This is the examination of the mechanics behind variation, that is, how it is produced, and how physical traits are passed on between parents and offspring. In order to do this, we need to know something about cell biology, embryology, and molecular genetics.

The sum of an individual's observable characteristics constitutes a phenotype. From this it can be said that each species contains a range of phenotypic variation. Knowing this, we might ask, what causes phenotypic variation? This is an interesting question, given that we all start out looking more or less the same at conception.

It's only as embryonic development proceeds that we start to obtain the characteristics that make us first vertebrates, then mammals, and then human beings. Our development from zygote to fully formed human being is conditioned by two things: a set of genetic instructions passed down to us from our parents called a genotype; and the environment in which this development is carried out. The genetic instructions that determine the growth and development stages of the zygote are contained within the nucleus.
 

The phenotype is a pattern of cells whose organization is determined by systems of information contained within our DNA (deoxyribonucleic acid). Types of DNA: Nuclear DNA is found in the nucleus of cells; it is inherited from both parents. Mitochondrial DNA is found outside of the nucleus of the cell, and is inherited along the female line only.

Fertilization and Cell Division
When fertilization first occurs, the resulting cell immediately begins to divide. As the divisions become more complex, cells become increasingly specialized and eventually take on different functions; for example: brain, gut, nerves, skin, etc.

The library of genetic information that controls phenotypic development are contained in long, threadlike structures called Chromosomes found in the nucleus of a cell. In the development of the zygote, the distribution of individual cells are not uniformly distributed. The effect is that they begin to take on more specialized functions. These functions are enabled by various proteins. Proteins are extremely important in the growth and development of all living organisms. 

RNA Ribonucleic Acid
RNA is a long strand-like structure that combines together in specific ways to build proteins. Varying combinations of their bases are responsible for the production of about 10,000 types of proteins in mammals. As such, RNA and the proteins they manufacture are the “tools” that allow the cell to both grow and subdivide.

Protein Functions
1. physiological - controlling such things as sight, smell, and hearing.

2. structural - controlling such things as the expansion and contraction of muscles and giving springiness to connective tissue (i.e. collagen in bone).

3. transportation - moving materials such as oxygen (hemoglobin in blood) from the lungs to tissues.

4. chemical - proteins known as enzymes function to digest things like food. Enzymes also carry out the process of that control and coordinate cell division.

Thus, proteins can be thought of as the body’s molecular tools that carry out specific genetic instructions which are encoded in DNA.

There are two processes that allow DNA to code for the life of an organism: DNA Replication and DNA Transcription.

DNA Replication is a process in which DNA replicates itself. The two strands of DNA that make up the double helix “unzip” and separate. Free floating nucleotides (phosphates, sugars, bases) within the cell then attach themselves to the appropriate bases found on the separated strands, forming two “copies” of the original DNA strand.

DNA Transcription is the process in which DNA is used as a "blueprint" for the synthesis of new RNA molecules. In DNA transcription, two intertwined strands of DNA partially “unzip”, and a single strand of RNA is created.

Genes and Genotypes
What do we actually mean when we use the term “gene”? We've seen that the DNA's function is that it carries the message that determines the appearance or phenotypic character of an organism.

We have also seen that DNA involves inheritance, because this message is transmitted from one generation to the next.  As such, we should think of a gene as "bits" of information that are carried by DNA that are passed on from parents to offspring. More specifically, a gene is defined as a section of DNA that codes for the development of a specific protein, which in turn, makes cells carry out certain functions.

Genetic Basis for Variation
The term Gene Locus refers to location of a particular gene on a chromosome. At any one particular locus on the chromosome, every individual will have two sets of information. The information contained within each "set" can either be the same or it can be different. The information itself is referred to as an allele. If both alleles at a gene locus are the same, then we say that the individual is homozygous. If both alleles at a gene locus are different, then we say that the individual is heterozygous.

This distinction is important because even though individuals may carry genetic information for one particular trait, they may not physically express it. For example, you may carry the allele for both black and blond hair at the gene locus controlling hair color, but only show black hair in your physical appearance. However, if your hair is a mixture of black and blond, then the effects of both alleles appear in the phenotype. This is referred to as Co-Dominance. In situations where the effects of only one allele appear in the phenotype, such as, black hair, then this allele is said to be Dominant while the allele controlling blond hair is said to be Recessive.

More Complex Patterns of Gene Interaction
So far all of the examples we have discussed have focused on a "one gene, one trait" or monogenic relationships, but things can get more complicated. In Polygenic situations, alleles associated with a single phenotypic trait are found at more than one locus on the chromosome.

Conclusion
The processes involved in the change of a species over time are rooted in the genetic variability of individuals and the resultant recombination of this material. To more fully understand the process of evolution, we now need to expand our view from the individual and look at populations of organisms, since this where we really see evolution at work.

Genes in Populations
Up until now, we have only looked at genetic variation at the level of the individual, now we are going to look at it at the population level. To do this, we should define what exactly we mean by population.  A Mendelian population refers to a group of organisms that are able to form mating pairs with others of their own kind.

Previously we talked about the amount of genetic variation inherent within individuals. When you take a group of individuals and redefine them as a population, you increase the potential for genetic variability many times over! This total amount of genetic variability within a Mendelian population is called a gene pool.

This pooled genetic information is what causes the range of phenotypic variation that we see in a Mendelian Population, and this is one of the reasons why we as human beings display such a wide range of physical variation within our species.  In some situations, species can become spatially isolated from one another by geographical constraints such as mountains, bodies of water, deserts, etc.. When this occurs, one or more sub groups may become isolated from the core group and become a sub-species.

Discontinuous and Continuous Variation
In discontinuous variation, phenotypic traits are either one thing, or another, there is no in between. In continuous variation, phenotypic traits are more blended so, rather than existing as discrete categories, they exist along a gradient. It is also important to note that the genes that control continuous variation are often found at more than one locus on a chromosome (which is defined as polygenic).

Gene Frequencies
Using Sickle Cell Anemia as an example, and from our Punnet Square, we know that the non-anemic phenotype is produced by the genotypes AA and AS and the anemic phenotype is only produced by the genotype SS because the S gene is recessive. Consequently, if we knew the frequencies in which these three genotypes appeared in a population, we could predict the impact that sickle cell anemia would have on that population.

Obviously, the ways in which the bearers of AA, AS, and SS genes mate with one another will influence the ways in which these alleles combine into new genotypes (and produce or not produce the phenotype for the disease). If we assume that everyone in a population has an equal chance of mating with any other individual within that population, then there should be predictable relationship in the frequency of the genes that can be calculated.

Hardy-Weinberg Theorem
This calculation of gene frequency can be stated mathematically using the Hardy-Weinberg Theorem. It is a method that can be used to calculate the expected frequency of genes in a hypothetical population that is considered stable (or free from evolutionary forces). We can use this these expected gene frequencies (of this hypothetical population) as a bench-mark for the comparison of real (or observed gene frequencies in a population) to determine whether a population is undergoing evolutionary change. The differences between the Expected and Observed frequencies will tell us whether evolution is at work, and the extent to which the population is evolving.

The Forces of Evolution
Working either alone or in combination, these produce different effects on a population because they alter the frequencies of genes and genotypes that will have definite evolutionary consequences.

1. Mutation - The primary means through which entirely new information can be added to genetic systems is by way of  mutation. Mutations can occur by way of changes in the chemical structure of the gene, or a change in the order of the chromosomes, or a change in the number of chromosomes.

2. Natural Selection - When populations become stable for long periods of time, they are said to be under the process of Stabilizing Selection. Directional Selection  is where there is pressure continuously selecting one trait or pattern over another in one direction. Diversifying Selection is where you have extremes being selected for at the expense of the center of the entire range of variation.

3. Genetic Drift - Genetic Drift is an important mechanism for producing genetic variation across populations. There are several processes that fall under the heading of genetic drift, including Fission, the Founder Effect and Gamete Sampling. Fission is the splitting of a population into sub-populations that differ from one another as well as the original population. When this split is uneven, the effect is likely to be more dramatic. The Founder Effect is demonstrated from a new population that is founded by only a few individuals who carry only a small fraction of the total genetic variation that was present in the parent population. The result of the founder effect is both a loss in variation (also referred to as an evolutionary "bottleneck"). Gamete Sampling describes the genetic change that we see from one generation to the next. While the genetic difference between ourselves and are parents might be quite small, when they are considered across a population, the effects are multiplied.

4. Gene Flow - Gene Flow is essentially the opposite of Fission. it acts to transport alleles from one population to another. It occurs as a result of intermarriage within another population or populations. In this regard, Gene Flow is often associated with cultural practices.

Interaction of Evolutionary Forces
So far we've discussed the various evolutionary forces acting on their own. However, the process of evolution actually involves the interaction of each of these four forces. The ways in which these forces act is often related to whether or not we are examining evolution within populations or between populations.

In general terms, both genetic drift and gene flow tend to be directional, with Genetic Drift decreasing variation within a population, and increasing variation between populations. On the other hand, Gene Flow works in the opposite direction, increasing variation within a population, and decreasing it between populations. Selection on the other hand can work in either direction in either situation. And, as a result, selection can either work with or against other forces of evolutionary change.

The end result, however, is that each population will show different dynamics, and it is highly improbable, if not impossible to predict the overall effect of these evolutionary forces on a population. Thus, evolutionary change is not predictable.

Macroevolution: The Origin and Evolution of Species
Speciation - the appearance of the new form that requires three conditions usually have to be satisfied: 1) reproductive isolation, 2) the development of species specific characteristics, and 3) the control of its own ecological niche. There are two main kinds of speciation processes. These are gradualism and punctuated equilibrium. Gradualism suggests that populations naturally change or evolve over time. Punctuated Equilibrium suggests that populations tend to develop to a state of stasis or equilibrium for long periods of time, and then occasionally, populations are forced into a new niche in an event that is referred to as punctuation. The result is that a new species is formed in an evolutionary burst in the new niche. Once established, the new species will then develop its own evolutionary stasis.

Adaptation - is the development of a position or “niche” within the environment. Each species assumes a special position within a particular environmental niche. The law of competitive exclusion states that if two co-existing species occupy environmental niches that are close enough to cause severe competition, it is inevitable that one of the two species will become extinct.

Stasis - can be defined as a period of evolutionary maturity when an adapted population in a stable environment. Once a species manages to colonize and adapt to a specific environmental niche, selection works to maintain stability.

Extinction - is defined of the disappearance of a species. Extinction is the inevitable fate that awaits all species. This might result in a number of ways, including: ecological change, species competition, and chance catastrophic events.

Species Interdependence in Evolution
Evolutionary processes are dependent on interactions between species. Improvements in one species lead to a selective advantage for that species. This means that as fitness increases in one evolutionary system, it will tend to decrease fitness in another system. The only way that a species involved in such a competition can maintain its fitness relative to the others is by, in turn, improving its design.

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