Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

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

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

1
Q

What does quantitative genetics focus on?

A

Continuous traits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are continuous traits?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are discrete traits?

A

Traits produced by a single locus (or a few)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How can discrete genes produce genes with continuously varying values?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

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

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is a quantitative trait loci (QTL)?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is a genetic map?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is a physical map?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

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

A

QTL Mapping
GWAS
Candidate loci

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How does QTL mapping work?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are recombinant inbred lines (RIL’S)?

A

Individuals are made up of different parental combinations due to recombination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are you looking for with QTL mapping?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is GWAS?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the general methodology for GWAS?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does a p-value indicate in GWAS?

A

The probability of seeing association by chance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

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

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the relative strengths of GWAS and QTL mapping?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are candidate loci genes?

A

Based on prior knowledge, you predict that genes are important

19
Q

What are follow up studies?

A

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

20
Q

What is the simplest model of nucleotide change?

A

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

21
Q

Why does the mutation rate not equal the substitution rate?

A

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

22
Q

Why are most mutations not substitutions?

A

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

23
Q

What is the measured rate of change?

A

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

24
Q

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

A

Transitions occur at greater frequency than transversions

25
Q

What is the 2-parameter model?

A

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

26
Q

How do you measure the substitution rate?

A

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

27
Q

What does the fossil rate of evolution mean?

A

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

28
Q

How do you calculate the rate of evolution?

A

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

29
Q

What does bradytelic mean?

A

Slow evolution

30
Q

What does horotelic mean?

A

Typical rate of evolution

31
Q

What does tachytelic mean?

A

Rapid evolution

32
Q

Why do rates of evolution vary?

A

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

33
Q

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

A

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

34
Q

What is the c-value paradox?

A

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)

35
Q

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

A

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

36
Q

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

A

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

37
Q

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

A

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

38
Q

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

A

50%

39
Q

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

A

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

40
Q

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

A

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

41
Q

What are the negative fitness effects of TE’s?

A

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

42
Q

What are the positive fitness effects of TE’s?

A

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

43
Q

What are some evolved defenses against TE’s?

A

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

Evolution (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions