skiphosoura
  1. The anterior part of the skull with the premaxillary crest and large teeth. Also seen is the humerus. Scale bar, 100 mm.
  2. The short caudal vertebrate with long zygapophyses and the elongate chevrons. Scale bar is 10 mm.
ca, caudal vertebra; cn, chevron; dr, dorsal rib; fe, femur; hu, humerus; pb, pubis; pm, premaxilla; wpx 1, wing phalanx 1. See also Figures S1, S2, S7, and S9

Figure 2 Simplified phylogeny of Macronychoptera showing the phylogenetic placement of Skiphosoura bavarica gen. et sp. nov
The new taxon is recovered outside of Pterodactyloidea as a late-diverging member of a grade of non-pterodactyloid monofenestratans. Note that Monofenestrata also lies within an earlier-diverging grade of “rhamphorhynchids” (Dorygnathus to Angustinaripterus) and that “rhamphorhynchines” (Rhamphorhynchini, Dearc, Angustinaripterus) here represent the closest relatives of Monofenestrata. See also Figure S10 and Table S2.
Figure 3 The transition of pterosaur proportions across the transition from early pterosaurs to the pterodactyloids
Upper left: Nopsca curves of the proportions of major elements of the skeleton scaled against the length of the humerus showing the transition of major proportions. Center: simplified phylogeny showing the transition of key characters in the evolution of pterodactyloids from the rhamphorhynchines and “through” the early monofenestratans. Skeletals showing the transition with representational taxa: Rhamphorhynchus, Dearc, Darwinopterus, Skiphosoura, and Pterodactylus. This shows the transitions of multiple features across the tree: (1) the increasing length of the skull and increase of the size of the naris before fusion to form the NAOF, (2) increase in the length of the cervical series, (3) proportional reduction in the length of the wingfinger and increase in the length of the proximal wing, (4) increase in the length of the first wing phalanx to be the longest of the four phalanges, (5) increase in the length of the wing metacarpal, (6) increase in the size of the prepubes, (7) reduction of the fifth toe, and (8) reduction and simplification of the tail. Reconstructions modified from Unwin,15 Wellnhofer,16 and Witton.1 These are not to scale but are all set to a uniform torso length.
See also Figures S1S8 and S11 and Table S1.
As Though to rub salt into creationist wounds, not only is this pterosaur from the Lower Tithonian (i.e. 148-150.8 million years old) but as the palaeontologist explain, it forms part of a transitional sequence of fossils showing how this group of reptiles evolved.
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