Cretaceous pterosaur diversification and extinction

Artist: Mark Witton

Few things are as disappointing as learning that no pterosaurs survived the K/Pg extinction. This has always been especially hard for me to emotionally accept due to their immense diversity. The typical explanation usually told is that they were wiped out with the non-avian dinosaurs after the chicxulub impact, and that they were barely alive by that time anyway because all the birds had filled up the flying niches. However recent evidence indicates that pterosaurs actually were doing very well up until 65 million years ago. Why they went extinct may have nothing to do with birds or a failure to diversify. Serial size reduction allowed for smaller pterosaurs to survive through other extinctions. Reaching sexual maturity before being fully grown allowed for smaller hatchlings maturing more quickly, allowing for more reduction in size by accelerating evolution somewhat. So if there were smaller pterosaurs at the end of the Cretaceous, AND pterosaurs have previously proven to be capable of relatively rapid phylogenetic size decreases, why did no pterosaurs survive?

The Cretaceous is more known for its giant, “small-plane sized” pterosaurs (Arambourgiania, Quetzalcoatlus, and one that’s been in the news more recently for “terrorizing” Transylvania: Hatzegopteryx). For background pterosaurs are split into two major suborders, with Rhamphorhynchoids being a paraphyletic group characterized by having teeth, long tails, and a cruropatagium that stretched between the feet (like how bats have it). Most were small and lacked bony head crests. They appeared in the Triassic and went extinct during the Cretaceous though there is no strong evidence to indicate they were outcompeted by pterodactyloids which is a common assumption.

Pterodactyloids, the other suborder, did not appear until the late Jurassic and were much more successful and diverse in the Cretaceous. While all pterosaurs are outstanding creatures, the pterosaurs this post is concerned with would all be pterodactlyoid members.

Rhamphorhynchoid on left, Pterodactyloid on right

No fossils of pterosaurs have been found from after the K/Pg extinction (and I don’t believe there ever will be 😦 ). But while there are certainly no pterosaurs alive today, there is a lot of evidence indicating that pterosaurs were actually quite diverse even at the end of the Cretaceous, and that some were even very small. The discovery of small pterosaurs from the late Cretaceous does seem to indicate that the reason for their clade’s total extinction was not simply because they were just “too large.”

Small pterosaurs may have been more abundant in Cretaceous than previously thought

A small azhdarchoid (azhdarchoids being the most recent common ancestor of Quetzalcoatlus and Tapejara, and all its descendents) pterosaur was discovered from the Campanian Northumberland Formation of British Columbia. With an estimated 1.5m wingspan, the pterosaur specimen is described as being about the size of a large seagull. The specimen found might not actually be an azcharchoid, but it certainly was from a pterosaur. Researchers were able to analyze the bones to determine whether or not it was juvenile or adult and found that the specimen was either fully grown or very close to being fully grown. For more on that, read the paper here.


Pterosaurs preserve terribly. They’re bones are hollow, their skeletons are fragile, they didn’t routinely die in nice, preserving environments. During the Cretaceous, pterosaurs shifted from marine to more non-marine habitats. This may account for the lack of data on small, difficult to preserve pterosaur fossils in the late Cretaceous. Terrestrial habitats do not preserve fragile fossils. Even much larger, denser bones do not often preserve well in terrestrial environments. The fossils that have been found from pterosaurs of this period are usually in very bad shape and are only fragments of the entire skeleton. Often times, fossils have to be looked at by many bird and pterosaur specialists before it can even be determined that the bone WAS from a pterosaur.  There is a lot of growing evidence suggesting that smaller pterosaurs in the late Cretaceous were not as rare as once believed.

Birds not the cause of pterosaur extinction

Pterosaurs were excellent fliers, almost definitely warm-blooded like birds (due to the energy expense of their lifestyle) and seemed able to adapt to a wide variety of niches. So it’s strange to imagine them going extinct due to their failure to diversify in the presence of birds. A study showed that pterosaurs actually diversified more after birds appeared. Pterosaurs had about a 160 million-year run on Earth and were relatively similar morphologically for the first 70 million years. They then began to experiment, trying out many modes of life. As birds became more successful, the pterosaurs actually responded by diversifying more. The emergence of birds (at least 50 million years after the first pterosaurs), encouraged the pterosaurs to try out new diets and feeding styles as seen by the rapid diversification of skull shapes in the fossil record. The general direction they went towards was much larger bodies. This was when the famous giant Quetzcoatlus types emerged.


  1. A small azhdarchoid pterosaur from the latest Cretaceous, the age of flying giants. Martin-Silverstone, Elizabeth, et al. Royal Society Open Science. 2016.
  2. Evolution of morphological disparity in pterosaurs. Katherine Prentice, Marcello Ruta, Michael Benton – Journal of Systematic Palaeontology – 2011





A microbe manipulating sex- and how it can fight Zika


A fan favorite, and probably the most successful genus on the planet–at least on land—the bacteria, Wolbachia infects an estimate between 40 to 65% of all arthropod and nematode species. This microbe is constantly drifting across the line between mutualist and parasite to it’s host. Some hosts are unable to survive and reproduce without a Wolbachia infection whilst others are killed by it.

Wolbachia as a mutualist

Plenty of species have become reliant on this microbe. The caterpillar of the spotted tentiform leaf miner uses Wolbachia to create green islands on yellowing leaves which remain fresh for munching on.

It provides a benefit to certain nematode worms, such as Brugia malayi and Wuchereria bancrofti which cause elephantiasis, and which cannot survive without a Wolbachia infection. Image1.jpg

Some Wolbachia bacteria provide metabolic advantages to their hosts such as in bed bugs who use it to synthesize B-vitamins that are absent in their blood meals. Wolbachia can even mediate iron metabolism in Drosophila.

But most exciting given the recent explosion of flavivirus infections (Zika traveling farther and farther north every summer for example), Wolbachia provides flies with resistance to many RNA viruses.

Wolbachia as a sex-determinator

In leafhoppers, Zyginidia pullula, females have two X chromosomes while males have only one X chromosome, yet when infected with Wolbachia, the X0 genetic males appeared to be female.

Some females of the Japanese butterfly, Eurema mandarin have a sex chromosome system where the males are (ZZ) and the females are (ZWEurema_blanda_on_flower_by_kadavoor.JPG). This incongruence between chromosomal and phenotypic sex can be explained by feminization of genetic males induced by Wolbachia. Two strains of WolbachiawCI and wFem, have been found in E. mandarina and the females having male chromosomes (ZZ) are consistently infected with both wCI and wFem. However females with only wCI are true females (ZW). Despite having male chromosomes, ZZ females are physically female and fully fertile.

A similar thing happens in woodlice (pillbugs? Roly-polys?), where all the ZZ males infected with Wolbachia develop as female. The W chromosome is sometimes lost entirely in these populations and sex is entirely determined by presence or absence of Wolbachia.

Who needs males?

Wolbachia has evolved into an intracellular parasite, and while it can infect many different organs, it is most famous for infecting the testes and the ovaries. Wolbachia are too large for sperm, but fit nicely into mature eggs so the infection is inherited maternally through the eggs.

So now the evolutionary dilemma that keeps Wolbachia on the balance between parasite and mutualist is, if males are an evolutionary dead-end, how does this intracellular parasite that needs its host to survive and reproduce, and it’s host species to continue thriving, evolve to both spread throughout populations but not allow evolutionary cheater strains to ruin everything? Wolbachia has developed numerous ways of targeting males to help itself spread such as:

  • Male killing- infected male larvae die, so more infected females are born
  • Feminization- where infected males develop as females or infertile pseudofemales
  • Parthenogenesis- when females reproduce without males
  • Cytoplasmic incompatibility (CI)- when Wolbachia-infected males can’t successfully reproduce with uninfected females or females infected with another Wolbachia strain.CI-causing Wolbachia interferes with the chromosomes during mitosis so they no longer divide in sync.
Warren et al, 2008, Nature Reviews, Microbiology.

Mosquitos carrying Wolbachia have a higher reproductive success when present in a population with mosquitoes not carrying Wolbachia. When a male mosquito carrying Wolbachia tries to mate with a female who is not carrying Wolbachia, the female’s eggs won’t hatch. However females with Wolbachia do not have this issue and produce perfectly healthy offspring which are all also carriers of Wolbachia. So you can imagine how the Wolbachia is able to sweep through a mosquito population. The female Wolbachia carriers have a much higher fitness than the non-carriers.

Scientists have taken advantage of this evolutionary strategy in fighting mosquito-transmitted viruses such as Dengue and Zika. The Aedes aegypti, a black-and-white striped species of mosquito infects people with Dengue virus which has no vaccine or real treatment and causes pains, fevers, rashes, and headaches. A plan (credited to evolution/ecology biologist, Scott O’Neill) to release Wolbachia infected mosquitos into the wild to lower dengue spread is becoming more and more popular. Wolbachia stops Aedes mosquitoes from carrying degue virus. Wolbachia carrying females have a selective advantage and should sweep through the population.

Wolbachia to rescue us from Dengue (and others?)- The original plan

An unusually virulent strain of Wolbachia the ‘popcorn’ strain, essentially halves the mosquito lifespand (it’s pretty gruesome, the bacteria essentially reproduce like crazy in the brains, eyes, and muscles filling up neurons). Dengue takes a long time to be able to reproduce and make it to the salivary glands so it can be transmitted, so only older mosquitos can transmit it.

Unfortunately Aedes (and Anopheles which transmist malaria) are not natural hosts of Wolbachia infections, so Scott O’Neill carefully developed a new symbiosis by injecting eggs. This took forever to work, until one lucky grad student was able to make it a success. Finally, an egg was stably infected and a line of Wolbachia-carrying Aedes was created. But after all that work, the strain was too virulent and the females did NOT have a selective advantage and actually had lower numbers of eggs with lower viabilities (honestly, they should have seen this coming really).


But none of that even ended up mattering because some other scientists figured out that Wolbachia stops dengue virus from replicating. Simply the presence of a nonvirulent strain of Wolbachia in the population was enough to stop the spread of dengue. So the team switched to a less virulent strain, wMel, and successfully started a line of wMel carrying Aedes mosquitos.

wMelwAlbB update and some critiques of the data

As amazing as Wolbachia is, it will take at least a few years to get significant results and many years to eliminate any particular mosquito-transmitted pathogen with this method. Some papers say Wolbachia was able to make not only dengue, but also Plasmodium and other flaviviruses less able to replicate, but others said the opposite. It would be kind of important to figure out how the Wolbachia is inhibiting the virus because no one seems to agree if it’s general or specific. But now with significant selective pressures on all these diseases I’d suspect it’d be easy to switch host vectors because mosquitos bite hosts, geographically spreading infections very far (potentially) exposing the virus to a wide variety of new potential hosts vector species.

In a 2016 paper looking at the progress of the wMel strains, they collected Ae. Aegypti after one year and it continued to have low levels of dengue (which implies it was passed around through tons of mosquitos and not a whole lot of apparent evolution has taken place in terms of resistance) but what if the some of the dengue viruses switched species?

They could try passing the dengue through many mosquitos perhaps in a mixed host population. Or basically just try to provide the virus with as many opportunities as you can for it to evolve in the hopes that you may understand potential mechanisms the different diseases may have to get around this one Wolbachia infected species of vectors.

While the paper shows wMelwAlbB, the superinfection, that strain of Wolbachia actually doesn’t appear to inhibit DENV very much. But later in the paper, it’s very dramatically different so it’s difficult to say if the data is actually supporting that the superinfection sweep will work.

As far as how they ensure the right strain is dominating all the time given selective pressures towards different mosquito sex alteration methods, that remains unanswered. Combined male-killing CI strains readily become extinct following invasion so CI strains are more selected for but sex-ratio distortion decreases male infection and therefore reduces the occurrence of CI meaning that you might expect selective pressure for evolution from CI to CI/sex ratio distortion to sex ratio distortion only.

Wolbachia’s potential

Using Wolbachia’s ability to stop mosquitos from carrying Zika, Dengue, Chikungunya, Plasmodium—the parasite responsible for malaria, may mean the eventual elimination of these diseases in humans.

It may even be used to someday stop nematode worms from causing blindness, disability, elephantitis etc in many millions of people every year.


Particularly inspiring about this story is how ecologists and evolutionary biologists ended up being the ones to figure out a way to eliminate viral infections. Yet more evidence that pre-med students or medical researcher hopefuls shouldn’t blow off biodiversity/ecology/evolution classes in college.


Kageyama, Daisuke, Satoko Narita, and Masaya Watanabe. “Insect Sex Determination Manipulated by Their Endosymbionts: Incidences, Mechanisms and Implications.” Insects 3.4 (2012): 161-99.

I contain multitudes: the microbes within us and a grander view of life. Ed Yong, 2016

Bacterium offers way to control dengue fever. Natasha Gilbert – Nature – 2011.

Establishment of a Wolbachia Superinfection in Aedes aegypti Mosquitoes as a Potential Approach for Future Resistance Management. D. Joubert-Thomas Walker-Lauren Carrington-Jyotika Bruyne-Duong Kien-Nhat Hoang-Nguyen Chau-Iñaki Iturbe-Ormaetxe-Cameron Simmons-Scott O’Neill – PLOS Pathogens – 2016



Homosexuality in animals

bottlenose_dolphin_1249780c.jpg Since it’s pride month, I thought the evolution of homosexuality warranted some attention. It turns out homosexuality is common throughout the animal kingdom, while homophobia is only seen in one species.

While sexuality is complex and seems to have a lot to do with epigenetics, as well as conditions in the uterus during fetal brain development, this variety is not limited to humans. Instead of thinking of humans as unique and separate from other animals, try to consider that brains, social structure, and cognitive ability exist on a spectrum with humans simply sometimes possessing a “higher degree” of whatever special unique thing we think we have. Such as love and sexuality. Homosexuality is especially common in primates and marine mammals (it’s correlated with intelligence in species). Same-sex relationships amongst animals strengthen social structures and can be particularly useful in systems with a lot of parental care, systems where the females outlive the males (humans?), and systems where not all males get an equal number of mates. Bottlenose dolphins for example are well-known for their bisexual behavior which strengthens social bonds.

When talking about homosexuality in nature, brief periods or episodes of homosexuality are actually pretty common. Male dominance mating (which is very common in giraffes), isn’t really “true homosexuality” because the males do not form any kind of bond, and the males will usually mate with females if they can. Cases of males or females rejecting the opposite sex and forming permanent pair bonds is more rare but absolutely happens.

Female-female couples

Young-albatross-female-couple-02.jpgA classic female-female coupling that actually makes a lot of evolutionary sense from a reproductive point of view, is the Laysan Albatross. The Laysan Albatross is monogamous and mates for life, and almost a third of the parent pairs are both female. This is useful as sometimes males will mate with more than the just their one female mate (basically he cheats on her in the hopes of making more offspring) and as the Albatross has evolved to require high parental care from both parents, female-female parents are actually a necessity in many cases where the father is absent.

Macaques are also rather known for their “lesbianism,” which in this case, has nothing to do with parenting and more to do with them just preferring sex with other female macaques. The males just can’t keep up.

Not all dominant mounting is males

While males mating with other males is very common, scientists have sometimes argued that a lot of that “mating” is simply the males exerting dominance over each other. Females do it to though, especially in the case of the female spotted hyenas who live in a matriarchy. The female hyena is even larger and more terrifying than the male hyena and leads the family.


gay-rams.jpgA study of gay sheep, was actually pretty historical as it really confirmed that there is a biological basis for sexual preference in animals. Sheep do seem to have a much higher rate of homosexuality than other animals where as many as 1 in 10 rams can be gay. Rams have undergone a lot of selective breeding which may provide some evidence that genes are involved in sexual preference. A region in the hypothalamus which is generally much bigger in rams than in ewes was found in gay rams to be the same size as the female’s. The hypothalamic region size variations effected levels of aromatase, an enzyme which converts androgens into estrogens. This supported the theory that hormones present during fetal development plays a role in determining sexual preference.


Bonobos are so closely related to us that it hardly seems worth it to mention them, but they are fascinating none the less. They exist in a peaceful (compared to chimps and humans) matriarchal society where sex occurs between basically every pairing you can imagine, excluding close family members (evolution doesn’t favor inbreeding). If you want to learn more about these super gay cousins of ours, I highly recommend primatologist, Frans de Waal’s books. He’s basically the top authority on bonobo sex. Really the best of the best.

Adoptive gay vulture dads
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In what may be one of the cutest stories I’ve read all year, two male griffon vultures from Amsterdam have recently been given the opportunity to raise a chick together. These two males are long-term mates who had been building nests together for months but were unable to produce an egg together (obviously). The zookeepers remarked that it was unfortunate as they were one of the most devoted culture couples observed.

Vultures are monogamous and have biparental care systems, so the males together could still make great parents. When a vulture egg was abandoned, and no heterosexual vultures would agree to incubate it, they gave the egg to the long-term male couple. The males ended up being very enthusiastic helicopter parents, proving that they could successfully hatch an egg even without a female helping. They carefully took turns incubating it, and when it hatched they proved to be protective, loving parents. The fathers have split their jobs equally, taking turns caring for their baby, looking for food, defending the nest, and feeding the baby.

Gay Penguins

Possibly the most famous gay couple in the animal kingdom is the penguin couple from the central park zoo, Roy and Silo. The two chinstrap penguins, where internationally celebrated for successfully hatching and caring for an egg they were given. Their caretakers noticed that they engaged in mating behaviors with one another and seemed to instinctually want an egg of their own, once seeming to try and hatch a rock that resembled an egg. Other gay penguin couples have been observed actually trying to steal eggs from other penguins, a behavior that’s not uncommon in heterosexual penguins either. Penguins typically engage in multiple long term relationships (kind of like humans do), and interestingly, many of them will switch around between male and female partners in their lifetime.



Oregon Health & Science University. “Biology Behind Homosexuality In Sheep, Study Confirms.” ScienceDaily. ScienceDaily, 9 March 2004.

Our Inner Ape, Frans de Waal

Polyploidy in tetrapods

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African Clawed Frog

Polyploidy is the condition where an organism possesses more than two sets of chromosomes. Most people probably only associate it with plants, as polyploidy in animals has been relatively understudied, and unisexuals—animals that are entirely female, are typically ignored because they use hybridization and parthenogenesis (though personally I think it may be male refusal to accept that they aren’t as permanent or resilient as they may have hoped—see the degenerate Y chromosome). The most famous female-only species are probably the New Mexico whiptails, Cnemidophorus neomexicanus, or “lesbian lizards,” a hybrid species of lizard that no longer involves males in their reproduction but still often perform courtship rituals to stimulate ovulation.

Females perform courtship rituals to stimulate ovulation. Nature is amazing.

Both parthenogenesis (when eggs develop with no fertilization) and hybridogenesis (fertilization occurs but paternal DNA isn’t passed on) are pretty common in amphibians. A more intriguing example than the lizards, though one that’s gotten less press until now, is the unisexual Ambystoma hybrid salamanders. This salamander ranges from triploid to pentaploid with Ambystoma nothagenes using genes from males from three different salamander species– Ambystoma lateraleAmbystoma texanum, and Ambystoma tigrinum.

The Ambystoma females always require sperm from a related species to fertilize their eggs and initiate development and generally just discard the sperm genome. Sometimes the unisexual sexually reproduces instead and there is a genome addition or genome replacement event where the maternal genome is discarded or the female acquires the male’s genes and then keeps only some of the genes after mating.

What’s kind of intriguing about this case of “kleptogenesis”, or gene stealing, is that the females basically express genes from the different males at a relatively equal rate. How exactly they choose which genes to use and which to throw away is not known, nor is how these genes come together to make a good hybrid.

Why do it? 

How Ambystoma, a six-million-year-old lineage, and how other polyploids/unisexuals/hybrid species survive when in competition with “regular” diploids living in the same spatial niche, is also not understood. It’s generally considered that polyploidy is a short-term strategy evolved in environments that are less stable. Which is why Ambystoma being a polyploid for so long is especially surprising.

Screen Shot 2017-06-15 at 6.28.34 PM
Ambystoma, female polyploid

While polyploidy can be advantageous, it’s initially unstable before becoming a competitive strategy. The presence of duplicated genes can help fuel diversification and evolutionary success.

Heterosis, gene redundancy, and asexual reproduction can all be considered advantages of polyploidy. Heterosis is essentially the ability to make better use of heterozygosity. Gene redundancy allows you to better diversity and provides a protection from harmful mutations. And asexual reproduction enables you to reproduce without a sexual mate around.

Polyploidy in animals is a case of convergent evolution where many fish and amphibians have acquired it separately. All the polyploids have acquired their genomes differently and in different ways. The unisexuals and males in the salamander group have higher gene exchange than other polyploids which may explain the “balance” in the genome not seen in other polyploids. Instead of gene silencing or dominance evolving, it seems natural selection has favored a more balanced genome because that’s just what worked for these girls. If you lose some gene contribution it’s less dramatic this way than if you’d put almost everything into one male salamander only for him to do something inconvenient like die or not show up to mate.

Faster regenerators

There’s some serious selective pressures for salamanders to survive injuries. They have the ability to regenerate tissue, so if part of their tails snap off, they can grow back. A study published in the Journal of Zoology showed that these polyploid all-female salamanders regenerate lost tissue 36% faster than other salamander species.

Within 10 weeks, after having had 40% of their tails cut off, the all-female salamanders had full length tails. The diploid sexually-reproducing relatives needed another 5 weeks to finish growing their tails.

The explanation may have to do with more genes meaning more proteins meaning faster regeneration. And if you can’t regenerate you don’t do so well so this could have been an added pressure to explain how this lineage was able to stay polyploid for six million years.


  1. J. Saccucci, R. D. Denton, M. L. Holding, H. L. Gibbs. Polyploid unisexual salamanders have higher tissue regeneration rates than diploid sexual relatives. Journal of Zoology, 2016;
  2. Comai, Luca. “The advantages and disadvantages of being polyploid.” Nature Reviews Genetics11 (2005)
  3. Kyle E. McElroy, Robert D. Denton, Joel Sharbrough, Laura Bankers, Maurine Neiman, H. Lisle Gibbs. Genome Expression Balance in a Triploid Trihybrid Vertebrate. Genome Biology and Evolution, 2017
  4. Evolutionary Significance of Whole-Genome Duplication. Mcgrath-M. Lynch – Polyploidy and Genome Evolution – 2012

The struggle against antibiotic resistance

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“Animals may be evolution’s icing, but bacteria are the cake.” –Andrew Knoll, Life on a Young Planet

Rapid evolution of multi-drug resistant bacteria due to overuse of antibiotics is one of the biggest threats facing humans today. Luckily scientists, motivated by terror of a superbug killing us all, have been working pretty hard recently on trying to solve this problem.


A new class of antibiotics was discovered with the help of a new device, the iChip. Humans have been unable to figure out how to isolate and culture most (99%) of the Earth’s bacteria, but the iChip was successfully used to culture previously unculturable soil bacteria, notably Eleftheria terrae. This bacteria was found to produce Teixobactin, an antibiotic that micorbes have an exceptionally difficult time evolving resistance to (like, so difficult none have been able to do it yet). Because most antibiotics are usually discovered by accident via fungi or other microbes, being unable to culture most of what was in the soil has been a pretty big barrier in our search. Teixobactin is active against gram-positive bacteria and works by inhibiting cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). Peptidoglycan is what makes up the thick walls of Gram-positive bacteria. Gram-negative bacteria also have peptidoglycan but in much smaller amounts and are protected by a second outer membrane which Gram positive bacteria do not have.

Screen Shot 2017-06-06 at 8.38.59 PM.pngStaphylococcus aureus (MRSA/VRSA) and Mycobacterium tuberculosis (TB), two ofthe biggest names in the antibiotic resistance crisis, were both killed by and unable to develop resistance to, Teixobactin.

Teixobactin is probably more robust against mutations of pathogens, because of its antibiotic mechanism is so unusual. Most antibiotics involve binding to relatively mutatable proteins. Teixobactin however, binds to much less mutatable fatty molecules.

Vancomycin 3.0

Vancomycin has been in use since 1958 and was once considered a last-resort drug because it seemed bacteria were not very good at developing resistance to it but it’s a pretty serious drug. It has a higher toxicity level than most antibiotics you’d usually be prescribed so it is used only for the treatment of life-threatening Gram-positive infections. It kills bacteria by preventing cell wall synthesis by binding to peptides ending in two copies of D-alanine. Unfortunately bacteria were able to replace a D-alanine with a D-lactate (D-lac). Scientists decided to fix this by creating a new vancomycin that binds to peptides ending in D-ala and D-lalc. Other scientists came up with ways to manipulate vancomycin to kill cells by stopping cell wall synthesis in a new way or causing the outer wall membrane to leak.

Screen Shot 2017-06-06 at 8.41.40 PM.png

The new vancomycin, vancomycin 3.0, has three antimicrobial targets in one antibiotic. It was shown to be effective against vancomycin resistant Enterococcus (VRE) and vancomycin resistant Staphylococcus (VRS). A three-pronged approach presumably means that for a bacterium to be resistant, it would have to have three non-lethal mutations to get around this drug.


Bacteriophages, viruses that infect bacteria, are also being used as a method to treat bacterial infections. While this concept is not especially new, it’s been relatively neglected by the U.S.. Phage therapy would take a long time to get FDA approval and it still needs a lot more research. The coevolution of bacteria and bacteriophages, while certainly studied a lot in model organisms, is an important factor to consider when blindly expecting phage therapy to work. The nice thing about phages over antibiotics, is that antibiotics can sometimes have unpleasant side-effects, cause allergic reactions, or have high toxicity to the people/animals taking them. Phage are harmless and extremely specific to their targets, unlike broad-spectrum antibiotics. However phage are huge spreaders of antibiotic resistant genes as they are relatively important engagers in horizontal gene transfer (where genes, instead of being inherited, are picked up and incorporated into a genome via viral infection or collection of raw DNA).

Phage therapy saves man with multidrug-resistant infection

credit:  Dr Graham Beards

In 2015, a four-phage cocktail was administered to target a man with a serious Acinetobacter baumannii infection which had been causing hallucinations and was killing his kidneys. This was the first instance of phages being used intravenously to treat someone almost dead due to an infection caused by a drug-resistant bacteria. Luckily he was married to a genius woman who happened to be an infectious-disease specialist and decided a phage-cocktail was his best bet. It was difficult trying to find the right bacteriophages but it worked in the end.

The Gram-negatives

One of the biggest struggles in finding new antibiotics is Gram-negative bacteria are often intrinsically resistant to antibiotics because their outer membrane is impermeable to large glycopeptide molecules, and so many antibiotics seem to target the cell wall.

Some Gram-negative bacteria that can cause pretty serious infections include Klebsiella (pneumonia, blood, wound), Acinetobacter (pneumonia, blood or wound infections), Pseudomonas aeruginosa (burns, wounds, respiratory), E. coli, Vibrio (Cholera), Yersinia pestis (“the plague”), and Neisseria gonorrhoeae (gonorrhea).

Neisseria gonorrhoeae

Luckily, a lot of these don’t usually infect people (the first three basically never infect healthy people), however antibiotic resistant sexually transmitted diseases are actually on the rise in the United States and could become a very serious and difficult to control problem pretty rapidly. Gonorrhea’s not really a big deal if you catch it early and treat it, but it’s asymptomatic in many people (making them untreated, unknowing carriers) and left ignored, causes infertility and pelvic inflammatory disease.

So even though we might feel relief at these new discoveries, keep in mind that no antibiotic will work on all bacterial pathogens, and allergies to antibiotics are very common so we can’t just be left with a single last-resort. We kind of need a lot of options.


  1. Okano, Akinori, Nicholas A. Isley, and Dale L. Boger. “Peripheral modifications of [Ψ[CH 2 NH]Tpg 4 ]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics.” Proceedings of the National Academy of Sciences (2017)
  2. “A new antibiotic kills pathogens without detectable resistance.” Ling et al (2015)


Coleoids exhibit unusual RNA editing

“It is widely known that the interestingness of an animal is proportional to how difficult it is to figure out where its butthole is. The octopus is therefore, very interesting.” -Zefrank1, True Facts About the Octopus

Coleoids, an evolutionary mystery

Squid, cuttlefish, and octopi are always intriguing to people because they represent the only branch other than vertebrates which have developed sophisticated behavior and intelligence. Them being much more closely related to oysters, and us being more closely related to sea cucumbers is pretty amazing. So seeing as understanding the cephalopod brain is the closest we could get to meeting an intelligent alien, it’s understandable these creatures are so popular even outside of career mollusk experts (the dream job).

The evolutionary journey to ridiculous intelligence might have involved exhibiting an unusual amount of RNA editing—about half their transcribed genes. The type of RNA editing the scientists are talking about is generally Adenosine to Inosine which behaves like a G nucleotide. This can have effects including altering the protein being translated, any secondary RNA structures, splicing, miRNA and siRNA, sequestration (localization), and heterochromatin formation.

RNA editing is a relatively undiscussed phenomenon because in almost every other animal, it doesn’t seem to amount to much that we can observe. Usually RNA editing does not result in codon changes, so observable protein changes. While RNA processing such as splicing and 5’ capping is common in eukaryotes, RNA editing to expand the proteome is not. Cephalopods however, use the edited RNA to make new proteins. So one octopus gene may produce many proteins as opposed to just one.

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Liscovitch-Brauer et al 2017


What makes people think it may be linked to their intelligence is that the RNA editing most often occurred in genes related to nervous system functions. Many of the RNA edits occurred in proteins controlling neural circuits and nerve cell excitability. And, especially cool, the Nautilus (a shelled cephalopod which has a smaller brain, less sophisticated nervous system and is not known for its intelligence), did not exhibit as high rates of RNA editing as the other cephalopods.

Why RNA editing?

It was previously shown that an octopus living in the Antarctic was able to adapt and survive the freezing temperatures via RNA editing to alter their potassium channels. Potassium channels which open and close during neuron firing, basically slow down in the cold so an RNA edit that resulting in a slightly different protein which performed better in the cold, was selected for. If RNA editing is so useful then why don’t more things do it all the time? The conservation of the flanking editing sites indicates a selective advantage, however this sophisticated RNA editing comes at an evolutionary cost of significantly slowing down mutation rate. Because so many sites are nonsynonymously edited the surrounding sequence conservation dramatically reduces the number of mutations and genomic polymorphisms in protein-coding regions. Essentially mutations occurring at an editing site, it can’t be edited anymore and so there’s more pressure to conserve sites.

We could think of it as strange that they evolved advanced RNA-editing, or maybe they just found a nice alternative to waiting around for mutations to fix in a population like we do, when they had those tentacles with minds of their own and those incredibly giant brains to fine-tune.

  1. RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses. Garrett-J. Rosenthal – Science – 2012
  2. Liscovitch-Brauer et al. Trade-off between transcriptome plasticity and genome evolution in cephalopods. Cell, 2017 DOI: 10.1016/j.cell.2017.03.025

by Irene Hoxie

Venezuelan equine encephalitis outbreaks- convergent evolution of a single amino acid substitution

Venezuelan equine encephalitis virus (VEEV) is a nasty virus in horses that causes CNS disorders, resulting in a high biphasic fever, decreased appetite, depression, lethargy, ataxia, stumbling, and in severe cases, nonsupperative meningoencephalitis. So basically, it’s a horse farmer’s nightmare. If it does manage to infect people it just causes some flu-like symptoms and then it’s over, but in horses it can spread through a herd and kill them all.

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Ecology of VEEV

VEEV continuously circulates by having an enzootic and epizootic strain where the enzootic strain passes through rodents and causes no viremia in horses. It is specific to the Culex mosquito and circles continuously in the rodent population relatively unnoticed by anyone.

Screen Shot 2017-06-01 at 5.38.25 PMBut every decade or so, epizootic strains emerge. These are not specific to a particular mosquito and cause viremia in horses, the amplifier for the epizootic strain. Subtypes of VEE and density of mosquito populations, as well as herd immunity determine how fast the disease will spread.

Serotypes IAB and IC are virulent in horses and produce high virus titers (epizootic).

A study that looked at the history of these outbreaks found there has been convergent evolution from the enzootic ID lineage.

Researchers identify key to epizootic VEEV

A study from 2006 (which in science time is forever ago, but which probably didn’t get the attention it deserved with the general public) wanted to identify mutations mediating emergence of epidemic serotype. They suspected that the origin of all epidemic strains involves enzootic strains and that these strains alter their serotype to induce high-titer viremia sufficient to be amplified in equines. Viruses usually have very small genomes which only contain a small number of proteins. Changing an amino acid can dramatically alter the way a protein may fold or interact with a receptor, so viruses that circulate in a reservoir, and then emerge as epidemics, could be the result of a small number of genetic changes.

2006 study

In this study, they performed phylogenetic analysis of alphaviruses in the VEE complex to determine genetic differences between the most recent ID strain before 1992-1993 outbreak, and the epidemic IC strain from the 1992-1993 outbreak. They then used reverse genetic approaches to recreate hypothetic emergence of a 1992-1993 outbreak and measured viremia titer and virulence.

They found that the key amino acid changes allowing for an epizootic outbreak were a glycine to an arginine at position 193 in the E2 envelope protein, and a threonine to an arginine at position 213 of the E2 envelope protein.

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E2 positive charge mutations have accompanied all epidemic emergences, so they tested these two mutations by making a clone of the “enzootic/epizootic border strain” ZPC738 and added either both mutations, or each one separately.

They found the Gly-193à Arg mutation had no effect on mAb reactivity; enzootic-specific Ab still reacted against strain ZPC738. The Thr-213àArg resulted in antigenicity change from enzootic (mAb 1A1B-9-reactive) to epidemic (1A3A-5-reactive). The Combination of both also resulted in IDàIC serotype change. Individual Arg substitutions had little effect on plaque size, but a combination of both resulted in plaques characteristic of epidemic strains

They ZPC738 clone had a low viremia as expected and the Arg-193 viruses did not produce detectable viremia with no disease seen. The Arg-213 virus however, increased virulence and viremia with the neurological disease and viremia titer consistent with epidemic phenotype.

The double mutant (Arg-213 and Arg-193) produced higher viremia 24hrs after infection but lower viremia 36-48hrs post infection.

The takeaway was that epidemic serotype IC VEEV can arise from a single mutation in enzootic serotype ID. Residue 213 responded to positive selection, and Arg substitution induced high-titer equine viremia. The high titer (104 to 106) and high mutation rate (on the order of 10-4 mutants/nucleotide) means RNA viruses likely have a mutation to be more virulent, broaden tropism, broaden host range, etc. at any given time. Which is terrifying to think about.

RNA virus evolution too often ignored in “vaccine wars”

This study shows the barriers for an outbreak are ecological conditions. Enzootic strains circulate continuously, so vaccines should continue to be used even when there’s no outbreak, which unfortunately often doesn’t happen because people don’t see the point in spending money on a vaccine if nobody’s horses are getting sick.

This paper or at least a summary should certainly be shown to more people as it provides direct evidence of just a single amino acid substitution causing an epidemic and is a great argument for continuing to vaccinate, even if a disease is not common anymore (because maybe it’s not common because the vaccine is stopping it from becoming an epidemic in humans). In the vaccine wars amongst humans, RNA virus evolution and ecology as well as RNA zoonosis is weirdly too often left out of the discussion.

Source: Venezuelan encephalitis emergence mediated by a phylogenetically predicted viral mutation. 2006. Michael Anishchenko, Richard A. Bowen, Slobodan Paessler, Laura Austgen, Ivorlyne P. Greene, and Scott C. Weaver