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Ancient origins. Yeast and other eukaryotes evolved from a mix of early microbial genomes.

Redrafting the Tree of Life

For more than a century, the "tree of life" has been the most popular metaphor for depicting evolutionary ties among Earth's flora, fauna, and microbes. But in the mid-1990s, new gene data about microbes threw some of the lowest branches into disarray. Now, some biologists are suggesting a new way to sketch it: Evidence of extensive gene switching between bacteria, microbes called archaea, and the first microbes with a nucleus--the eukaryotes--means that the lowest branches should be drawn as a ring with different groups of organisms spinning off over time.

Over the past 2 decades, systematists have increasingly relied on differences in gene sequences to determine kinships among species. As a result, microbiologists now call "bacteria" prokaryotes and have divided that group into bacteria and archaea. However, they have been unable to decide which prokaryotic group gave rise to the seemingly more complex eukaryotes that evolved into the myriads of multicellular plants and animals.

To sort out these relationships, Maria Rivera and James Lake of the University of California, Los Angeles, designed a sophisticated computer program to examine the genomes of two yeast species and 25 bacteria and archaea. They were especially interested in when one organism's genome had gotten entangled with another's because of gene transfers, which presumably occur after ingestion. They also looked for cases when two genomes had merged.The results indicated that eukaryotes got their nuclear genomes from a fusion of an ancient bacterium and an archaeon similar to the eocyta, which thrive in high temperatures. Also, the data imply that early in life's history, many microbes picked up genes by swallowing their neighbor's DNA, Rivera and Lake report in the 9 September issue of Nature. This situation isn't captured by a tree diagram, which implies that groups descended from a common ancestor. Instead, they suggest that these relationships are best represented by a ring. By this view, frequent gene and genome mixing keep some organisms from evolving their own genomic identities.The ring depiction is an accurate representation of how eukaryotes came about, says T. Martin Embley of the University of Newcastle upon Tyne, U.K. But, he notes, "the paper is bound to cause a stir." Patrick Forterre of the University of Paris-Sud in Orsay, France, worries that the analysis is weak because it doesn't incorporate enough eukaryotic genes.

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