One reason that it matters whether or not species coexist in structured communities is because of so-called 'emergent properties' of associations of species. Thus, communities were long thought to have properties, or characteristics, that were not discernible, nor predictable, from knowledge of the species as individual entities. The properties of a set of species interacting with each other in a community were emergent in the sense that one had to study the community to know about, understand, or explain them. These characteristics of species 'emerged' from the community as the unit of study.
There has been widespread discussion of the concept of emergent properties in ecological investigations. Some of this discussion is, to say the least, confusing. For example, some properties of a set of species are simply collective properties due to grouping them into a set (whether or not such grouping is appropriate). Often, the diversity of species in a community is considered to be an emergent property, because it cannot exist for the individual species. In fact, this is a collective property that can be determined from the properties of the component species. An analogy is the average size of individuals of a population of deer. This is not a property of the individual deer, but can be calculated from their individual sizes. It does not 'require' study of the population as an entity.
Emergent properties may exist. For example, natural selection may operate on individuals because of their interactions with (and only with) other members of a community. If this were the case, clearly the community would have to be studied as a unit; the process (the property) could not be found (would not emerge) from study of only the component species.
As with other issues about communities, the concept of emergent properties is confusing, because the term means various and different things. To some, it means properties that become apparent when the scale of observation is changed, but this does not apply in the context of communities. The observations that are interpreted to be indicating the evidence of a community are at a particular scale; it makes no sense to change the scale.
To others, emergent properties are those that are unexpected to find in an assemblage because not enough information was available about its components. Using this definition, emergent properties are those that are found by studying communities, but that were not known from information about the component species. Ignorance about components does not make a more holistic study the best option - the community would still have to be understood in terms of its components for that ignorance to be dispelled. Apart from that, any such property could only possibly 'emerge' once. Once the property is known for one assemblage, it can be predicted for another assemblage from similar knowledge about the components of that assemblage. This scarcely defines emergent properties of communities in a useful manner.
The third and, probably, philosophically most useful meaning of emergent properties is that they exist in a community, but cannot possibly be derived from knowledge of components of the community. Thus, reductionist studies of ecology will fail to provide understanding of communities because studying the components will not lead to understanding of the community as a whole.
So, for communities to be appropriate units of study, not only must they have some definable structure (as above), but also they must have emergent properties, so that subcomponents (i.e., the populations of different species) and their interactions are not appropriate units. This makes the practical usefulness of the concept of a community very difficult to demonstrate. Whether or not trying to demonstrate that existence of emergent properties is useful is a moot point, because it can distract from the real task of understanding the ecology of the observed assemblage.
A final comment on emergent properties is that many ecologists have holistic views about the way organisms operate, based on patterns of energy flow through ecosystems. Properties of ecosystems that make them appropriate units for study presumably include emergence. This makes the use of ecosystems even more problematic than the definitional problems briefly discussed earlier.
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