Enlarge / Portion of a reproduction of cave paintings in France, showing rhinos (among other species). (credit: JEFF PACHOUD)

For most people, an extinct species is an abstraction, a set of bones they might have seen on display in a museum. For Gennady Boeskorov, they are things he has interacted with directly, studying their fur, their skin, their internal organs—experiencing these animals much as they existed thousands of years ago. Some of the well-preserved Pleistocene animals he has worked with include the mummified remains of woolly mammoths (Mammuthus primigenius), an extinct form of rabbit (Lepus tanaiticus), and cave lion cubs (Panthera spelaea).

His latest paper also makes it clear that woolly rhinoceroses belong on this list. Boeskorov is a senior researcher at the Diamond and Precious Metals Geology Institute, Siberian Branch of the Russian Academy of Sciences, as well as a professor at the North-Eastern Federal University in Yakutsk. This July, he and his colleagues described the relatively recent discovery of three woolly rhinoceros mummies, one of which is new to science, in a paper published in the journal Doklady Earth Sciences.

Woolly rhinos (Coelodonta antiquitatis) were stocky, long-haired, two-horned denizens that inhabited Eurasia during the Pleistocene, a period that includes the most recent glacial expansion. They coexisted with woolly mammoths, placing second on the list of largest animals in this ecosystem (behind their tusked proboscidean coevals), and shared a similar dense coat of hair to protect against the cold.

Enlarge (credit: BirdImages)

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.

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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.

Enlarge / The African Lungfish, showing it's thin, wispy fins. (credit: feathercollector)

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.

Enlarge / The fossil in question, oriented with its head to the left. (credit: 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.

Enlarge / Half of the upper arm bone of this species can fit comfortably in the palm of a modern human hand. (credit: 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.

Enlarge (credit: Aurich Lawson | Getty Images)

There are no wild ligers. Indeed, hybrids were once thought to be rare in nature—and of little consequence in an evolutionary sense. But now we know they can play an important role in speciation—the creation of new, genetically distinct populations.

As it turns out, hybridization in nature is quite common. Some 25 percent of plant species hybridize and some 10 percent of animals do the same.

“Hybridization as an event is rare,” said Jeremie Fant, a conservation scientist with the Chicago Botanic Garden who has worked on plant hybridization. “But in evolutionary history, it's been very common. Hybrids in the plant kingdom are everywhere. They are scattered through most lineages. When hybridization does occur, it can have important evolutionary impacts.”

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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.

Enlarge (credit: UNIVERSITY OF LAUSANNE)

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.

Enlarge (credit: C. Marsicano)

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.

Enlarge (credit: LEONELLO CALVETTI/SCIENCE PHOTO LIBRARY)

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.

Enlarge / The Baishiya Karst Cave, where the recently analyzed samples were obtained. (credit: Dongju Zhang’s group (Lanzhou University))

For well over a century, we had the opportunity to study Neanderthals—their bones, the items they left behind, their distribution across Eurasia. So, when we finally obtained the sequence of their genome and discovered that we share a genetic legacy with them, it was easy to place the discoveries into context. By contrast, we had no idea Denisovans existed until sequencing DNA from a small finger bone revealed that yet another relative of modern humans had roamed Asia in the recent past.

Since then, we've learned little more. The frequency of their DNA in modern human populations suggests that they were likely concentrated in East Asia. But we've only discovered fragments of bone and a few teeth since then, so we can't even make very informed guesses as to what they might have looked like. On Wednesday, an international group of researchers described finds from a cave on the Tibetan Plateau that had been occupied by Denisovans, which tell us a bit more about these relatives: what they ate. And that appears to be anything they could get their hands on.

The Baishiya Karst Cave

The finds come from a site called the Baishiya Karst Cave, which is perched on a cliff on the northeast of the Tibetan Plateau. It's located at a high altitude (over 3,000 meters or nearly 11,000 feet) but borders a high open plain, as you can see in the picture below.

Enlarge / An artist's conception of one of the last mammoths of Wrangel Island. (credit: 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).