Topic 2: Genetic Variation, Markers, HWE

Question 1

What is genetic variation? (3 things)

Answer 1

Genetic variation refers to the differences:
1. Among the genomes of members of the same species
2. Among genomes of individuals in populations of the same species
3. Assessed as variation in phenotype, protein sequence, and DNA sequence

Question 2

What is a polymorphism?

Answer 2

When a phenotypic character or a gene (locus) has more than one state in a population (more than one allele exists)

Question 3

What is a genetic marker? What is a requirement of using genetic markers?

Answer 3

A KNOWN genetic polymorphism associated with a specific locus on a chromosome that can be identified with a simple assay.
We MUST asses homologous loci within and across individuals.W

Question 4

What are the criteria for genetic markers? (6)

Answer 4

1. Do not need to know the mode of inheritance
2. Does the marker provide dominant (only one allele observed, or cannot determine allelism), or codominant data(both alleles observed0?
3. What is the marker mutation rate
4. Abundance in genome
5. Information content per locus
6. Ease of expense of genotyping

Question 5

What are molecular markers?

Answer 5

DNA or protein segments used as markers to study forensics, mating systems (parentage), population structure, gene flow, speciation, hybridization, and systematics
They are used to study complex (quantitative) traits in natural populations

Question 6

What were population genetics originally used to investigate?

Answer 6

Used to investigate allele frequency changes over time for conspicuous phenotypic polymorphisms. This addressed questions related to selection and hybridization
Few traits are inherited in a mendelian fashion

Question 7

What is an important thing to be noted about phenotypic markers?

Answer 7

Very few morphological markers are determined by a single gene and inherited in a simple fashion, most of them are polygenic and are continuously distributed

Question 8

How do you calculate genotype freqency?

Answer 8

Number of individuals with that genotype divided by the total.

Question 9

How do you calculate allele frequency using genotype counts?

Answer 9

2(homozygotes) + (heterozygotes) divided by 2(total)

Question 10

How do you calculate observed heterozygosity?

Answer 10

Number of heterozygotes divided by total individuals

Question 11

What are the advantages of assessing phenotypic variation?

Answer 11

Trait is directly linked to selection, easy to genotype (discreet), and field work provides other data collection

Question 12

What are the limitations to assessing phenotypic variation?

Answer 12

Mode of trait inheritance difficult to determine in the wild, limited scope because most traits are polygenic, limited genetic variation (2 alleles), and unable to distinguish between homozygous dominant and heterozygous dominant as they look the same.

Question 13

What are proteins? What are they made of?

Answer 13

Proteins are polypeptide chains of amino acids encoded by codons in DNA.
There are 20 different amino acids each with a different R group (reactive), and am amino group (NH2) and a carboxyl group (COOH). They are joined together by peptide bonds formed by condensation reaction of the amino group and the carboxyl group with the removal of water.

Question 14

What are the four protein structures?

Answer 14

1. Primary: chain of amino acids
2. Secondary: regular substructure, alpha helix and beta sheets
3. Tertiary: 3D folding
4. Quaternary: aggregation of polypeptides

Question 15

What are 5 advantages of examining protein variation over phenotypic variation?

Answer 15

1. Variation is genetically determined (no effect of the environment)
2. They show mendelian inheritance (known mode of inheritance)
3. They are ubiquitous (all organisms have proteins)
4. They are generic
5. Amino acid sequences may show more variation than phenotypes

Question 16

What is the method by which you analyze protein variation?

Answer 16

Protein gel electrophoresis, where you can run proteins down a gel towards a positive charge and see how much and how large they are in relation to other controls.

Question 17

What does replacement of an amino acid do? How many amino acids are there that can change the charge of a protein?

Answer 17

Can effect the charge and or the shape of the protein. There are 4 main amino acids that can change the charge of a protein (aspartic acid, arginine, lysine, glutamic acid), and these can be charged or uncharged depending on the pH of the buffer in which they occur

Question 18

How are allozymes made?

Answer 18

Mutations in DNA that cause changes in the protein structure of an enzyme are called allozymes. These are variant forms of an enzyme that are coded by different alleles at a locus. These will migrate differently on a gel, thus you can tell them apart

Question 19

How do you determine whether a loci is polymorphic?

Answer 19

If you look at enough copies of a gene in a population, you will almost always find more than one allele per locus (some rare), therefore every gene is technically polymorphic, however some alleles are so rare that they should not be considered (example is any with a frequency of 0.01).
Instead, the way to determine whether a locus is polymorphic is to find the most common allele at that locus and if it has a frequency LESS THAN 0.95 then it is considered to be polymorphic.

Question 20

How do you determine the proportion of polymorphic loci?

Answer 20

Take the number of loci that were determined to be polymorphic and divide them by the total number of loci analyzed.

Question 21

What are the three measurement of variation used in this topic?

Answer 21

Proportion of polymorphic loci
Number of alleles (allelic diversity)
Gene diversity (expected heterozygosity)

Question 22

What is allelic diversity?

Answer 22

Measured as the number of alleles observed in a sample (often denoted as k)
May be expressed as an average in population over loci, or average at a locus over populations.

Question 23

How do you calculate average allelic diversity over populations for one loci?

Answer 23

You count the number of possible alleles in each population for the loci, then divide by the number of populations. This gives you average alleles for those loci per population

Question 24

How do you calculate the average allelic diversity of a population over multiple loci.

Answer 24

Add up the number of alleles in each loci, then divide by the total number of loci. This gives you average alleles per locus

Question 25

What is expected heterozygosity? What is it also called?

Answer 25

It is a measure of genetic diversity based on HWE. You calculate it from allele frequencies using Hardy-Weinberg equations.

Question 26

What are the assumptions made by HWE?

Answer 26

No migration
No mutation
Infinitely large population (NO DRIFT)
Random mating
No natural selection
If all these assumptions are held then there could be no evolution

Question 27

How do you calculate expected heterozygosity and what is it?

Answer 27

It is the probability that an individual in a population will be a heterozygote at a locus.
Calculate it by doing 1- the sum of the homozygosity (1-pi^2)or the sum of the heterozygotes (2pipj)

Question 28

How do you calculate average expected heterozygosity of a population?

Answer 28

You sum the heterozygosity at all loci of interest then divide by the number of loci.