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Symbiogenesis is the merging of two separate organisms to form a single new organism. The idea originated with Konstantin Mereschkowsky in his 1926 book Symbiogenesis and the Origin of Species, which proposed that chloroplasts originate from cyanobacteria captured by a protozoan. Today both chloroplasts and mitochondria are believed to have such an origin; this is the endosymbiotic theory.

In Acquiring Genomes: A Theory of the Origins of Species, biologist Dr. Lynn Margulis argued that symbiogenesis is a primary force in evolution. According to her theory, acquisition and accumulation of random mutations are not sufficient to explain how inherited variations occur; rather, new organelles, bodies, organs, and species arise from symbiogenesis. Whereas the classical interpretation of evolution (neo-Darwinism) emphasizes competition as the main force behind evolution, Margulis emphasizes cooperation.

Many ecologists agree, but this idea has little support from other evolutionary biologists. They see little evidence that symbiogenesis has had a major impact on eukaryotic life, or that much of its diversification can be attributed to it. Other than the two examples of mitochondria and chloroplasts, there is no clear evidence of other major traits or transitions that can be attributed to symbiogenesis.

It is a fundamental principle of classical neo-Darwinism, or population genetics theory, that mutations arise one at a time and either spread through the population or not, depending on whether they offer an individual fitness advantage. There is a major body of scientific work, both theoretical and experimental, based on this paradigm. Those who have worked in the field tend to regard its foundation as unassailable.

Nevertheless, the neo-Darwinist perspective remains vulnerable to challenges like that of Margulis because its experimental support comes overwhelmingly from the laboratory, not from the wild. We understand clearly how artificial selection works in the laboratory, but there is legitimate controversy over whether nature's laboratory works in just this way. Indeed, genome mapping techniques have revealed that family trees of the major taxa appear to be extensively cross-linked—possibly due to lateral transfer of genes carried by bacteria, as Margulis predicted.

• Margulis, Lynn and Dorion Sagan. "Acquiring Genomes: A Theory of the Origins of Species", Perseus Books Group, 2002 ISBN 0-465-04391-7