Encapsulation is the process by which a set of distinct objects combine to act as a single unit. Individual fish, for example, form a school by aligning their movements with their neighbors. Because smaller objects usually merge into larger wholes, encapsulation is often linked to questions of scale. Encapsulation is closely associated with the idea of emergence. The whole emerges when individuals become subsumed within a group in relation to the outside world. There are many examples in ecology. Ecosystems are communities of interacting organisms; populations are groups of interbreeding organisms; and schools, flocks, and herds are groups of animals moving in coordinated fashion. In all of these cases, the individuals may not be permanently bound to the group, unlike cells within the human body. Cellular slime molds present an intermediate case in which cells sometimes act independently but at other times aggregate to form a multicellular individual.

Various ecological theories are based on the assumption that encapsulation plays an important role in ecosystem structure and function. The concept of ecosystem compartments implies that a community is formed of distinct groups (compartments) consisting of mutually interacting species, but the interactions between the groups are limited.

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