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This Is Your Ancestor

When microbiologist Mitchell Sogin decided to trace human evolution to its roots, he had no idea he might find sponges.

By Jack McClintock and Richard Barnes
Nov 10, 2004 12:00 AMOct 9, 2019 8:37 PM


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Draw a line back through time from today’s person, panda, porpoise, pelican, or perch and it ought to end with their earliest progenitor. In the mists of the ancient past, a single organism must have given rise to us all. But that raises an interesting question: Where did this animal come from? What did it look like? And what are its nearest living relatives?

To understand what the first animals looked like, Mitchell Sogin, an evolutionary microbiologist at the Marine Biological Laboratory in Woods Hole, Massachusetts, used advanced automated DNA technology and computing power to trace the molecular evolution of dozens of today’s oldest known species—jellyfish, sea anemones, sponges, mollusks, starfish—back to their common point of origin. When he grouped the species in the precise order of their appearance on Earth, from less complex to more complex, he landed on sponges.  

Even Sogin was taken aback. “Sponges didn’t seem like animals—they didn’t go seeking prey, didn’t have 4 legs—or 10 legs. Show Joe Blow a sponge and it looks like cauliflower. But it’s not. It’s an animal.” Perhaps even more intriguing, Sogin uncovered something older in the animal line than sponges that isn’t an animal: fungi. “That’s surprising,” Sogin says. His findings have implications for evolutionary studies and may even shed light on the shape of extraterrestrial life. The discoveries have already made contributions to medicine. “He’s a pioneer in the systematic application of this method,” says evolutionary biologist W. Ford Doolittle of Dalhousie University in Nova Scotia. “It’s a very great achievement.”

Not bad for a Chicago kid who “never expected to become a scientist” and in fact had “no driving career ambitions” when he went to school. Now, sitting in his cluttered Woods Hole office, the soft-spoken biologist says, “It seems to be the big questions that appeal to me.” He opened his lab in 1989 with 5 people (now 10) and eight years later founded the Josephine Bay Paul Center for Comparative Molecular Biology, which he directs. Both are funded by the National Institutes of Health, the National Science Foundation, and NASA. He gazes out the window at icy Eel Pond and Buzzard’s Bay beyond it, then throws a wistful glance at a photo of Woods Hole in summer, when he sails his wife’s 41-foot Beneteau sloop, Origins.

Sogin and his colleagues are examining basic questions not only in linear molecular evolution but also in molecular ecology, molecular biodiversity, the evolution of genomes, and parasitology. Questions posed decades ago by Carl Woese, his mentor at the University of Illinois, and other scientists—such as how the essential unit of life, the cell, came into being—are still unanswered. Sogin says, “I’m obsessed with finding our origins—where we come from and where we are.”

There are 9,000 species growing up to eight feet tall, from the tropics to the Arctic. They don’t visibly move or stalk prey or appear to mate; they just sit there as the world’s oceans pass through their pores, filtering as little as an ounce of food from a ton of seawater. Many even live in freshwater. Sponges are multicellular, but the cells don’t add up to much: no tissues, muscles, organs, nerves, or brain. But this simplicity can be deceptive. Some sponges come armed with glasslike skeletal spikes, microscopic and as beautiful as snowflakes. Some, like the fire sponge of Hawaii, have surface toxins that can cause excruciating pain to humans—and in which scientists have begun to discover antitumor and anti-inflammatory agents.

The sponge is the earliest, most primitive multicelled animal, Sogin says. Some scientists believe the ability to grow different cell types started animals on the evolutionary road to becoming humans. With just a few kinds of cells, only loosely connected, the sponge manages to produce a variety of asymmetrical shapes, from cups and fans to tubes and piecrust shapes. Sponges survive handsomely on their own and can even shelter other sea creatures: Scientists found a large sponge in the Gulf of Mexico hosting 16,000 snapping shrimp and 1,000 other aquatic animals. The sponge’s cells, its calcium carbonate or glasslike silica spicules, and the mass of collagen that forms its visible body all create a network of tunnels and chambers, with little flailing hairs called cilia on the walls that wave the water through and filter out plankton and waste. No matter how large the sponge, it can eat only what its individual cells can absorb.

Sponges are also the earliest sexual reproducers; most are hermaphroditic, producing both eggs and sperm, which they release into the water. The sperm drift along until they find their way into the tunnels and caves of another sponge. But the sponge has other reproductive options. If you push one through a sieve, breaking free its individual cells, these cells will drift until they find each other, then stick together and create an exact genetic duplicate of the parent. If wounded, a sponge doesn’t need to grow new tissue; it simply moves old cells into the wound to close it. These techniques have helped sponges survive at least 500 million years. A few have remarkable capabilities. One, living in a Mediterranean underwater cave, traps small crustaceans with the sharp, glassy spikes jutting from its body, then surrounds them with its cells and digests them.

Biologist Calhoun Bond, then at the University of North Carolina at Chapel Hill, found in 1986 that sponges don’t just sit still—many actually move. Using time-lapse microscopy, he filmed freshwater sponges slowly crawling across the bottom of their containers. He found that larger, saltwater sponges do the same by extruding flat paddlelike extensions of their bodies and pulling themselves along, often climbing the sides of their glass tanks in labs. One sponge, a lavender beauty called Heliclona loosanoffi, moved four millimeters a day.

With so many curious characteristics, sponges have always been hard for taxonomists to place. Although some biologists have suspected they are more animal than plant, others have considered them to be outside the evolutionary line that led to multicelled metazoans—today’s animals. Until recently, neither side had a good way to prove its case.

Scientists have traditionally arranged the living world largely by morphology, or shape, and by the fossil record. If two organisms shared characteristics—suckers on their arms, opposable thumbs, green feathers, or yellow feet—they were thought to be related. The more characteristics they shared, the closer the relationship. That was simple: An octopus doesn’t much resemble an orangutan, so they are correctly not classified together. But the method was crude, easily supporting ambiguity and error. As scientists went deeper into evolutionary history and closer to the base of the tree of life, the harder it became to know how closely related organisms are.

“The most significant problem was that there was no quantitative way to compare; therefore, subjectivity crept into the construction of evolutionary history based on morphology,” Sogin says. We needed something more sophisticated, something objective, and DNA seemed like the answer. But scientists couldn’t compare the complete genetic makeup of individuals—each has millions of components. “You could sequence the genomes for each organism to see how similar they are,” Sogin says, smiling slightly at how immense a chore that would be. “But that’s not practical; it’d be like looking at the New York City telephone directory compared to the Mexico City directory. You could line up similar names, but it wouldn’t be very informative.”

Sogin thought he had a better idea. He reasoned that he could examine a limited number of genes that are present in every organism, and by comparing those and counting the differences between them, he could get quantitative measures of the similarities in any two organisms. If the two had similar gene sequences for a gene that conferred the same trait, he could infer a common ancestry. If the gene sequences were very different, he would know they diverged a long time ago because they had evolved away from each other—simple, logical, objective.

“We didn’t have a specific hypothesis,” Sogin says. “We said, ‘Let’s see if we can construct an objective [evolutionary] tree’”—and, in the process, identify Earth’s first animal.

But which genetic sequence to pick? It had to be one that existed in all organisms and did the same job. It had to have evolved slowly enough so that one could still see genetic similarities but quickly enough to see differences. The sequence had to be easy to isolate but couldn’t jump inexplicably from one organism to another, as some genes do. It so happened that, back in 1977, Carl Woese, Sogin’s mentor, had employed one particular gene sequence to identify a previously unknown form of life, the archaea, a discovery that transformed science’s view of biology. The sequence is called ribosomal RNA, which is used by cells to create protein. It fit Sogin’s criteria perfectly.

Sogin began collecting and sifting through marine organisms—algae, fungi, sponges, jellyfish, anemones, mollusks—cutting them up and extracting DNA, adding enzymes, concentrating the DNA and sequencing the genes, reducing them to strips of code, comparing their ribosomal RNA, and applying algorithms to measure their relationship with one another and with insects, worms, fish, birds, and mammals. At the time Sogin started, 20 years ago, when DNA sequencing was in its infancy, such a project was even more ambitious than it appears now. Today Sogin concedes nonchalantly that it was “a technically difficult problem.” A given genome might contain anywhere from 10 million to 3 billion base pairs, and Sogin was searching for just 2,000—“a needle in a haystack.” It took a year to isolate and sequence one gene from a red sponge when he began in the early 1980s, all by hand with manual DNA sequencing gels. As he worked, gene technology improved. Within a few years, he was able to sequence 10 to 15 genes a year. Today he can do 1,000 overnight. The answers came in parts, but as he pieced them together, the findings became clear.

Clear, but not simple. Rummaging for reprints of scientific articles to illustrate his point, Sogin says the more he looked—and he’s not finished—the more complicated the picture became. He makes a sketch and points with his pen. The sponge was indeed at the base of animal lineage, and just above it were the cnidarians, such as jellyfish, anemones, and corals. They, like the sponge, have a saclike body form. They developed tentacles and an opening like a mouth at one end. But there were other forms of life lower down the line of descent that scientists might not have expected. Suddenly, they made sense. One of the sponge’s cell types is the distinctively shaped choanocyte, a cell equipped with a tiny long filament, called a flagellum, surrounded by a collar studded with even tinier hairs called microvilli. Thousands of these flagella beat constantly at the water and move it past the sponge’s feeding cells.

As it happens, Sogin found that the sponge’s immediate evolutionary predecessors are the choanoflagellates, which represent what life would have looked like just before animals in the form of sponges emerged. The similarity in names is no accident, for these are single-celled creatures, with whiplike flagella surrounded by a collar of microvilli, and they bear an amazing resemblance to the choanocyte cells of sponges. A few of them even clump loosely together into colonies, bringing evolution to the very brink of the animal age. Scientists had long suspected that the choanoflagellates could have been the nearest things to animals without actually being animals. At the University of Wisconsin in Madison, molecular biologists Nicole King and Sean Carroll recently verified Sogin’s results and took the story a sentence or two further. They analyzed a different genetic sequence and found “strong support that the choanoflagellates are very close relatives of animals,” as King says. In one species, they discovered a particular molecule previously found only in multicelled animals. They concluded that the choanoflagellates appear to contain the “genetic tool kit” from which the first animals were made.

The only thing older in the same line, the line leading directly to animals and to us, are the fungi. “This is revolutionary,” Sogin says, pushing back thick, graying hair. “Animals and sponges share a common evolutionary history from fungi.”

Until Sogin was able to prove otherwise, “we thought fungi were related to plants or somehow were just colorless plants,” he says. “Plants had seeds, fungi had spores, and so on. Scientists used to publish fungi articles in plant journals. But the work does not support that. We’ve shown that fungi and plants are very different from each other, and fungi are actually more closely related to animals.” With a pen, he taps his evolutionary tree sketch. Green plants form one branch, and the fungi and animals are farther along on another branch.

Does all this mean humans are just highly evolved mushrooms? “I’d say we share a common, unique evolutionary history with fungi,” Sogin says. “There was a single ancestral group of organisms, and some split off to become fungi and some split off to become animals.” The latter have become us.

Sogin’s findings have more than theoretical importance. “The fact that fungi and animals share a common evolutionary history tells us more about fungal infections, for example,” Sogin says—from simple ones like ringworm and athlete’s foot to more difficult cases, including those implicated in heart disease. “It might explain why fungal infections are so difficult to treat—they’re more like us than we thought. They’re similar targets. The more different two organisms are, the easier it may be to target a pathogen without damage to the host. That helps us make decisions about what model organisms are worth investing biomedical research in. It might affect the treatment of heart disease.” Endocarditis, for instance, an inflammation of the heart muscle, can be caused by either a bacterium or a fungus—the yeast Candida albicans.

The animal kinship to fungi could revolutionize medicine. For example, thousands of HIV patients have been killed by Pneumocystis carinii, which until recently was believed to be a parasitic protozoan related to malaria. Sogin and his colleagues discovered something different. “When we sequenced the pneumocystis, we found it was related to a fungus,” he says. “We’ve been trying to treat it with the drugs used against malaria, but it would be better to use those drugs that are used on fungi. And since pneumocystis can’t be cultivated in the lab, if you’re looking for a research model, you’ll look for something close that can: fungi.”

But it’s with the sponge that pre-animals began to take shape, Sogin believes, because the sponge was first to grow different cell types. For all their simplicity, sponges have “a lot of organization.” With their choanoflagellate-like choanocyte cells and a second type of cell, an archaeocyte, that can shift shape and function as needed to absorb food, secrete new skin, or reproduce, they became the first multicellular animals. All the other animals emerged from this simple architecture and are built upon this platform. After the sponges and cnidarians came the worms—the first creatures with bilateral symmetry, after which came an “explosion,” as Sogin calls it, of big-animal phyla. A bilaterally symmetrical animal, different from front to back but a mirror image of itself from side to side, has many subtle and not-so-subtle advantages, among them the ability to move purposefully forward in quest of prey, for instance.

All this raises new questions. What would our early, pre-animal ancestors have looked like? If we evolved from a kind of sponge, why do sponges still exist, unevolved? What can our spongy/fungi forebears tell us about life today?

Nobody can precisely describe those early sponges, but it’s most likely that they resembled today’s sponges. “We can find diatoms today, horseshoe crabs today, that look almost identical to how they looked before in a morphological sense,” Sogin says. “You might argue that they haven’t evolved. Yet everything evolves—genetically, we evolve—and today’s sponge isn’t genetically identical to the sponge that might be in the fossil record.” If it weren’t for Sogin’s work, we might, on the basis of appearance, still think of them as identical.

“Learning how organisms evolved might hold the key to knowing what might happen to us in the future,” Sogin says. “We can use these molecules to create predictive models and see how changes in the environment altered microbial growth patterns and then, in a feedback loop, how these growth patterns affect the environment—how they create a model of ecological change.” It might even shed light on the possibility of life elsewhere in the universe.

“We’ve got a long way to go, studying how eukaryotes [multicelled creatures] can live in extreme environments, like acidic environments, which brings up big questions like life in space,” Sogin says, leaning back in his chair. Any life found in outer space, he speculates, will most likely resemble early, primitive life on Earth—something like a sponge.

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