A crucial differences between the Cavalier-Smith (2006) model and the ‘standard’ three domain model of Woese et al. (1990) are that the standard model perceives the archaebacteria as an ancient (over 3.5 billion years old) group of prokaryotes which was the ancestor of eukaryotes, whereas Cavalier-Smith views the Archaebacteria as appearing for the first time less than 800 million years ago and being sisters to eukaryotes, rather than ancestors.
Generally speaking I find the Cavalier-Smith model much more convincing because it is based on integration of such a broad range of data (Cavalier-Smith, 2006, 2010a & b); so I accept Cavalier-Smith’s basic narrative from the first appearance of living cells about 3.5 billion years ago to the emergence of eukaryotes from an actinobacterial ancestor. I disagree with Cavalier-Smith’s version of the origin of eukaryotes which I think is wrong because it is totally dismissive of fungi, and so animal centric that it equates the origin of phagocytosis with the origin of eukaryotes (e.g. “...the origin of phagocytosis by prey engulfment (which indirectly made the eukaryote cell...)...” Cavalier-Smith, 2010a, p. 123). This extreme position is taken without suggesting what selective advantage there might be in the essential intermediate steps towards phagocytosis. Phagocytosis requires water management, precise membrane management of endocytosis and exocytosis, and full cytoskeletal management of enzyme, vesicle and vacuole movement and distribution. Although the selective advantage of the complete process is self-evident now; I can’t see nutritional selective advantage(s) for any distant animal-ancestors in partially completed steps of the overall process. However, Martin et al. (2003) suggested that osmotrophy had to precede phagotrophy in eukaryote evolution, because without importers, food vacuoles are useless. As all present day fungi are osmotrophs it may be that at least this aspect of the fungal life style is an ancestral feature of the earliest eukaryotes. I will argue below (and you can read the full story in my new book: Moore, 2013) that there are other aspects of the fungal life style that could have contributed to assembly of the array of processes that might have enabled the emergence of phagotrophy in those early eukaryotes from which the animal lifestyle emerged.
Updated December 7, 2016