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Pterocystida Cavalier-Smith and Heyden, 2007 stat. n.

Phylogenetic diagnosis: The least inclusive clade, containing Pterocystis devonica, Raphidiophrys heterophryoidea and Choanocystis curvata, but not Acanthocystis nichollsi.

Raphidista
Centrohelids typically covered with an in-compact layer of flattened siliceous scales, which consist of upper and lower plates, connected by internal radial septae or with two types of scales: scales of the inner layer are flattened, simple in structure, usually ornamented with an axial rib, outer scales with a cylindrical shaft attached to a heart-shaped base-plate, which provides bilateral symmetry.

      • Raphidiophryidae
      • Choanocystidae

Pterista
Centrohelids covered with two contrasting types of siliceous scales: tangential inner plate-scales usually without a hollow and inrolled margin; outer scales typically consisting of a leaf-like blade with an axial rib, usually in various degrees extended at one end; the outer scale-base may be rounded or truncated and may be in the same plane as the blade or somewhat bent away from it or markedly extended as a distinct shelf or basal disc; siliceous scales may be secondarily missing with or without replacing it with organic spicules.

      • Oxnerellidae
      • Pterocystidae
      • Heterophryidae 

Spiculophryidae (incertae sedis):
Centrohelids typically lacking silica scales but with numerous thin, pointed organic spicules tapering towards acute apices.

 
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