Family resemblance can indeed be elusive, or we wouldn't have "check the mailman" jokes. Scientists who try to infer who's related to whom among all creatures past and present can therefore be forgiven for taking 150 years to figure out this one: slime molds, mushrooms and other fungi are more closely related to you, me and other animals than they are to plants.
The conclusion that fungi should be classified with humans in the group called "opisthokonts" is based on the discovery that the reproductive cells of both (sperm, in the case of people) are propelled by a single little flagellum that whips back and forth as if the very continuity of the species depended on it—which, come to think of it, it does.
Charles Darwin hardly suspected that figuring out who's descended from whom would be this hard, but he knew it was important: The only drawing in his 1859 opus, "The Origin of Species," shows a tree of life. Ever since his rudimentary attempt at showing the family tree of species living and extinct, evolutionary biologists have been ardent arborists.
Working first with anatomical and fossil evidence and lately with genetic clues, they have moved from the original division of life into plants and animals (a tree with two main trunks) to a scheme with three, then five, then back to three major trunks.
"Progress has gone in fits and starts as technology has advanced," says biologist Sandra Baldauf of the University of York, England. But with the revolution in genome sequencing, "the first truly comprehensive outline of the tree seems to be emerging."
Presentations at a conference last year and five papers in Friday's issue of the journal Science show that the tree of life is undergoing major overhauls. There are even new ideas about "which end is up," says Prof. Baldauf. Scientists used to think that single-celled protozoa and bacteria were the most ancient living things, and therefore formed the roots of the tree. Animals and fungi were sitting pretty in the crown, having branched off from other species fairly late in the game. But new genetic evidence hints that the first ancestors of animals split off from the rest of the tree at least 1.5 billion years ago.
Either way, all the new genetic data are clearly saying that the last common ancestor of everything "was a far more complex organism than previously envisioned," she says. There is no fossil evidence of what it was, but the emerging theory is that life got complex fast.
Molecular biology scored its first major tree-of-life shake-up in 1977, when biologists Carl Woese and George Fox used DNA sequences to infer that the tree has three main trunks. Bacteria constitute one trunk. Eukaryotes (everything whose cells have a nucleus, which means plants, animals, fungi and even lowly pond scum) make up a second. And the newly named Archaea, ancient microbes, are the third.
Nowadays, scientists routinely compare genome sequences to estimate relatedness among species, on the assumption that the greater the differences between those sequences the more-distantly related the organisms are. "Now that you can sequence genomes, you can begin to define evolutionary questions Darwin couldn't even imagine, such as what genetic changes led to new species," says Prof. Woese, of the University of Illinois at Urbana-Champaign.
At the American Museum of Natural History in New York, the cluster of computers dubbed Demeter reconstructs family trees based on DNA sequences. It's a mammoth task (yes, scientists are pretty sure that mammoths are on the branch with mastodons and elephants): of 1.7 million known species, and somewhere between four million and 10 million yet to be catalogued, only about 80,000 have a semi-well-established place on the tree of life.
Among the successes of Demeter and her predecessors is showing that life probably moved from water onto land only once in its 3.7 billion-year history, says the museum's Ward Wheeler. According to his genealogies, birds, crocodiles and dinosaurs are cousins, with mammals related only distantly. Crocs are closer to birds and dinos than to other reptiles.
Although schoolchildren used to be taught that amphibians were the ancestors of reptiles, reptiles and mammals are more closely related, says herpetologist Harry Greene of Cornell University in Ithaca, N.Y. In fact, pythons retain genes for hind legs, but apparently are perfectly content with a leg-free existence. And everything with four limbs, including people, is a child of ancient swimmers.
"It turns out we're really all fish," says Prof. Greene, a notion that makes an ape-like ancestor relatively appealing.
"That humans are just a leaf on this tree of life is one of the most significant ideas that Homo sapiens has ever come up with," says entomologist David Maddison of the University of Arizona, Tucson. In 1994 he launched the Tree of Life Web Project, which reflects the work of more than 350 scientists in 21 countries.
But although assembling the tree of life is fundamentally an exercise in basic science, not to mention ever-more humility as scientists discover who our cousins are, it also holds out the promise of practical payoffs. Understanding the genealogy should shed light on why diseases jump from one species to others, as AIDS, severe acute respiratory syndrome and many influenzas have, and how pathogens become more virulent as they evolve. It may also point to new sources of natural medicines like the breast-cancer drug Taxol, which comes from the Pacific yew tree. If the goal is compounds that work in people, we might do well to look in our relatives—like slime molds.
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