We have reviewed here the evidence that all the three hydrogenosomes that have been studied so far in more detail are functionally and structurally distinct. They evolved independently in the various evolutionary lines of unicellular eukaryotes in the course of adaptation to anaerobic environments. Nevertheless, all available evidence supports the interpretation that all these three types of hydrogenosomes are the consequence of evolutionary tinkering starting with a mitochondrial-type organelle, which, however, was clearly different from the present-day textbook mitochondria (cf. Gabaldon and Huynen 2003, 2004). The discovery of a missing link, which combines a mitochondrial with a hydrogenosomal metabolism (Boxma et al. 2005), terminates the discussions about an inherent weakness of the endosymbiont hypothesis because it reveals the existence of anaerobic eukaryotes which combine an anaerobic and an aerobic metabolism as postulated in the hydrogen hypothesis (Martin and Müller 1998; Martin 2005). These findings allow an extrapolation to the more exotic, more degenerated members of the "mitochondrial" family: mitosomes and mitochondrial remnants (Fig. 7.1). Also these organelles are much more likely to be retrograde, highly adapted members of the mitochondrial family than the results of different, independent endosymbioses.
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