Rearranging the Branches on a New Tree of Life

  • A Tale Told by DNA: The Tree of Life


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    A diner sits down to a salad containing mushrooms and lettuce.

    In the universal genealogy of life, the mushrooms are more closely related to the lettuce than to the diner, right?


    As part of an outpouring of research that is revolutionizing notions about the genetic, biochemical, structural and evolutionary relationships among living things, fungi like mushrooms have now been revealed as being closer to animals like humans than to plants like lettuce.

    Genetic comparisons place fungi closer to man than to plants.

    The revelation is just one of many emerging new ideas about family ties in the upper reaches of the earth's 3.5-billion-year-old tree of life, in particular ties among plants and between them and other higher forms of existence.

    Scientists are consequently having to rethink some long-held ideas about evolution.

    The tree of life, which essentially maps the path of evolution, has simple single-celled organisms at its base and plants, animals and fungi -- and a newly delineated kingdom that includes kelp -- at its crown.

    For most of the history of science, experts have drawn the tree by comparing the gross surface features of various creatures.

    Fungi, for example, were lumped with plants because they look much like them and grow in one spot.

    But now, by comparing organisms' genetic material and microscopic internal structures, scientists are drawing the tree all over again.

    It used to be, for instance, that higher organisms were divided into two kingdoms, plants and animals.

    The revised crown of the tree of life now includes five kingdoms: red algae, green plants, animals, fungi and a more recently discovered group called stramenopiles, most of which look like plants but are not, because they do not perform photosynthesis.

    "Brown" water plants like tiny diatoms and giant kelp share so many characteristics with stramenopiles that they have been lumped with them.

    All five of these kingdoms have lineages that trace back to different one-celled organisms.

    Among this grouping of kingdoms, the green plants have been the most intensively reanalyzed.

    They had been divided simply into green algae and land plants; now they are seen to be a far more various but closely related set of groupings, from fresh-water algae on one end of the evolutionary scale to flowering plants on the other.

    Moreover, some kinds of organisms are being reassigned from one kingdom to another.

    Some slime molds, for instance, have long been classified with fungi, but now are considered stramenopiles.

    As the tree of life has been re-drawn, scientists have also had to revise some of their ideas about how evolution has proceeded.

    It now appears, for instance, that plants first colonized the land not from the oceans but from fresh water -- with some of the land plants recolonizing the ocean as green seaweed.

    And as the revision proceeds, scientists are moving tantalizingly close to identifying the first land plant and the first flowering plant.

    The revision is also providing road maps that could enable scientists to speed up the search for naturally occurring medicines and the development of new strains of drought-resistant crops. But it is primarily the sheer intellectual excitement of figuring out one of nature's grand designs that has lately galvanized the efforts of hundreds of scientists.

    "It is at least as exciting as exploring the cosmos," says Dr. Brent Mishler, a biologist and green-plant specialist at the University of California at Berkeley, who is a leader in the effort.

    The reanalysis accepts and builds on a recent, fundamental realignment of all living things into three basic groups: simple bacteria, archaea and eukarya (or eukaryotes).

    Simple bacteria have no cell nuclei. Archaea are bacteria of ancient origin that today often live in hostile environments like hot springs and are believed by many scientists to have represented the first life on earth.

    Eukarya -- the group that includes people -- are characterized by complex cells that have nuclei and specialized internal structures to process energy. They are the basis of all higher life; the cells of plants, animals, fungi and stramenopiles are eukaryotes.

    The first simple bacteria emerged at least as far back as 3.5 billion years ago, about a billion years after the earth's formation. Eukarotic cells had materialized by at least 2 billion years ago, maybe earlier.

    They evolved, scientists believe, by ingesting other species of cells and then, instead of digesting them, adopting them as permanent, genetically reproducible parts of themselves -- like the chloroplasts that enable plants to convert solar radiation into chemical energy and the mitochondria that process that energy in both plant and animal cells. Because plants give off oxygen in photosynthesis, they also produced an oxygen-rich atmosphere, eventually enabling oxygen-breathing animals like people to evolve.

    The higher groupings of life -- what some scientists call the eukaryote crown groups -- may have appeared in something of an evolutionary "big bang" about a billion years ago.

    In this efflorescence of life, some eukaryotic cells combined to form multicelled organisms and then began to diversify dramatically. Although their flowering has been spectacular, they constitute only a few small branches of the entire tree of life. Microbes of immense variety still rule the planet, and compared to them the crown eukaryotes are "almost evolutionary afterthoughts," said Dr. Mitchell Sogin, an evolutionary biologist at the Marine Biological Laboratory at Woods Hole, Mass.

    Nevertheless, recent research on the higher forms, particularly plants, has been especially revealing.

    This was clear from a flood of evidence presented this month at the 16th International Botanical Congress in St. Louis, a worldwide gathering of botanists which takes place every six years.

    There, a team of 200 scientists from 12 countries reported the first results of a five-year, Federally supported research effort on the green-plant portion of the tree of life.

    The result of the project, called Deep Green, is said to be the most complete reconstruction of any part of the tree so far. While much uncertainty over details remains, the scientists said, the main outlines of green-plant genealogy and evolution now are clear.

    Green plants, in the form of algae, first appeared in the cavalcade of evolution about the same time as the explosion of multicelled life a billion or so years ago.

    For perhaps 500 million years, the algae were confined to the water.

    Without water, they could not reproduce; the only way sperm cells could reach egg cells was to swim or float to them.

    But eventually, according to the new thinking, some of these algal species found their way from the ocean to fresh water, where they inhabited shoreline environments that were sometimes dry and sometimes wet.

    Special genetic adaptations to dryness and to damaging ultraviolet radiation from the sun enabled these pioneer algae to survive when water receded, according to this idea, and they were able to reproduce when the water rose.

    Mosses and ferns fit this category even today -- they grow in spots that are sometimes wet -- and they were the first land plants.

    The next landmark in plant evolution was the appearance of seed plants, called gymnosperms, about 425 million years ago.

    This eliminated the need for sperm cells to swim free in the environment; now the male reproductive cells were contained in pollen. The innovation proved much more effective a means of reproduction, and with it, the first big plants like cone-bearing trees developed, and green plants for the first time became ecologically dominant on land. Conifers are today's descendants of these plants.

    The latest of these fundamental branchings was the appearance of flowering plants about 150 million years ago.

    These plants, called angiosperms, have an advantage in that their seeds are protected by the fleshy bodies of their fruits.

    The lineages of many angiosperms run in a virtually straight line from then till now: several groups of modern angiosperms, like sycamores, walnuts, oaks and dogwoods, also graced the countryside in the era of the dinosaurs more than 65 million years ago.

    "If you had been wandering around with those dinosaurs, the landscape wouldn't have looked that unfamiliar to you," Dr. Peter R. Crane, the director of Britain's Royal Botanic Gardens at Kew, said in St. Louis.

    There would be some differences, he and others said; most of the flowers of that era were smaller and less colorful than modern ones, and neither big flowers like sunflowers nor grasses had yet evolved.

    Scientists have not yet identified the original single-celled organism from which all plants evolved, or the first land plant, or the first flowering plant. But they are on the scent.

    In St. Louis, an early alga called mesostigma, still growing on the earth, was presented as a "living fossil" believed to have evolved just before the first land plants. Two other freshwater algae are seen as promising candidates as closest living relatives of the land plants.

    Similarly, a small cream-colored flower called amborella, found only on the island of New Caledonia in the South Pacific, was revealed in St. Louis as the oldest known living flowering plant.

    While it is not the "Eve" of angiosperms, Dr. Mishler said, it is close to that original ancestor and thus provides a model for what it might have been like.

    At each stage of plant evolution, scientists now believe, only one family lineage was able to surmount the considerable environmental obstacles to its emergence.

    For instance, just one among many groups of algae succeeded in making the transition to land.

    The result is that all plants are more closely related than had once been thought.

    This emerges quite clearly in the case of red, green and brown chloroplasts, the engines of photosynthesis and the structures that define plants.

    For a long time, scientists thought that red, green and brown plants acquired different types of chloroplasts at different times.

    But now it appears that all chloroplasts stem from one group of blue-green bacteria and are in fact more closely related to one another than are the plants themselves.

    For that matter, it now appears that all forms of higher life, for all their divisions, are more closely related than is commonly believed; people are closer to green plants, for example, than to the E. coli bacteria that inhabit the human intestinal tract, and closer still to fungi.

    One consequence of the latter relationship, experts say, is that treating fungal infections in people is an exacting business; the wrong treatment might harm the person as well as the fungus.

    Humans are brothers and sisters not just to each other, it seems, but to the rest of life as well. Copyright 1999 The New York Times Company