evolution

dna-from-mammoth-remains-reveals-the-history-of-the-last-surviving-population

DNA from mammoth remains reveals the history of the last surviving population

ancient DNA, Biology, evolution, Genetics, Genomics, mammoths, Science, Wrangel Island / /

Sole survivors —

The mammoths of Wrangel Island purged a lot of harmful mutations before dying off.

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A dark, snowy vista with a single mammoth walking past the rib cage of another of its kind.

Enlarge / An artist’s conception of one of the last mammoths of Wrangel Island.

Beth Zaiken

A small group of woolly mammoths became trapped on Wrangel Island around 10,000 years ago when rising sea levels separated the island from mainland Siberia. Small, isolated populations of animals lead to inbreeding and genetic defects, and it has long been thought that the Wrangel Island mammoths ultimately succumbed to this problem about 4,000 years ago.

A paper in Cell on Thursday, however, compared 50,000 years of genomes from mainland and isolated Wrangel Island mammoths and found that this was not the case. What the authors of the paper discovered not only challenges our understanding of this isolated group of mammoths and the evolution of small populations, it also has important implications for conservation efforts today.

A severe bottleneck

It’s the culmination of years of genetic sequencing by members of the international team behind this new paper. They studied 21 mammoth genomes—13 of which were newly sequenced by lead author Marianne Dehasque; others had been sequenced years prior by co-authors Patrícia Pečnerová, Foteini Kanellidou, and Héloïse Muller. The genomes were obtained from Siberian woolly mammoths (Mammuthus primigenius), both from the mainland and the island before and after it became isolated. The oldest genome was from a female Siberian mammoth who died about 52,300 years ago. The youngest were from Wrangel Island male mammoths who perished right around the time the last of these mammoths died out (one of them died just 4,333 years ago).

Wrangel Island, north of Siberia has an extensive tundra.

Enlarge / Wrangel Island, north of Siberia has an extensive tundra.

Love Dalén

It’s a remarkable and revealing time span: The sample included mammoths from a population that started out large and genetically healthy, went through isolation, and eventually went extinct.

Mammoths, the team noted in their paper, experienced a “climatically turbulent period,” particularly during an episode of rapid warming called the Bølling-Allerød interstadial (approximately 14,700 to 12,900 years ago)—a time that others have suggested might have led to local woolly mammoth extinctions. However, the genomes of mammoths studied through this time period don’t indicate that the warming had any adverse effects.

Adverse effects only appeared—and drastically so—once the population was isolated on that island.

The team’s simulations indicate that, at its smallest, the total population of Wrangel Island mammoths was fewer than 10 individuals. This represents a severe population bottleneck. This was seen genetically through increased runs of homozygosity within the genome, caused when both parents contribute nearly identical chromosomes, both derived from a recent ancestor. The runs of homozygosity within isolated Wrangel Island mammoths were four times as great as those before sea levels rose.

Despite that dangerously tiny number of mammoths, they recovered. The population size, as well as inbreeding level and genetic diversity, remained stable for the next 6,000 years until their extinction. Unlike the initial population bottleneck, genomic signatures over time seem to indicate inbreeding eventually shifted to pairings of more distant relatives, suggesting either a larger mammoth population or a change in behavior.

Within 20 generations, their simulations indicate, the population size would have increased to about 200–300 mammoths. This is consistent with the slower decrease in heterozygosity that they found in the genome.

Long-lasting negative effects

The Wrangel Island mammoths may have survived despite the odds, and harmful genetic defects may not have been the reason for their extinction, but the research suggests their story is complicated.

At about 7,608 square kilometers today, a bit larger than the island of Crete, Wrangel Island would have offered a fair amount of space and resources, although these were large animals. For 6,000 years following their isolation, for example, they suffered from inbreeding depression, which refers to increased mortality as a result of inbreeding and its resulting defects.

That inbreeding also boosted the purging of harmful mutations. That may sound like a good thing—and it can be—but it typically occurs because individuals carrying two copies of harmful mutations die or fail to reproduce. So it’s good only if the population survives it.

The team’s results show that purging genetic mutations can be a lengthy evolutionary process. Lead author Marianne Dehasque is a paleogeneticist who completed her PhD at the Centre for Palaeogenetics. She explained to Ars that, “Purging harmful mutations for over 6,000 years basically indicates long-lasting negative effects caused by these extremely harmful mutations. Since purging in the Wrangel Island population went on for such a long time, it indicates that the population was experiencing negative effects from these mutations up until its extinction.”

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when-did-humans-start-social-knowledge-accumulation?

When did humans start social knowledge accumulation?

Biology, evolution, Human behavior, Science, social learning / /
Two worked pieces of stone, one an axe head, and one a scraper.

A key aspect of humans’ evolutionary success is the fact that we don’t have to learn how to do things from scratch. Our societies have developed various ways—from formal education to YouTube videos—to convey what others have learned. This makes learning how to do things far easier than learning by doing, and it gives us more space to experiment; we can learn to build new things or handle tasks more efficiently, then pass information on how to do so on to others.

Some of our closer relatives, like chimps and bonobos, learn from their fellow species-members. They don’t seem to engage in this iterative process of improvement—they don’t, in technical terms, have a cumulative culture where new technologies are built on past knowledge. So, when did humans develop this ability?

Based on a new analysis of stone toolmaking, two researchers are arguing that the ability is relatively recent, dating to just 600,000 years ago. That’s roughly the same time our ancestors and the Neanderthals went their separate ways.

Accumulating culture

It’s pretty obvious that a lot of our technology builds on past efforts. If you’re reading this on a mobile platform, then you’re benefitting from the fact that smartphones were derived from personal computers and that software required working hardware to happen. But for millions of years, human technology lacked the sort of clear building blocks that would help us identify when an archeological artifact is derived from earlier work. So, how do you go about studying the origin of cumulative culture?

Jonathan Paige and Charles Perreault, the researchers behind the new study, took a pretty straightforward approach. To start with, they focused on stone tools since these are the only things that are well-preserved across our species’ history. In many cases, the styles of tools remained constant for hundreds of thousands of years. This gives us enough examples that we’ve been able to figure out how these tools were manufactured, in many cases learning to make them ourselves.

Their argument in the paper they’ve just published is that the sophistication of these tools provides a measure of when cultural accumulation started. “As new knapping techniques are discovered, the frontiers of the possible design space expand,” they argue. “These more complex technologies are also more difficult to discover, master, and teach.”

The question then becomes one of when humans made the key shift: from simply teaching the next generation to make the same sort of tools to using that knowledge as a foundation to build something new. Paige and Perreault argue that it’s a matter of how complex it is to make the tool: “Generations of improvements, modifications, and lucky errors can generate technologies and know-how well beyond what a single naive individual could invent independently within their lifetime.”

When did humans start social knowledge accumulation? Read More »

to-kill-the-competition,-bacteria-throw-pieces-of-dead-viruses-at-them

To kill the competition, bacteria throw pieces of dead viruses at them

bacteria, Biology, evolution, phages, Science / /

Murderous —

A network of mutual murder ensures that diverse populations of bacteria survive.

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A green, lawn like background with an orange item consisting of legs, a narrow shaft, and a polygonal head.

Enlarge / This is an intact phage. A tailocin looks like one of these with its head cut off.

Long before humans became interested in killing bacteria, viruses were on the job. Viruses that attack bacteria, termed “phages” (short for bacteriophage), were first identified by their ability to create bare patches on the surface of culture plates that were otherwise covered by a lawn of bacteria. After playing critical roles in the early development of molecular biology, a number of phages have been developed as potential therapies to be used when antibiotic resistance limits the effectiveness of traditional medicines.

But we’re relative latecomers in terms of turning phages into tools. Researchers have described a number of cases where bacteria have maintained pieces of disabled viruses in their genomes and converted them into weapons that can be used to kill other bacteria that might otherwise compete for resources. I only just became aware of that weaponization, thanks to a new study showing that this process has helped maintain diverse bacterial populations for centuries.

Evolving a killer

The new work started when researchers were studying the population of bacteria associated with a plant growing wild in Germany. The population included diverse members of the genus Pseudomonas, which can include plant pathogens. Normally, when bacteria infect a new victim, a single strain expands dramatically as it successfully exploits its host. In this case, though, the Pseudomonas population contained a variety of different strains that appeared to maintain a stable competition.

To learn more, the researchers obtained over 1,500 individual genomes from the bacterial population. Over 99 percent of those genomes contained pieces of virus, with the average bacterial strain having two separate chunks of virus lurking in their genomes. All of these had missing parts compared to a functional virus, suggesting they were the product of a virus that had inserted in the past but had since picked up damage that disabled them.

On its own, that’s not shocking. Lots of genomes (including our own) have plenty of disabled viruses in them. But bacteria tend to eliminate extraneous DNA from their genomes fairly quickly. In this case, one particular viral sequence appeared to date back to the common ancestor of many of the strains since all of them had the virus inserted at the same location of the genome, and all instances of this particular virus had been disabled by losing the same set of genes. The researchers termed this sequence VC2.

Many phages have a stereotypical structure: a large “head” that contains their genetic material, perched on top of a stalk that ends in a set of “legs” that help latch on to their bacterial victims. Once the legs make contact, a stalk contracts, an action that helps transfer the virus’ genome into the bacterial cell. In VC2’s case, all copies of it lacked the genes for producing the head section, as well as all the genes needed for processing its genome during infection.

This made the researchers suspect VC2 was something called a “tailocin.” These are former phages that have been domesticated by bacteria so they can be used to harm the bacteria’s potential competition. Bacteria with a tailocin can produce partial phages that consist only of the legs and stalk. These tailocins can still find and latch on to other bacteria, but when the stalk contracts, there’s no genome to inject. Instead, this just opens a hole in the membrane of their victim, partially eliminating the boundary of the cell and allowing some of its contents to leak out, leading to its death.

An evolutionary free-for-all

To confirm that the VC2 sequence encodes a tailocin, the researchers grew some bacteria that contained the sequence, purified proteins from it, and used electron microscopy to confirm that they contained headless phages. Exposing other bacteria to the tailocin, they found that while the strain that produced it was immune, many other strains growing in the same environment were killed by it. When the team deleted the genes that encode key parts of the tailocin, the killing went away.

The researchers hypothesize that the system is used to kill off potential competition but that many strains have evolved resistance to the tailocin.

When the researchers did a genetic screen to identify resistant mutants, they found that resistance was provided by mutations that interfered with the production of complex sugar molecules that are found on proteins that end up on the exterior of cells. At the same time, most of the genetic differences among the VC2 genes occur in the proteins that encode the legs, which latch on to these sugars.

So it appears that every bacterial strain is both an aggressor and a victim, and there’s an evolutionary arms race that leads to a complex collection of pairwise interactions among the strains—think of a rock/paper/scissors game with dozens of options. And the arms race has a history. Using old samples, the researchers show that many of the variations in these genes have been around for at least 200 years.

Evolutionary competitions are often viewed as a simple one-against-one fight, probably because it’s an easy way to think about them. But the reality is that most are more akin to a chaotic bar room brawl—one where it’s rare for any faction to obtain a permanent advantage.

Science, 2024. DOI: 10.1126/science.ado0713  (About DOIs).

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Bizarre egg-laying mammals once ruled Australia—then lost their teeth

Biology, echidna, evolution, fossils, monotremes, paleontology, Platypus, Science / /

Eggs came first, no chickens involved —

Finds may indicate what the common ancestor of the platypus and echidna looked like.

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A small animal with spiky fur and a long snout strides over grey soil.

Enlarge / The echidna, an egg-laying mammal, doesn’t develop teeth.

Outliers among mammals, monotremes lay eggs instead of giving birth to live young. Only two types of monotremes, the platypus and echidna, still exist, but more monotreme species were around about 100 million years ago. Some of them might possibly be even weirder than their descendants.

Monotreme fossils found in refuse from the opal mines of Lightning Ridge, Australia, have now revealed the opalized jawbones of three previously unknown species that lived during the Cenomanian age of the early Cretaceous. Unlike modern monotremes, these species had teeth. They also include a creature that appears to have been a mashup of a platypus and echidna—an “echidnapus.”

Fossil fragments of three known species from the same era were also found, meaning that at least six monotreme species coexisted in what is now Lightning Ridge. According to the researchers who unearthed these new species, the creatures may have once been as common in Australia as marsupials are today.

“[This is] the most diverse monotreme assemblage on record,” they said in a study recently published in Alcheringa: An Australasian Journal of Paleontology.

The Echidnapus emerges

Named Opalios spendens, the “echidnapus” shows similarities to both ornithorhynchoids (the platypus and similar species) and tachyglossids (echidna and similar species). It is thought to have evolved before the common ancestor of either extant monotreme.

The O. splendens holotype had been fossilized in opal like the other Lightning Ridge specimens, but unlike some, it is preserved so well that the internal structure of its bones is visible. Every mammalian fossil from Lightning Ridge has been identified as a monotreme based partly on their peculiarly large dental canals. While the fossil evidence suggests the jaw and snout of O. splendens are narrow and curved, similar to those of an echidna, it simultaneously displays platypus features.

So what relates the echidnapus to a platypus? Despite its jaw being echidna-like at first glance, its dentary, or the part of the jaw that bears the teeth, is similar in size to that of the platypus ancestor Ornithorhynchus anatinus. Other features related more closely to the platypus than the echidna have to do with its ramus, or the part of the jaw that attaches to the skull. It has a short ascending ramus (the rear end) and twisted horizontal ramus (the front end) that are seen in other ornithorhynchoids.

Another platypus-like feature of O. splendens is the flatness of the front of its lower jaw, which is consistent with the flatness of the platypus snout. The size of its jaw also suggests a body size closer to that of a platypus. Though the echidnapus had characteristics of both surviving monotremes, neither of those have the teeth found on this fossil.

My, what teeth you don’t have

Cretaceous monotremes might not have had as many teeth as the echidnapus, but they all had some teeth. The other two new monotreme species that lived among the Lightning Ridge fauna were Dharragarra aurora and Parvopalus clytiei, and the jaw structure of each of these species is either closer to the platypus or the echidna. D. aurora has the slightly twisted jaw and enlarged canal in its mandible that are characteristic of an ornithorhynchoid. It might even be on the branch that gave rise the platypus.

P. clytiei is the second smallest known monotreme (after another extinct species named Teinolophos trusleri). It was more of an echidna type, with a snout that was curved and deep like that of a tachyglossid rather than flat like that of an ornithorhynchoid. It also had teeth, though fewer than the echidnapus. Why did those teeth end up disappearing altogether in modern monotremes?

Monotremes without teeth came onto the scene when the platypus (Ornithorhynchus anatinus) appeared during the Pleistocene, which began 2.6 million years ago. The researchers think competition for food caused the disappearance of teeth in the platypus—the spread of the Australo-New Guinean water rat may have affected which prey platypuses hunted for. Water rats eat mostly fish and shellfish along with some insects, which are also thought to have been part of the diet of ancient ornithorhynchoids. Turning to softer food to avoid competition may explain why the platypus evolved to be toothless.

As for echidnas, tachyglossids are thought to have lost their teeth after they diverged from ornithorhynchoids near the end of the Cretaceous. Echidnas are insectivores, grinding the hard shells of beetles and ants with spines inside their mouths, so have no need for teeth.

Although there is some idea of what happened to their teeth, the fate of the diverse species of Cretaceous monotremes, which were not only toothy but mostly larger than the modern platypus and echidna, remains unknown. The end of the Cretaceous brought a mass extinction triggered by the Chicxulub asteroid. Clearly, some monotremes survived it, but no monotreme fossils from the time have surfaced yet.

“It is unclear whether diverse monotreme fauna survived the end-Cretaceous mass extinction event, and subsequently persisted,” the researchers said in the same study. “Filling this mysterious interval of monotreme diversity and adaptive development should be a primary focus for research in the future.”

Alcheringa: An Australasian Journal of Palaeontology, 2024. DOI: 10.1080/03115518.2024.2348753

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dinosaurs-needed-to-be-cold-enough-that-being-warm-blooded-mattered

Dinosaurs needed to be cold enough that being warm-blooded mattered

Biology, climate change, dinosaurs, evolution, paleontology, Science, warm blooded / /

Some like it less hot —

Two groups of dinosaurs moved to cooler climes during a period of climate change.

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Image of a feathered dinosaur against a white background.

Enlarge / Later theropods had multiple adaptations to varied temperatures.

Dinosaurs were once assumed to have been ectothermic, or cold-blooded, an idea that makes sense given that they were reptiles. While scientists had previously discovered evidence of dinosaur species that were warm-blooded, though what could have triggered this adaptation remained unknown. A team of researchers now think that dinosaurs that already had some cold tolerance evolved endothermy, or warm-bloodedness, to adapt when they migrated to regions with cooler temperatures. They also think they’ve found a possible reason for the trek.

Using the Mesozoic fossil record, evolutionary trees, climate models, and geography, plus factoring in a drastic climate change event that caused global warming, the team found that theropods (predators and bird ancestors such as velociraptor and T. rex) and ornithischians (such as triceratops and stegosaurus) must have made their way to colder regions during the Early Jurassic. Lower temperatures are thought to have selected for species that were partly adapted to endothermy.

“The early invasion of cool niches… [suggests] an early attainment of homeothermic (possibly endothermic) physiology in [certain species], enabling them to colonize and persist in even extreme latitudes since the Early Jurassic,” the researchers said in a study recently published in Current Biology.

Hot real estate

During the Mesozoic Era, which lasted from 230 to 66 million years ago, proto-dinosaurs known as dinosauromorphs began to diversify in hot and dry climates. Early sauropods, ornithischians, and theropods all tended to stay in these regions.

Sauropods (such as brontosaurus and diplodocus) would become the only dinosaur groups to bask in the heat—the fossil record shows that sauropods tended to stay in warmer areas, even if there was less food. This suggests the need for sunlight and heat associated with ectothermy. They might have been capable of surviving in colder temperatures but not adapted enough to make it for long, according to one hypothesis.

It’s also possible that living in cooler areas meant too much competition with other types of dinosaurs, as the theropods and ornithiscians did end up moving into these cooler areas.

Almost apocalypse

Beyond the ecological opportunities that may have drawn dinosaurs to the cooler territories, it’s possible they were driven away from the warm ones. Around 183 million years ago, there was a perturbation in the carbon cycle, along with extreme volcanism that belched out massive amounts of methane, sulfur dioxide, and mercury. Life on Earth suffered through scorching heat, acid rain, and wildfires. Known as the Early Jurassic Jenkyns Event, the researchers now think that these disruptions pushed theropod and ornithischian dinosaurs to cooler climates because temperatures in warmer zones went above the optimal temperatures for their survival.

The theropods and ornithischians that escaped the effects of the Jenkyns event may have had a key adaptation to cooler climes; many dinosaurs from these groups are now thought to have been feathered. Feathers can be used to both trap and release heat, which would have allowed feathered dinosaurs to regulate their body temperature in more diverse climates. Modern birds use their feathers the same way.

Dinosaur species with feathers or special structures that improved heat management could have been homeothermic, which means they would have been able to maintain their body temperature with metabolic activity or even endothermic.

Beyond the dinosaurs that migrated to high latitudes and adapted to a drop in temperature, endothermy might have led to the rise of new species and lineages of dinosaurs. It could have contributed to the rise of Avialae, the clade that includes birds—the only actual dinosaurs still around—and traces all the way back to their earliest ancestors.

“[Our findings] provide novel insights into the origin of avian endothermy, suggesting that this evolutionary trajectory within theropods… likely started in the latest Early Jurassic,” the researchers said in the same study.

That really is something to think about next time a sparrow flies by.

Current Biology, 2024.  DOI: 10.1016/j.cub.2024.04.051

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researchers-make-a-plastic-that-includes-bacteria-that-can-digest-it

Researchers make a plastic that includes bacteria that can digest it

bacteria, Biology, chemistry, evolution, materials science, plastics, Science / /

It’s alive! —

Bacterial spores strengthen the plastic, then revive to digest it in landfills.

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Image of two containers of dirt, one with a degraded piece of plastic in it.

Han Sol Kim

One reason plastic waste persists in the environment is because there’s not much that can eat it. The chemical structure of most polymers is stable and different enough from existing food sources that bacteria didn’t have enzymes that could digest them. Evolution has started to change that situation, though, and a number of strains have been identified that can digest some common plastics.

An international team of researchers has decided to take advantage of those strains and bundle plastic-eating bacteria into the plastic. To keep them from eating it while it’s in use, the bacteria is mixed in as inactive spores that should (mostly—more on this below) only start digesting the plastic once it’s released into the environment. To get this to work, the researchers had to evolve a bacterial strain that could tolerate the manufacturing process. It turns out that the evolved bacteria made the plastic even stronger.

Bacteria meet plastics

Plastics are formed of polymers, long chains of identical molecules linked together by chemical bonds. While they can be broken down chemically, the process is often energy-intensive and doesn’t leave useful chemicals behind. One alternative is to get bacteria to do it for us. If they’ve got an enzyme that breaks the chemical bonds of a polymer, they can often use the resulting small molecules as an energy source.

The problem has been that the chemical linkages in the polymers are often distinct from the chemicals that living things have come across in the past, so enzymes that break down polymers have been rare. But, with dozens of years of exposure to plastics, that’s starting to change, and a number of plastic-eating bacterial strains have been discovered recently.

This breakdown process still requires that the bacteria and plastics find each other in the environment, though. So a team of researchers decided to put the bacteria in the plastic itself.

The plastic they worked with is called thermoplastic polyurethane (TPU), something you can find everywhere from bicycle inner tubes to the coating on your ethernet cables. Conveniently, there are already bacteria that have been identified that can break down TPU, including a species called Bacillus subtilis, a harmless soil bacterium that has also colonized our digestive tracts. B. subtilis also has a feature that makes it very useful for this work: It forms spores.

This feature handles one of the biggest problems with incorporating bacteria into materials: The materials often don’t provide an environment where living things can thrive. Spores, on the other hand, are used by bacteria to wait out otherwise intolerable conditions, and then return to normal growth when things improve. The idea behind the new work is that B. subtilis spores remain in suspended animation while the TPU is in use and then re-activate and digest it once it’s disposed of.

In practical terms, this works because spores only reactivate once nutritional conditions are sufficiently promising. An Ethernet cable or the inside of a bike tire is unlikely to see conditions that will wake the bacteria. But if that same TPU ends up in a landfill or even the side of the road, nutrients in the soil could trigger the spores to get to work digesting it.

The researchers’ initial problem was that the manufacturing of TPU products usually involves extruding the plastic at high temperatures, which are normally used to kill bacteria. In this case, they found that a typical manufacturing temperature (130° C) killed over 90 percent of the B. subtilis spores in just one minute.

So, they started out by exposing B. subtilis spores to lower temperatures and short periods of heat that were enough to kill most of the bacteria. The survivors were grown up, made to sporulate, and then exposed to a slightly longer period of heat or even higher temperatures. Over time, B. subtilis evolved the ability to tolerate a half hour of temperatures that would kill most of the original strain. The resulting strain was then incorporated into TPU, which was then formed into plastics through a normal extrusion process.

You might expect that putting a bunch of biological material into a plastic would weaken it. But the opposite turned out to be true, as various measures of its tensile strength showed that the spore-containing plastic was stronger than pure plastic. It turns out that the spores have a water-repelling surface that interacts strongly with the polymer strands in the plastic. The heat-resistant strain of bacteria repelled water even more strongly, and plastics made with these spores was tougher still.

To simulate landfilling or litter with the plastic, the researchers placed them in compost. Even without any bacteria, there were organisms present that could degrade it; by five months in the compost, plain TPU lost nearly half its mass. But with B. subtilis spores incorporated, the plastic lost 93 percent of its mass over the same time period.

This doesn’t mean our plastics problem is solved. Obviously, TPU breaks down relatively easily. There are lots of plastics that don’t break down significantly, and may not be compatible with incorporating bacterial spores. In addition, it’s possible that some TPU uses would expose the plastic to environments that would activate the spores—something like food handling or buried cabling. Still, it’s possible this new breakdown process can provide a solution in some cases, making it worth exploring further.

Nature Communications, 2024. DOI: 10.1038/s41467-024-47132-8  (About DOIs).

Listing image by Han Sol Kim

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researchers-find-a-new-organelle-evolving

Researchers find a new organelle evolving

biochemistry, Biology, endosymbiosis, evolution, nitrogen, organelle, Science / /
Image of a single celled algae.

Enlarge / A photo of Braarudosphaera bigelowii with the nitroplast indicated by an arrowhead.

The complex cells that underlie animals and plants have a large collection of what are called organelles—compartments surrounded by membranes that perform specialized functions. Two of these were formed through a process called endosymbiosis, in which a once free-living organism is incorporated into a cell. These are the mitochondrion, where a former bacteria now handles the task of converting chemical energy into useful forms, and the chloroplast, where photosynthesis happens.

The fact that there are only a few cases of organelles that evolved through endosymbiosis suggests that it’s an extremely rare event. Yet researchers may have found a new case, in which an organelle devoted to fixing nitrogen from the atmosphere is in the process of evolving. The resulting organelle, termed a nitroplast, is still in the process of specialization.

Getting nitrogen

Nitrogen is one of the elements central to life. Every DNA base, every amino acid in a protein contains at least one, and often several, nitrogen atoms. But nitrogen is remarkably difficult for life to get ahold of. N2 molecules might be extremely abundant in our atmosphere, but they’re extremely difficult to break apart. The enzymes that can, called nitrogenases, are only found in bacteria, and they don’t work in the presence of oxygen. Other organisms have to get nitrogen from their environment, which is one of the reasons we use so much energy to supply nitrogen fertilizers to many crops.

Some plants (notably legumes), however, can obtain nitrogen via a symbiotic relationship with bacteria. These plants form specialized nodules that provide a habitat for the nitrogen-producing bacteria. This relationship is a form of endosymbiosis, where microbes take up residence inside an organism’s body or cells, with each organism typically providing chemicals that the other needs.

In more extreme cases, endosymbiosis can become obligatory. with neither organism able to survive without the other. In many insects, endosymbionts are passed on to offspring during the production of eggs, and the microbes themselves often lack key genes that would allow them to live independently.

But even states like this fall short of the situation found in mitochondria and chloroplasts. These organelles are thoroughly integrated into the cell, being duplicated and distributed when cells divide. They also have minimal genomes, with most of their proteins made by the cell and imported into the organelles. This level of integration is the product of over a billion years of evolution since the endosymbiotic relationship first started.

It’s also apparently a difficult process, based on its apparent rarity. Beyond mitochondria and chloroplasts, there’s only one confirmed example of a more recent endosymbiosis between eukaryotes and a bacterial species. (There are a number of cases where eukaryotic algae have been incorporated by other eukaryotes. Because these cells have compatible genetics, this occurs with a higher frequency.)

That’s why finding another example is such an exciting prospect.

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DNA parasite now plays key role in making critical nerve cell protein

Biology, evolution, Genetics, Genomics, myelin, neurobiology, Science, transposons / /

Domesticated viruses —

An RNA has been adopted to help the production of myelin, a key nerve protein.

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Graphic depiction of a nerve cell with a myelin coated axon.

Human brains (and the brains of other vertebrates) are able to process information faster because of myelin, a fatty substance that forms a protective sheath over the axons of our nerve cells and speeds up their impulses. How did our neurons evolve myelin sheaths? Part of the answer—which was unknown until now—almost sounds like science fiction.

Led by scientists from Altos Labs-Cambridge Institute of Science, a team of researchers has uncovered a bit of the gnarly past of how myelin ended up covering vertebrate neurons: a molecular parasite has been messing with our genes. Sequences derived from an ancient virus help regulate a gene that encodes a component of myelin, helping explain why vertebrates have an edge when it comes to their brains.

Prehistoric infection

Myelin is a fatty material produced by oligodendrocyte cells in the central nervous system and Schwann cells in the peripheral nervous system. Its insulating properties allow neurons to zap impulses to one another at faster speeds and greater lengths. Our brains can be complex in part because myelin enables longer, narrower axons, which means more nerves can be stacked together.

The un-myelinated brain cells of many invertebrates often need to rely on wider—and therefore fewer—axons for impulse conduction. Rapid impulse conduction makes quicker reactions possible, whether that means fleeing danger or capturing prey.

So, how do we make myelin? A key player in its production appears to be a type of molecular parasite called a retrotransposon.

Like other transposons, retrotransposons can move to new locations in the genome through an RNA intermediate. However, most retrotransposons in our genome have picked up too many mutations to move about anymore.

RNLTR12-int is a retrotransposon that is thought to have originally entered our ancestors’ genome as a virus. Rat genomes now have over 100 copies of the retrotransposon.

An RNA made by RNLTR12-int helps produce myelin by binding to a transcription factor or a protein that regulates the activity of other genes. The RNA/protein combination binds to DNA near the gene for myelin basic protein, or MBP, a major component of myelin.

“MBP is essential for the membrane growth and compression of [central nervous system] myelin,” the researchers said in a study recently published in Cell.

Technical knockout

To find out whether RNLTR12-int really was behind the regulation of MBP and, therefore, myelin production, the research team had to knock its level down and see if myelination still happened. They first experimented on rat brains before moving on to zebrafish and frogs.

When they inhibited RNLTR12-int, the results were drastic. In the central nervous system, genetically edited rats produced 98 percent less MBP than those where the gene was left unedited. The absence of RNLTR12-int also caused the oligodendrocytes that produce myelin to develop much simpler structures than they would normally form. When RNLTR12-int was knocked out in the peripheral nervous system, it reduced myelin produced by Schwann cells.

The researchers used a SOX10 antibody to show that SOX10 bound to the RNLTR12-int transcript in vivo. This was an important result, since there are lots of non-coding RNAs made by cells, and it wasn’t clear whether any RNA would work or if it was specific to RNLTR12-int.

Do these results hold up in other jawed vertebrates? Using CRISPR-CAS9 to perform knockout tests with retrotransposons related to RNLTR12-int in frogs and zebrafish showed similar results.

Myelination has enriched the vertebrate brain so it can work like never before. This is why the term “brain food” is literal. Healthy fats are so important for our brains; they help form myelin since it is a fatty acid. Think about that next time you’re pulling an all-nighter while reaching for a handful of nuts.

Cell, 2024. DOI: 10.1016/j.cell.2024.01.011

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Robo-dinosaur scares grasshoppers to shed light on why dinos evolved feathers

dinosaurs, evolution, paleobiology, paleontology, robotics, Science / /

What’s the point of half a wing? —

The feathers may have helped dinosaurs frighten and flush out prey.

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Grasshoppers, beware! Robopteryx is here to flush you from your hiding place.

Enlarge / Grasshoppers, beware! Robopteryx is here to flush you from your hiding place.

Jinseok Park, Piotr Jablonski et al., 2024

Scientists in South Korea built a robotic dinosaur and used it to startle grasshoppers to learn more about why dinosaurs evolved feathers, according to a recent paper published in the journal Scientific Reports. The results suggest that certain dinosaurs may have employed a hunting strategy in which they flapped their proto-wings to flush out prey, and this behavior may have led to the evolution of larger and stiffer feathers.

As reported previously, feathers are the defining feature of birds, but that wasn’t always the case. For millions of years, various species of dinosaurs sported feathers, some of which have left behind fossilized impressions. For the most part, the feathers we’ve found have been attached to smaller dinosaurs, many of them along the lineage that gave rise to birds—although in 2012, scientists discovered three nearly complete skeletons of a “gigantic” feathered dinosaur species, Yutyrannus huali, related to the ancestors of Tyrannosaurus Rex.

Various types of dino-feathers have been found in the fossil record over the last 30 years, such as so-called pennaceous feathers (present in most modern birds). These were found on distal forelimbs of certain species like Caudipteryx, serving as proto-wings that were too small to use for flight, as well as around the tip of the tail as plumage. Paleontologists remain unsure of the function of pennaceous feathers—what use could there be for half a wing? A broad range of hypotheses have been proposed: foraging or hunting, pouncing or immobilizing prey, brooding, gliding, or wing-assisted incline running, among others.

Caudipteryx zoui skeleton at the Löwentor Museum in Stuttgart, Germany.” height=”475″ src=”https://cdn.arstechnica.net/wp-content/uploads/2024/02/dino2-640×475.jpg” width=”640″>

Enlarge / Mounted Caudipteryx zoui skeleton at the Löwentor Museum in Stuttgart, Germany.

Co-author Jinseok Park of Seoul National University in South Korea and colleagues thought the pennaceous feathers might have been used to flush out potential prey from hiding places so they could be more easily caught. It’s a strategy employed by certain modern bird species, like roadrunners, and typically involves a visual display of the plumage on wings and tails.

There is evidence that this flush-pursuit hunting strategy evolved multiple times. According to Park et al., it’s based on the “rare enemy effect,” i.e., certain prey (like insects) wouldn’t be capable of responding to different predators in different ways and would not respond effectively to an unusual flush-pursuit strategy. Rather than escaping a predator, the insects fly toward their own demise. “The use of plumage to flush prey could have increased the frequency of chase after escaping prey, thus amplifying the importance of plumage in drag-based or lift-based maneuvering for a successful pursuit,” the authors wrote.  “This, in turn, could have led to the larger and stiffer feathers for faster movements and more visual flush displays.”

To test their hypothesis, Park et al. constructed a robot dinosaur they dubbed “Robopteryx,” using Caudipteryx as a model. They built the robot’s body out of aluminum, with the proto-wings and tail plumage made from black paper and plastic ribbing. The head was made of black polystyrene, the wing folds were made of black elastic stocking, and the whole contraption was covered in felt. They scanned the scientific literature on Caudipteryx to determine resting posture angles and motion ranges. The motion of the forelimbs and tail was controlled by a mechanism controlled by custom software running on a mobile phone.

Robopteryx faces off against a grasshopper and prepares to flap its wings.

Enlarge / Robopteryx faces off against a grasshopper and prepares to flap its wings.

Jinseok Park, Piotr Jablonski et al., 2024

Park et al. then conducted experiments with the robot performing motions consistent with a flush display using the band-winged grasshopper (a likely prey), which has relatively simple neural circuits. They placed a wooden stick with scale marks next to the grasshopper and photographed it to record its body orientation relative to the robot, and then made the robot’s forelimbs and tail flap to mimic a flush display. If the grasshopper escaped, they ended the individual test; if the grasshopper didn’t respond, they slowly moved the robot closer and closer using a long beam. The team also attached electrodes to grasshoppers in the lab to measure neural spikes as the insects were shown projected Cauderyx animations of a flush display on a flat-screen monitor.

The results: around half the grasshoppers fled in response to Robopteryx without feathers, compared to over 90 percent when feathered wings flapped. They also measured stronger neural signals when feathers were present. For Park et al., this is solid evidence in support of their hypothesis that a flush-pursuit hunting strategy may have been a factor in the evolution of pennaceous feathers. “Our results emphasize the significance of considering sensory aspects of predator-prey interactions in the studies of major evolutionary innovations among predatory species,” the authors wrote.

Not everyone is convinced by these results. “It seems to me to be very unlikely that a structure as complex as a pennaceous feather would evolve for such a specific behavioral role,” Steven Salisbury of the University of Queensland in Australia, who was not involved with the research, told New Scientist. “I am sure there are lots of ways to scare grasshoppers other than to flap some feathers at it. You can have feathers to scare grasshoppers and you can have them to insulate and incubate eggs. They’re good for display, the stabilization of body position when running, and, of course, for gliding and powered flight. Feathers help for all sorts of things.”

Scientific Reports, 2024. DOI: 10.1038/s41598-023-50225-x  (About DOIs).

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New E. coli strain will accelerate evolution of the genes of your choice

biochemistry, Biology, E. coli, evolution, mutation rate, mutations, Science / /

Making mutants —

Strain eliminates the trade-offs of a high mutation rate.

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Woman holding a plate of bacteria with clusters of bacteria on it.

Genetic mutations are essential for innovation and evolution, yet too many—or the wrong ones—can be fatal. So researchers at Cambridge established a synthetic “orthogonal” DNA replication system in E. coli that they can use as a risk-free way to generate and study such mutations. It is orthogonal because it is completely separate from the system that E. coli uses to copy its actual genome, which contains the genes E. coli needs to survive.

The genes in the orthogonal system are copied with an extraordinarily error-prone DNA replication enzyme, which spurs rapid evolution by generating many random mutations. This goes on while E. coli’s genes are replicated by its normal high-fidelity DNA copying enzyme. The two enzymes work alongside each other, each doing their own thing but not interfering with the other’s genes.

Engineering rapid mutation

Such a cool idea, right? The scientists stole it from nature. Yeast already has a system like this, with a set of genes copied by a dedicated enzyme that doesn’t replicate the rest of the genome. But E. coli is much easier to work with than yeast, and its population can double in 20 minutes, so you can get a lot of rounds of replication and evolution done fast.

The researchers generated the system by pillaging a phage—a virus that infects E. coli. They took out all of the phage genes that allow the phage to grow uncontrollably until it bursts the E. coli cell it infected open. The engineering left only a cassette containing the genes responsible for copying the phage genome. Once this cassette was inserted into the E. coli genome, it could simultaneously replicate at least three different strings of genes placed next to it in the DNA, maintaining them for over a hundred generations—all while leaving the rest of the E. coli genome to be copied by other enzymes.

The scientists then tweaked the mutation rate of the orthogonal DNA-replicating enzyme, eventually enhancing it 1,000-fold. To test if the system could be used to evolve new functions, they inserted a gene for resistance to one antibiotic and saw how long it took for that gene to mutate into one conferring resistance to a different antibiotic. Within twelve days, they got 150 times more resistance to the new antibiotic. They also inserted the gene encoding green fluorescent protein and increased its fluorescence over 1,000-fold in five days.

Evolving detoxification

Not 20 pages later, in the same issue of Science, Frances Arnold’s lab has a paper that provides evidence of how powerful this approach could be. This team directed the evolution of an enzyme the old-fashioned way: through sequential rounds of random mutagenesis and selection for the desired trait. Arnold won The Nobel Prize in Chemistry 2018 for the directed evolution of enzymes, so she knows what she’s about. In this recent work, her lab generated an enzyme that can biodegrade volatile methyl siloxanes. We make megatons of these compounds every year to stick in cleaning products, shampoos and lotions, and industrial products, but they linger in the environment. They contain carbon-silicon bonds, which were never a thing until humans made them about 80 years ago; since nature never made these bonds, there is no natural way to break them, either.

“Directed evolution with siloxane was particularly challenging,” the authors note in their introduction, for various technical reasons. “We started from an enzyme we had previously engineered for other chemistry on siloxanes—that enzyme, unlike the natural enzyme, showed a tiny bit of activity for siloxane Si-C bond cleavage. The overall project, however, from initial discovery to figuring out how to measure what we wanted, took several years,” Arnold said. And it is only the first step in possibly rendering siloxanes biodegradable. The accelerated continuous evolution that the new orthologous system allows will hopefully greatly facilitate the development of enzymes and other proteins like this that will have applications in research, medicine, and industry.

We do not (yet) have machines that can efficiently assemble long stretches of DNA or make proteins. But cells do these things extremely efficiently, and E. coli cells have long been the ones used in the lab as little factories, churning out whatever genes or proteins researchers program into them. Now E. coli can be used for one more molecular task—they can be little hotbeds of evolution.

Science, 2024.  DOI: 10.1126/science.adi5554, 10.1126/science.adk1281

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our-oldest-microbial-ancestors-were-way-ahead-of-their-time

Our oldest microbial ancestors were way ahead of their time

Biology, eukaryotes, evolution, paleontology, Science / /

Going Golgi —

Specialized internal structures were present over 1.5 billion years ago.

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computer generated image of membrane structures inside a cell

Enlarge / The Golgi apparatus, shown here in light green, may have been involved in building internal structures in cells.

ARTUR PLAWGO / SCIENCE PHOTO LIBRARY

Before Neanderthals and Denisovans, before vaguely humanoid primates, proto-mammals, or fish that crawled out of the ocean to become the first terrestrial animals, our earliest ancestors were microbes.

More complex organisms like ourselves descend from eukaryotes, which have a nuclear membrane around their DNA (as opposed to prokaryotes, which don’t). Eukaryotes were thought to have evolved a few billion years ago, during the late Palaeoproterozoic period, and started diversifying by around 800 million years ago. Their diversification was not well understood. Now, a team of researchers led by UC Santa Barbara paleontologist Leigh Ann Riedman discovered eukaryote microfossils that are 1.64 billion years old, yet had already diversified and had surprisingly sophisticated features.

“High levels of eukaryotic species richness and morphological disparity suggest that although late Palaeoproterozoic [fossils] preserve our oldest record of eukaryotes, the eukaryotic clade has a much deeper history,” Riedman and her team said in a study recently published in Papers in Paleontology.

Really, really, really old tricks

During the late Palaeoproterozoic, eukaryotes most likely evolved in the wake of several major changes on Earth, including a drastic increase in atmospheric oxygen and shifts in ocean chemistry. This could have been anywhere from 3 billion to 2.3 billion years ago. Riedman’s team explored the layers of sedimentary rock in the Limbunya region of Australia’s Birrindudu basin. The fossils they unearthed included a total of 26 taxa, as well as 10 species that had not been described before. One of them is Limbunyasphaera operculata, a species of the new genus Limbunyasphera.

What makes L. operculata so distinct is that it has a feature that appears to be evidence of a survival mechanism used by modern eukaryotes. There are some extant microbes that form a protective cyst so they can make it through harsh conditions. When things are more tolerable, they produce an enzyme that dissolves a part of the cyst wall into an opening, or pylome, that makes it possible for them to creep out. This opening also has a lid, or operculum. These were both observed in L. operculata.

While splits in fossilized single-cell organisms may be the result of taphonomic processes that break the cell wall, complex structures such as a pylome and operculum are not found in prokaryotic organisms, and therefore suggest that a species must be eukaryotic.

Didn’t know they could do that

Some of the previously known species of extinct eukaryotes also surprised the scientists with unexpectedly advanced features. Satka favosa had a vesicle in the cell that was enclosed by a membrane with platelike structures. Another species, Birrindudutuba brigandinia, also had plates identified around its vesicles, although none of its plates were as diverse in shape as those seen in different S. favosa individuals. Those plates came in a large variety of shapes and sizes, which could mean that what has been termed S. favosa is more than one species.

The plated vesicle of S. favosa is what led Riedman to determine that the species must have been eukaryotic, because the plates are possible indicators that Golgi bodies existed in these organisms. After the endoplasmic reticulum of a cell synthesizes proteins and lipids, Golgi bodies process and package those substances depending on where they have to go next. Riedman and her team think that Golgi or Golgi-like bodies transported materials within the cell to form plates around vesicles, such as the ones seen in S. favosa. The hypothetical Golgi bodies themselves are not thought to have had these plates.

This sort of complex sorting of cellular contents is a feature of all modern eukaryotes. “Taxa including Satka favosa… are considered [eukaryotes] because they have a complex, platy vesicle construction,” the researchers said in the study. These new fossils suggest that it arose pretty early in their history.

Eukaryotes have evidently been much more complex and diverse than we thought for hundreds of millions of years longer than we thought. There might be even older samples out there. While fossil evidence of eukaryotes from near their origin eludes us, samples upwards of a billion years old, such as those found by Riedman and her team, are telling us more than ever about their—and therefore our—evolution.

Papers in Paleontology, 2023.  DOI: 10.1002/spp2.1538

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