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Siloxia split from its ancestor when a mutation in a biochemical pathway changed the production of cage-like oligosiloxanes to long siloxane polymers. This resulted in more rubber-like silicone instead of resin in the membranes. Some methane-poor environments caused this pathway to yield polymers of silica instead of silicone due to the lack of hydrocarbon groups to add to siloxane chains.

This added complexity to silicon biochemistry triggered a burst of speciation. Some species, especially in hydrocarbon-rich and oxygen-poor environments, retain silicone production and cause deposits of it to build up in the sediment. Other species form strong silica cell walls which offer defense and osmotic regulation, allowing them to live in a wider array of environments. In terrestrial soils, silica-forming Siloxia produce relatively simple glass shells, while in salty or fresh waters they may be spiked as a response to higher predation. Due to the orange pigments used in photosynthesis, all Siloxia species are restricted to light-limited habitats such as deep or turbid water, benthic soils, or moist terrestrial soils just below the surface.