When Josefin Stiller was growing up in Berlin, she loved reading about Greek gods in an encyclopedia of mythology. She often lost track of their relationships, however—their feuds, trysts, and betrayals—as she flipped among the entries. Frustrated, she wrote each name on a card and started to arrange children beneath parents on a desk in her bedroom. As lineages became clear, so did family dramas. Sons killed fathers; uncles kidnapped nieces; siblings fell in love. “I wonder if this experience of reconstructing a family tree primed me to appreciate trees and the powerful insights they hold,” Stiller told me in a recent e-mail.
Years later, as a graduate student in biology, Stiller worked on an evolutionary tree for seahorses and their relatives, using DNA to understand the ancestry of different species. Then, in 2017, she moved to the University of Copenhagen and joined B10K, a scientific collaboration that aims to sequence the genome of every bird species—more than ten thousand in all—and to reveal their connections in a comprehensive tree. The amount of data and computing power required for this mission is almost unfathomable, but the final product should be as simple in principle as the diagram Stiller had assembled as a child. “Everything in biology has a history, and we can show this history as a bifurcating tree,” she said.
Birds are the most diverse vertebrates on land, and they have always been central to ideas about the natural world. In 1837, a taxonomist in London told Charles Darwin that the finches he had shot and carelessly lumped together in the Galápagos Islands were, in fact, many different species. Darwin wondered whether the finches might have shared a common ancestor from mainland South America—whether all of life might have evolved through a process of “descent with modification”—and he drew a rudimentary tree in his private notebook, beneath the words “I think.” The tree showed how a single ancestral population could branch into many species, each with its own evolutionary path. “On the Origin of Species,” published twenty-two years later, includes only one diagram: an evolutionary tree. The tree of life became for biology what the periodic table was for chemistry—both a foundation and an emblem for the field. “The time will come I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of nature,” Darwin wrote to a friend.
The rise of genome sequencing, at the turn of the twenty-first century, seemed to bring Darwin’s dream within reach. “It is now realistic to conceive of reconstructing the entire Tree of Life—eventually to include all of the living and extinct species,” Joel Cracraft, the curator of birds at the American Museum of Natural History, wrote, in 2004. The naturalist E. O. Wilson predicted that such a tree could unify biology. Its value to such fields as agriculture, conservation, and medicine would be incalculable; evolutionary trees have already deepened our understanding of SARS-CoV-2, the virus that causes COVID-19. By mapping a major branch on the tree of life, B10K aims to light the way.
When Stiller joined the project, her colleagues were combing through museums and laboratories to sample three hundred and sixty-three bird species, chosen carefully to represent the diversity of living birds. With help from four supercomputers in three different countries, they began to compare each bird’s DNA to figure out how they were related. “I think there was always this idea that, once we sequence full genomes, we will be able to solve it,” Stiller told me. But, early in the process, she encountered an evolutionary enigma called Opisthocomus hoazin. “I was completely amazed by this bird,” she said.
Hoatzins, which live along oxbow lakes in tropical South America, have blood-red eyes, blue cheeks, and crests of spiky auburn feathers. Their chicks have primitive claws on their tiny wings and respond to danger by plunging into water and then clawing their way back to their nests—a trait that inspired some ornithologists to link them to dinosaurs. Other taxonomists argued that the hoatzin is closely related to pheasants, cuckoos, pigeons, and a group of African birds called turacos. Alejandro Grajal, the director of Seattle’s Woodland Park Zoo, said that the bird looks like a “punk-rock chicken,” and smells like manure because it digests leaves through bacterial fermentation, similar to a cow.
DNA research has not solved the mysteries of the hoatzin; it has deepened them. One 2014 analysis suggested that the bird’s closest living relatives are cranes and shorebirds such as gulls and plovers. Another, in 2020, concluded that this clumsy flier is a sister species to a group that includes tiny, hovering hummingbirds and high-speed swifts. “Frankly, there is no one in the world who knows what hoatzins are,” Cracraft, who is now a member of B10K, said. The hoatzin may be more than a missing piece of the evolutionary puzzle. It may be a sphinx with a riddle that many biologists are reluctant to consider: What if the pattern of evolution is not actually a tree?
Fossils that resemble hoatzins have been found in Europe and Africa, but today the birds can be found only in the river basins of the Amazon and Orinoco of South America. I live in Germany, so I visited them in Berlin’s Museum of Natural History, where cabinets are filled with thousands of stuffed birds. Sylke Frahnert, the bird curator, kept two taxidermy hoatzins on a shelf near the cuckoos and turacos, which seems as good a place as any. Over the years, there have been so many conflicting trees of birds, she told me. “You would have been crazy to change the collection with every one.” One of the museum’s hoatzins was shot in Brazil more than two centuries ago, and the years have drained the color from its face. I had heard that even the specimens smell like manure, but Frahnert warned me not to sniff them, since birds were once preserved with arsenic.
In the eighteenth century, natural-history museums started using anatomical similarities to classify plants and animals into increasingly specific categories: class, order, family, genus, species. Darwin realized that species share traits because their ancestors were one and the same. Fish, amphibians, reptiles, birds, and mammals all have spines, but not because God had given them to each creature separately; rather, the spine suggested a “common parent” living long ago. The construction of evolutionary trees was dubbed “phylogeny,” literally meaning “the generation of species,” by the zoologist Ernst Haeckel. The more traits two species shared, the theory went, the more recently they had shared a common ancestor. Human beings and other great apes evolved from a common ancestor millions of years ago, but even human beings and bacteria have a common ancestor—the first known living organisms, which date to three and a half billion years ago.
Hoatzins—“in some respects the most aberrant of birds,” according to one Victorian ornithologist—were a problem from the beginning. Early European naturalists described them as pheasants, and the first major tree for birds, published in 1888 by Max Fürbringer, placed them on the fowl branch. But, by the early nineteen-hundreds, some scientists were comparing hoatzins and cuckoos on the basis of traits such as jaws and feathers, and others were noting similarities between hoatzins and turacos, pigeons, barn owls, and rails. Even the hoatzin’s parasites defied classification: they hosted feather lice found on no other birds.
One crucial problem in phylogeny was convergent evolution. Sometimes natural selection nudges two organisms toward the same trait. Birds and bats independently evolved the ability to fly. Swifts and swallows each evolved into aerodynamic insectivores with nearly identical silhouettes, but traits such as their vocal organs and foot bones reveal that they are only distantly related. Because taxonomists often disagreed about things such as how to distinguish common ancestry from convergent evolution, the literature grew thick with conflicting trees, to the point that some twentieth-century biologists seemed ready to give up. “The construction of phylogenetic trees has opened the door to a wave of uninhibited speculation,” one wrote in 1959. “Science ends where comparative morphology, comparative physiology, comparative ethology have failed us.”
Phylogeny made a comeback in the seventies and eighties, after the German entomologist Willi Hennig developed more rigorous criteria for identifying common ancestry and drawing evolutionary trees. These innovations laid a foundation for a new wave of research that did not rely solely on physical specimens but, rather, on the emerging science of DNA. “Organisms are related to one another by the degree to which they share genetic information,” two ornithologists wrote in the early nineties, adding that genetics could reveal “a different view of the process of evolution and its effects.” The typical bird genome is a string of more than a billion base pairs that mutate randomly over time. Scientists can compare the same parts of the genome across multiple species to estimate their evolutionary closeness. Typically, species that share mutations have a more recent common ancestor, and species that do not are more distantly related.
Early sequencing was expensive and tedious, but, by the beginning of the twenty-first century, a signal was emerging from the noise. The journal Nature published an article about the promise of a single unified tree of life. But its author also identified a complication: each genome contains many different genes, and each one could generate a different evolutionary tree.
In 2001, a paper in the Proceedings of the Royal Society identified a pair of bird siblings as unlikely as Arnold Schwarzenegger and Danny DeVito: the flamingo’s closest relative was a little diving bird called a grebe. “That was probably the single most astounding result that anybody’s ever gotten,” Peter Houde, an avian biologist from New Mexico State University, told me. Ornithologists had always reasoned that grebes were closely related to short-legged loons, whereas tall wading birds such as flamingos, storks, and herons probably had a long-legged common ancestor.
That was the first domino to fall. In 2008, Science published a new avian tree based on DNA. Research led by Shannon Hackett, Rebecca Kimball, and Sushma Reddy, scientists affiliated with the Field Museum and the University of Florida, examined nineteen parts of the genomes of a hundred and sixty-nine avian species. The “root” of their tree resembled trees based on physical specimens: large, flightless birds such as ostriches, emus, and kiwis—known collectively as ratites—were first to diverge from all the others, followed by land fowl and waterfowl. The remaining ninety-five per cent of living birds, from parrots to penguins and pigeons, are known as “modern birds” and descended from a common ancestor, probably around the time that an asteroid hit the earth, sixty-six million years ago, and the dinosaurs went extinct. The youngest order—passerines, which include all songbirds—branched out into a staggering six thousand species in the span of tens of millions of years. The genetic tree for modern birds was decked with relationships that few, if any, taxonomists had guessed from anatomy; key groups such as parrots, owls, woodpeckers, vultures, and cranes shifted places.
Scientists had long assumed, for example, that daytime hunters such as hawks, eagles, and falcons all descended from a single bird of prey. But, in the genetic tree, hawks and eagles shared a branch with vultures, yet falcons turned out to be closer relatives of passerines and parrots. This meant that the peregrine falcon is more closely related to colorful macaws and tiny sparrows than to any hawk or eagle. The traditional explanation for flightlessness in ratites—that a common ancestor diverged into ostriches, emus, rheas, cassowaries, and kiwis after the southern continents split apart—also collapsed. DNA showed that the ratites also included flying birds called tinamous, suggesting that the group evolved flightlessness at least three separate times. “That study revolutionized our understanding of how the major groups of living birds are related to each other,” Daniel J. Field, an avian paleontologist at the University of Cambridge, said. Bird-watching guides had to reorganize their contents to reflect the new relationships.
This content was originally published here.