1. Gene Frequency and Natural Selection
Spring Feb 2015

2. Relationship between Gene Frequency and Natural Selection
Random genetic mutations occurs
Inherent Variation
Sexual reproduction
Natural Selection
Influences from the surrounding environment
Eliminating incompetent individuals
Does not produce perfect organisms
Highly selective and specific
(According to Hardy-Weinberg, changes in frequency will not occur in a population if these five conditions are not met.)
No mutations
No natural selection
Very large population
Random mating
No gene flow
Gene/Allele frequency: It is the proportion of genes/alleles in a specific population. It shows the true genetic diversity of a species’ population or the variety within its gene pool. Gene frequency is based on the genotype, not the phenotype.
Natural Selection is a gradual process in which beneficial traits are accumulated and detrimental traits are exterminated through selective pressures. Each subsequent generation will also undergo this process, further fine tuning the traits that prove most useful and hindering the more unfortunate individuals from reproducing.
We know that the Hardy-Weinberg principle states that allele and genotype frequencies will remain constant over different generations, given that there is an absence of other evolutionary influences
The Hardy-Weinberg equilibrium can be applied to the population only if:
No mutations
No natural selection
Very large population
Random mating
No gene flow
The Hardy-Weinberg equilibrium can be disturbed by a number of forces- including mutations, natural selection, nonrandom mating, genetic drift, and gene flow (Reece).
Likewise, nonrandom mating (i.e. sexual selection) disrupts the Hardy- Weinberg equilibrium because this type of behavior typically encourages directional or disruptive selection, resulting in changes to the gene frequency.
Another factor that can upset this equilibrium is genetic drift, which occurs when allele frequencies grow higher or lower by chance and typically takes place in small populations.
Gene flow, which occurs when breeding between two populations transfers new alleles into a population, can also alter the gene frequency equilibrium.
Since all of these disruptive forces occur commonly in nature, the Hardy-Weinberg equilibrium rarely applies in reality; therefore, this principle describes an idealized state, and genetic variations in nature can be measured as changes from this equilibrium state.
With this we can see how gene frequency and natural selection are related to each.
Explain how, what, why is common to gene frequency and natural selection.
Allele/gene frequencies tend to shift towards the phenotype that is best suited for the current environment. Natural selection weeds out the unfit individuals and allows better adapted individuals to breed more frequently, eventually increasing the frequency of "preferred" allele combinations.
Natural selection acts on an individual’s ability to survive and reproduce in a specific environment, which is determined by its phenotype, the physical manifestation of the alleles it has inherited. Natural selection changes the gene frequency within a population by selecting certain phenotypes over others. This leads to indirect sexual selection of the more able individuals. Mutations are completely random, but natural selection is a process that imposes a rigorous filter on what mutations make it through to future generations.
Nature cannot build new traits from the ground up but instead augments existing structures to fulfill different needs. Instead of adding a new feature that would be advantageous, natural selection changes what is already present to suit new environmental conditions. A prime example of this is the homologous structures shared amongst vertebrates.

3. Natural Selection Methods
Different populations of prey
Different predators
Adaptation by prey and predators
Different environments
Natural disaster-bottleneck effect
Different rates of survival and reproduction of prey populations
Explain how you modeled gene frequency and natural selection in a few bullet points
We simulated the process of natural selection by placing multi-colored paper dots on a multi-colored mat.
We then let predators eat this prey randomly and observed how the different colors were adapted to their environment and were therefore able to survive and reproduce.
We let the predators as well as the prey adapt to the changing circumstances.
We demonstrated directional selection for certain colors, when a predator would attack a specific color, as it stood out as an extreme color in its environment.
Furthermore we changed the environment to observe whether some of the prey were better suited for survival in this different set of circumstances.
Finally, we produced a bottleneck effect by simulating a natural disaster that wiped out the majority of the individuals and some of the populations.

4. Gene Frequency Methods
A starting population of 50 individuals represented by 100 alleles (beads) were picked out of the cup at random; this essentially signifies random mating.
Allele pairs were added or removed based on the rate of survival to replicate the introduction of selective pressures.
The allele pairs were then counted and beads were added depending on the rate of survival and reproduction for each case.
Beads were picked out in pairs at random again, these signify individuals of the second generation.
This process was repeated for six generations for all runs except for one case due to a shortage of beads.
That run was carried out until the fourth generation; therefore, all comparative analysis can only be carried out to the fourth generation and forecasting was used for the subsequent generations.
The rates of survival and reproduction for our various runs are greatly exaggerated, with rates rare- if ever found in nature.
The exaggeration is so that we can see the explosive/depressive effects of adaptability, or lack thereof, to a given environmental condition.
We ran a series of experiments under different conditions with controlled factors in an attempt to determine how effective the Hardy-Weinberg equilibrium is in predicting allele frequency within actual populations found in nature.
Comparing the results of running this experiment under different conditions demonstrated more precisely what type of selection is favored by altering the independent variables (directional, disruptive, and stabilizing selection).
Using the data we determined changes in allele frequency under different sets of environmental pressures. (explosive/depressive effects of adaptability or lack thereof)
Finally we tested the validity of the Hardy-Weinberg principle and demonstrated this concept in a controlled laboratory environment
Base case
-33% ww
-100% ww
Positive Mutation -100% ww
Negative Mutation

5. Gene Frequency Results
According to the graph, each of the genotype frequencies remain constant, therefore reinforcing the fundamental points outlined in the Hardy Weinberg principle.
The first case is a base case or control case. This base case essentially demonstrates the fundamental principles of Hardy Weinberg; some of which include but not limited to random mating, the absence of natural selection and mutations, and all members of the population surviving and having equal reproduction rates.
According to the graph, each of the genotype frequencies remain constant, therefore reinforcing the fundamental points outlined in the Hardy Weinberg principle.

6. This graph entails the projections of the genotype frequency percentages up for future generations.
This next case contravenes the principle in two such ways: this case comprises of the presence of natural selection and mutations.
Mutations disrupt the equilibrium of allele frequencies by introducing new allele combinations into a population. Certain combinations of alleles may harm, help, or not effect an organism. This has an effect on the reproductive success of the organisms within the population. Harmful or helpful phenotypes result in either a directional or disruptive selection, changing the gene frequency. Neutral phenotypic mutations will result in a stabilizing selection, making the Hardy-Weinberg equilibrium still applicable.
This graph entails the projections of the genotype frequency percentages up for future generations. The pair of alleles with 0% survival (green) showed a decreasing trendline, those who remained neutral (no mutations) (light blue and dark blue) showed a constant projection (furthering propagating the HW concept), and the pair of alleles with a positive survival rate (purple and orange) continued to increase logarithmically.

7. Natural Selection Results
First Environment
Population Size Data G1 G2 G3 G4 G5 G6
Blue 20 28 40 12 13
Light Purple 33 37
Orange 35 1
Yellow 32
Green 16
Pink 21 9
Dark Purple 29 24
Aqua
Natural selection can be caused by natural adaptations and extinctions or manipulation by human intervention.
By simulating selective pressures, natural selection can be replicated in a laboratory setting.
Species (light purple) that hid along the edges of the environment and species that blended into the colors of the environment were successful in surviving and reproducing.
In the data table here, we can see that G1-3 are for the first environment, while G4-6.
We found that the green and pink species did not do well in the first environment.
When clustered together, species of the same color died out faster and were unable to survive and reproduce as much as the rest of the species present.
In the second environment, when the predators attacked, we found that green, orange, yellow, and pink either died off or very few were left.
Second Environment

8. According to the first Figure (Populations with Projected Decay), the population counts in the first 6 generations fluctuated, but mainly had decreased in numbers.
The second figure displays the combined representation of all of the species
According to the first Figure (Populations with Projected Decay), the population counts in the first 6 generations fluctuated, but mainly had decreased in numbers.
It illustrates the population counts when forecasted up to generation 12; essentially, all of the species had a declining logarithmic trend line.
It exhibits the concept of natural selection; species who are unfit for survival from predators continued to decrease.
The Figure (Populations with Projected Growth) also shows the forecasted trend lines for the light purple and aqua (introduced in generation 4 after the green species died out) species; they have increasing trend lines.
It illustrates the concept of natural selection in such a way that species who evaded the predator were able to survive and reproduce more successfully than the other species who weren’t able to hide.
The second figure displays the combined representation of all of the species; there is a definite decline in population size of each species for generations 1 through 6 for the orange, yellow, and green species and a definite increase in population sizes.
The natural environment “selects” for specific traits in certain environments. The ability of the blue dots to thrive in the first environment, yet diminish in size in the second environment demonstrates this concept.
As we can see Some predators adapted to certain kinds of prey, specifically selecting certain colors of dots.
Some colors were visible better in the first environment, whereas other colors stood out more in the second; this had a direct impact on the survival rate, as the more visible ones were “eaten” at a higher rate.
Survival is linked to frequency of reproduction, perpetuating beneficial mutations and weeding out the disadvantageous mutations.

9. Gene Frequency vs. Natural Selection
Selection against one genotype can result in an overall positive effect on others by freeing up resources such as food and habitat.
Fluctuations within subsets of a population are normal, overall change in allele frequency is usually gradual unless a subset completely dies out.
As the homozygous recessive white phenotype is declining, there are resources for the heterozygous and homozygous red phenotypes, so there is less competition for food, mates, and resources for the red subset of the population, causing an increase in the frequency of the red allele.
The selection for the red allele could be due to multiple evolutionary techniques:
Directional selection: when conditions favor individuals exhibiting one extreme phenotypic range and shifts the populations frequency curve in favor of that characteristic.
Sexual selection: a form of selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates. The case exhibiting the negative 100% homozygous recessive could be caused by an extreme sexual selection, where the white simply could not obtain mates, and therefore they did not contribute their alleles to the gene pool of the next generation. This causes a drastic decrease in the white allele, as the only ones that survive are due to the heterozygous red individuals that carry a copy of it in their genetic makeup.
Another cause of this allele fluctuation could be due to gene flow, a mechanism of natural selection. In this case, the white alleles may not have been able to survive in a changed environment, as they could not camouflage, and in an attempt to adapt, they migrated out of the population to a new environment.

10. Conclusions
Natural selection and allele frequency are closely related, if natural selection is in action, then allele frequencies are changing.
The correlation between natural selection and gene frequency can be modeled in the laboratory using simple non-living systems, in living systems with much greater complexity, and can probably be modeled using highly sophisticated computer programs.
The allele frequency of the previous generation determines the phenotypic distribution of the current generation.
Natural selection acts upon this generation to refine the positive traits, weeding out the negative traits due to selective pressures such as predation, sexual selection, and relative fitness.
Therefore natural selection is a direct cause of allele fluctuation within a population.
Natural selection is the process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of these traits.
Adaptations arise due to this selection.
These adaptations cause allele frequencies to change in favor of the traits better suited for adapting.
The Hardy-Weinberg principle assesses if natural selection is in action and if evolution is acting on a population.
There are five conditions that must be met in order for the Hardy-Weinberg equilibrium to occur.
If not all of these conditions are met, then natural selection is acting on the population, and allele frequencies are changing.
This principle demonstrates the interconnection between natural selection and allele frequencies because natural selection acts on the phenotypic characteristics of the individuals in a population, and these characteristics arise due to inherited genes, and thus natural selection selects for specific alleles, and is a direct cause of allele frequency.

11. References
Reece, J. (2011). Campbell biology Jane B. Reece ... [et al.]. (9th ed.). Boston: Benjamin
Cummings.
The Paleontological Research Institution and its Museum of the Earth. Types of Natural Selection.
NY. Paleontological Research Institution. [cited 2015 Feb 19]. Available from
Philip McClean. Evolutionary Genetics [Internet]. Bison (ND): North Dakota State University; 1997 [updated 1998; cited 2015 Feb 25]. Available from:
"Modern Theories of Evolution: Hardy-Weinberg Equilibrium Model."Modern Theories of Evolution: Hardy-Weinberg Equilibrium Model. Available from: