Does natural selection apply to entire populations as it does to individual organisms?
Unit of selection

Your question is about the concept of unit of selection. Selection acts on any populations of things that have heritable features which explain at least part of the fitness variance in this population. The "things" can be genes, cells, organisms, groups of organisms, species, lineages, etc...

The standard is to view selection acting on population of individuals. But of course, selection can also act on populations of groups of individuals (or populations of populations if you prefer) or populations of species. When talking about selection on a population of groups of individuals, we talk about group selection (a concept very related to kin selection) When talk about selection on a population of species, we talk about species selection (or lineage selection). 

Social evolution and altruism

An altruistic phenotype is defined as being a phenotype that is causing a decrease in the fitness of the carrier of the phenotype coupled with an increase in the fitness of one or more recipient individuals. Altruism can evolve at a level, only by selection applying at levels above it.

Imagine for example a population of individuals. If one individual mutates and as a result display a behaviour of donating food to the others. The cost for this individual is -0.5 and the benefit for the recipient is say 0.7. In absence of reciprocity, this mutation will not be passed on on future generations because  this individual carrying it have lower fitness. Therefore altruism should not evolve in this population. Imagine however if there are many populations and that some populations are altruistic and other aren't. Then, the altruistic population will likely outcompete the non-altruistic populations and therefore over time only the altruistic populations will remain.

It is by the way the existence of an altruistic behaviour that brought to wonder about the level at which selection can act.

The field that studies the evolution of such social phenotypes is called social evolution