DNA Sequence Variation

Question 1

Study of genetic variation in a group of individuals of the same species, and the evolutionary forces that shape this variation

Answer 1

Population genetics

Question 2

describes two or more sequence variants at a DNA site

Answer 2

polymorphism

Question 3

differences in individual base pairs

Answer 3

single nucleotide polymorphisms (SNPs)

Question 4

1. A change in a single nucleotide can create or remove a restriction enzyme recognition sequence
2. The difference in fragment sizes following restriction enzyme digestion is ____
3. PCR amplification around an RFLP followed by restriction enzyme digestion and separation of the fragments on an agarose gel

Answer 4

Detecting SNPs: Restriction fragment length polymorphisms

Question 5

1. slides/chips with oligonucleotides (probes) covalently attached
2. can contain thousands of probes
3. A fluorescently-labeled DNA sample is hybridized to the probes, but will only bind if the sequence matches
4. Fluorescent signal is read for each probe and used to identify the SNPs found in DNA sample

Answer 5

Detecting SNPs: Microarrays

Question 6

Duplications or losses of stretches of DNA sequence

Answer 6

Copy number variants (CNVs)

Question 7

common CNVs

Answer 7

Simple sequence length polymorphisms (SSLPs)

Question 8

SSLPs: short tandem repeats (STRS), <13bp sequences

Answer 8

microsatellites

Question 9

SSLPs: variable number of tandem repeats (VNTRs), repeats of 13-25 bp sequences

Answer 9

minisatellites

Question 10

linked combinations of alleles

Answer 10

haplotypes

Question 11

show relationships among haplotypes

Answer 11

haplotype networks

Question 12

influenced by a combination of genetic and environmental factors

Answer 12

Complex traits (quantitative traits)

Question 13

Complex traits with infinite phenotype possibilities

Answer 13

continuous

Question 14

complex traits with many discrete possibilities

Answer 14

meristic

Question 15

proportion of phenotypic variance due to genetic differences among individuals in a population
0 = all phenotypic variation due to environment
1= all phenotypic variation due to genetics

Answer 15

Broad-sense heritability (H^2)

Question 16

1. Heritability estimates rely on population and environment in one particular study
2. We often underestimated (how much environmental sampling was included?)
3. Cannot compare heritability estimates between groups

Answer 16

Important caveats when calculating broad-sense heritability

Question 17

Can offspring phenotypes be predicted from parental phenotypes?

Can only be calculated if alleles for a locus are additive, looks at correlation between parent and offspring phenotypes

Answer 17

Narrow-sense heritability (h^2)