So what are the facts and inferences upon which the Theory of Evolution is based? Two of its foundational observations are deeply interrelated and based on empirical observations associated with plant and animal breeding and the charateristics of natural populations. The first is the fact that whatever type of organism we examine, if we look carefully enough, making accurate measurements of visible and behavioral traits (this description of the organism is known as its phenotype), we find that individuals vary with respect to one another. More to the point, plant and animal breeders recognized that the offspring of controlled matings between individuals often displayed phenotypes similar to those of their parents, indicating that phenotypic traits can be inherited. Over many generations, domestic animal and plant breeders used what is now known as artificial selection to generate the range of domesticated plants and animals with highly exaggerated phenotypes. For example, beginning ~10,000 years ago plant breeders in Mesoamerica developed modern corn (maize) by the selective breeding of variants of the grass teosinte.68 All of the various breeds of dogs, from the tiny to the rather gigantic, appear to be derived from a common ancestor that lived between ~19,000 to 32,000 years ago (although as always, be skeptical; it could be that exactly where and when this common ancestor lived could be revised).69 In all cases, the crafting of specific domesticated organisms followed the same pattern.
Organisms with desirable (or desired) traits were selected for breeding with one another. Organisms that did not have these traits were discarded and not permitted to breed. This process, carried out over hundreds to thousands of generations, led to organisms that display distinct or exaggerated forms of the selected trait. What is crucial to understand is that this strategy could work only if different versions of the trait were present in the original selected population and at least a part of this phenotypic variation was due to genetic, that is heritable, factors. Originally, what these heritable factors were was completely unclear, but we can refer to them as the organism’s genotype, even though early plant and animal breeders would never have used that term.
This implies that different organisms have different genotypes and that different genotypes produce different phenotypes, but where genotypic differences came from was completely unclear to early plant and animal breeders. Were they imprinted on the organism in some way based on its experiences or were they the result of environmental factors? Was the genotype stable or could it be modified by experience? How were genotypic factors passed from generation to generation? And how, exactly, did a particular genotype produce or influence a specific phenotypic trait. As we will see, at least superficially, this last question still remains poorly resolved for many phenotypes.
68 Molecular Evidence and the Evolution of Maize: http://link.springer.com/article/10.1007/BF02860472
69 From wild animals to domestic pets, an evolutionary view of domestication: http://www.pnas.org/content/106/Supp...nt_1/9971.full