Lecture 15 - Measuring Evolution

Question 1

What is homology?

Answer 1

Similarity due to common descent.

Question 2

What is convergent evolution?

Answer 2

The independent evolution of shared derived traits that were not present in the common ancestor (known as analogous structures or homoplasies).
- Usually due to similar environmental niches
- E.g., Australian and African Golden moles

Question 3

What is meant by character reversal?

Answer 3

When a species loses the derived trait and reverts back to the ancestral form.
- E.g., Fleas
- Belong in a clade of winged insects (i.e., wings are the derived trait), but have lost their own wings

Question 4

What are the problems associated with morphology when measuring evolution?

Answer 4

• Convergent evolution
• Character reversal
• Erratic rates of morphological evolution (e.g., living fossils vs artificial selection in dogs)

Question 5

What is molecular homology?

Answer 5

Molecular homology due to common descent.
- “Conserved sites”

Question 6

How is molecular homology ascertained?

Answer 6

Based on sequence similarity.

Question 7

How do we quantify sequence similarity?

Answer 7

Hamming Distance (or Degree of Divergence):
The proportion of differences (n/N) for two sequences of length N that differ at n sites.
- Number of differences over number of comparisons
- This will give us a % divergence, and from that we can obtain % similarity

Question 8

What do we have to do to prove similarity is due to common descent (and not due to random chance)?

Answer 8

Homology is simply a hypothesis!

Thus, we first have to consider the null hypothesis…
“How probable is it that we would observe the level of similarity if they were not homologous?”

Question 9

What should be taken into account when trying to establish homology?

Answer 9

Overall length of the sequence (as well as sequence similarity).

(SEE LECTURE 19 part 1 @ 27 MINS)

Question 10

What is another source of sequence similarity (that does NOT necessarily indicate homology)?

Answer 10

Similarity can be due to common mutational processes (e.g., repeat expansions) and other phenomena.
- These should be avoided in homology assessment!

Question 11

What two things must be considered during homology assessment?

Answer 11

1. Overall length of the sequence
2. Sequence complexity (to avoid low complexity sequences containing repeats etc.)

Question 12

What are analogous sequences?

Answer 12

Sequences that are similar but not homologous, rather due to chance and reoccurring evolutionary processes.

Question 13

Why might we get dissimilar sequences that are actually homologous?

Answer 13

Due to the build up of evolutionary changes since their divergence.

Question 14

What is mutation rate (µ)?

Answer 14

The rate at which mutations occur in a sequence per unit time.

Question 15

What is the estimated mutation rate in the human genome (i.e., mutation rate across the entire genome)?

Answer 15

1 new mutation every 10^8 base pairs per generation.

Taking into account the size of the human genome, this implies…
- 30 new mutations in each gamete
- 60 new mutations per generation

Question 15

What is the estimated mutation rate in the human genome (i.e., mutation rate across the entire genome)?

Answer 15

1 new mutation every 10^8 base pairs per generation.

Taking into account the size of the human genome, this implies…
- 30 new mutations in each gamete
- 60 new mutations per generation

Question 16

What is the estimated mutation rate in the human genome (i.e., mutation rate across the entire genome)?

Answer 16

1 new mutation every 10^8 base pairs per generation.

Taking into account the size of the human genome, this implies…
- 30 new mutations in each gamete
- 60 new mutations per generation

Question 17

What is the estimated mutation rate in the human genome (i.e., mutation rate across the entire genome)?

Answer 17

1 new mutation every 10^8 base pairs per generation.

Taking into account the size of the human genome, this implies…
- 30 new mutations in each gamete
- 60 new mutations per generation

Question 17

What is the estimated mutation rate in the human genome (i.e., mutation rate across the entire genome)?

Answer 17

1 new mutation every 10^8 base pairs per generation.

Taking into account the size of the human genome, this implies…
- 30 new mutations in each gamete
- 60 new mutations per generation

Question 18

What are the two evolutionary processes that cause the change in frequency of the mutation in a population over time?

Answer 18

1. Random genetic drift
2. Selection

Question 19

If an allele has a negative impact on fitness, what selection will occur?

Answer 19

Negative selection (purifying selection).

Question 20

If an allele has a positive impact on fitness, what selection will occur?

Answer 20

Positive selection (adaptive evolution).

Question 21

What does the strength of selection depend on?

Answer 21

1. The size of the fitness effect
2. The size of the population (e.g., harder for selection to act in smaller populations, where genetic drift is stronger).

Question 22

What is meant by balancing selection?

Answer 22

May act to maintain multiple alleles in the population over a longer period of time than we would expect through drift.

Question 23

What is a substitution event?

Answer 23

Where a new allele arises by mutation and then goes on to reach fixation.

Question 24

What is responsible for all fixed differences in sequences between species?

Answer 24

Substitution events.
- Molecular evolution can be described as a series of substitutions

Question 25

What can the rate of molecular evolution often be described as?

Answer 25

The rate of substitution.

Question 26

What does a substitution event concern?

Answer 26

Substitutions of genes or alleles (NOT nucleotide substitutions).

Question 27

What is the Neo-Darwinian model (Panselectionism)?

Answer 27

In this model…
- Selection is the strongest force of evolution
- Genetic drift (randomness) is mostly irrelevant

This was all based on assumptions (in accordance to what was seen at the morphological level, and not considering the molecular level).

Question 28

What did Hubby and Lewontin observe (1966)?

Answer 28

Uncovered surprising amounts of genetic variation.
- Through studying protein variation in Drosophila

Posed the question: Could all this genetic variation really be due to selection alone?

Question 29

What did Zuckerkandl & Pauling do (1962)?

Answer 29

Measured the “molecular distance” (i.e., number of amino acid differences) between pairs of haemoglobin molecules from different species.

Found that the number of AA differences between species pairs correlated extremely well with their estimated divergence times from the fossil record.

Thus proposed the idea of the Molecular Clock - the older the evolutionary split, the more AA differences you observe (a clock-like rate).

Question 30

What did Motoo Kimura propose (1968)?

Answer 30

The Neutral Theory of Evolution.
- Most observed genetic variation is selectively neutral
- Thus, their frequency is driven by drift alone
- Most substitution events occur by drift, and not selection
- Negative selection also plays an important (but silent) role here, removing deleterious mutations and working to keep the status quo (i.e., prevent substitution)

Question 31

How does neutral theory explain the abundance of polymorphism?

Answer 31

When we observe polymorphisms, we are catching them in the act of genetic drift (i.e., catching a snapshot of their random journal to fixation or extinction).

Question 32

What is the chance that a NEUTRAL ALLELE will “get lucky” and reach fixation?

Answer 32

The probability of fixation of a neutral allele is simply equal to its current frequency in the population.
- E.g., if the allele is at 10% frequency, it has a 1 in 10 (10%) chance of becoming fixed

Question 33

What is the probability of a new neutral mutation reaching fixation/extinction?

Answer 33

Reaching fixation = 1/2N
Reaching extinction = 1 - 1/2N

So new mutations are much more likely to go extinct than to ever reach fixation.

Question 34

What is the rate of substitution (k)?

Answer 34

The number of new mutations reaching fixation per unit time. Also known as the rate of evolution.

Question 35

What doe the rate of substitution (k) depend on?

Answer 35

Depends on…
1. Rate of mutation (µ)
2. The probability of the mutation reaching fixation (1/2N for neutral sites)

Question 36

What do we observe when studying substitution events at neutral sites?

Answer 36

Substitution events at neutral sites occur at a regular, predictable rate.
- This idea underlies the Molecular Clock
- 1/k = time between consecutive fixation events

Question 37

What is the rate of neutral evolution?

Answer 37

The number of new mutations reaching fixation per unit time. Also known as the rate of neutral substitution.

Question 38

What is the rate of neutral substitution/evolution equal to?

Answer 38

It is simply equal to the rate of mutation (µ).
- This explains the ticking of our molecular clock

(SEE LECTURE 16 part 2 @ 23 mins)

Question 39

How does the rate of neutral substitution being equal to the rate of mutation explain the ticking of our molecular clock?

Answer 39

Due to the vast majority of observed substitutions being neutral (or nearly neutral), they will become fixed at the same clock-like rate at which mutations occur!