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Secondary and tertiary endosymbiosis

It is now established that Chromalveolata is paraphyletic to Rhizaria.

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Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga that contained a chloroplast. These chloroplasts are known as secondary plastids.

While primary chloroplasts have a double membrane from their cyanobacterial ancestor, secondary chloroplasts have additional membranes outside of the original two, as a result of the secondary endosymbiotic event, when a nonphotosynthetic eukaryote engulfed a chloroplast-containing alga but failed to digest it—much like the cyanobacterium at the beginning of this story. The engulfed alga was broken down, leaving only its chloroplast, and sometimes its cell membrane and nucleus, forming a chloroplast with three or four membranes —the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the phagosomal vacuole from the host's cell membrane.

The genes in the phagocytosed eukaryote's nucleus are often transferred to the secondary host's nucleus. Cryptomonads and chlorarachniophytes retain the phagocytosed eukaryote's nucleus, an object called a nucleomorph, located between the second and third membranes of the chloroplast.

All secondary chloroplasts come from green and red algae —no secondary chloroplasts from glaucophytes have been observed, probably because glaucophytes are relatively rare in nature, making them less likely to have been taken up by another eukaryote.