Neanderthal Genes Influence Contemporary Humans’ Skull Shape, Brain Size


Individuals carrying these ancient ancestors’ DNA are more likely to have slightly elongated, rather than rounded, brains

The researchers are quick to point out that their findings don’t suggest a link between brain size or shape and behavior, but instead offer an exploration of the genetic evolution of modern brains (Philipp Gunz)

By Meilan Solly

smithsonian.com
December 14, 2018

Neanderthals may have gone extinct some 40,000 years ago, but thanks to long-ago species interbreeding, their genes live on in modern humans.

The implications of this genetic inheritance remain largely unclear, although previous studies have proposed links with disease immunity, hair color and even sleeping patterns. Now, Carl Zimmer reports for The New York Times, a study recently published in Current Biology offers yet another example of Neanderthals’ influence on Homo sapiens: Compared to individuals lacking Neanderthal DNA, carriers are more likely to have slightly elongated, rather than rounded, brains.

This tendency makes sense given Neanderthals’ distinctive elongated skull shape, which Science magazine’s Ann Gibbons likens to a football, as opposed to modern humans’ more basketball-shaped skulls. It would be logical to assume this stretched out shape reflects similarly protracted brains, but as lead author Philipp Gunz of Germany’s Max Planck Institute for Evolutionary Anthropology tells Live Science’s Charles Q. Choi, brain tissue doesn’t fossilize, making it difficult to pinpoint the “underlying biology” of Neanderthal skulls.

To overcome this obstacle, Gunz and his colleagues used computed tomography (CT) scanning to generate imprints of seven Neanderthal and 19 modern human skulls’ interior braincases. Based on this data, the team established a “globularity index” capable of measuring how globular (rounded) or elongated the brain is. Next, Dyani Lewis writes for Cosmos, the researchers applied this measure to magnetic resonance imaging (MRI) scans of around 4,500 contemporary humans of European ancestry, and then compared these figures to genomic data cataloguing participants’ share of Neanderthal DNA fragments.

Two specific genes emerged in correlation with slightly less globular heads, according to The New York Times’ Zimmer: UBR4, which is linked to the generation of neurons, and PHLPP1, which controls the production of a neuron-insulating sleeve called myelin. Both UBR4 and PHLPP1 affect significant regions of the brain, including the part of the forebrain called the putamen, which forms part of the basal ganglia, and the cerebellum. As Sarah Sloat explains for Inverse, the basal ganglia influences cognitive functions such as skill learning, fine motor control and planning, while the cerebellum assists in language processing, motor movement and working memory.

In modern human brains, PHLPP1 likely produces extra myelin in the cerebellum; UBR4 may make neurons grow faster in the putamen. Comparatively, Science’s Gibbons notes, Neanderthal variants may lower UBR4 expression in the basal ganglia and reduce the myelination of axions in the cerebellum—phenomena that could contribute to small differences in neural connectivity and the cerebellum’s regulation of motor skills and speech, the study’s lead author Simon Fisher of the Netherlands’ Max Planck Institute for Psycholinguistics tells Gibbons .

Still, the effects of such gene variations are probably negligible in living humans, merely adding a slight, barely discernible elongation to the skull.

“Brain shape differences are one of the key distinctions between ourselves and Neanderthals,” Darren Curnoe, a paleoanthropologist from Australia’s University of New South Wales who was not involved in the study, tells Cosmos, “and very likely underpins some of the major behavioural differences between our species.”

In an interview with The New York Times, Fisher adds that the evolution of UBR4 and PHLPP1 genes could reflect modern humans’ development of sophisticated language, tool-making and similarly advanced behaviors.

But, Gunz is quick to point out, the researchers are not issuing a decisive statement on the genes controlling brain shape, nor the effects of such genes on modern humans carrying fragments of Neanderthal DNA: “I don’t want to sound like I’m promoting some new kind of phrenology,” he tells Cosmos. “We’re not trying to argue that brain shape is under any direct selection, and brain shape is directly related to behaviour at all.”

We Still Don’t Know Why the Reign of the Dinosaurs Ended


The asteroid strike on the Yucatán Peninsula 66 million years ago is only part of the story

Dino Asteroid Strike
Although the asteroid strike that created Chicxulub crater in modern-day Mexico dramatically affected life on Earth, the fiery crash isn’t the whole story of the fate of the dinosaurs.

The reason our planet lost the terrible lizards of eras long past may seem self-evident. About 66 million years ago, an asteroid came screaming out of the sky and smacked into what is now the Yucatán Peninsula of Mexico. The devastation that followed was unprecedented, with tsunamis, an overheated atmosphere, darkened skies, a terrible cold snap, and other apocalyptic ecological events clearing away an estimated seventy five percent of known life on Earth.

Paleontologists know this catastrophe as the K/Pg extinction event because it marks the transition from the Cretaceous into the Paleogene period of Earth’s history. But even though it has been studied constantly, the details of this event still puzzle experts. The case wasn’t closed with the recognition of the impact crater in the 1990s, and exactly how the extinction played out—what differentiated the living from the dead—continues to inspire paleontologists to dig into the cataclysm of the Cretaceous.

To better understand the full story, researchers are pulling back from the moment of impact to examine the broader patterns of life at the time. Dinosaurs were not living in a stable and lush Mesozoic utopia, nor were they the only organisms around at the time—far from it. The world was changing around them as it always had. As the Cretaceous drew to a close, sea levels were dropping, the climate was trending toward a cooler world, and a part of prehistoric India called the Deccan Traps was bubbling with intense volcanic activity. Sorting through how these changes affected life on Earth is no simple task, particularly after the cataclysmic meteorite mixed things up in the rock record, but paleontologists are sifting through the wreckage to better understand what happened.

“In order to get an idea of what happened in the wake of the asteroid impact, we need solid baseline data on what rates of background extinction were like before the K/Pg took place,” Natural History Museum paleontologist Paul Barrett says. A moment of catastrophe can only make sense within the broader context of life before and after. “This would make the difference between the cataclysmic events at Chicxulub being either the primary cause of the extinction or merely the coup de grace that finished off an ecosystem whose resilience had been gradually worn away.”

Asteroid Impact
An artist’s rendering of an asteroid impacting the Earth. (NASA / Don Davis)

While the K/Pg extinction was a global crisis, how it played out at various locales around the planet is largely unknown. The amount of information at any given location depends on how well the relevant rock layers are preserved and how accessible they are to scientists. Some of the best exposures happen to be located in western North America, where there’s a continuous sequence of sedimentary layers recording the end of the Cretaceous straight through to the beginning of the Paleogene. These rocks offer before and after shots of the extinction, and it’s these exposures that has allowed Royal Saskatchewan Museum paleontologist Emily Bamforth to investigate what was happening in the 300,000 years leading up to the explosive close of the Cretaceous.

Looking at the geologic record of southwest Saskatchewan, Bamforth says, local conditions such as the frequency of forest fires and the characteristics of a particular habitat were as important as what was happening on a global scale when determining patterns of ancient biodiversity. “I think this is an important message to keep in mind when thinking of causes of the extinction,” Bamforth says. “Each different ecosystem could have had its own smaller scale biodiversity drivers that were in operation before the extinction, which underlay the big, global factors.” What was good for turtles, amphibians, plants, dinosaurs and other organisms in one place might not have been beneficial in another, underscoring that we can’t comprehend global shifts without the foundation of local diversity. “Ecosystems are complicated things, and I think that is worth keeping in mind when considering the cause and duration of the mass extinction,” Bamforth says.

As far as Saskatchewan goes, the ecological community at the time leading up to the extinction was like a big game of Jenga. “The tower remains standing, but factors like climate change are slowly pulling blocks out from it, weakening the system and making it vulnerable,” Bamforth says. The constantly shifting ecological stability made major upsets—like an asteroid striking at the wrong place, at the wrong time—especially disastrous.

This picture of shifting ecosystems inverts the focus of the K/Pg disaster. While the reason non-avian dinosaurs and other organisms died off always grabs our attention, it’s been harder for scientists to determine why the survivors were able to pass through to the next chapter of life’s history.

Species that survived the impact were typically small, semi-aquatic or made burrows, and able to subsist on a variety of foods, but there are some key contradictions. There were some small non-avian dinosaurs that had these advantages and still went extinct, and many reptiles, birds and mammals died out despite belonging to broader groups that persisted. The badger-sized mammal Didelphodon didn’t make it, for example, nor did the ancient bird Avisaurus, among others.

“This is something I struggle to explain,” Barrett says. Generally speaking, smaller dinosaurs and other animals should have had better chances at survival than their larger relatives, but this was not always the case.

T. Rex
Tyrannosaurus rex lived in the western United States from about 66 to 68 million years ago, right up until the K/Pg extinction event. (Smithsonian National Museum of Natural History)

Pat Holroyd of the University of California Museum of Paleontology likens these investigations to what happens in the wake of airline accidents. “They go in and they gather all the data and they try to figure out, ‘Well, ok, why did the people in the tail section survive, and the people in the other parts of the plane didn’t make it?’” Holroyd says. And while such disasters may be singular events with unique causes, it’s still possible to look at multiple incidents collectively to identify patterns and inform what we may think of as a singular event.

As far as the K/Pg extinction goes, the patterns are still emerging. Holroyd estimates that much of the relevant research about which species survived the impact has only been published or uploaded to the Paleobiology Database in the last decade. This new information allowed Holroyd and colleagues to study patterns of turnover—how long species persisted on land and in associated freshwater habitats—long before and after the asteroid impact. The team’s findings were presented earlier this fall at the annual Society of Vertebrate Paleontology meeting in Albuquerque, New Mexico.

Some of the patterns were familiar. Fish, turtles, amphibians and crocodylians all generally fared better than strictly terrestrial organisms. “People have been observing this pattern since at least the 50s, and probably before,” Holroyd says. But the resilience of waterbound species had never been quantified in detail before, and the new analysis is revealing that the solution to the extinction pattern puzzle may have been right in front of us all along.

The surprise, Holroyd found, was that the difference between the survivors and the extinct of the K/Pg event mimicked a pattern that has held true for tens of millions of years before and after the asteroid impact. Species living on land, particularly large species, tend not to persist as long as those living in freshwater environments. Terrestrial species often go extinct at a greater rate than those in aquatic environments even without a massive catastrophe to take them out of the picture. Species that lived in and around freshwater habitats appear to have persisted longer even when there wasn’t a crisis, and when the extinction at the end of the Cretaceous struck in full force, these organisms had an advantage over their purely terrestrial neighbors.

But even in their relatively safe aquatic environments, everything wasn’t peachy for water-faring animals. Holroyd notes that Cretaceous turtles, for example, lost fifty percent of their diversity globally, although only about twenty percent in the more localized area of western North America, further underscoring the importance of understanding local versus global patterns. Even lineages that can be considered “survivors” still suffered losses and may not have bounced back to their former glory. Marsupial mammals, for example, survived the mass extinction as a group but had their diversity and abundance drastically cut back.

Chicxulub Crater
A shaded relief image of Mexico’s Yucatan Peninsula showing the indication of the Chicxulub impact crater. (NASA / JPL)

How local ecosystems were affected by these changes is the next step toward understanding how the extinction event affected the world. Holroyd points to the familiar “three-horned face” Triceratops as an example. This dinosaur was ubiquitous across much of western North America at the end of the Cretaceous and was clearly a major component of its ecosystem. These animals were the bison of their time, and, given how large herbivores alter their habitats through grazing and migration, the extinction of Triceratops undoubtedly had major implications for ecosystems recovering in the wake of the Cretaceous catastrophe. Plants that may have relied on Triceratops to disperse seeds would have suffered, for example, whereas other plants that were trampled down by the dinosaurs might have grown more freely. How these ecological pieces fit, and what they mean for life’s recovery after the extinction, have yet to fully come into focus.

“The western interior of North America gives us our only detailed window on what happened to life on land during the K/Pg extinction, but it’s totally unclear if this was typical,” Barrett says. “We don’t know much about how the intensity of the extinction varied around the world,” especially in locations that were geographically distant from the asteroid strike. “It seems unlikely that a one-size-fits-all model would be responsible” for cutting down organisms as different from each other as Edmontosaurus on land and coil-shelled ammonites in the seas, among so many other species lost to the Cretaceous. Research in Europe, South America, Asia and Australia is just beginning to form the basis of a much sought-after global picture of the most famous extinction event in history.

“It’s like one gigantic jigsaw puzzle that we’ve started to turn up more of the pieces to,” Bamforth says. The resulting picture of this critical moment in Earth’s history will only be revealed in time.

The theory of evolution has its origins in the Galápagos.


Now climate change is rapidly heating the ocean here.
Darwin’s creatures are threatened.

ALCEDO VOLCANO, Galápagos — When the clouds break, the equatorial sun bears down on the crater of this steaming volcano, revealing a watery landscape where the theory of evolution began to be conceived.

Across a shallow strip of sea lies the island of Santiago, where Charles Darwin once sighted marine iguanas, the only lizard that scours the ocean for food. Finches, the product of slow generational flux, dart by. Now, in the era of climate change, they might be no match for the whims of natural selection.

In the struggle against extinction on these islands, Darwin saw a blueprint for the origin of every species, including humans.

Yet not even Darwin could have imagined what awaited the Galápagos, where the stage is set for perhaps the greatest evolutionary test yet.

Marine iguanas on Fernandina Island.

As climate change warms the world’s oceans, these islands are a crucible. And scientists are worried. Not only do the Galápagos sit at the intersection of three ocean currents, they are in the cross hairs of one of the world’s most destructive weather patterns, El Niño, which causes rapid, extreme ocean heating across the Eastern Pacific tropics.

Research published in 2014 by more than a dozen climate scientists warned that rising ocean temperatures were making El Niño both more frequent and more intense. Unesco, the United Nations educational and cultural agency, now warns the Galápagos Islands are one of the places most vulnerable to the impacts of climate change.

“You can see them laying one or two eggs and being attacked by the ants,” said Christian Sevilla, a conservationist at the national park here. “They’re just throwing off the rest of the eggs as they walk off trying to escape, with the ants still biting at their legs.”

(Not without irony, Darwin was a predator of the tortoises well before the ants were. “The young tortoises make excellent soup,” he wrote in 1839.)

Mr. Sevilla and other workers at the park are now considering mitigation efforts to try to protect threatened species from the more frequent El Niño events that have come with climate change. The park already has a program to breed giant tortoises in captivity.

Chicken Bones May Be the Legacy of Our Time


A new study argues that the sheer abundance of chicken consumption, coupled with the strange skeletons of modern chickens, will leave a unique fingerprint

 

Some experts say we are now in the era of the “Anthropocene,” a term used to describe humans’ unprecedented influence on the planet. When our civilization is long gone, the Earth will continue to bear the effects of the time we spent here—effects like nuclear isotopes in sedimentary rock, and the fossilized remains of plastic on the ocean floor and concrete on land. But perhaps more than anything else, according to a new study, the great legacy of our time will be chicken bones. Lots and lots of chicken bones.

chickenisthefuture

Writing in Royal Society Open Science, a team of researchers argues that the remains of domesticated chickens (Gallus gallus domecustis) will be a major and unique marker of our changing biosphere. For one thing, there are just so many of them. With a standing population of more than 22.7 billion, domesticated chickens far outnumber the world’s most abundant wild bird—the red-billed quelea, which has a population of about 1.5 billion. According to James Gorman of the New York Times, if you combined the mass of all these chickens, it would be greater than that of all other birds.

The world is home to such a huge number of chickens because humans can’t stop eating them. Chicken consumption is growing faster than the consumption of any other type of meat—more than 65 billion chickens were slaughtered in 2016 alone—and it is on pace to surpass pork soon as the world’s most consumed meat.

With an abundance of chicken dinners comes an abundance of chicken remains. In the wild, bird carcasses are prone to decay and are not often fossilized. But organic materials preserve well in landfills, which is where many chicken remains discarded by humans end up. Thus, these chicken bones don’t degrade, according to the study authors—they mummify. For this reason, lead study author Carys E. Bennett tells Sam Wong of New Scientist that chickens are “a potential future fossil of this age.”

The modern chicken’s strange and singular features also make it a good candidate to represent the current era of human-directed change. The domestication of chickens started around 8,000 years ago, but humans have come up with a number of innovations to feed our growing hunger for chicken products. Modern broiler chickens, which is the variety farmed for meat, are bred to be four or five times heavier than they were in the 1950s. They are transported to slaughterhouses once they reach an age of between five and seven weeks, which may seem like a short lifespan, but in reality, they would not be able to survive much longer.

“In one study, increasing their slaughter age from five weeks to nine weeks resulted in a sevenfold increase in mortality rate,” the study authors write. “The rapid growth of leg and breast muscle tissue leads to a relative decrease in the size of other organs such as the heart and lungs, which restricts their function and thus longevity. Changes in the centre of gravity of the body, reduced pelvic limb muscle mass and increased pectoral muscle mass cause poor locomotion and frequent lameness.”

These chickens are, unsurprisingly, unlike any the world has seen before. The study authors compared data on modern broilers to zooarchaeological information recorded by the Museum of London Archaeology. Today’s domestic chickens are descended from a bird called the red junglefowl, Gallus gallus, and related species that might have bread with G. gallus, Andrew Lawler and Jerry Adler explain for Smithsonian magazine. The researchers found that between the 14th and 17th centuries, domestication caused chickens to become noticeably larger than their wild progenitors. But those chickens had nothing on the fowls of today. “There has been a steady increase in growth rate since 1964,” the study authors write, “and the growth rate of modern broilers is now three times higher than that of the red junglefowl.”

So the next time you tuck into a plate of drumsticks or wings, remember: archaeologists of the future may one day be able to find and identify your meal.

Why Did Humans Lose Their Fur?


We are the naked apes of the world, having shed most of our body hair long ago.

 

Homo neanderthalensis
Homo neanderthalensis, the earlier relatives of Homo sapiens, also evolved to shed most of their body hair. (Reconstruction based on Shanidar 1 by John Gurche / National Museum of Natural History)

Millions of modern humans ask themselves the same question every morning while looking in the mirror: Why am I so hairy? As a society, we spend millions of dollars per year on lip waxing, eyebrow threading, laser hair removal, and face and leg shaving, not to mention the cash we hand over to Supercuts or the neighborhood salon. But it turns out we are asking the wrong question—at least according to scientists who study human genetics and evolution. For them, the big mystery is why we are so hairless.

Evolutionary theorists have put forth numerous hypotheses for why humans became the naked mole rats of the primate world. Did we adapt to semi-aquatic environments? Does bare skin help us sweat to keep cool while hunting during the heat of the day? Did losing our fur allow us to read each other’s emotional responses such as fuming or blushing? Scientists aren’t exactly sure, but biologists are beginning to understand the physical mechanism that makes humans the naked apes. In particular, a recent study in the journal Cell Reports has begun to depilate the mystery at the molecular and genetic level.

Sarah Millar, co-senior author of the new study and a dermatology professor at the University of Pennsylvania’s Perelman School of Medicine, explains that scientists are largely at a loss to explain why different hair patterns appear across human bodies. “We have really long hair on our scalps and short hair in other regions, and we’re hairless on our palms and the underside of our wrists and the soles of our feet,” she says. “No one understands really at all how these differences arise.”

In many mammals, an area known as the plantar skin, which is akin to the underside of the wrist in humans, is hairless, along with the footpads. But in a few species, including polar bears and rabbits, the plantar area is covered in fur. A researcher studying the plantar region of rabbits noticed that an inhibitor protein, called Dickkopf 2 or Dkk2, was not present in high levels, giving the team the fist clue that Dkk2 may be fundamental to hair growth. When the team looked at the hairless plantar region of mice, they found that there were high levels of Dkk2, suggesting the protein might keep bits of skin hairless by blocking a signaling pathway called WNT, which is known to control hair growth.

To investigate, the team compared normally developing mice with a group that had a mutation which prevents Dkk2 from being produced. They found that the mutant mice had hair growing on their plantar skin, providing more evidence that the inhibitor plays a role in determining what’s furry and what’s not.

But Millar suspects that the Dkk2 protein is not the end of the story. The hair that developed on the plantar skin of the mice with the mutation was shorter, finer and less evenly spaced than the rest of the animals’ hair. “Dkk2 is enough to prevent hair from growing, but not to get rid of all control mechanisms. There’s a lot more to look at.”

Even without the full picture, the finding could be important in future research into conditions like baldness, since the WNT pathway is likely still present in chrome domes—it’s just being blocked by Dkk2 or similar inhibitors in humans. Millar says understanding the way the inhibitor system works could also help in research of other skin conditions like psoriasis and vitiligo, which causes a blotchy loss of coloration on the skin.

Australopithecus afarensis
A reconstruction of the head of human ancestor Australopithecus afarensis, an extinct hominin that lived between about 3 and 4 million years ago. The famous Lucy skeleton belongs to the species Australopithecus afarensis

With a greater understanding of how skin is rendered hairless, the big question remaining is why humans became almost entirely hairless apes. Millar says there are some obvious reasons—for instance, having hair on our palms and wrists would make knapping stone tools or operating machinery rather difficult, and so human ancestors who lost this hair may have had an advantage. The reason the rest of our body lost its fur, however, has been up for debate for decades.

One popular idea that has gone in and out of favor since it was proposed is called the aquatic ape theory. The hypothesis suggests that human ancestors lived on the savannahs of Africa, gathering and hunting prey. But during the dry season, they would move to oases and lakesides and wade into shallow waters to collect aquatic tubers, shellfish or other food sources. The hypothesis suggests that, since hair is not a very good insulator in water, our species lost our fur and developed a layer of fat. The hypothesis even suggests that we might have developed bipedalism due to its advantages when wading into shallow water. But this idea, which has been around for decades, hasn’t received much support from the fossil record and isn’t taken seriously by most researchers.

A more widely accepted theory is that, when human ancestors moved from the cool shady forests into the savannah, they developed a new method of thermoregulation. Losing all that fur made it possible for hominins to hunt during the day in the hot grasslands without overheating. An increase in sweat glands, many more than other primates, also kept early humans on the cool side. The development of fire and clothing meant that humans could keep cool during the day and cozy up at night.

But these are not the only possibilities, and perhaps the loss of hair is due to a combination of factors. Evolutionary scientist Mark Pagel at the University of Reading has also proposed that going fur-less reduced the impact of lice and other parasites. Humans kept some patches of hair, like the stuff on our heads which protects from the sun and the stuff on our pubic regions which retains secreted pheromones. But the more hairless we got, Pagel says, the more attractive it became, and a stretch of hairless hide turned into a potent advertisement of a healthy, parasite-free mate.

One of the most intriguing theories is that the loss of hair on the face and some of the hair around the genitals may have helped with emotional communication. Mark Changizi, an evolutionary neurobiologist and director of human cognition at the research company 2AI, studies vision and color theory, and he says the reason for our hairless bodies may be in our eyes. While many animals have two types of cones, or the receptors in the eye that detect color, humans have three. Other animals that have three cones or more, like birds and reptiles, can see in a wide range of wavelengths in the visible light spectrum. But our third cone is unusual—it gives us a little extra power to detect hues right in the middle of the spectrum, allowing humans to pick out a vast range of shades that seem unnecessary for hunting or tracking.

Changizi proposes that the third cone allows us to communicate nonverbally by observing color changes in the face. “Having those two cones detecting wavelengths side by side is what you want if you want to be sensitive to oxygenation of hemoglobin under the skin to understand health or emotional changes,” he says. For instance, a baby whose skin looks a little green or blue can indicate illness, a pink blush might indicate sexual attraction, and a face flushing with red could indicate anger, even in people with darker skin tones. But the only way to see all of these emotional states is if humans lose their fur, especially on their faces.

In a 2006 paper in Biology Letters, Changizi found that primates with bare faces and sometimes bare rumps also tended to have three cones like humans, while fuzzy-faced monkeys lived their lives with just two cones. According to the paper, hairless faces and color vision seem to run together.

Millar says that it’s unlikely that her work will help us directly figure out whether humans are swimming apes, sweaty monkeys or blushing primates. But combining the new study’s molecular evidence of how hair grows with physical traits observed in humans will get us closer to the truth—or at least closer to a fuller, shinier head of hair.

Sharks Have Existed More or Less Unchanged For Millions of Years, Until Now


Shark populations off the east coast of Australia have been declining over the past 55 years with little sign of recovery, according to research published in the journal Communications Biology.

Coastal shark numbers are continuing a 50-year decline, contradicting popular theories of exploding shark populations, according to an analysis of Queensland Shark Control Program data.

University of Queensland and Griffith University researchers analysed data from the program, which has used baited drumlines and nets since 1962 to and now covers 1,760 km of the Queensland coastline.

Chris Brown from Griffith’s Australian Rivers Institute says the results show consistent and widespread declines of apex sharks — tiger white sharks and hammerheads — along Queensland’s coastline.

main article image

“We were surprised at how rapid these declines were, especially in the early years of the shark control program. We had to use specialist statistical methods to properly estimate the declines, because they occurred so quickly,” says Brown.

“We were also surprised to find the declines were so consistent across different regions.”

Some species, such as hammerhead sharks, were recognised internationally as being at risk of extinction.

“Sharks are an important part of Australia’s identity. They are also survivors that have been around for hundreds of millions of years, surviving through the extinction of dinosaurs,” he says.

“It would be a great tragedy if we lost these species because of preventable human causes.

“Sharks play important roles in ecosystems as scavengers and predators, and they are indicators of healthy ecosystems. These declines are concerning because they suggest the health of coastal ecosystems is also declining.”

George Roff, a UQ School of Biological Sciences researcher, says historical baselines of Queensland shark populations are largely unknown despite a long history of shark exploitation by recreational and commercial fisheries.

“Explorers in the 19th century once described Australian coastlines as being chock-full of sharks, yet we don’t have a clear idea of how many sharks there used to be on Queensland beaches,” he says.

“Shark populations around the world have declined substantially in recent decades, with many species being listed as vulnerable and endangered.”

Researchers discuss their findings:

The research team reconstructed historical records of shark catches to explore changes in the number and sizes of sharks over the past half century.

“What we found is that large apex sharks such as hammerheads, tigers and white sharks, have declined by 74 to 92 per cent along Queensland’s coast,” Roff says.

“And the chance of zero catch – catching no sharks at any given beach per year – has increased by as much as seven-fold.

“The average size of sharks has also declined – tiger sharks and hammerhead sharks are getting smaller.”

“We will never know the exact numbers of sharks in our oceans more than half a century ago, but the data points to radical changes in our coastal ecosystems since the 1960s.

“The data acts as a window into the past, revealing what was natural on our beaches, and provides important context for how we manage sharks.

“What may appear to be increases in shark numbers is in reality a fraction of past baselines, and the long-term trend shows ongoing declines.

“While often perceived as a danger to the public, sharks play important ecological roles in coastal ecosystems.

“Large apex sharks are able to prey on larger animals such as turtles, dolphins and dugongs, and their widespread movement patterns along the coastline connects coral reefs, seagrass beds and coastal ecosystems.

“Such losses of apex sharks is likely to have changed the structure of coastal food webs over the past half century.”

How Neanderthal DNA might have shaped some human brains


Gene variants acquired through interbreeding seem to give some people with European ancestry more elongated brains.

 

 

CT scans of a neanderthal cranium (l) and a modern human (r) rotating on a black background

Neanderthal skulls (left) are more elongated than modern-human skulls.

No human has the brain of a Neanderthal — but some have hints of its shape.

The brain shape of some people with European ancestry is influenced by Neanderthal DNA acquired through interbreeding tens of thousands of years ago, researchers report on 13 December in Current Biology1.

These DNA variants seem to affect the expression of two genes in such a way as to make the brains of some humans slightly less round, and more like the Neanderthals’ elongated brains.

“It’s a really subtle shift in the overall roundedness,” says team member Philipp Gunz, a palaeoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “I don’t think you would see it with your naked eye. These are not people that would look Neanderthal-like.”

The Neanderthal DNA variants alter gene expression in brain regions involved in planning, coordination and learning of movements. These faculties are used in speech and language, but there is no indication that the Neanderthal DNA affects cognition in modern humans.

Instead, the researchers say, their discovery points to biological changes that might have endowed the human brain with its distinct shape.

Changing brains

Earlier this year, Gunz and two colleagues determined that the rounded brain shape of modern humans evolved gradually, reaching its current appearance between 35,000 and 100,000 years ago2. The earliest human fossils from across Africa, dating to around 200,000–300,000 years ago, have large yet elongated brains. “There really is something going on in the brain that changes over time in the Homo sapiens lineage,” says Gunz.

Given that brains don’t fossilize well, looking at how Neanderthal DNA affects human biology is one of the only ways to study differences between the species, says Tony Capra, an evolutionary geneticist at Vanderbilt University in Nashville, Tennessee. “We’re never going to be able to dig up a Neanderthal brain intact and compare it to our brain,” he says.

So the team set out to identify DNA variants that contributed to humans’ rounded brains. They hypothesized that some Neanderthal variants — which all humans with Eurasian ancestry carry — might affect H. sapiens brain shape and make it more elongated.

They first analysed brain scans from 4,468 people of European ancestry, and quantified their overall roundedness. The researchers then tested whether any of about 50,000 Neanderthal DNA variants known to occur in some modern humans were associated with difference in their brain shape.

They pinpointed variants near two genes. The variants don’t alter the shape of the proteins those genes encode — but rather, where in the brain they are made.

Neanderthal variants near a gene called UBR4, which has a role in making neurons, reduce that gene’s expression in deep brain structures called the basal ganglia.

People with a Neanderthal variant near a gene called PHLPP1, which is involved in building the fatty sheaths that insulate nerves, have greater expression of that gene in their cerebellums.

Important function

Cedric Boeckx, a neuroscientist at the Catalan Institute for Research and Advanced Studies in Barcelona, Spain, is intrigued by the brain regions in which expression of these genes is altered, which have previously been linked to human cognition, and to either the absence of or suppression of Neanderthal genes.

For example, a 2017 study found that the expression of Neanderthal genes tends to be suppressed in the basal ganglia and cerebellum3, suggesting that the human versions of the genes are important to brain function.

Speech and tool use are also likely to depend on exquisite motor control underpinned by these regions, notes Simon Fisher, a neurogeneticist at the Max Planck Institute for Psycholinguistics in Nijmegen, the Netherlands, who led the latest study.

Fisher co-discovered a gene implicated in language, FOXP2, that influences brain circuits in the basal ganglia and cerebellum. A study in 2014 found that FOXP2 lies in a large swathe of the human genome that contains no Neanderthal variants.4

Yet the researchers say there is no evidence that the variants they identified in the new study affect language or any trait other than brain shape.

And, both Fisher and Boeckx say that many more genes, active in different parts of brain, probably also affect the brain’s roundedness. “We don’t see this as something where this is a single gene that magically changed brain shape,” Fisher says.

Next, his team plans to look for more variants that affect this trait in the UK Biobank database, which is gathering brain scans and genome data for 100,000 people. “We need to go and find more of these genes,” he says.

Ancient Aquatic Flora Was among the First Flowering Plants


Pyrenees fossils suggest the Montsechia lived up to 130 million years ago and is the earliest known example of a fully submerged aquatic flowering plant

Ancient Aquatic Flora Was among the First Flowering Plants
This is a large intact specimen of the fossil, Montsechia. Usually only small fragmentary pieces of the fossil are found.   

 

Photosynthesis – the ability to convert energy from the sun into fuel – first appeared on Earth in single-celled organisms, which eventually evolved into algae, then mosses, then ferns. Flowering plants, now such a familiar part of our landscape, didn’t evolve until the Jurassic period, after dinosaurs and mammals had already hit the scene. At this time, insects were diversifying, and the evolving plants used the emerging bugs to carry their own genetic material from plant to plant. Flowering plants, also known as angiosperms, are a product of this early version of sex and its exchange of genetic material – so important in evolution.

A recent discovery and analysis of fossilized plants has opened up the discussion of the nature and relationships of these early plants. First found in the lithographic limestone being mined in the Pyrenees Mountains over 100 years ago, these fossils, with their strange sprawling stems, were little understood. Some thought they were mosses, some considered them to be conifers, but few recognized the fossils as flowering plants.

Now my colleagues and I, on a team of paleobotantists led by Bernard Gomez of Lyon, France, have presented evidence that this fossil, Montsechia, which lived as long ago as 130 million years, is the earliest known example of a fully submerged aquatic flowering plant. After careful analysis of hundreds of well-preserved newly collected fossils from northeastern Spain, we believe Montsechia flowered underwater and was pollinated underwater, living in a similar fashion to the plantCeratophyllum that’s found around the world today.

Flowers are all about sex and getting new genetic material into the breeding line. Montsechia is an example of a very early line of evolution that solved this challenge in a new and novel way – relying on water to disperse its pollen, not the wind or animal pollinators.

The plant we see in these new old fossils
Based on the many fossil examples we examined, Montsechia floated in freshwater lakes and was submerged in the water. It had a spreading growth, branching freely. This flowering plant didn’t display any of the showy blossoms we tend to associate with flowers. But because it contains seeds enclosed in a fruit, the basic characteristic of angiosperms, it is classified as a flowering plant.

We’ve found two forms of this fossil: one form has leaves that are small and closely pressed to the stem. On this form, we frequently saw mature fruits.

The other form has leaves that extend out from the stems and only rarely are mature seeds found attached. We saw the two leaf types associated together at the same fossil localities.

Today, many flowers are made up of petals and then male stamens (with filaments and anthers that produce pollen) and female carpels (which mature into fruits and contain the seeds, like peas in a pod). We didn’t identify any male flowers or remains of where they were borne on the stems in Montsechia. It appears they had separate flowers to contain pollen organs and carpels.

Fishing around for the first flower
When asking the question of what the first flower in the world was like, 30 years ago some botanists said that magnolias were the typical form. Later, others suggested that perhaps water lily flowers may be a better choice.

Then the tools of molecular systematics allowed botanists to use DNA and RNA from the nuclei and chloroplasts of plant cells to puzzle out relationships based on molecular characteristics. That’s when a genus calledAmborella, found living today only in New Caledonia, gained favor as a possible first flowering plant.

Another contender, Ceratophyllum, was also once thought to be basal to all flowering plants before being displaced by Amborella, and its position in the angiosperms has been uncertain since. Montsechia, at 130 million years old – among the oldest megafossil remains known of any flowering plant – is in the lineage of Ceratophyllum. This makes this lineage of flowering plants one of the oldest known and suggests that underwaterCeratophyllum is back in the running to be the original flowering plant.

Ceratophyllum, modern descendent of first flower
Ceratophyllum consists of six species found around the world today in the single genus in its own order, Ceratophyllales. These plants, known as foxtails, live in freshwater lakes on all continents of the world today, save Antarctica.

These modern-day descendents ofMontsechia have separate male and female flowers with no sepals or petals, just simple reproductive organs, like stamens and carpels. When they reproduce, the stamens release the anthers that contain the pollen to float up to the water’s surface. Then the pollen is released and begins to slowly sink through the water column. As it descends, being moved by water currents, a branched pollen tube grows out. When the pollen tube makes it into the vicinity of a female, a branch will find a small hole enter and pollinate. This is how the plant fertilizes and creates a seed.

Because of the water dispersal of the pollen there is genetic mixing or outcrossing, just as if an insect had carried the pollen.

The fossil fruits of Montsechia also have a similar small pore in the fruit wall, and the seed is positioned similarly as those of Ceratophyllum today. This suggests that these very ancient flowers flowered underwater, were very simple in nature (no beautiful petals yet) and were pollinated underwater. This very early and inventive way for flowering plants to manage their reproduction so early in their evolution is impressive.

Montsechia places the Ceratophyllumlineage as one of the oldest of all the flowering plants and suggests that we need to reevaluate the nature of the evolution of the original angiosperm again.

Why Red Algae Never Packed Their Bags for Land


Red algae have shockingly few genes for a multicellular organism – far fewer than a single-celled green alga – and this may explain why they never colonized land.

Why Red Algae Never Packed Their Bags for Land

Red algae are the great “also-ran” of plant evolution. Though they are by far the most diverse seaweeds in the ocean, they rarely occur in freshwater and never on land, and so almost no one has ever heard of them (though if you’ve ever eaten sushi, you’ve certainly had an intimate red algal encounter).

Why this might be has long been a mystery. But a team of European scientists discovered in 2013 that they have shockingly few genes for a multicellular organism – far fewer even than several single-celled green algae. And this may explain why such a diverse and abundant group of algae never packed their bags for land and why, when you look outside your window, you see a sea of green and not red. What happened to the poor red algae? But first, you may be wondering something even more basic — what are red algae?

Red algae — again, seaweed — are red thanks to the light-harvesting pigment phycoerythrin. Red light does not penetrate water well. Blue light does – it is the last color to disappear in the twilight zone. Phycoerythrin absorbs and harvests energy from blue light and reflects red, which gives algae that possess it an advantage in living in deeper water. Of course, red algae also have chlorophyll like other photosynthetic organisms, and not all red algae look red. Some appear blue or green due to an abundance of other pigments and a dearth of phycoerythrin. Some red algae don’t look like seaweeds and actually build hard skeletons for themselves like coral and are called, aptly, “coralline algae“.

Two famous economically important products are made from red algae. Carrageenans, the gelatinous texturing agents that make everything from ice cream to salad dressing creamy smooth, are extracted from their cell walls. And nori – the ubiquitous seaweed sushi wrapper — is made from red algae in spite of its dried dark olive hue.

Red algae have been around a long time. They represent the first identifiable fossils we have of complex, sexually reproducing life. Yet they have also long been known to possess certain quirks. One of the quirkiest: they lack flagella, beating cellular tails so widespread that even we have them (or rather, men do) along with such distant relatives as ferns and fungus-like plant pathogens called water molds. Red algae also lack centrioles, the cellular microstructures that help orchestrate cell division, although conifers, flowering plants, and most fungi also lack them.

The red alga scientists sequenced was Irish moss – Chondrus crispus – a seaweed commonly found strewn around the coasts of the north Atlantic Ocean. In its genome they found 9,606 genes. For comparison, the single-celled green alga Chlamydomonas reinhardtii has 14,516 genes while the pedestrian green plant Arabidopsis thaliana has 27,416 genes. That a large, complex organism can operate comfortably with only two-thirds of the genes of a single-celled organism is an impressive and startling discovery.

To reiterate: This organism

can run on 2/3 of the number of genes it takes to power this:

Not to scale (obviously). Most chlamydomonas range from 10-30 micrometers in length. Creative Commons Ninghui Shi.

Chondrus also seems to have stripped down its genome to the essentials, eliminating genes that perform redundant functions in other organisms. It has 82 genes for making ribosomes, compared with 349 in the green plant Arabidopsis. What genes it does have are very closely spaced.

In addition to lacking any flagella-specific genes — which was no surprise given that red algae have no flagella – irish moss possessed only one light-sensing protein: a cryptochrome. Light sensing proteins permit organisms to “see”; yours are located in your retina. Plants use their light-sensing proteins to direct their growth and development, and most have several. So for a photosynthetic organism to possess only one was another big surprise.

C. crispus also has very few introns – sections of RNA inside genes that get edited out during the production of proteins. The few it has are small and probably serve vital regulatory functions, increasing or decreasing protein production as conditions warrant. The rest of the eukaryotes – all Earthly life except for bacteria and archaea — have introns galore.

Together, this evidence led the team of scientists to suggest that the red algae experienced an “evolutionary bottleneck” – an event in which the population of red algae and their genomes shrank drastically. The scientists propose that sometime soon after red algae evolved they adapted to an environment that exerted strong selective pressure for small body size, the ability to get by on very little food, or perhaps both. The consequence was the drastic reduction in genome size, pruning introns, non-coding DNA, and superfluous genes from the genome.

What might have precipitated this bottleneck? The authors suggest that the habits of the red algae Cyanidioschyzon merolae and Galdieria suphuraria may hold a clue: they both live in hot, acidic water. A genome squeeze induced by such an extreme environment may also explain why Chondrus has an unusually high number of genes with no known counterparts in other organisms. Once red algae left the confines of their acid bath, they may have been forced to reinvent genes from scratch for many functions needed in ordinary seawater.

It isn’t apparent why acidic hot water should favor small genomes, but it apparently does in living red algae. Since cyanobacteria(blue-green algae) – the probable chief competitors of early red algae – are known to avoid the stuff, these forbidding environments may have provided a golden opportunity for early red algae to thrive in a place few other organisms were exploiting. On the other hand, their trial by fire may have condemned them to eternal imprisonment in the sea. Without a large and redundant genome from which evolution could play and easily create new genes, they lacked the genetic potential necessary to leave the ocean for the brave new world of land.

Reference

Collén, Jonas, Betina Porcel, Wilfrid Carré, Steven G. Ball, Cristian Chaparro, Thierry Tonon, Tristan Barbeyron et al. “Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.” Proceedings of the National Academy of Sciences 110, no. 13 (2013): 5247-5252.

How the First Plant Came to Be


A genetic analysis reveals the ancient, complex–and symbiotic–roots of photosynthesis in plants

How the First Plant Came to Be

Earth is the planet of the plants—and it all can be traced back to one green cell. The world’s lush profusion of photosynthesizers—from towering redwoods to ubiquitous diatoms—owe their existence to a tiny alga eons ago that swallowed a cyanobacteria and turned it into an internal solar power plant.

By studying the genetics of a glaucophyte—one of a group of just 13 unique microscopic freshwater blue-green algae, sometimes called “living fossils”—an international consortium of scientists led by molecular bioscientist Dana Price of Rutgers University, has elucidated the evolutionary history of plants. The glaucophyte Cyanophora paradoxa still retains a less domesticated version of this original cyanobacteria than most other plants.

According to the analysis of C. paradoxa‘s genome of roughly 70 million base pairs, this capture must have occurred only once because most modern plants share the genes that make the merger of photosynthesizer and larger host cell possible. That union required cooperation not just from the original host and the formerly free-ranging photosynthesizer but also, apparently, from a bacterial parasite. Chlamydia-like cells, such as Legionella (which includes the species that causes Legionnaire’s disease), provided the genes that enable the ferrying of food from domesticated cyanobacteria, now known as plastids, or chloroplasts, to the host cell.

“These three entities forged the nascent organelle, and the process was aided by multiple horizontal gene transfers as well from other bacteria,” explains biologist Debashish Bhattacharya of Rutgers University, whose lab led the work published in Science on February 17. “Gene recruitment [was] likely ongoing” before the new way of life prospered and the hardened cell walls of most plants came into being.

In fact, such a confluence of events is so rare that evolutionary biologists have found only one other example: the photosynthetic amoeba Paulinella domesticated cyanobacteria roughly 60 million years ago. “The amoeba plastid is still a ‘work in progress’ in evolutionary terms,” Bhattacharya notes. “We are now analyzing the genome sequence from Paulinella to gain some answers” as to how these events occur.

The work provides the strongest support yet for the hypothesis of late biologist Lynn Margulis, who first proposed in the 1960s to widespread criticism the theory that all modern plant cells derived from such a symbiotic union, notes biologist Frederick Spiegel of the University of Arkansas in Fayetteville, who was not involved in the work. That thinking suggests that all plants are actually chimeras—hybrid creatures cobbled together from the genetic bits of this ancestral union, including the enabling parasitic bacteria.

The remaining question is why this complex union took place roughly 1.6 billion years ago. One suggestion is that local conditions may have made it more beneficial for predators of cyanobacteria to stop eating and start absorbing, due to a scarcity of prey and an abundance of sunlight. “When the food runs out but sunlight is abundant, then photosynthesis works better” to support an organism, Bhattacharya notes. And from that forced union a supergroup of extremely successful organisms—the plants—sprang.

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