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Apicomplexa consist entirely of parasitic genera occurring in a wide spectrum of invertebrates and vertebrates, including humans. It is assumed that ancestral apicomplexans parasitized marine annelids and that their adaptation to a parasitic lifestyle and further radiation took place before the era of vertebrates, spreading first to other marine invertebrates (crustaceans, turbellarians, echinoderms, etc.), then freshwater and terrestrial invertebrates, and finally vertebrates. In contrast to apicomplexan etiologic agents of globally significant human and animal diseases (e.g. malaria, toxoplasmosis, cryptosporidiosis), which have been well studied, the enormously diversified basal apicomplexan lineages restricted to invertebrate hosts remain poorly understood, despite being important from an evolutionary perspective due to their basal phylogenetic position. Several early-dispersed apicomplexan branches are hypothesised, e.g. blastogregarines, archigregarines, eugregarines and neogregarines, agamococcidia, protococcidia and cryptosporidia.These exhibit an enormous diversity in both dimension and cell architecture, depending on their surrounding environment and parasitism strategy, and appear to be perfect examples of coevolution between parasites and their hosts.

Apicomplexans exhibit highly specific adaptations for invading and surviving within their hosts. These have evolved under distinct evolutionary pressures, resulting in diverse host-parasite interactions. The highly specialized, motile invasive stage of apicomplexan parasites, the zoite, is equipped with a set of sophisticated organelles and a cytoskeleton dedicated to reaching and invading the host cell. The zoite exhibits high cell polarity by having an anterior pole equipped with a unique invasion apparatus, the apical complex, consisting of specialised secretory organelles (rhoptries, micronemes), polar ring(s) and a conoid. This apparatus, traditionally used as the best-defined feature for Apicomplexa, can also be found in other Myzozoa, a group comprising apicomplexans, dinoflagellates and several lineages of free-living predatory or parasitic flagellates that employ a myzocytosis-based mode of feeding. It is probable that the evolution of Apicomplexa progressed from myzocytotic predation to myzocytotic extracellular parasitism, as exhibited by some gregarines and cryptosporidia, and finally to intracellular parasitism, typical for coccidia. The Apicomplexa demonstrate two main determinative evolutionary trends: i) the origination of epicellular parasitism, observed mostly in gregarines, with subsequent modification of the attachment apparatus and motility mode in the vegetative stage (trophozoite); and ii) origination of intracellular parasitism in typical coccidia and Aconoidasida, accompanied by a rejection of trophozoite polarity and motility.