Conclusion

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The inventory of the diversity of eukaryotes and their modern classification carried out mainly through sequence data has led us to revise our vision of their evolution. The old dichotomy between animal and plant had been undermined by the discovery of a first type of cell without nucleus, bacteria, then a second still without nucleus, archaea. Modern phylogenies have shown that this dichotomy, as well as a partition into four realms, is also not valid for eukaryotes (Figure ). On the contrary, from these phylogenies, a story seems to emerge that would begin with a small biflagellate protozoan which, to feed itself, would have phagocytosed bacteria through its ventral groove, in agreement with the theory of the phagotrophic origin of the eukaryotic cell. Indeed, eukaryotes exhibiting this biology are present in Amorphea, Excavata and Diaphoretickes. Additionally, they appear to plug into the base of trees from all three of these groups, suggesting that this type of lifestyle and makeup is ancestral. This ancestor would therefore already have acquired all of the attributes of the eukaryotic cell: a nucleus with a sexual cycle, the reticulum/golgi system associated with the nucleus and the capacity to perform endocytosis/exocytosis, an actin and tubulin cytoskeleton with associated structures such as flagella but also probably pseudopodia, and finally mitochondria potentially capable of breathing oxygen, but also probably capable of producing hydrogen in anoxia.

The fate of this small protozoan was complex because it evolved from other ways of living repetitively (Figure ). It was able to maintain a phagotrophic lifestyle, but often perfected its prey capture system. The flagella have changed: disappearance of one of the two flagella and displacement of its insertion backwards in Opisthokonta and some Diaphoretickes, multiplication to give ciliature, particularly in Ciliophora, but also in Opalinata and Pseudociliata. The amoebic form has been favored and the pseudopods have adopted various morphologies, lobed, filiform, reticulated, radiating, etc., the different types favoring either hunting or fishing for prey. The trophic form increased in size to recurrently adopt a plasmodium-like form. The way of dispersing has also evolved, often with the establishment of an aggregative multicellularity. The predatory lifestyle culminated, of course, in animals where the increase in size involved the establishment of a complex multicellularity. In this group, phagotrophy was replaced by ingestion, a process identical in its course, but adapted to an organism with a mouth and a stomach.

The phagotrophy was lost more or less gradually either as a result of endosymbiosis of a cyanobacterium or after the establishment of an osmotrophic diet. We have seen the complexity of the placement of plastids in different groups of algae, explaining the mosaic of photosynthetic taxa. Osmotrophy has been adopted primarily by fungal-like organisms that emerge at least twice during evolution. In this case, it probably responds to the increasing availability in ecosystems of complex plant matter following the appearance of algae, then plants. It has also been adopted by parasitic organisms, especially those that live inside their host’s cells. Parasitism has been adopted recurrently during evolution (Figure 349). Parasitism engages in a race for so-called Red Queen evolution. One of the results of this race is the status quo, even the emergence of mosaic organizations where each of the two partners lives as a mutualist. These complex organisms then have a selective advantage and can invade ecosystems. The establishment of the eukaryotic cell is the result of such a phenomenon. This is repeated recurrently with the establishment of plastids, lichens, various syntrophies … In many lineages, these phenomena have been accompanied by the establishment of a more or less complex multicellularity. This takes its most successful forms in animals, plants, but also in Dikarya and Phaeophyta.

In summary, we must substitute a tree where the main branches are defined by the morphology or the lifestyle (Figure 63), with one where the main and secondary branches are essentially defined by phylogenic and molecular signatures combined with ultrastructural data (Figure )…

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