We provide data and analysis to support the hypothesis that the ancestor of
animal mitochondria (Mt) and many primitive amitochondrial (a-Mt) eukaryot
es was a fusion microbe composed of a Clostridium-like eubacterium and a Su
lfolobus-like archaebacterium. The analysis is based on several observation
s: (i) The genome signatures (dinucleotide relative abundance values) of Cl
ostridium and Sulfolobus are compatible (sufficiently similar) and each has
significantly more similarity in genome signatures with animal Mt sequence
s than do all other available prokaryotes. That stable fusions may require
compatibility in genome signatures is suggested by the compatibility of pla
smids and hosts. (ii) The expanded energy metabolism of the fusion organism
was strongly selective for cementing such a fusion. (iii) The molecular ap
paratus of endospore formation in Clostridium serves as raw material for th
e development of the nucleus and cytoplasm of the eukaryotic cell.