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Linnaeus, following Aristotle, classified living things into two kingdoms: plants and animals. Additionally, he classified members of each kingdom in a nested hierarchy (expanded after his death): phylum, class, order, family, genus and species. Scientific acceptance of Darwin's theory of evolution allowed biologists to view this scheme as a tree, with descendant branches diverging from a common ancestral stem. However, in the 19th century, following the work of Darwin and Haeckel, evidence began to accumulate that the two-kingdom scheme was too narrow to express the rich diversity of life. Microorganisms, first discovered after the invention of the microscope by van Leeuwenhoek, posed a challenge to the two-kingdom classification: many of them resembled neither plants nor animals. Fungi also posed a problem, as their mode of nutrition and cellular structure was so different from that of plants. Various classifications were put forward, with three or more kingdoms.
In 1969, Robert Whittaker proposed his classification of life into five kingdoms: monera (bacteria), protista (now known as protoctista - water-dwelling microbes, such as amoebae), plants, fungi and animals.
The five kingdom scheme co-existed with a scheme dividing life into two main divisions: prokaryotes, or organisms without a cell nucleus, whose DNA floats freely within the cell (bacteria, etc.) and eukaryotes, whose DNA is stored in a nucleus (animals, plants, fungi, and protoctista).
In her book "Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth", Lynn Margulis (with Karlene Schwartz) proposed a unified two domain-five kingdom system. In contrast to the usual "tree of life" metaphor, Margulis used the illustration of a hand, with prokaryotic monera corresponding to the thumb, and the four other eukaryotic kingdoms corresponding to the fingers of a hand. As Stephen Jay Gould notes in his foreword to the book, in this new taxonomy, "the greatest division is not even between plants and animals, but within the once-ignored microorganisms - the prokaryotic Monera and the eukaryotic Protoctista."
Research in the 1990s showed that prokaryotes are far more diverse than anyone had suspected, and a new three-domain classification has emerged. Living things (with the exception of viruses) are now classified into three domains: Bacteria, Archaea (microorganisms that live in extreme habitats) and Eukaryotes.
The Tree of Life - taken from "San Jose Mercury", September 20, 1999. Article by Glennda Chui.
Because these three domains, the major lineages of the tree of life, are thought to have swapped a lot of their genes in the past (a phenomenon known as lateral gene transfer), mutated several times at the same sites in their genes (saturation), undergone gene duplication (non-orthologous replacement), acquired foreign genes (through eating), discarded different genes (differential gene loss) and evolved at different rates (giving rise to the long branch attraction phenomenon), the rooting of the tree of life is contentious, with a bewildering variety of views: (i) prokaryotes, being simpler in their cell organisation, evolved first, and split into bacteria and archaea, while eukaryotes later branched off from the archaea (the standard view); (ii) all three domains diverged at the same time from a common source; (iii) eukaryotes represent the root of the tree of life, while prokaryotes are simplified life forms that arose through gene loss and other reductive mechanisms; (iv) eukaryotes arose from a merging of bacteria and archaea; (v) a fourth branch of the tree, now lost, contributed genes to the eukaryotes; and (vi) there is no unique "tree of life", but rather a tangled thicket of trees (or a net, as Doolittle (2000) describes it): owing to the prevalence of gene-swapping (lateral gene transfer) between different domains of organisms in the past, different genes in the same organism have different family trees, so the same organism can be classified in different ways, depending on which of its genes we examine. Proponents of the last view also question the idea that all living things diverged from a common ancestral stock, and suggest that there may be many ancestral roots.
The Tree of Life: a current view. Courtesy of "The Scientist", Volume 16, Issue 18, September 16, 2002 (article by Maher: "Uprooting the tree of life"). Image: Ned Shaw.
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