Eukaryotes are chimeric in that their DNA is the fusion of more than one genome. Phylogenetic analyses of eukar-yotic genes result in many conflicting results, some eukaryotic genes appear most recently derived from archea, while others from bacteria. If these conflicts were infrequent, horizontal gene flow could be an adequate explanation. However, these conflicts are frequent and appear to fall into distinct categories. Genes involved in the maintenance and manipulation of the genetic code appear to be most recently derived from archea, whereas genes that are involved in metabolic processes are most similar to those of bacteria. Thus, it appears that at least two organisms are responsible for the major contributions to the eukaryotic genome and thus any theory on the evolution of eukaryotes must be one that can account for this pattern.
Curiously, genes believed to be of bacterial origin are sometimes grouped most closely with Gram-negative bacteria (like Rickettsia), while others are grouped most closely with Gram-positive bacteria (suggesting at least three major contributors). Debate exists however concerning whether these two groups are each monophyletic (consisting of a common ancestor and its descendents).
The Archezoa were (as many of these organisms are now being placed elsewhere) a group containing various eukaryotes that lacked mitochondria (amitochondriates) and often lacked or possessed 'primitive' versions of some eukaryotic traits. They are largely parasitic, inhabiting low oxygen environments, and were believed to descend from an ancient eukaryote before the acquisition of mitochondria. Recent phylogenetic analyses however have shown that many of these species are relatively recent with highly simplified structures resulting from their parasitism and anoxic environments. Structures similar to mitochondria have been found in many (though they may lack DNA) as well as nuclear genes normally associated with mitochondrial DNA.
Before the demise of Archezoa scientists had a rather gradual interpretation of eukaryotic evolution from simple cells to more complicated eukaryotes gradually with eukaryotic lineages diverging along the way acting as living fossils of earlier versions. With recent discoveries however, scientists are now ofthe opinion that most ofthe major features of eukaryotes (nucleus, cytoskeleton, ability to endocytose, and mitochondria) evolved very rapidly. It is now believed that if any early diverging lineages existed, they are now extinct and did not contribute to modern lineages.
No matter the theories concerning the origin of eukaryotes, there are hypotheses that can account for their chimeric nature. Woese has proposed that early in the evolution of eukaryotes horizontal gene flow was much more common, and as genomes became more complex and integrated these rates decreased. Doolittle posits that the advent of the cytoskeleton and ability to phagocytoze gave eukaryotes the potential to incorporate DNA from ingested organisms. Over time, numerous organisms contributed to the genome of early eukaryotes. While it is difficult to test either of these hypotheses, if future comprehensive phylogenetic analyses across a great many organisms point to 'few' donors for the origin of eukar-yotes, then these ideas would be disproved.
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