PATTERNS OF GENETIC VARIATION

Question 1

Single Nucleotide Polymorphisms (SNPs)

Answer 1

Variations at a single nucleotide position in DNA. Different alleles can lead to different traits.

Question 2

Insertions and Deletions (INDELs):

Answer 2

Variations where nucleotides are inserted or deleted, causing differences in allele length

Question 3

Copy Number Variants (CNVs):

Answer 3

: Variations in the number of copies of a particular gene or genomic region.

Question 4

Large Structural Variants:

Answer 4

Significant alterations in chromosome structure, including rearrangements, fissions, and fusions.

Question 5

How do SNPs contribute to genetic variation?

Answer 5

SNPs are different alleles at a specific nucleotide position.

Example: A to T change in a specific gene can cause conditions like sickle-cell anemia.

Individuals with genotype TT are affected, while AA or AT are not.

SNP frequency can vary in populations, often influenced by environmental factors like malaria prevalence.

Question 6

What is nucleotide diversity (Pi) and how is it calculated?

Answer 6

Pi (π): A measure of nucleotide differences among sequences.

Calculation:
π
=
TotalPairwiseDifferences
NumberofComparisons
×
NumberofSites
π=
NumberofComparisons×NumberofSites
TotalPairwiseDifferences
​

Example: For three sequences (A, B, C), with total pairwise differences of 12, the calculation is:
12
3
×
40
=
0.1
3×40
12
​
=0.1 or 10% nucleotide diversity, indicating relatively high diversity.

Question 7

What are INDELs and their implications for genetic variation?

Answer 7

INDELs occur when one allele is longer or shorter than another due to insertion or deletion of nucleotides.

Can arise from replication errors, causing frameshifts and altering gene expression.

Generally detrimental, leading to negative effects on phenotype and health.

Question 8

Allele frequency (P) of allele A

Answer 8

P

NumberofAalleles
Totalalleles
P=
Totalalleles
NumberofAalleles

If there are 11 A alleles out of 20 total alleles,
P
=
11
20
=
0.55
P=
20
11
​
=0.55
​

Question 9

Allele frequency (Q) of allele T

Answer 9

Q

NumberofTalleles
Totalalleles
Q=
Totalalleles
NumberofTalleles
​
If there are 9 T alleles,
Q
=
9
20
=
0.45
Q=
20
9
​
=0.45

Q=1−P.

Question 10

What are Copy Number Variants (CNVs) and their significance?

Answer 10

CNVs involve variations in the number of copies of a specific DNA segment.

Arise from duplications, deletions, or repeats.

Example: In Huntington’s disease, an increase in the number of CAG repeats (>35) can cause neural degradation

Question 11

What are large structural variants and their significance in genetics?

Answer 11

Large structural variants involve significant genomic rearrangements.

Useful for describing expected genotypic frequencies under the Hardy-Weinberg equilibrium, which assumes:

Sexual diploid organisms, non-overlapping generations, random mating.

Question 12

Genotypic frequencies:

Answer 12

Homozygous dominant: P^2

Homozygous recessive: Q^2

Heterozygous: 2PQ

Question 13

What causes deviations from expected Hardy-Weinberg frequencies?

Answer 13

1.Non-random mating (assortative or disassortative)
2.Mutations
3.Natural selection
4.Genetic drift
5.Migration

Question 14

What is assortative mating and its implications?

Answer 14

Definition: Individuals with similar phenotypes or genotypes are more likely to mate.

Types:
Positive Assortative Mating: Choosing mates with similar traits.

Negative Assortative Mating: Choosing mates with different traits.

Implications: Increases genetic similarity within populations, potentially affecting trait distributions.

Question 15

What is disassortative mating and its benefits?

Answer 15

Definition: Preference for mating with individuals who have different traits.

Implications:

Promotes genetic diversity and heterozygosity, beneficial for population health and adaptability.

Increases variability in traits, reducing the risk of inbreeding.

Examples:
Assortative Mating: Bird species where females choose mates with similar plumage.
Disassortative Mating: Fish species that select contrasting coloration mates.

Question 16

What are inversions in genetics?

Answer 16

Definition: Occurs when a chromosome breaks and is repaired in the opposite orientation, preventing recombination.

Implications: Can lead to genetic variations without impairing function.

Question 17

What are fission and fusion in chromosome structure?

Answer 17

Fission: A single chromosome breaks into two separate chromosomes.

Fusion: Two non-homologous chromosomes join together into one chromosome.

Implications: These structural changes often do not impair gene function.

Question 18

What is genetic variation and how does it arise?

Answer 18

Genetic variation refers to differences in DNA among individuals, arising from random mutations. These mutations can be beneficial, neutral, or harmful, depending largely on environmental context.

Question 19

What does “random” mean in the context of mutations?

Answer 19

Random Mutations: Occur without any specific direction or purpose, arising by chance.

Lack of targeted outcomes means mutations do not evolve in response to an organism’s needs.

Question 20

What are the common mechanisms that lead to mutations?

Answer 20

Errors in DNA Replication or Repair: Mistakes during these processes can introduce mutations.

Mutations are independent of selection pressure; selection acts only after mutations occur.

Question 21

How do different types of mutations vary in frequency?

Answer 21

Certain mutations have higher probabilities of occurring. For example, Single Nucleotide Polymorphisms (SNPs) are more common than large structural variants.

Question 22

How do organisms use random mutations for adaptation?

Answer 22

Organisms rely on random mutations to adapt to new environments, as they cannot predict which mutations will be beneficial. Mutations occur randomly concerning their fitness effects.

Question 23

How can some bacteria influence their mutation rates?

Answer 23

Under environmental stress, certain bacteria can manipulate their mutation rates to increase the likelihood of acquiring beneficial mutations that help them survive.

Question 24

What qualifies as a structural variant?

Answer 24

A structural variant must involve a difference greater than 1000 base pairs (bp), leading to noticeable changes in chromosome structure.

Question 25

: What are potential reasons for deviations from expected allele frequencies?

Answer 25

Inbreeding: Leads to increased homozygosity.

Assortative Mating: Preference for similar phenotypes.

Disruptive Selection: Favors extreme phenotypes.

Heterozygote Disadvantage: When heterozygotes have lower fitness.