Based on the stereotypical hairpin structure, researchers have scanned genomes and found over 38,000 likely precursors; nearly 50,000 mature microRNAs have been discovered by sequencing all the RNA found in cells from a variety of species. While found widely in animals, they’ve also been discovered in plants, raising the possibility that they existed in a single-celled ancestral organism.
While some microRNA genes, including lin-4 and let-7, have dramatic phenotypes when mutated, many have weak or confusing effects. This is likely in part due to the fact that a single microRNA can bind to and regulate a variety of genes and so may have a mix of effects when mutated. In other cases, several different microRNAs may bind to the same messenger RNA, creating a redundancy that makes the loss of a single microRNA difficult to detect.
Nevertheless, there’s plenty of evidence that, collectively, they’re essential for normal development in many organisms and tissues. Knocking out the gene that encodes the Dicer protein, which is needed for forming mature microRNAs, causes early embryonic lethality. Knockouts of the gene in specific cell types cause a variety of defects. For example, B cells never mature if Dicer is lost in that cell lineage, and a knockout in nerve cells causes microcephaly and limiting branching of connections among neurons, leading the animals to die shortly after birth.
This being the Medicine prize, the Nobel Committee also cite a number of human genetic diseases that are caused by mutations in microRNA genes.
Overall, the award highlights just how complex life is at the cellular level. There’s a fair number of genes that have to be made by every cell simply to enable their survival. But as for the rest, they exist embedded in complex regulatory networks that interact to ensure that proteins are made only where and when they’re needed, and often degraded if they somehow get made anyway. And every now and then, fundamental research in an oddball species is still telling us unexpected things about those networks.
Tracing the lineages of agricultural ants to their most recent common ancestor revealed that the ancestor probably lived through the end-Cretaceous mass extinction—the one that killed off the dinosaurs. The researchers argue that the two were almost certainly related. Current models suggest that there was so much dust in the atmosphere after the impact that set off the mass extinction that photosynthesis shut down for nearly two years, meaning minimal plant life. By contrast, the huge amount of dead material would allow fungi to flourish. So, it’s not surprising that ants started to adapt to use what was available to them.
That explains the huge cluster of species that cooperate with fungi. However, most of the species that engage in organized farming don’t appear until roughly 35 million years after the mass extinction, at the end of the Eocene (that’s about 33 million years before the present period). The researchers suggest that the climate changes that accompanied the transition to the Oligocene included a drying out of the tropical Americas, where the fungus-farming ants had evolved. This would cut down on the availability of fungi in the wild, potentially selecting for the ability of species that could propagate fungal species on their own.
This also corresponds to the origins of the yeast strains used by farming ants, as well as the most specialized agricultural fungal species. But it doesn’t account for the origin of coral fungus farmers, which seems to have occurred roughly 10 million years later.
The work gives us a much clearer picture of the origin of agriculture in ants and some reasonable hypotheses regarding the selective pressures that might have led to its evolution. In the long term, however, the biggest advance here may be the resources generated during this study. Ultimately, we’d like to understand the genetic basis for the changes in the ants’ behavior, as well as how the fungi have adapted to better provide for their farmers. To do that, we’ll need to compare the genomes of agricultural species with their free-living relatives. The DNA gathered for this study will ultimately be needed to pursue those questions.
It seems like common sense that being smart should increase the chances of survival in wild animals. Yet for a long time, scientists couldn’t demonstrate that because it was unclear how to tell exactly if a lion or a crocodile or a mountain chickadee was actually smart or not. Our best shots, so far, were looking at indirect metrics like brain size or doing lab tests of various cognitive skills such as reversal learning, an ability that can help an animal adapt to a changing environment.
But a new, large-scale study on wild mountain chickadees, led by Joseph Welklin, an evolutionary biologist at the University of Nevada, showed that neither brain size nor reversal learning skills were correlated with survival. What mattered most for chickadees, small birds that save stashes of food, was simply remembering where they cached all their food. A chickadee didn’t need to be a genius to survive; it just needed to be good at its job.
Testing bird brains
“Chickadees cache one food item in one location, and they do this across a big area. They can have tens of thousands of caches. They do this in the fall and then, in the winter, they use a special kind of spatial memory to find those caches and retrieve the food. They are little birds, weight is like 12 grams, and they need to eat almost all the time. If they don’t eat for a few hours, they die,” explains Vladimir Pravosudov, an ornithologist at the University of Nevada and senior co-author of the study.
The team chose the chickadees to study the impact cognitive skills had on survival because the failure to find their caches was their most common cause of death. This way, the team hoped, the impact of other factors like predation or disease would be minimized.
First, however, Welklin and his colleagues had to come up with a way to test cognitive skills in a fairly large population of chickadees. They did it by placing a metal square with two smart feeders attached to each side among the trees where the chickadees lived. “The feeders were equipped with RFID receivers that recognized the signal whenever a chickadee, previously marked with a microchip-fitted leg band, landed near them and opened the doors to dispense a single seed,” Welklin says. After a few days spent getting the chickadees familiar with the door-opening mechanism, the team started running tests.
The first task was aimed at testing how good different chickadees were at their most important job: associating a location with food and remembering where it was. To this end, each of the 227 chickadees participating in the study was assigned just one feeder that opened when they landed on it; all the other feeders remained closed. A chickadee’s performance was measured by the number of trials it needed to figure out which feeder would serve it, and how many errors (landings on the wrong feeders) it made over four days. “If you were to find the right feeder at random, it should take you 3.5 trials on average. All the birds learned and performed way better than chance,” Pravosudov says.
The second task was meant to test reversal learning skills, widely considered the best predictor of survival. Once the chickadees learned the location of the reward-dispensing feeders, the locations were changed. The goal was to see how fast the birds would adapt to this change.
Once the results of both tests were in, the team monitored the birds using their microchip bands, catching them and changing the bands every year, for over six years. “Part of the reason that’s never been done in the past is just because it takes so much work,” says Welklin. But the work paid off in the end.
Rapa Nui, often referred to as Easter Island, is one of the most remote populated islands in the world. It’s so distant that Europeans didn’t stumble onto it until centuries after they had started exploring the Pacific. When they arrived, though, they found that the relatively small island supported a population of thousands, one that had built imposing monumental statues called moai. Arguments over how this population got there and what happened once it did have gone on ever since.
Some of these arguments, such as the idea that the island’s indigenous people had traveled there from South America, have since been put to rest. Genomes from people native to the island show that its original population was part of the Polynesian expansion across the Pacific. But others, such as the role of ecological collapse in limiting the island’s population and altering its culture, continue to be debated.
Researchers have now obtained genome sequence from the remains of 15 Rapa Nui natives who predate European contact. And they indicate that the population of the island appears to have grown slowly and steadily, without any sign of a bottleneck that could be associated with an ecological collapse. And roughly 10 percent of the genomes appear to have a Native American source that likely dates from roughly the same time that the island was settled.
Out of the museum
The remains that provided these genomes weren’t found on Rapa Nui, at least not recently. Instead, they reside at the Muséum National d’Histoire Naturelle in France, having been obtained at some uncertain point in the past. Their presence there is a point of contention for the indigenous people of Rapa Nui, but the researchers behind the new work had the cooperation of the islanders in this project, having worked with them extensively. The researchers’ description of these interactions could be viewed as a model for how this sort of work should be done:
Throughout the course of the study, we met with representatives of the Rapanui community on the island, the Comisión de Desarrollo Rapa Nui and the Comisión Asesora de Monumentos Nacionales, where we presented our research goals and ongoing results. Both commissions voted in favor of us continuing with the research… We presented the research project in public talks, a short video and radio interviews on the island, giving us the opportunity to inquire about the questions that are most relevant to the Rapanui community. These discussions have informed the research topics we investigated in this work.
Given the questionable record-keeping at various points in the past, one of the goals of this work was simply to determine whether these remains truly had originated on Rapa Nui. That was unambiguously true. All comparisons with genomes of modern populations show that all 15 of these genomes have a Polynesian origin and are most closely related to modern residents of Rapa Nui. “The confirmation of the origin of these individuals through genomic analyses will inform repatriation efforts led by the Rapa Nui Repatriation Program (Ka Haka Hoki Mai Te Mana Tupuna),” the authors suggest.
A second question was whether the remains predate European contact. The researchers attempted to perform carbon dating, but it produced dates that made no sense. Some of the remains had dates that were potentially after they had been collected, according to museum records. And all of them were from the 1800s, well after European contact and introduced diseases had shrunk the native population and mixed in DNA from non-Polynesians. Yet none of the genomes showed more than one percent European ancestry, a fraction low enough to be ascribed to a spurious statistical fluke.
So the precise date these individuals lived is uncertain. But the genetic data clearly indicates that they were born prior to the arrival of Europeans. They can therefore tell us about what the population was experiencing in the period between Rapa Nui’s settlement and the arrival of colonial powers.
Back from the Americas
While these genomes showed no sign of European ancestry, they were not fully Polynesian. Instead, roughly 10 percent of the genome appeared to be derived from a Native American population. This is the highest percentage seen in any Polynesian population, including some that show hints of Native American contact that dates to before Europeans arrived on the scene.
Isolating these DNA sequences and comparing them to populations from across the world showed that the group most closely related to the one who contributed to the Rapa Nui population presently resides in the central Andes region of South America. That’s in contrast to the earlier results, which suggested the contact was with populations further north in South America.
Enlarge/ The African Lungfish, showing it’s thin, wispy fins.
When it was first discovered, the coelacanth caused a lot of excitement. It was a living example of a group of fish that was thought to only exist as fossils. And not just any group of fish. With their long, stalk-like fins, coelacanths and their kin are thought to include the ancestors of all vertebrates that aren’t fish—the tetrapods, or vertebrates with four limbs. Meaning, among a lot of other things, us.
Since then, however, evidence has piled up that we’re more closely related to lungfish, which live in freshwater and are found in Africa, Australia, and South America. But lungfish are a bit weird. The African and South American species have seen the limb-like fins of their ancestors reduced to thin, floppy strands. And getting some perspective on their evolutionary history has proven difficult because they have the largest genomes known in animals, with the South American lungfish genome containing over 90 billion base pairs. That’s 30 times the amount of DNA we have.
But new sequencing technology has made tackling that sort of challenge manageable, and an international collaboration has now completed the largest genome ever, one where all but one chromosome carry more DNA than is found in the human genome. The work points to a history where the South American lungfish has been adding 3 billion extra bases of DNA every 10 million years for the last 200 million years, all without adding a significant number of new genes. Instead, it seems to have lost the ability to keep junk DNA in check.
Going long
The work was enabled by a technology generically termed “long-read sequencing.” Most of the genomes that were completed were done using short reads, typically in the area of 100–200 base pairs long. The secret was to do enough sequencing that, on average, every base in the genome should be sequenced multiple times. Given that, a cleverly designed computer program could figure out where two bits of sequence overlapped and register that as a single, longer piece of sequence, repeating the process until the computer spit out long strings of contiguous bases.
The problem is that most non-microbial species have stretches of repeated sequence (think hundreds of copies of the bases G and A in a row) that were longer than a few hundred bases long—and nearly identical sequences that show up in multiple locations of the genome. These would be impossible to match to a unique location, and so the output of the genome assembly software would have lots of gaps of unknown length and sequence.
This creates extreme difficulty for genomes like that of the lungfish, which is filled with non-functional “junk” DNA, all of which is typically repetitive. The software tends to produce a genome that’s more gap than sequence.
Long-read technology gets around that by doing exactly what its name implies. Rather than being able to sequence fragments of 200 bases or so, it can generate sequences that are thousands of base pairs long, easily covering the entire repeat that would have otherwise created a gap. One early version of long-read technology involved stuffing long DNA molecules through pores and watching for different voltage changes across the pore as different bases passed through it. Another had a DNA copying enzyme make a duplicate of a long strand and watch for fluorescence changes as different bases were added. These early versions tended to be a bit error-prone but have since been improved, and several newer competing technologies are now on the market.
Back in 2021, researchers used this technology to complete the genome of the Australian lungfish—the one that maintains the limb-like fins of the ancestors that gave rise to tetrapods. Now they’re back with the genomes from African and South American species. These species seem to have gone their separate ways during the breakup of the supercontinent Gondwana, a process that started nearly 200 million years ago. And having the genomes of all three should give us some perspective on the features that are common to all lungfish species, and thus are more likely to have been shared with the distant ancestors that gave rise to tetrapods.
Enlarge/ The fossil in question, oriented with its head to the left.
Yang Jie / Zhang Xiguang
Around half a billion years ago, in what is now the Yunnan Province of China, a tiny larva was trapped in mud. Hundreds of millions of years later, after the mud had long since become the black shales of the Yuan’shan formation, the larva surfaced again, a meticulously preserved time capsule that would unearth more about the evolution of arthropods.
Youti yuanshi is barely visible to the naked eye. Roughly the size of a poppy seed, it is preserved so well that its exoskeleton is almost completely intact, and even the outlines of what were once its internal organs can be seen through the lens of a microscope. Durham University researchers who examined it were able to see features of both ancient and modern arthropods. Some of these features told them how the simpler, more wormlike ancestors of living arthropods evolved into more complex organisms.
The research team also found that Y. yuanshi, which existed during the Cambrian Explosion (when most of the main animal groups started to appear on the fossil record), has certain features in common with extant arthropods, such as crabs, velvet worms, and tardigrades. “The deep evolutionary position of Youti yuanshi… illuminat[es] the internal anatomical changes that propelled the rise and diversification of [arthropods],” they said in a study recently published in Nature.
Inside out and outside in
While many fossils preserved in muddy environments like the Yuan’shan formation are flattened by compression, Y. yuanshi remained three-dimensional, making it easier to examine. So what exactly did this larva look like on the outside and inside?
The research team could immediately tell that Y. yuanshi was a lobopodian. Lobopodians are a group of extinct arthropods with long bodies and stubby legs, or lobopods. There is a pair of lobopods in the middle of each of its twenty segments, and these segments also get progressively shorter from the front to back of the body. Though soft tissue was not preserved, spherical outlines suggest an eye on each side of the head, though whether these were compound eyes is unknown. This creature had a stomodeum—the precursor to a mouth—but no anus. It would have had to both take in food and dispose of waste through its mouth.
Youti yuanshi has a cavity, known as the perivisceral cavity, that surrounds the outline of a tube that is thought to have once been the gut. The creature’s gut ends without an opening, which explains its lack of an anus. Inside each segment, there is a pair of voids toward the middle. The researchers think these are evidence of digestive glands, especially after comparing them to digestive glands in the fossils of other arthropods from the same era.
A ring around the mouth of the larva was once a circumoral nerve ring, which connected with nerves that extend to eyes and appendages in the first segment. Inside its head is a void that contained the brain. The shape of this empty chamber gives some insight into how the brain was structured. From what the researchers could see, the brain of Y. yuanshi had wedge-shaped frontal portion, and the rest of the brain was divided into two sections, as evidenced by the outline of a membrane in between them.
Way, way, way back then and now
Given its physical characteristics, the researchers think that Y. yuanshi displays features of both extinct and extant arthropods. Some are ancestral characteristics present in all arthropods, living and extinct. Others are ancestral characteristics that may have been present in extinct arthropods but are only present in some living arthropods.
Among the features present in all arthropods today is the protocerebrum; its evolutionary precursor was the circumoral nerve ring present in Y. yuanshi. The protocerebrum is the first segment of the arthropod brain, which controls the eyes and appendages, such as antennae in velvet worms and the mouthparts in tardigrades. Another feature of Y. yuanshi present in extant and extinct arthropods is its circulatory system, which is similar to that of modern arthropods, especially crustaceans.
Lobopods are a morphological feature of Y. yuanshi that are now found only in some arthropods—tardigrades and velvet worms. Many more species of lobopodians existed during the Cambrian. The lobopodians also had a distinctively structured circulatory system in their legs and other appendages, which is closest to that of velvet worms.
“The architecture of the nervous system informs the early configuration of the [arthropod] brain and its associated appendages and sensory organs, clarifying homologies across [arthropods],” the researchers said in the same study.
Yuti yuanshi is still holding on to some mysteries. They mostly have to do with the fact that it is a larva—what it looked like as an adult can only be guessed at, and it’s possible that this species developed compound eyes or flaps for swimming by the time it reached adulthood. Whether it is the larva of an already-known species of extinct lobopod is an open question. Maybe the answers are buried somewhere in the Yuan’shan shale.
Enlarge/ Half of the upper arm bone of this species can fit comfortably in the palm of a modern human hand.
Yousuke Kaifu
The discovery of Homo floresiensis, often termed a hobbit, confused a lot of people. Not only was it tiny in stature, but it shared some features with both Homo erectus and earlier Australopithecus species and lived well after the origin of modern humans. So, its precise position within the hominin family tree has been the subject of ongoing debate—one that hasn’t been clarified by the discovery of the similarly diminutive Homo luzonensis in the Philippines.
Today, researchers are releasing a paper that describes bones from a diminutive hominin that occupied the island of Flores much earlier than the hobbits. And they argue that, while it still shares an odd mix of features, it is most closely related to Homo erectus, the first hominin species to spread across the globe.
Remarkably small
The bones come from a site on Flores called Mata Menge, where the bones were found in a large layer of sediment. Slight wear suggests that many of them were probably brought to the site by a gentle flood. Dating from layers above and below where the fossils were found limits their age to somewhere between 650,000 and 775,000 years ago. Most of the remains are teeth and fragments of jaw bone, which can be suggestive of body size, but not definitive. But the new finds include a fragment of the upper arm bone, the humerus, which is more directly proportional to body size.
The researchers argue that the bone is broken at roughly the mid-point of the humerus, meaning that the full-sized bone was twice its length. Based on the relationship between humerus length and body size, they estimate that the individual it came from was only a bit above a meter tall.
They also took a slice from the center of the sample and imaged the cells present in the bone when it fossilized. These suggest that the fossil came from a fully mature adult. That makes its dimensions, including the diameter of the bone, the smallest yet found. It is, to quote the paper, “smaller than LB1 (H. floresiensis) and any other adult individuals of small-bodied fossil hominins (Australopithecus and H. naledi.” So, even by the standards of small species, the new fossils belong to an extremely small individual.
As for what these individuals are related to, the answers are (once again) complicated. The morphology of the humerus is most closely related to the H. floresiensis individuals who resided on Flores hundreds of thousands of years later. Beyond that, it’s most similar to H. naledi. From there, its shape appears to be equally distant from various species, including both H. erectus and various species of Australopithecus. The teeth show a variety of affinities but are generally closest to members of the Homo genus.
So, the authors make two arguments. One is that the fossils come from the ancestors of the hobbits and belong to the same species, indicating that they inhabited Flores for at least half a million years. The second is that it’s a branch off the population of H. erectus, a species that was similar in stature to modern humans. The population would have evolved a shorter stature once isolated on Flores.
Nothing makes a lot of sense
That’s the argument, at least. There will undoubtedly be different opinions among paleontologists, however. Some had already argued that H. floresiensis was an offshoot of H. erectus and will be happy to accept this as new evidence. But the species is such a hodge-podge of features of earlier and contemporary species that it has been easy for others to make contrary arguments.
Even if those arguments were settled, there’s the issue of how it got there. Even at times of significantly lower sea levels, Flores would have required a significant ocean crossing from what is now Java, where H. erectus is known to have been present, and which was connected to Asia at the time. There’s no indication that any species that came before modern humans had developed boating technology, and some have suggested that the population was established on Flores after being swept there on tsunami debris. Once present, the island environment could have selected for a smaller body size.
But then there’s the issue of Homo luzonensis, which shared a similar body size but inhabited a very different island. That would seem to require a second event that was also unlikely: either a second ocean passage involving individuals from Flores or another ocean trip by H. erectus followed by similar evolution of smaller body size, despite a potentially different environment.
It’s clear that, while the new finds tell us something about the Flores population, they’re not going to settle any arguments.
In the early 2000s, local fossil collector Mohamed ‘Ou Said’ Ben Moula discovered numerous fossils at Fezouata Shale, a site in Morocco known for its well-preserved fossils from the Early Ordovician period, roughly 480 million years ago. Recently, a team of researchers at the University of Lausanne (UNIL) studied 100 of these fossils and identified one of them as the earliest ancestor of modern-day chelicerates, a group that includes spiders, scorpions, and horseshoe crabs.
The fossil preserves the species Setapedites abundantis, a tiny animal that crawled and swam near the bottom of a 100–200-meter-deep ocean near the South Pole 478 million years ago. It was 5 to 10 millimeters long and fed on organic matter in the seafloor sediments. “Fossils of what is now known as S. abundantis have been found early on—one specimen mentioned in the 2010 paper that recognized the importance of this biota. However, this creature wasn’t studied in detail before simply because scientists focused on other taxa first,” Pierre Gueriau, one of the researchers and a junior lecturer at UNIL, told Ars Technica.
The study from Gueriau and his team is the first to describe S. abundantis and its connection to modern-day chelicerates (also called euchelicerates). It holds great significance, because “the origin of chelicerates has been one of the most tangled knots in the arthropod tree of life, as there has been a lack of fossils between 503 to 430 million years ago,” Gueriau added.
An ancestor of spiders
The study authors used X-ray scanners to reconstruct the anatomy of 100 fossils from the Fezouata Shale in 3D. When they compared the anatomical features of these ancient animals with those of chelicerates, they noticed several similarities between S. abundantis and various ancient and modern-day arthropods, including horseshoe crabs, scorpions, and spiders.
For instance, the nature and arrangement of the head appendages or ‘legs’ in S. abundantis were homologous with those of present-day horseshoe crabs and Cambrian arthropods that existed between 540 to 480 million years ago. Moreover, like spiders and scorpions, the organism exhibited body tagmosis, where the body is organized into different functional sections.
“Setapedites abundantis contributes to our understandings of the origin and early evolution of two key euchelicerate characters: the transition from biramous to uniramous prosomal appendages, and body tagmosis,” the study authors note.
Currently, two Cambrian-era arthropods, Mollisonia plenovenatrix and Habelia optata are generally considered the earliest ancestors of chelicerates (not all scientists accept this idea). Both lived around 500 million years ago. When we asked how these two differ from S. abundantis, Gueriau replied, “Habelia and Mollisonia represent at best early-branching lineages in the phylogenetic tree. While S. abundantis is found to represent, together with a couple of other fossils, the earliest branching lineage within chelicerates.”
This means Habelia and Mollisonia are relatives of the ancestors of modern-day chelicerates. On the other side, S. abundantis represents the first group that split after the chelicerate clade was established, making it the earliest member of the lineage. “These findings bring us closer to untangling the origin story of arthropods, as they allow us to fill the anatomical gap between Cambrian arthropods and early-branching chelicerates,” Gueriau told Ars Technica.
S. abundantis connects other fossils
The researchers faced many challenges during their study. For instance, the small size of the fossils made observations and interpretation complicated. They overcame this limitation by examining a large number of specimens—fortunately, S. abundantis fossils were abundant in the samples they studied. However, these fossils have yet to reveal all their secrets.
“Some of S. abundantis’ anatomical features allow for a deeper understanding of the early evolution of the chelicerate group and may even link other fossil forms, whose relationships are still highly debated, to this group,” Gueriau said. For instance, the study authors noticed a ventral protrusion at the rear of the organism. Such a feature is observed for the first time in chelicerates but is known in other primitive arthropods.
“This trait could thus bring together many other fossils with chelicerates and further resolve the early branches of the arthropod tree. So the next step for this research is to investigate deeper this feature on a wide range of fossils and its phylogenetic implications,” Gueriau added.
Rupendra Brahambhatt is an experienced journalist and filmmaker. He covers science and culture news, and for the last five years, he has been actively working with some of the most innovative news agencies, magazines, and media brands operating in different parts of the globe.
The basic outline of the interactions between modern humans and Neanderthals is now well established. The two came in contact as modern humans began their major expansion out of Africa, which occurred roughly 60,000 years ago. Humans picked up some Neanderthal DNA through interbreeding, while the Neanderthal population, always fairly small, was swept away by the waves of new arrivals.
But there are some aspects of this big-picture view that don’t entirely line up with the data. While it nicely explains the fact that Neanderthal sequences are far more common in non-African populations, it doesn’t account for the fact that every African population we’ve looked at has some DNA that matches up with Neanderthal DNA.
A study published on Thursday argues that much of this match came about because an early modern human population also left Africa and interbred with Neanderthals. But in this case, the result was to introduce modern human DNA to the Neanderthal population. The study shows that this DNA accounts for a lot of Neanderthals’ genetic diversity, suggesting that their population was even smaller than earlier estimates had suggested.
Out of Africa early
This study isn’t the first to suggest that modern humans and their genes met Neanderthals well in advance of our major out-of-Africa expansion. The key to understanding this is the genome of a Neanderthal from the Altai region of Siberia, which dates from roughly 120,000 years ago. That’s well before modern humans expanded out of Africa, yet its genome has some regions that have excellent matches to the human genome but are absent from the Denisovan lineage.
One explanation for this is that these are segments of Neanderthal DNA that were later picked up by the population that expanded out of Africa. The problem with that view is that most of these sequences also show up in African populations. So, researchers advanced the idea that an ancestral population of modern humans left Africa about 200,000 years ago, and some of its DNA was retained by Siberian Neanderthals. That’s consistent with some fossil finds that place anatomically modern humans in the Mideast at roughly the same time.
There is, however, an alternative explanation: Some of the population that expanded out of Africa 60,000 years ago and picked up Neanderthal DNA migrated back to Africa, taking the Neanderthal DNA with them. That has led to a small bit of the Neanderthal DNA persisting within African populations.
To sort this all out, a research team based at Princeton University focused on the Neanderthal DNA found in Africans, taking advantage of the fact that we now have a much larger array of completed human genomes (approximately 2,000 of them).
The work was based on a simple hypothesis. All of our work on Neanderthal DNA indicates that their population was relatively small, and thus had less genetic diversity than modern humans did. If that’s the case, then the addition of modern human DNA to the Neanderthal population should have boosted its genetic diversity. If so, then the stretches of “Neanderthal” DNA found in African populations should include some of the more diverse regions of the Neanderthal genome.
Gaiasia jennyae, a newly discovered freshwater apex predator with a body length reaching 4.5 meters, lurked in the swamps and lakes around 280 million years ago. Its wide, flattened head had powerful jaws full of huge fangs, ready to capture any prey unlucky enough to swim past.
The problem is, to the best of our knowledge, it shouldn’t have been that large, should have been extinct tens of millions of years before the time it apparently lived, and shouldn’t have been found in northern Namibia. “Gaiasia is the first really good look we have at an entirely different ecosystem we didn’t expect to find,” says Jason Pardo, a postdoctoral fellow at Field Museum of Natural History in Chicago. Pardo is co-author of a study on the Gaiasia jennyae discovery recently published in Nature.
Common ancestry
“Tetrapods were the animals that crawled out of the water around 380 million years ago, maybe a little earlier,” Pardo explains. These ancient creatures, also known as stem tetrapods, were the common ancestors of modern reptiles, amphibians, mammals, and birds. “Those animals lived up to what we call the end of Carboniferous, about 370–300 million years ago. Few made it through, and they lasted longer, but they mostly went extinct around 370 million ago,” he adds.
This is why the discovery of Gaiasia jennyae in the 280 million-year-old rocks of Namibia was so surprising. Not only wasn’t it extinct when the rocks it was found in were laid down, but it was dominating its ecosystem as an apex predator. By today’s standards, it was like stumbling upon a secluded island hosting animals that should have been dead for 70 million years, like a living, breathing T-rex.
“The skull of gaiasia we have found is about 67 centimeters long. We also have a front end of her upper body. We know she was at minimum 2.5 meters long, probably 3.5, 4.5 meters—big head and a long, salamander-like body,” says Pardo. He told Ars that gaiasia was a suction feeder: she opened her jaws under water, which created a vacuum that sucked her prey right in. But the large, interlocked fangs reveal that a powerful bite was also one of her weapons, probably used to hunt bigger animals. “We suspect gaiasia fed on bony fish, freshwater sharks, and maybe even other, smaller gaiasia,” says Pardo, suggesting it was a rather slow, ambush-based predator.
But considering where it was found, the fact that it had enough prey to ambush is perhaps even more of a shocker than the animal itself.
Location, location, location
“Continents were organized differently 270–280 million years ago,” says Pardo. Back then, one megacontinent called Pangea had already broken into two supercontinents. The northern supercontinent called Laurasia included parts of modern North America, Russia, and China. The southern supercontinent, the home of gaiasia, was called Gondwana, which consisted of today’s India, Africa, South America, Australia, and Antarctica. And Gondwana back then was pretty cold.
“Some researchers hypothesize that the entire continent was covered in glacial ice, much like we saw in North America and Europe during the ice ages 10,000 years ago,” says Pardo. “Others claim that it was more patchy—there were those patches where ice was not present,” he adds. Still, 280 million years ago, northern Namibia was around 60 degrees southern latitude—roughly where the northernmost reaches of Antarctica are today.
“Historically, we thought tetrapods [of that time] were living much like modern crocodiles. They were cold-blooded, and if you are cold-blooded the only way to get large and maintain activity would be to be in a very hot environment. We believed such animals couldn’t live in colder environments. Gaiasia shows that it is absolutely not the case,” Pardo claims. And this turned upside-down lots of what we knew about life on Earth back in gaiasia’s time.
One of the challenges of working with ancient DNA samples is that damage accumulates over time, breaking up the structure of the double helix into ever smaller fragments. In the samples we’ve worked with, these fragments scatter and mix with contaminants, making reconstructing a genome a large technical challenge.
But a dramatic paper released on Thursday shows that this isn’t always true. Damage does create progressively smaller fragments of DNA over time. But, if they’re trapped in the right sort of material, they’ll stay right where they are, essentially preserving some key features of ancient chromosomes even as the underlying DNA decays. Researchers have now used that to detail the chromosome structure of mammoths, with some implications for how these mammals regulated some key genes.
DNA meets Hi-C
The backbone of DNA’s double helix consists of alternating sugars and phosphates, chemically linked together (the bases of DNA are chemically linked to these sugars). Damage from things like radiation can break these chemical linkages, with fragmentation increasing over time. When samples reach the age of something like a Neanderthal, very few fragments are longer than 100 base pairs. Since chromosomes are millions of base pairs long, it was thought that this would inevitably destroy their structure, as many of the fragments would simply diffuse away.
But that will only be true if the medium they’re in allows diffusion. And some scientists suspected that permafrost, which preserves the tissue of some now-extinct Arctic animals, might block that diffusion. So, they set out to test this using mammoth tissues, obtained from a sample termed YakInf that’s roughly 50,000 years old.
The challenge is that the molecular techniques we use to probe chromosomes take place in liquid solutions, where fragments would just drift away from each other in any case. So, the team focused on an approach termed Hi-C, which specifically preserves information about which bits of DNA were close to each other. It does this by exposing chromosomes to a chemical that will link any pieces of DNA that are close physical proximity. So, even if those pieces are fragments, they’ll be stuck to each other by the time they end up in a liquid solution.
A few enzymes are then used to convert these linked molecules to a single piece of DNA, which is then sequenced. This data, which will contain sequence information from two different parts of the genome, then tells us that those parts were once close to each other inside a cell.
Interpreting Hi-C
On its own, a single bit of data like this isn’t especially interesting; two bits of genome might end up next to each other at random. But when you have millions of bits of data like this, you can start to construct a map of how the genome is structured.
There are two basic rules governing the pattern of interactions we’d expect to see. The first is that interactions within a chromosome are going to be more common than interactions between two chromosomes. And, within a chromosome, parts that are physically closer to each other on the molecule are more likely to interact than those that are farther apart.
So, if you are looking at a specific segment of, say, chromosome 12, most of the locations Hi-C will find it interacting with will also be on chromosome 12. And the frequency of interactions will go up as you move to sequences that are ever closer to the one you’re interested in.
On its own, you can use Hi-C to help reconstruct a chromosome even if you start with nothing but fragments. But the exceptions to the expected pattern also tell us things about biology. For example, genes that are active tend to be on loops of DNA, with the two ends of the loop held together by proteins; the same is true for inactive genes. Interactions within these loops tend to be more frequent than interactions between them, subtly altering the frequency with which two fragments end up linked together during Hi-C.
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).
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.”
