Having divided the formation of the phenotype into a patterning node and non-heritable nodes, I want to spend some time discussing what is and isn’t part of the phenotype.
The phenotype is the interface of an object with its environment. Everything, even rocks, have a phenotype. It is probably useful to use a somewhat philosophical concept of the “phenotype” being the sum of all aspects of the organism that interacts with the environment, or conceptually a gestalt concept of the totality of the organism’s appearance behavior and physiology.
Such a concept of phenotype is not particularly useful, thus, it is convenient to divide the phenotype into “characters” or “traits” (I will use the two more or less interchangeably). A trait is a measurable aspect of the phenotype that is of interest to us. Thus, for example, many flowers have ultraviolet nectar guides that attract pollinators. Humans were unable to detect ultraviolet radiation until it was discovered by Johann Ritter in 1801 (http://coolcosmos.ipac.caltech.edu/cosmic_classroom/classroom_activities/ritter_bio.html). Basically, the distinction I am making between phenotype and trait means that nectar guides were always part of the phenotype of flowers, but didn’t become traits until 1801, when humans were able to detect them. Finally, given that a trait is a particular measurable aspect of the phenotype, I will use the term “trait state” (or character state) to refer to the value that a given individual has for a particular trait. Thus, for the trait “height” my trait state is five feet five inches.
Aspects of the phenotype obviously include those traits that are of interest to evolutionary biologists, such as body weight, running speed, amylase activity, foraging behavior, but also traits that are generally not of interest because they are ephemeral, or have little chance of being heritable. Examples of the latter would include such things as the time since the last meal, what that meal was, tattoos, and other body art, and the color clothes a person wears. We don’t normally think of these as “traits”; however, an important aspect of the phenotype are non-heritable changes, such as adding a person tattoo, or whether or not a lizard has lost its tail.
My definition of evolution is about the gain and loss of individuals. This raises an issue about traits that change over time. Many of these traits will be of trivial interest. For example whether you are inhaling or exhaling would seem to be part, if perhaps an uninteresting part, of your phenotype at any given moment. On the other hand, weight is clearly part of the phenotype of an organism, and it can fluctuate with development and time. The question is how to deal with traits that change, whether slowly or quickly. My own solution, and maybe other have a different solution, is to think of an individual’s phenotype as a vector through time. In this view every trait has two values, the trait value, and the age at which the trait was measured. Thus, we could measure body weight at age 6, 18, and 32. These would all presumably be different. We could also number of fingers on the left hand, and discover that in nearly all cases this was constant. In the finger number example, while the time element is technically there, there is little reason to keep track of it.
When I talk about multilevel selection it will also be useful to think of the phenotype as including some aspects of the social environment. For example, there will be times when the size of the group an individual experiences can be treated as a trait of the individual. This is best left for a later discussion, briefly, however, these supra-individual level traits will be useful to consider when features of the group affects an individual’s fitness
It is worth discussing genes at this point as an example of what is and isn’t part of the phenotype. In particular, genes actually have three more or less independent functions.
First, they are passed from parent to offspring, and they carry with them information. This is traditionally what one thinks of when referring casually to genes. Basically genes are units of heritable information that is passed vertically between generations. It is worth noting that as we have gotten a better handle on the structure of the genome, the concept of what a gene really is has become less clear. That is, a gene is a strip of DNA, but it may be DNA that is transcribed and translated into a protein, DNA that is transcribed into the many of the various RNA’s without being translated into a protein, or it might be one of the many controlling elements. For our purposes it really doesn’t matter, the first function is that it is information that is passed from parent to offspring.
Second, genes are part of the patterning node, and as such they participate in the formation of the phenotype. This is a distinct function from the inheritance aspect, a point that is made very obvious by the single celled Prtotist, Paramecium. Paramecium have two nuclei, a micronucleus and a macronucleus. Briefly, the micronucleus is reserved for reproduction, and is only used for transmitting information when the cell divides. On the other hand, the macronucleus has multiple copies of the genome, and functions in protein synthesis and the management of the cell. In animals we have only a single nucleus that functions both for information transfer and protein synthesis; however, even here there are cells that become “polytene” meaning that they have multiple copies of the genome. These tend to be cells that will no longer divide, but have a heavy protein synthesis load, such as salivary gland cells in Drosophila, and liver cells in humans.
Figure: Drawing of a Paramecium (http://www.flickr.com/photos/worldworldworld/4095866648/sizes/o/in/photostream/). The micro nucleus, which divides when the cell divides, transmits information between the mother and daughter cell. The macronucleus has multiple copies of the genome and produces the proteins and RNA that interact with the environment to produce the phenotype.
The third aspect of genes is that they are part of the phenotype. That is, they are traits of an individual since they have a sequence, and a position in the chromosome. As such they have to be considered part of the phenotype. For example, there are circumstances in which we might want to identify and select animals with a particular allele at a particular locus. In this case we are in fact selecting for those animals that have the trait state of having the desired gene sequence at the locus of interest. Typically we are selecting for individuals with certain alleles because we hope it will have a desired effect on some other trait; however, this is correctly viewed as a “correlated response to selection”. That is, we are selecting individuals with the desired gene sequence, and the phenotype changes because it is correlated with the genic phenotype. (I have not talked about it, so this has to remain an aside; however, notice that even in this case selection is on individuals, not genes. With the exception of transposable elements I have not been able to come up with a single example that can legitimately be called “genic selection”. I will talk about this when I discuss selection.)
Thus, in summary, the gene sequence, and corollaries such as the location of a band on a gel, can be considered to be part of the phenotype. The information that the gene carries, and its function in the patterning node in creating other characteristics of the organism is not part of the phenotype.