Wednesday, July 9, 2014

Background to pop gen

Here's some quick and dirty background info for those curious about population genetics. It'll be simplified for wider popular appeal, but hopefully not overly simplified. I won't talk about population genetics itself, per se, since that'd be a bit too time-consuming for me to provide right now. But the background should provide enough knowledge to get people started on learning about population genetics on their own.

1. DNA. The first thing to know is that we're made up of DNA. DNA is a molecule that resides in us and encodes all our genetic information. We can think of it as containing all the instructions for how to make a human being.

2. Genes. DNA is composed of genes. Genes are segments of DNA that give humans form and/or function. Genes are also passed on from one parent to their child.

3. Allele. An allele is an alternative form of a gene. A variant. For example, different eye colors (e.g. blue, brown).

4. Genome. A person's genome is all the genetic info in a single person. This is all the DNA in a person.

Usually when we refer to DNA, we're talking about the DNA in a person's chromosomes aka chromosomal DNA. But there's also what's called mitochondrial DNA. That is, DNA in a person's mitochondria as well.

There are further distinctions but this should suffice for our purposes.

At any rate, a person's genome would include all the DNA.

5. Population. A population is all the organisms in a given set that can interbreed with one another. Actually, this is a very basic definition. It isn't perfect by any means, and debatable. But we'll just stick with this for now.

6. Evolution. A basic definition of evolution is a change in the frequencies of genes/alleles in a given population. Again, somewhat debatable, or at least requiring more elaboration, but we'll move on.

7. According to neo-Darwinian evolutionary theory, there are at least five factors that can influence the frequency of the genes/alleles in a population:

a. Natural selection. This is based on fitness. This is when the fitter or fittest individuals of a population survive (e.g. thick coated foxes are more fit to survive in the Arctic than thin coated foxes), pass on their genes/alleles, and thus their genes/alleles become more frequent in a population.

b. Sexual selection. This is based on sexual attractiveness. This is when the more sexually attractive individuals of a population mate and have the most offspring, thus passing on their genes/alleles, and thus their genes/alleles become more frequent in a population.

c. Gene migration. This is based on movement. This is when new individuals with new genes/alleles migrate into or out of another population, thus changing the frequency of genes/alleles in a population.

d. Genetic drift. This is based on chance. This is when random chance events (e.g. bugs getting stepped on, floods wiping out half the population) lead to changes in the frequency of genes/alleles in a population.

e. Mutations. This is based on anomalies in the genetic code. This is when mistakes in DNA lead to new genes/alleles.

7. Equilibrium. Specifically, Hardy-Weinberg equilibrium. A population is said to be in (Hardy-Weinberg) equilibrium when none of the previously mentioned factors are in operation. It also assumes all individuals in a given population capable of breeding are breeding and each produces the same number of offspring.

That is, natural selection is not at work. Sexual selection is completely random. There are no new migrants into or out of a population. There is a huge population size in order to moot random chance events affecting the frequency of genes/alleles in a population. Finally, no mutations ever occur.

8. Finally, as the cornerstone of population genetics, we have what's called the Hardy-Weinberg equation. The equation is: p2 + 2pq + q2 = 1.

We can think the equation in the following way.

Consider three basic types of genes/alleles. Say we have XX genes/alles representing dominant genes/alleles, xx representing recessive genes/alleles, and Xx representing mixed dominant and recessive genes/alleles.

Accordingly, the "p2" in the equation refers to what's called homozygous dominant genes/alleles. The "q2" refers to what's called homozygous recessive genes/alleles. And the "2pq" refers to what's called heterozygous genes/alleles.

If we know 40% of a given population posses homozygous dominant genes/alleles, then we know p2 = 0.4.

If p2 = 0.4, then p = 0.63 (approx).

That means q = 1 - 0.63 = 0.37.

While q2 = 0.137.

And 2pq = 0.466.

Thus, since we know p2 = 0.4, 2pq = 0.466, and q2 = 0.137, then we know 40% of the population possesses homozygous dominant genes (e.g. XX), 46.6% of the population possesses heterozygous genes/alles (e.g. Xx), and 13.7% of the population possesses homozygous recessive genes/alleles.

Wednesday, July 9, 2014

Background to pop gen

Here's some quick and dirty background info for those curious about population genetics. It'll be simplified for wider popular appeal, but hopefully not overly simplified. I won't talk about population genetics itself, per se, since that'd be a bit too time-consuming for me to provide right now. But the background should provide enough knowledge to get people started on learning about population genetics on their own.

1. DNA. The first thing to know is that we're made up of DNA. DNA is a molecule that resides in us and encodes all our genetic information. We can think of it as containing all the instructions for how to make a human being.

2. Genes. DNA is composed of genes. Genes are segments of DNA that give humans form and/or function. Genes are also passed on from one parent to their child.

3. Allele. An allele is an alternative form of a gene. A variant. For example, different eye colors (e.g. blue, brown).

4. Genome. A person's genome is all the genetic info in a single person. This is all the DNA in a person.

Usually when we refer to DNA, we're talking about the DNA in a person's chromosomes aka chromosomal DNA. But there's also what's called mitochondrial DNA. That is, DNA in a person's mitochondria as well.

There are further distinctions but this should suffice for our purposes.

At any rate, a person's genome would include all the DNA.

5. Population. A population is all the organisms in a given set that can interbreed with one another. Actually, this is a very basic definition. It isn't perfect by any means, and debatable. But we'll just stick with this for now.

6. Evolution. A basic definition of evolution is a change in the frequencies of genes/alleles in a given population. Again, somewhat debatable, or at least requiring more elaboration, but we'll move on.

7. According to neo-Darwinian evolutionary theory, there are at least five factors that can influence the frequency of the genes/alleles in a population:

a. Natural selection. This is based on fitness. This is when the fitter or fittest individuals of a population survive (e.g. thick coated foxes are more fit to survive in the Arctic than thin coated foxes), pass on their genes/alleles, and thus their genes/alleles become more frequent in a population.

b. Sexual selection. This is based on sexual attractiveness. This is when the more sexually attractive individuals of a population mate and have the most offspring, thus passing on their genes/alleles, and thus their genes/alleles become more frequent in a population.

c. Gene migration. This is based on movement. This is when new individuals with new genes/alleles migrate into or out of another population, thus changing the frequency of genes/alleles in a population.

d. Genetic drift. This is based on chance. This is when random chance events (e.g. bugs getting stepped on, floods wiping out half the population) lead to changes in the frequency of genes/alleles in a population.

e. Mutations. This is based on anomalies in the genetic code. This is when mistakes in DNA lead to new genes/alleles.

7. Equilibrium. Specifically, Hardy-Weinberg equilibrium. A population is said to be in (Hardy-Weinberg) equilibrium when none of the previously mentioned factors are in operation. It also assumes all individuals in a given population capable of breeding are breeding and each produces the same number of offspring.

That is, natural selection is not at work. Sexual selection is completely random. There are no new migrants into or out of a population. There is a huge population size in order to moot random chance events affecting the frequency of genes/alleles in a population. Finally, no mutations ever occur.

8. Finally, as the cornerstone of population genetics, we have what's called the Hardy-Weinberg equation. The equation is: p2 + 2pq + q2 = 1.

We can think the equation in the following way.

Consider three basic types of genes/alleles. Say we have XX genes/alles representing dominant genes/alleles, xx representing recessive genes/alleles, and Xx representing mixed dominant and recessive genes/alleles.

Accordingly, the "p2" in the equation refers to what's called homozygous dominant genes/alleles. The "q2" refers to what's called homozygous recessive genes/alleles. And the "2pq" refers to what's called heterozygous genes/alleles.

If we know 40% of a given population posses homozygous dominant genes/alleles, then we know p2 = 0.4.

If p2 = 0.4, then p = 0.63 (approx).

That means q = 1 - 0.63 = 0.37.

While q2 = 0.137.

And 2pq = 0.466.

Thus, since we know p2 = 0.4, 2pq = 0.466, and q2 = 0.137, then we know 40% of the population possesses homozygous dominant genes (e.g. XX), 46.6% of the population possesses heterozygous genes/alles (e.g. Xx), and 13.7% of the population possesses homozygous recessive genes/alleles.