The first animal genus defined purely by genetic characters represents a new era for classifying animals

Charlie Wood writes:

The world’s simplest known animal is so poorly understood that it doesn’t even have a common name. Formally called Trichoplax adhaerens for the way it adheres to glassware, the amorphous blob isn’t much to look at. At just a few millimeters across, the creature resembles a squashed sandwich in which the top layer protects, the bottom layer crawls, and the slimy stuffing sticks it all together. With no organs and just a handful of cell types, the most interesting thing about T. adhaerens might just be how stunningly boring it is.

“I was fascinated when I first heard about this thing because it has no real defined body,” said Michael Eitel, an evolutionary biologist at the Ludwig Maximilian University in Germany. “There’s no mouth, there’s no back, no nerve cells, nothing.”

But after spending four years painstakingly reconstructing the blob’s genome, Eitel might know more about the organism than anyone else on the planet. In particular, he has looked closely enough at its genetic code to learn what visual inspections failed to reveal. The variety of creature that biologists have long called T. adhaerens is really at least two, and perhaps as many as a dozen, anatomically identical but genetically distinct “cryptic species” of animals. The discovery sets a precedent for taxonomy, the science of naming organisms, as the first time a new animal genus has been defined not by appearance, but by pure genetics.

The modern taxonomic system, little changed since Carl Linnaeus laid it out in the 1750s, attempts to chop the sprawling tree of life into seven tidy levels that grant every species a unique label. The two-part scientific name (such as Homo sapiens) represents the tail end of a branching path through this tree, starting from the thickest limbs, the kingdoms, and ending at the finest twigs, the genus (Homo) and then the species (sapiens). The path tells you everything there is to know about the organism’s relationship to other groups of creatures, at least in theory. [Continue reading…]

The microbiologist who fundamentally changed the way we think about evolution and the origins of life

David Quammen writes:

On Nov. 3, 1977, a new scientific revolution was heralded to the world — but it came cryptically, in slightly confused form. The front page of that day’s New York Times carried a headline: “Scientists Discover a Form of Life That Predates Higher Organisms.” A photograph showed a man named Carl R. Woese, a microbiologist at the University of Illinois in Urbana, with his feet up on his office desk. He was 50ish, with unruly hair, wearing a sport shirt and Adidas sneakers. Behind him was a blackboard, on which was scrawled a simple treelike figure in chalk. The article, by a veteran Times reporter named Richard D. Lyons, began:

Scientists studying the evolution of primitive organisms reported today the existence of a separate form of life that is hard to find in nature. They described it as a “third kingdom” of living material, composed of ancestral cells that abhor oxygen, digest carbon dioxide and produce methane.

This “separate form of life” would become known as the archaea, reflecting the impression that these organisms were primitive, primordial, especially old. They were single-celled creatures, simple in structure, with no cell nucleus. Through a microscope, they looked like bacteria, and they had been mistaken for bacteria by all earlier microbiologists. They lived in extreme environments, at least some of them — hot springs, salty lakes, sewage — and some had unusual metabolic habits, such as metabolizing without oxygen and, as the Times account said, producing methane.

But these archaea, these whatevers, were drastically unlike bacteria if you looked at their DNA, which is what (indirectly) Woese had done. They lacked certain bits that characterized all bacteria, and they contained other bits that shouldn’t have been present. They constituted a “third kingdom” of living creatures because they fit within neither of the existing two, the bacterial kingdom (bacteria) and the kingdom of everything else (eukarya), including animals and plants, amoebas and fungi, you and me.

Charles Darwin himself suggested (first in an early notebook, later in “On the Origin of Species”) that the history of life could be drawn as a tree — all creatures originating in a single trunk, then diverging into different lineages like major limbs, branches and twigs, with leaves of the canopy representing the multiplicity of living species. But if that simile was valid, then the prevailing tree of 1977, the orthodox image of life’s history, was wrong. It showed two major limbs arising from the trunk. According to what Woese had just announced to the world, it ought to show three.

Woese was a rebel researcher, obscure but ingenious, crotchety, driven. He had his Warholian 15 minutes of fame on the front page of The Times, and then disappeared back into his lab in Urbana, scarcely touched by popular limelight throughout the remaining 35 years of his career. But he is the most important biologist of the 20th century that you’ve never heard of. He asked profound questions that few other scientists had asked. He created a method — clumsy and dangerous, but effective — for answering those questions. And in the process, he effectively founded a new branch of science.

It began with a casual suggestion made to Woese by Francis Crick, the co-discoverer of DNA’s structure, who mentioned passingly in a scientific paper that certain long molecules in living creatures, because they are built of multiple small units, coded in sequences that change gradually over time, could serve as signatures of the relatedness between one form of life and another. The more similar the sequence, the closer the relative. In other words, comparing such molecules could reveal phylogeny. The new branch of science is called molecular phylogenetics. Wrinkle your nose at that fancy phrase, if you will, and I’ll wrinkle with you, but in fact what it means is fairly simple: reading the ancient history of life from the different sequences built into such molecules. The molecules mainly in question were DNA, RNA and a few select proteins. Carried far beyond Woese and his lab, these efforts have brought unexpected and unimaginable discoveries, fundamentally reshaping what we think we know about life’s history, the process of evolution and the functional parts of living beings, including ourselves.

Woese vanished into his lab, but his insights and methods, and his successors in applying them, have produced in particular one cardinal revelation: The tree of life is not a tree. That old metaphor is obsolete. Life’s history has been far more tangled. [Continue reading…]

The new story of humanity’s origins in Africa

Ed Yong writes:

There is a decades-old origin story for our species, in which we descended from a group of hominids who lived somewhere in Africa around 200,000 years ago. Some scientists have placed that origin in East Africa; others championed a southern birthplace. In either case, the narrative always begins in one spot. Those ancestral hominids, probably Homo heidelbergensis, slowly accumulated the characteristic features of our species—the rounded skull, small face, prominent chin, advanced tools, and sophisticated culture. From that early cradle, we then spread throughout Africa, and eventually the world.

But some scientists are now arguing that this textbook narrative is wrong in its simplicity, linearity, and geography. Yes, we evolved from ancestral hominids in Africa, but we did it in a complicated fashion—one that involves the entire continent.

Consider the ancient human fossils from a Moroccan cave called Jebel Irhoud, which were described just last year. These 315,000-year-old bones are the oldest known fossils of Homo sapiens. They not only pushed back the proposed dawn of our species, but they added northwest Africa to the list of possible origin sites. They also had an odd combination of features, combining the flat faces of modern humans with the elongated skulls of ancient species like Homo erectus. From the front, they could have passed for us; from the side, they would have stood out.

Fossils from all over Africa have modern and ancient traits in varied combinations, including the 260,000-year-old Florisbad skull from South Africa; the 195,000-year-old remains from Omo Kibish in Ethiopia; and the 160,000-year-old Herto skull, also from Ethiopia. Some scientists have argued that these remains represent different subspecies of Homo sapiens, or different species altogether.

But perhaps they really were all Homo sapiens, and our species simply used to be far more diverse than we currently are. “If you look at skulls, you’ll see different features of modern humans arising in different locations at different times,” says Eleanor Scerri, an archaeologist at the University of Oxford. And the reason for that, she says, is that “we’re a species with multiple African origins.” [Continue reading…]

Mice don’t know when to let it go, either

Erica Goode reports:

Suppose that, seeking a fun evening out, you pay $175 for a ticket to a new Broadway musical. Seated in the balcony, you quickly realize that the acting is bad, the sets are ugly and no one, you suspect, will go home humming the melodies.

Do you head out the door at the intermission, or stick it out for the duration?

Studies of human decision-making suggest that most people will stay put, even though money spent in the past logically should have no bearing on the choice.

This “sunk cost fallacy,” as economists call it, is one of many ways that humans allow emotions to affect their choices, sometimes to their own detriment. But the tendency to factor past investments into decision-making is apparently not limited to Homo sapiens.

In a study published on Thursday in the journal Science, investigators at the University of Minnesota reported that mice and rats were just as likely as humans to be influenced by sunk costs. [Continue reading…]

What enabled animal life to get more complex and diverse during the Cambrian explosion?

Jordana Cepelewicz writes:

When Emma Hammarlund of Lund University in Sweden first reached out to her colleague Sven Påhlman for help with her research, he was skeptical he’d have much insight to offer. He was a tumor biologist, after all, and she was a geobiologist, someone who studied the interplay between living organisms and their environment. Påhlman didn’t see how his work could possibly inform her search for answers about the rapid proliferation and diversification of animal life that, half a billion years ago, forever changed Earth’s evolutionary landscape.

In spite of Påhlman’s initial reservations, however, the pair has collaborated over the past four years to put forth a new interdisciplinary hypothesis, published in Nature Ecology & Evolution earlier this year, explaining why it took so long for animals to burst onto the scene.

For most of its 4.5-billion-year history, Earth has sustained life — but that life was largely limited to microbial organisms: bacteria, plankton, algae. Not until about 540 million years ago did larger, more complex species begin to dominate the oceans, but within just a few tens of millions of years (a blip on the evolutionary timescale), the planet had filled up with all kinds of animals. The fossil record from that period shows the beginnings of almost all modern animal lineages: animals with shells and animals with spines, animals that swam and animals that burrowed, animals that could hunt and animals that could defend themselves from predators.

Like many biologists, Hammarlund wondered why it took so long for complex animals to emerge — and why, when they finally did, it happened so suddenly. One of the leading theories about this hotly debated question holds that a skyrocketing rise in atmospheric oxygen around that time triggered what’s known as the Cambrian explosion. Earlier, when oxygen was scarce, the simple animals in the seas had anaerobic metabolisms that did not depend on it, and they even found oxygen problematic if not toxic. By shifting to aerobic respiration, however, animals gained an enormous metabolic advantage because the amount of energy that cells could produce per respiration cycle increased nearly twentyfold. That extra energy may have been what powered the greater complexity witnessed during the Cambrian period: increased biomass, improvements in their cellular systems, more complex body structures, and the capacity for energy-intensive movement and predation. [Continue reading…]

Tiny brains of extinct human relative had complex features

The New York Times reports:

What makes humans so smart? For a long time the answer was simple: our big brains.

But new research into the tiny noggins of a recently discovered human relative called Homo naledi may challenge that notion. The findings, published Monday, suggest that when it comes to developing complex brains, size isn’t all that matters.

In 2013 scientists excavating a cave in South Africa found remains of Homo naledi, an extinct hominin now thought to have lived 236,000 to 335,000 years ago. Based on the cranial remains, the researchers concluded it had a small brain only about the size of an orange or your fist. Recently, they took another look at the skull fragments and found imprints left behind by the brain. The impressions suggest that despite its tiny size, Homo naledi’s brain shared a similar shape and structure with that of modern human brains, which are three times as large.

“We’ve now seen that you can package the complexity of a large brain in a tiny packet,” said Lee Berger, a paleoanthropologist at Wits University in South Africa and an author of the paper published in the journal Proceedings of the National Academy of Sciences. “Almost in one fell swoop we slayed the sacred cow that complexity in the hominid brain was directly associated with increasing brain size.” [Continue reading…]

Evolution tracks predictable ways of being

Ed Yong writes:

Most people go to Hawaii for the golden beaches, the turquoise seas, or the stunning weather. Rosemary Gillespie went for the spiders.

Situated around 2,400 miles from the nearest continent, the Hawaiian Islands are about as remote as it’s possible for islands to be. In the last 5 million years, they’ve been repeatedly colonized by far-traveling animals, which then diversified into dozens of new species. Honeycreeper birds, fruit flies, carnivorous caterpillars … all of these creatures reached Hawaii, and evolved into wondrous arrays of unique forms.

So did the spiders. There are happy-face spiders whose abdomens look like emojis, and which Gillespie started studying in 1987. There are appropriately named long-jawed spiders, which caught her attention years later. Spiders have so repeatedly radiated on Hawaii that scientists often discover entirely new groups of species at once, allowing them to have some taxonomic fun. One genus was named Orsonwelles and each species is named after one of the director’s films; another group is named after all the characters from the film Predator. “The diversity is extraordinary,” says Gillespie, an evolutionary biologist at UC Berkeley.

The most spectacular of these spider dynasties, Gillespie says, are the stick spiders. They’re so-named because some of them have long, distended abdomens that make them look like twigs. “You only see them at night, walking around the understory very slowly,” Gillespie says. “They’re kind of like sloths.” Murderous sloths, though: Their sluggish movements allow them to sneak up on other spiders and kill them.

During the day, stick spiders hide, relying on their camouflage to protect them from the beaks of honeycreepers. Each of Hawaii’s islands has species of stick spider that come in three distinctive colors—shiny gold, dark brown, and matte white. Go to Oahu and you’ll find all three kinds. Head to East Maui and you’ll see the same trio. It would be tempting to think that the same three species of stick spider, one for each color, have traveled throughout the island chain. But the truth is much stranger.

Gillespie has shown that the gold spiders on Oahu belong to a different species from those on Kauai or Molokai. In fact, they’re more closely related to their brown and white neighbors from Oahu. Time and again, these spiders have arrived on new islands and evolved into new species—but always in one of three basic ways. A gold spider arrives on Oahu, and diversified into gold, brown, and white species. Another gold spider hops across to Maui and again diversified into gold, brown, and white species. “They repeatedly evolve the same forms,” says Gillespie.

Gillespie has seen this same pattern before, among Hawaii’s long-jawed goblin spiders. Each island has its own representatives of the four basic types: green, maroon, small brown, and large brown. At first, Gillespie assumed that all the green species were related to each other. But the spiders’ DNA revealed that the ones that live on the same islands are most closely related, regardless of their colors. They too have hopped from one island to another, radiating into the same four varieties wherever they land.

One of the most common misunderstandings about evolution is that it is a random process. Mutations are random, yes, but those mutations then rise and fall in ways that are anything but random. [Continue reading…]

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We reconstructed the genome of the ‘first animal’

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By Jordi Paps, University of Essex

The first animals emerged on Earth at least 541m years ago, according to the fossil record. What they looked like is the subject of an ongoing debate, but they’re traditionally thought to have been similar to sponges.

Like today’s animals, they were made up of many, many different cells doing different jobs, programmed by thousands of different genes. But where did all these genes come from? Was the emergence of animals a small step in evolution, or did it represent a big leap in the DNA that carries the instructions for life?

To answer these questions and more, my colleague and I have reconstructed the set of genetic instructions (a minimal genome) present in the last common ancestor of all animals. By comparing this ancestral animal genome to those of other ancient lifeforms, we’ve shown that the emergence of animals involved a lot of very novel changes in DNA. What’s more, some of these changes were so essential to the biology of animals that they are still found in most modern animals after more than 500m years of independent evolution. In fact, most of our own genes are descended from this “first animal”.

Previous research on lifeforms that are closely related to animals – single-celled organisms such as choanoflagellates, filastereans and ichthyosporeans – has shown they share many genes with their animal cousins. This means that these genes are older than animals themselves and date back to some common ancestor of all these creatures. So the recycling of old genes into new functions, a kind of genome tinkering, must have been an important force in the origin of animals.

But Professor Peter Holland and I wanted to find out which new genes emerged when animals evolved. We used sophisticated computer programs to compare 1.5m proteins (the molecules that genes contain the instructions for) across 62 living genomes, making a total of 2.25 trillion comparisons to find out which genes are shared between different organisms today.

[Read more…]

Are we smart enough to know how smart animals are?

Frans de Waal asks: are we smart enough to know how smart animals are?

Just as attitudes of superiority within segments of human culture are often expressions of ignorance, humans collectively — especially when subject to the dislocating effects of technological dependence — tend to underestimate the levels of awareness and cognitive skills of creatures who live mostly outside our sight. This tendency translates into presuppositions that need to be challenged by what de Waal calls his “cognitive ripple rule”:

Every cognitive capacity that we discover is going to be older and more widespread than initially thought.

In a review of de Waal’s book, Are We Smart Enough to Know How Smart Animals Are?, Ludwig Huber notes that there are a multitude of illustrations of the fact that brain size does not correlate with cognitive capacities.

Whereas we once thought of humans as having unique capabilities in learning and the use of tools, we now know these attributes place us in a set of species that also includes bees. Our prior assumptions about seemingly robotic behavior in such creatures turns out to have been an expression of our own anthropocentric prejudices.

Huber writes:

Various doctrines of human cognitive superiority are made plausible by a comparison of human beings and the chimpanzees. For questions of evolutionary cognition, this focus is one-sided. Consider the evolution of cooperation in social insects, such as the Matabele ant (Megaponera analis). After a termite attack, these ants provide medical services. Having called for help by means of a chemical signal, injured ants are brought back to the nest. Their increased chance of recovery benefits the entire colony. Red forest ants (Myrmica rubra) have the ability to perform simple arithmetic operations and to convey the results to other ants.

When it comes to adaptations in animals that require sophisticated neural control, evolution offers other spectacular examples. The banded archerfish (Toxotes jaculatrix) is able to spit a stream of water at its prey, compensating for refraction at the boundary between air and water. It can also track the distance of its prey, so that the jet develops its greatest force just before impact. Laboratory experiments show that the banded archerfish spits on target even when the trajectory of its prey varies. Spit hunting is a technique that requires the same timing used in throwing, an activity otherwise regarded as unique in the animal kingdom. In human beings, the development of throwing has led to an enormous further development of the brain. And the archerfish? The calculations required for its extraordinary hunting technique are based on the interplay of about six neurons. Neural mini-networks could therefore be much more widespread in the animal kingdom than previously thought.

Research on honeybees (Apis mellifera) has brought to light the cognitive capabilities of minibrains. Honeybees have no brains in the real sense. Their neuronal density, however, is among the highest in insects, with roughly 960 thousand neurons—far fewer than any vertebrate. Even if the brain size of honeybees is normalized to their body size, their relative brain size is lower than most vertebrates. Insect behavior should be less complex, less flexible, and less modifiable than vertebrate behavior. But honeybees learn quickly how to extract pollen and nectar from a large number of different flowers. They care for their young, organize the distribution of tasks, and, with the help of the waggle dance, they inform each other about the location and quality of distant food and water.

Early research by Karl von Frisch suggested that such abilities cannot be the result of inflexible information processing and rigid behavioral programs. Honeybees learn and they remember. The most recent experimental research has, in confirming this conclusion, created an astonishing picture of the honeybee’s cognitive competence. Their representation of the world does not consist entirely of associative chains. It is far more complex, flexible, and integrative. Honeybees show configural conditioning, biconditional discrimination, context-dependent learning and remembering, and even some forms of concept formation. Bees are able to classify images based on such abstract features as bilateral symmetry and radial symmetry; they can comprehend landscapes in a general way, and spontaneously come to classify new images. They have recently been promoted to the set of species capable of social learning and tool use.

In any case, the much smaller brain of the bee does not appear to be a fundamental limitation for comparable cognitive processes, or at least their performance. Jumping spiders and cephalopods are similarly instructive. The similarities between mammals and bees are astonishing, but they cannot be traced to homologous neurological developments. As long as the animal’s neural architecture remains unknown, we cannot determine the cause of their similarity. [Continue reading…]

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Neanderthals developed art earlier than modern humans

Carl Zimmer writes:

The two new studies don’t just indicate that Neanderthals could make cave art and jewelry. They also establish that Neanderthals were making these things long before modern humans — a blow to the idea that they simply copied their cousins.

The earliest known cave paintings made by modern humans are only about 40,000 years old, while Neanderthal cave art is at least 24,000 years older. The oldest known shell jewelry made by modern humans is about 70,000 years old, but Neanderthals were making it 45,000 years before then.

“These results imply that Neanderthals were not apart from these developments,” said Dr. Zilhão. “For all practical purposes, they were modern humans, too.”

The new studies raise another intriguing possibility, said Clive Finlayson, director of the Gibraltar Museum: that the capacity for symbolic thought was already present 600,000 years ago in the ancestors of both Neanderthals and modern humans. [Continue reading…]