A colony of clones
Clinging to boat hulls, docks, and rocks along the California coast are strange, colorful patches looking like melted jewels. These are colonies of Botryllus schlosseri, a species of colonial tunicate, or sea squirt. Though they appear as a single organism, each patch is a society of hundreds of genetically identical individuals, called zooids, embedded in a shared gelatinous matrix called a tunic. All the zooids in a colony are connected by a common network of blood vessels, sharing blood, nutrients, and stem cells.
The life of Botryllus begins as a free-swimming tadpole-like larva, complete with a primitive spinal cord (notochord). After a short mobile phase, the larva settles onto a surface and undergoes a radical metamorphosis, absorbing most of its chordate features to become a sessile, filter-feeding adult. This founding individual, or oozooid, then begins to replicate itself through a weekly cycle of asexual budding, giving rise to the entire colony of clones. Each week, the adult zooids die off in a synchronized wave of apoptosis and are replaced by a new generation of buds, while the colony's stem cells persist for the life of the organism.
To fuse or to fight
When two separate Botryllus schlosseri colonies grow until their edges touch, a dramatic decision is made: friend or foe. The choice is governed by a single, highly variable genetic region called the Botryllus histocompatibility factor (BHF) locus, also known as Fu/HC. If the two colonies share at least one of the two alleles at this locus, they are deemed compatible. Their external blood vessels, called ampullae, will fuse, merging the two colonies into one larger chimera with a shared circulatory system. Once fused, stem cells can travel between the once-separate colonies. In some cases, the stem cells of one colony can completely take over the other's reproductive organs, turning the loser into an incubator for the winner's offspring.
If the colonies do not share an allele, they reject each other in a violent, localized war. Their circulatory systems do not connect. Instead, cytotoxic cells migrate from the blood vessels into the tunic and attack the opposing colony. This triggers an inflammatory reaction where the interacting ampullae are destroyed, leading to cell death and the formation of a necrotic, black scar tissue between the two colonies. This highly specific rejection is sophisticated form of innate immunity, like organ transplant rejection in vertebrates, and it is the only known example in a non-vertebrate animal. This system allows colonies to avoid fusing with genetically distinct rivals, preventing a potential takeover by "parasitic" stem cells from an unrelated colony.