Lecture2

Question 1

What is the most abundant TE(transposal elements) in human:

Answer 1

Most abundant in human: Alu I (>1 million copies, 10% of genome)

Question 2

What is the most Biggest TE in human

Answer 2

LINE-1(~17% of genome)

Question 3

only active TEs in human genome are?

Answer 3

Alu and LINE-1

Question 4

Drift is.... in smaller populations, => Selection is weaker in ....populations
A) Stronger, Stronger
B)Stronger, Weaker
C)Weaker, Stronger
D)Weaker, Weaker

Answer 4

B) Drift is stronger in smaller populations => Selection is weaker in smaller populations

Question 5

The fate of mutations is determined by…..

Answer 5

Fate of mutations is determined by drift and selection

Question 6

Expectations can be estimated with proper models from regions that are assumed to have no function (=
evolve neutrally)
True or False?

Answer 6

True

Question 7

To what questions does each answer?
Causal role functionality:
Selected effects functionality:

Answer 7

Causal role functionality: “what something does”

Selected effects functionality: Why?

Question 8

Biological things that do something, but are not selected can hardly be called functional
True?

Answer 8

Yes, True

Question 9

Genetic drift occurs due to populations of finite size
• If there is no selection of an allele
(s=0) what will happen?
• The probability of fixation is
equal to the (2)

Answer 9

1) one allele will eventually fix

2) mutation rate (μ)

Question 10

(1)………. (e.g. per bp and generation) generates
2Ne*μ each generation.
(2) Rate of…. is 1/2Ne
The probability of….. is equal to the…. rate (μ)

Answer 10

1)Mutation rate μ
2) Rate of fixation is 1/2Ne
=> The probability of fixation is equal to the mutation rate (μ)

Question 11

What is the other name of Purifying selection?

Answer 11

=Negative or stabilizing selection

Question 12

What are the feature of purifying selection?

Answer 12

• If an allele decreases fitness it is
less likely to have offspring
• It will be found less often in the
population (i.e. has a low
frequency)
• It will be less likely to fix in the
population
• It will be less likely to be found as
a difference between two species

Question 13

How we can estimate the amount of functional DNA in the Genome?

Answer 13

1) comparing the human genome to other species (= identify
regions with fewer fixed mutations (=substitutions) than
expected)
2) Comparing human genomes among each other (=identify
regions with fewer segregating mutations (polymorphisms)
than expected)
3) Mutational load estimates by asking how much function is
compatible with a deleterious mutation rate and the genome

Question 14

A fitness of less than one indicates that the mutant was

Answer 14

less fit than the wild type, so the mutation was

deleterious

Question 15

A fitness of zero indicates that

Answer 15

no mutated progeny were recovered, and that the mutation was therefore lethal. (all of them dead)

Question 16

Purifying selection leads to conserved residues

True or False?

Answer 16

True

Question 17

Which is which one? haha
quantify rate of change leading to amino acid changes (=…) and rate of change leading to no amino acid change (=..)
Ks, Ka

Answer 17

quantify rate of change leading to amino acid changes

=ka) and rate of change leading to no amino acid change (=ks

Question 18

…. can be seen as neutral mutation rate μ

Its Ka or Ks?

Answer 18

Ks

Question 19

The amount of constraint varies among different groups of proteins (probably largely due to the structure of different proteins)
Right?

Answer 19

yes!

Question 20

at functional sites variations do not exist resp. are rarer than at neutral sites
True or False?

Answer 20

True

Question 21

the allele frequency at functional sites is skewed towards rarer alleles.
True or False?

Answer 21

True

Question 22

Why are rare alleles more frequent?

Answer 22

• The DNA sequences are related by a genealogy (tree)
• If mutations occur randomly on such a genealogy rare
mutations are more frequent