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We plan to simulate a breeding population and determine the minimum number of individuals necessary to maintain a healthy gene pool based on a given trait with ‘x’ number of alleles.



We will experiment with the initial number of organisms of each gender necessary to ensure that no ‘inbreeding’ (defined initially as either filial mating or mating with first cousins) occurs.

Interim Report

Problem Definition:
Inbreeding is a problem facing many species of endangered animals today. Inbreeding, or the mating between two closely related individuals, enables recessive, detrimental alleles to be expressed. These rare traits would normally be suppressed when a carrier and non-carrier mate. However, when two closely related individuals mate there is a high probability that they carry similar recessive alleles of certain genes, including detrimental ones. Thus, inbreeding produces offspring that have a high probability of expressing detrimental characteristics that further weaken the population of endangered animals.

We plan to write a program that will determine the effects of a detrimental, recessive allele in a breeding population and determine what number of organisms is needed to make the allele non-harmful.

Problem Solution:

We will create a program that models a breeding population and introduce any number of genes will a number of alleles. We will track the effect the detrimental alleles have on the population and change the number of initial organisms to determine the minimum number of organisms needed to reduce inbreeding and decrease the presence of a detrimental allele. Mating will be random and the detrimental allele will cause homozygous individuals to exhibit a decrease in fitness (the number of viable offspring left).

Progress to Date:

We have researched various endangered species including captive tigers and wild pandas and spotted owls, and the effects inbreeding has had on them. We have also examined the effects habitat loss has had on the animals and how this has affected the health of the breeding population. Generally, inbreeding reduces reproductive ability, which even further reduces the already limited number of endangered individuals. Reduced habitat isolates one population from another and does not allow closely related individuals to disperse over a large habitat, as they would normally. These factors greatly increase the chance of inbreeding. Captive breeding programs, such as for the Sumatran and Bengal tiger also face problems with inbreeding even though they control which tigers mate. There are a limited number of tigers from other zoos to choose from when breeding tigers and the distance each tiger must travel, the age and health of the animal must also be considered.

We have a basic breeding program where male and female organisms mate randomly at a determined number of times per year. Currently, we have added no detrimental characteristics that can be passed on to offspring and to control growth rate, the organisms die at a certain predetermined age. Each organism contains properties such as its age, gender, parents, and unique identification number so that we can keep track of each individual organism. We are able to track mating between individuals and record the id number of the male and female involved, the number, gender, and id numbers of the offspring produced. Also, we can graph the number of individuals in the entire population; currently this graph is near exponential as individuals are dying after they mate more than once and produce offspring.

Expected Results:

We plan to test our current breeding program by introducing one gene with two alleles. This gene will only be for testing purposes and being homozygous for either allele or heterozygous will have no effect on the animal. We will measure the frequency of each allele using the Hardy-Weinberg (H-W) equation. The frequency of each allele should remain constant through each generation if our simulation conforms to the five stipulations of the H-W equation; a large population, random mating, no mutations, no migration between populations, and no natural selection.

After we ensure that our program conforms to the H-W requirements we will expand upon it and introduce a gene where being homozygous for the two recessive alleles will prove harmful in some way, such as reduced mating, fewer offspring produced, or early death. We will change the population size to find the minimum number of organisms needed to ensure that this allele would not wipe out the population, the recessive allele will either continue to be present in heterozygous form or may eventually be wiped out entirely if homozygous recessive individuals display a decrease in fitness. The recessive allele will be present in one heterozygous individual that will exhibit the healthy phenotype of a homozygous dominant individual. We will monitor consanguine mating between individuals and determine how this effects the population; the effects should be somewhat detrimental as the recessive allele can be present in its homozygous form if two closely related individuals carry the allele. We will then add factors such as habitat loss and population isolation and observe how these factors influence the population. As we have learned concerning the wild Giant Panda, these should both be detrimental to the health of the species.

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