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Unformatted text preview: vol. 154, supplement the american naturalist october 1999 The Tangled Web: Gene Genealogies and the Origin of Eukaryotes Laura A. Katz * Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063; and Program in Organismic and Evolutionary Biology, University of Massachusetts—Amherst, Amherst, Massachusetts 01003 abstract: Accessing data from the genomes of organisms (indi- vidual genes) and analyzing these data using sophisticated alignment and phylogenetic methods led to the expectation that we would be able to paint a clear picture of the evolution of eukaryotes. Previous analyses based on morphology and ultrastructure failed to pinpoint both the sister taxon to eukaryotes and the branching order of eu- karyotic lineages. However, the expectation that molecular data would provide resolution has not been met since a growing number of gene genealogies present conflicting hypotheses for the origin and diversification of eukaryotes. Instead of reconstructing a simple bi- furcating tree of life, these gene genealogies have generated a complex picture of eukaryotic genomes whereby ancient lateral transfers (of individual genes or perhaps even entire genomes) has tangled the evolutionary history of eukaryotes. Resolution of these conflicting genealogies comes in recognizing that eukaryotes are chimeric, con- taining genetic information from multiple ancestral lineages. Keywords: origin of eukaryotes, chimerism, multiple gene genealogies, tree of life. The initial step in determining the evolutionary history of eukaryotes is to define them clearly. Eukaryotes were named for the presence of a nucleus. Antoni Van Leeu- wenhoek, who, in the seventeenth century, was the first to turn a microscope onto the natural world, described the morphology of microbial eukaryotes and prokaryotes in great detail (Dobell 1932). However, the significance of the nucleus as a distinguishing character was not recog- nized until the 1930s, when living organisms are divided into eukaryotes (organisms with a “true” nucleus) and prokaryotes (organisms that evolved before the nucleus; Chatton 1937). This concept was further elaborated by * E-mail: [email protected]; URL: http://www.science.smith.edu/biology/lkatz. Am. Nat. 1999. Vol. 154, pp. S137–S145. q 1999 by The University of Chicago. 0003-0147/1999/15404S-0004$03.00. All rights reserved. Stanier and his colleagues who recognized the acquisition of a nucleus as a defining characteristic in distinguishing forms of life on Earth (e.g., Stanier and van Niel 1941, 1962). Hence, any theory to explain the origin of eukar- yotes must adequately address the origin of this defining feature. A second defining feature of eukaryotes is the presence of a cytoskeleton. This complex structure, composed of both microtubules and microfilaments, is involved in a multitude of eukaryotic processes including motility, phag- ocytosis, morphological differentiation, and cell division....
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