Quiz 5 (Quantitative Genetics, Rates of Evolution, Genome Evolution)

Question 1

What does quantitative genetics focus on?

Answer 1

Continuous traits

Question 2

What are continuous traits?

Answer 2

Traits produced by a large number of genes, usually have a phenotypic range
ex: height, skin color, weight

Question 3

What are discrete traits?

Answer 3

Traits produced by a single locus (or a few)

Question 4

How can discrete genes produce genes with continuously varying values?

Answer 4

A 2-locus example (assuming all allele frequencies = 0.5)
Let A1 = 2 cm, A2 = 1 cm & B1 = 3 cm, B2 = 2cm
An individual that is A1A1B2B2 would be 10 cm,
An individual that is A2A2B2B2 would be 6 cm

Question 5

What is the correlation between # of loci and the number of combinations?

Answer 5

As the amount of loci increases, the number of combinations increases very quickly
ex: 1 loci = 3 possible genotype combinations,
5 loci = 243 possible genotype combinations
10 loci = 59049 possible genotype combinations

Question 6

What is a quantitative trait loci (QTL)?

Answer 6

A region of the genome that we can identify that influences quantitative traits

Question 7

What is a genetic map?

Answer 7

One way to map genes based on recombination rates (measured in centi-morgans)

Question 8

What is a physical map?

Answer 8

Another way to map genes based on sequencing the genome (measured in bp or Mb)

Question 9

What are the 3 methods to determine the genes that influence quantitative traits?

Answer 9

QTL Mapping
GWAS
Candidate loci

Question 10

How does QTL mapping work?

Answer 10

Start with 2 parents who differ in the trait of interest
Make genetic maps of each parent; each map is made with some unique markers and some shared
Cross the parents to make an F1 generation
Inbreed/Self the F1 generation to create recombinant inbred lines

Question 11

What are recombinant inbred lines (RIL’S)?

Answer 11

Individuals are made up of different parental combinations due to recombination

Question 12

What are you looking for with QTL mapping?

Answer 12

How correlated the genetic markers are with phenotypes
You can conclude that somewhere close to the marker, there is at least 1 gene that’s causing the trait

Question 13

What is GWAS?

Answer 13

QTL’s on a larger scale, done with thousands of individuals instead of 2 parents
Single nucleotide differences in individuals are analyzed with a statistics test

Question 14

What is the general methodology for GWAS?

Answer 14

Generate a p-value for each SNP (single nucleotide polymorphism)
Correct for multiple comparisons
p-values below some threshold are statistically significant
Generate a manhattan plot

Question 15

What does a p-value indicate in GWAS?

Answer 15

The probability of seeing association by chance

Question 16

Why do you have to correct for multiple comparisons in GWAS?

Answer 16

When comparing multiple p-values, false significances can occur (false-positives)

Question 17

What are the relative strengths of GWAS and QTL mapping?

Answer 17

It is more likely that relevant variation will be present since in QTL only the variation between parents is assessable
Associated markers are likely close to relevant genes
GWAS is expensive compared to QTL mapping

Question 18

What are candidate loci genes?

Answer 18

Based on prior knowledge, you predict that genes are important

Question 19

What are follow up studies?

Answer 19

Targeted mutagenesis: figure out which mutations affect function
Cell culture: apply evolutionarily relevant treatments
Expression: expression level of a trait may be the evolutionary mechanism rather than changes in the protein
KO: genes that are knocked out to assess effect of that gene
Gene Phylogeny: assess the evolutionary origin

Question 20

What is the simplest model of nucleotide change?

Answer 20

Equal probability that a base will change into one of the other three
Null model
Has single parameter, α = rate of change

Question 21

Why does the mutation rate not equal the substitution rate?

Answer 21

Mutations occur in individuals and can spread through selection or drift
If the mutation replaces the original basepair in the population then it is a substitution

Question 22

Why are most mutations not substitutions?

Answer 22

Most non-synonymous mutations are deleterious and will be lost
Most neutral mutations are lost by drift (not acted upon by selection)

Question 23

What is the measured rate of change?

Answer 23

The average rate is estimated to be 5 x 10^-9 substitutions/site/generation

Question 24

Why is a single parameter not good enough to explain nucleotide change?

Answer 24

Transitions occur at greater frequency than transversions

Question 25

What is the 2-parameter model?

Answer 25

There are different rates for transitions and transversions Transition: α (alpha) Transversion: β (beta)

Question 26

How do you measure the substitution rate?

Answer 26

Divide the number of substitutions by the number of bp sequences and divide by the amount of time (x2 since both species have had the same amount of time to accumulate substitutions) Units = subs/site/time

Question 27

What does the fossil rate of evolution mean?

Answer 27

How rapidly a character (usually a fossil such as bones, teeth, or shells) in a species or a lineage evolved over time

Question 28

How do you calculate the rate of evolution?

Answer 28

t1 = older sample t2 = younger sample Δt = t1 - t2 (older - younger) x1 = average value of the character at t1 x2 = average value of the character at t2 Units = Darwins

Question 29

What does bradytelic mean?

Answer 29

Slow evolution

Question 30

What does horotelic mean?

Answer 30

Typical rate of evolution

Question 31

What does tachytelic mean?

Answer 31

Rapid evolution

Question 32

Why do rates of evolution vary?

Answer 32

Rates might be more rapid during periods of speciation More genetically complex forms can evolve more extreme forms than lesser complex forms since there are more genes for variation that selection can act on Some groups evolve more rapidly that others Artifact of the data

Question 33

Why do artifacts of the data cause the rates of evolution to vary?

Answer 33

Evolution varies over time and changes direction, so short intervals are more likely to capture short term rapid changes and gives the appearance of greater amounts of change

Question 34

What is the c-value paradox?

Answer 34

A c-value is the measure of diploid genome size in picograms Humans are much more complex than onions yet their genome is 3x as large (onion test)

Question 35

For eukaryote DNA viruses, bacteriophages, and prokaryotes, what is the DNA content and the proportion that codes for proteins?

Answer 35

1:1 ratio between genome size and the amount of genome dedicated to coding proteins (100%)

Question 36

For unicellular eukaryotes, what is the DNA content & the proportion that codes for proteins?

Answer 36

Over 50% of the genome to coding regions start to fall off

Question 37

For land plants and animals, what is the DNA content & the proportion that codes for proteins?

Answer 37

Less than 1% of the genome length not for making proteins

Question 38

How much of the human genome do TE's make up?

Answer 38

50%

Question 39

What are transposable elements (TE's or mobile genetic elements)?

Answer 39

Segments of DNA with the ability to insert itself into the genome and use the machinery of the cell to replicate

Question 40

Why are TE's more prominent in Eukaryotes vs. Prokaryotes?

Answer 40

Prokaryotes tend to have larger population sizes which selection will act to eliminate them TE's are generally neutral so they can escape selection

Question 41

What are the negative fitness effects of TE's?

Answer 41

Often neutral so no negative effect on the fitness of the host Have the ability to insert themselves into coding regions which can have serious consequences for the host decreasing their fitness

Question 42

What are the positive fitness effects of TE's?

Answer 42

Can rarely lead to beneficial variation via regulatory elements & gene duplication

Question 43

What are some evolved defenses against TE's?

Answer 43

Methylation: TE's often highly methylated so they can't be transcribed and replicated RNAi: these target TE's and render them immobile after transcription