Ecology is the study of plants and animals at home, that is to say, in their natural environment (from the Greek word oikos, a house). Evolutionary ecology is the branch of this subject that considers how organisms have evolved to become adapted to their environment, including in this term their interactions with members of their own and other species (the biotic environment) as well as the physical environment; it examines the selective pressures imposed by the environment and the evolutionary response to these pressures. Darwin (1859) proposed natural selection as a unifying principle to explain two things: the transmutation of species and the adaptation of organisms to their environment. Evolutionary ecology takes the second of these as its field of study. Its aim is to explain, in the light of current knowledge, "how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation that most justly excites our admiration." — Michael Bulmer (1994)

Evolutionary ecology, as noted and in less-strict terms, is the study of the evolution of adaptations. That is, those morphological, physiological, or behavioral changes that result in increased Darwinian fitness, i.e., increased ability to survive and, especially, to reproduce. Many of these adaptations are straightforward in terms of our ability to understand how an organism benefits. Other adaptations are more subtle, however, and therefore it is more difficult to conceptualize just how they are beneficial. Furthermore, as noted, the evolution of adaptations does not occur within a vacuum. Instead, adaptations ensue within the context of the organism's evolutionary history, what adaptations already are present, the genetic system employed by a species, and a population's potential to generate useful, that is, adaptive mutations. One can view evolutionary ecology, i.e., the evolution of these adaptations, from the perspective of the optimization of phenotypes, in terms of either phenotype function or phenotype contribution to an organism's evolutionary fitness or, of course, both. One can also study evolutionary ecology in terms of tradeoffs, not just in terms of optimization of specific phenotypes but also in terms of how changes in one phenotype/adaptation can affect the functioning of other phenotypes/adaptations.

Evolutionary ecology in very broad terms is simply the study of the "Why" of phenotype, i.e., ultimate causation, rather than the study of the "How" of phenotype, a.k.a., in terms of proximate causation. Biology thus can be subdivided into physiological studies (the study of how, which includes such things as biochemistry as well as much of genetics, i.e., proximate issues), the study of how organism interact with their environments as considered independently of evolutionary history (the more proximate causation side ecology), evolutionary relationships between organisms (phylogenetics), and also evolutionary ecology (the more ultimate causation side of ecology). In addition, and for completeness, biology also consists of numerous applied disciplines, such as medicine, dentistry, and agriculture.

With evolutionary ecological approaches we can take "a cost-benefit view of" adaptations where benefits represent fitness-increasing aspects while costs present fitness-decreasing aspects (Mackinnon and Marsh, 2010). Generally an adaptation, operating within the context in which it evolved, would be expected to provide net fitness benefits to its carrier, that is, where benefits outweigh costs. Such costs can be energetic, can be due to costly increases in the bulk of an organism (issues one sees particularly among flying animals such as birds), can result in decreased functioning of other aspects of an organism, can require increased time to develop (thereby extending generation times), can directly take the place of other adaptations (e.g., loss of forelimb functionality, again with birds, towards increased flight efficiency), etc. Note that explicit to this view is that adaptations do not necessarily present cost-free increases in carrier fitness. Instead, and as noted, typically there will be tradeoffs where the fitness of an organism is increased in one respect but decreased in another. This idea of adaptation costs and benefits may be a useful perspective particularly for microbiologists to take since it is in a sense a more proximate way of viewing what otherwise are issues of ultimate causation, that is, an approach where one can begin with the actual adaptation rather than with some hypothetical utility. I'll go even further and suggest that microbiology is at its best when considering adaptations from a cost-benefit outlook, with the more possible costs and benefits that one can consider when study a particular organism aspect, the better.

This latter perspective is closer to how microbiology traditionally has been practiced, particularly in the pre-genomics era. It is important to realize that microbiological investigation often will go into more mechanistic detail, however, especially in terms of determining the proximate bases of adaptations, i.e., what molecules do what and how. An evolutionary ecologist with a phenotypic bent, by contrast, while still interested in mechanisms, often will not be as interested in the specific, mechanistic underpinnings of adaptations. Thus we can consider a spectrum, where evolutionary ecology with a more genotypic emphasis (adaptation as increase in fitness) forming one end; traditional, especially molecular microbiology forming the other; and somewhere in the middle lies evolutionary ecology with its more phenotypic emphasis, that is where mechanistic details of adaptations are not of central importance.

Another way of defining evolutionary ecology is specifically in terms of its ties to the concept of organismal fitness. One can view this relationship in terms of phenotypic versus genotypic or ecological versus evolutionary biological concerns. On the one hand, there are many scientists who come at evolutionary ecology from the evolutionary biology side of the divide, whose major concern is with change in genotype through time. In this case, genotypes can be and often are viewed in terms of differences in organismal fitness. Differences in fitness thus can be determined between different genotypes and greater fitness viewed as an adaptation. Alternatively, it is possible to start with adaptations, not defining those adaptations solely in terms of fitness, and this can be seen as a more ecological perspective. In this case the specific means by which an adaptation results in greater fitness is the central issue. That is, the primary questions are why or how an adaptation mechanistically gives rise to an increase in fitness, rather than simply that such an increase has occurred or that it may be linked with specific changes to nucleotide sequences.

Another rough differentiation among biological disciplines. Here particularly the emphasis on phenotype by evolutionary ecology is differentiated from the more genotypic emphasis of phylogenetics (as a subset of evolutionary biology). Less evolutionarily oriented aspects of ecology – more proximate emphases versus the more ultimate emphasis of evolutionary ecology – are more oriented towards environmental or ecosystem functioning than is evolutionary ecology. Evolutionary ecology thus, essentially, is the evolution of phenotype and particularly as viewed within the context of organism interactions with their environments. Evolutionary ecology, along with physiology, is the study of organism functioning. In comparing organisms, evolutionary ecology is also concerned with the functional meaning of differences, and how those differences may promote environment interactions as well as fitness, versus simply the comparison of organisms (phylogenetics) or the simply functional interactions with environments (indicated in the table as utility).

These various perspectives may be considered to represent something of cycle of biological interest, where adaptations, as phenotype, are underlain by developmental biology, biochemistry, and molecular genetics. These molecular aspects with or without consideration of phenotypic plasticity are, in turn, consequences of the expression of genotype. Evolutionary biology thus is concerned with changes in genotype through time, and different genotypes can display differences in fitness. Fitness, in turn, may be understood in terms of the phenotypic details of adaptation, which are underlain by molecular details, and so on. In terms of flow of information, however, the direction is from genotype to molecular phenotype to organismal phenotype to fitness, plus back again via the process of natural selection (the latter consists of environment acting on phenotype that results in distinctions among genotypes that are more than just in terms of differences in nucleotide sequence). It is a philosophical short-circuiting of this flow to describe genotype as going directly to fitness, as though through some "black box", though not necessarily an invalid short circuiting. Nonetheless, the point still holds that fitness can be viewed as a concept that links the ecological with the evolutionary biological. Whether viewed from a genotypic or phenotypic perspective, that linkage embodies the discipline of evolutionary ecology.

Here we will tend to place a great deal of emphasis on evolutionary ecology while considering microbial population biology/microbial evolution. In part this is a consequence of the personal inclinations of the author. Additionally we can differentiate evolution into that which is adaptive and that which is not explicitly adaptive. While the latter, non-Darwinian evolution is crucial to appreciate, what is interesting about microorganisms, particularly to microbiologists, is what they do. What microorganisms do can be viewed explicitly in terms of microbial adaptation, i.e., Darwinian evolution. In short, evolution occurs exclusively within an ecological context, that is, in terms of organism interactions with environments, and to a large extent interest in microorganisms is synonymous with interest in microorganism phenotypic properties, particularly in terms of microorganism interactions with their environments (which, for example, includes interactions with our own bodies). The evolution of phenotype in turn can be viewed in terms of adaptations, and the evolution of adaptations is the province of evolutionary ecology.