lec17: genetic variation; models and measurement

Question 1

looking at all the evolutionary forces that can influence genetic diversity, heritable variation, and also evolution.
what are the 5 factors that influence patterns of genetic diversity and evolution?

Answer 1

1. mutation
2. recombination
3. random genetic drift
4. natural selection
5. migration (gene flow)

Question 2

mutation influence

Answer 2

• 1 individual base pair of DNA sequence in the genome have a mutation from G to T
• represents the increase in genetic variation in populations
• ultimate source of genetic variation
• caused by error during replication or DNA repair (not directed)

Question 3

recombination influence

Answer 3

• can’t just consider one base pair of DNA but 2
• creates new combinations of mutations due to recombination from eg. GA to GC base pairs (a process by which pieces of DNA are broken and recombined to produce new combinations of alleles)
• so recombination works with existing variation that accumulated through mutation and is creating NEW COMBINATIONS
• increases genetic variation in population

Question 4

random genetic drift influence

Answer 4

• the change in frequency of an existing gene variant in the population due to random chance
• eg. lost of G alleles
  GA
  GA
  AC
  AA
  AC
  AC
  ↓
  AC
  AA
  AC
  AC
  AC
  AA
• Genetic drift may cause gene variants to disappear completely and thereby, acts to reduce genetic variation in populations
• genetic drift can cause evolutionary change, where evolution is the change in genotype composition or genotype frequencies through time but it’s not adaptive
• caused by RANDOM SAMPLING effects every generation
• more important for populations that are smaller. the smaller your sample/population size the greater impact of random effects of genetic drift
• so genetic drift acts stronger in smaller population

Question 5

random genetic drift is also a force that can drive evolution in population but does it lead to adaptation?

Answer 5

NO. genetic drift can cause evolutionary change, where evolution is the change in genotype composition or genotype frequencies through time but it’s not adaptive and leads to decrease in genetic variation

Question 6

what are the 3 types of natural selection influences

Answer 6

a. negative (purifying) selection
b. positive (directional) selection (adaptation)
c. selection favouring diversity

Question 7

negative (purifying) selection

Answer 7

• reduces genetic variation in populations
• mutations that reduce fitness are REMOVED by natural selection (if you have a new mutation that reduces the probability of survival and reproduction, natural selection will act to remove that new mutation rather than act to favour it and so negative selection removes genetic variation and therefore reduced the amount of genetic variation that we see in pop)

GTG –> GGG

Question 8

positive (directional) selection (adaptation)

Answer 8

• decreases genetic variation in populations (because it’s acting to favour the new mutation over the G’s)
• mutations that increase fitness will become FIXED in a population

GTG –> TTT

• a new mutation T that conferse some benefits (eg. produced some new defences against herbivore that’s going to spread through the population more likely and become fixed eventually; fixed means all individuals now have that T) and natural selection is favouring it over the G’s eliminating the G’s
• that’s what Darwin’s was really focused on; thinking about new beneficial variation that might spread because it increases the probability of survival and reproduction

Question 9

selection favouring diversity

Answer 9

• increases or retains genetic variation in populations
• natural selection can act to MAINTAIN diversity over the long term (eg. heterozygote advantage)

GGGTGG –> TGTTGG

• lead to maintenance of both T and G alleles in populations, maintaining diversity over the longer time frame
• if for whatever reason the heterozygous genotype has higher fitness and confers some selective advantage than either of the 2 homozygous, then natural selection will favour heterozygous, favouring keeping both of these alleles around

Question 10

migration (gene flow) influence

Answer 10

• increases genetic diversity in populations
• migration influences the STRUCTURING of diversity/variation over a large spatial scale

pop1 –> pop2
(somewhat these pop were isolated so each pop have somewhat different genetic variation in the pop)
↓
pop2
(a more diverse sequence)

Question 11

what happens if there’s low migration and if there’s high migration (its influence to population)

Answer 11

populations might start to diverge in their genetic variation whereas in high migration they become more homogenized

Low migration rates often lead to low genetic variation within populations and increased population differentiation over time. by “increased population differentiation” it’s referring that the divergence of genetic characteristics between different populations, not within a single population

high migration rates between populations result in low genetic differentiation between those populations. Within a population, high migration rates contribute to increased genetic variation because individuals from different populations bring in diverse genetic materia

Question 12

now we know that different processes can increase or decrease genetic diversity within population. what is still being debated and what is not being debated.

Answer 12

what people don’t debate is in order to explain adaptation, we have to invoke natural selection. but overall in terms of the genetic variation and genetic composition of populations, what is the relative roles of these different forces? this is still being debated.

so to conclude: many controversies in evolutionary biology concern the RELATIVE IMPORTANCE OF THESE FORCES IN EVOLUTION.

Question 13

how can we measure genetic variation now that we understand that all these forces influences genetic diversity?

Answer 13

through the metrics
- heterozygosity (H)
- polymorphism (P)

Question 14

if we can measure the genetic variation, what might we be able to address?

Answer 14

if we can measure it we might be able to address what is the relative importance of these forces.

Question 15

heterozygosity (H)

Answer 15

• fraction of individuals that are heterozygous averaged across gene loci (loci/locus is one sight or region that we are focused on for quantifying genetic variation)
• recall from Mendelian genetics: heterozygote individuals have both alleles

another way to think about heterozygosity is if we randomly pick 2 individuals from this population and take one copy from one individual and one copy from another, what’s the chance that they’re different from each other?

Question 16

if more individuals are heterozygous, is there more or less genetic variation?

Answer 16

MORE

Question 17

polymorphism (P)

Answer 17

• proportion of gene loci that have 2 or more alleles in the population (looking across genes or across sites and asking what fraction of those genes are variable)

Question 18

what’s the difference between heterozygosity and polymorphism?

Answer 18

polymorphism is when there are two or more possibilities of a trait on a gene. Heterozygosity is the condition of having two different alleles at a locus

Question 19

can you have one without the other (heterozygosity and polymorphism)?

Answer 19

• a locus can be polymorphic without being heterozygous
• you can’t have heterozygosity without a gene being polymorphism because you have to have genetic variation there
• but you can have polymorphism without heterozygosity if different individuals were homozygous but for different alleles

Question 20

what maintains genetic variation (2)?

Answer 20

1. mutation-selection balance
2. selection maintaining variation

Question 21

mutation-selection balance

Answer 21

The dynamic equilibrium between the introduction of new genetic variants through mutation and the removal of less fit variants by natural selection, ensuring the persistence of genetic diversity within a population.

• Less Fit Types Reintroduced by Mutation: Mutations constantly introduce new genetic variants into a population. Some of these mutations may result in less fit individuals or genotypes.
• Followed by Selection Acting to Remove Them: Natural selection acts to remove less fit individuals from a population. However, if the mutation rate is high enough, new less fit variants will be continuously reintroduced, creating a balance where selection and mutation counteract each other. This balance results in the persistence of genetic variation within the population.

Question 22

selection maintaining variation

Answer 22

Mechanisms, such as heterozygote advantage, frequency-dependent selection, and environmental variability, that actively work to preserve genetic diversity within a population by balancing the selective pressures on different genetic variants

• heterozygote advantage
• frequency-dependent selection
• fitness varies in space or time
• umbrella term “balancing selection”

Question 23

what did the two schools (classical and balance school) differ?

Answer 23

in their predictions on how much genetic variation occurs in natural population (side note: and what evolutionary force is most important in maintaining variation?)

Question 24

who were the two people in classical school and two people in balance school?

Answer 24

classical: Morgan, Muller
balance: Dobzhansky, Ford

Question 25

based on the two models of population genetic variation (classical abalance) what did each believe (4 each)?

Answer 25

classical:
- negative selection
- low heterozygosity
- low polymorphism
- wild type is normal genotype (thinking there’s one common genotype called wild type)

balance
- heterozygote advantage
- high heterozygosity
- high polymorphism
- selection favour diversity

Question 26

how was genetic diversity studied (2+ex for each):

Answer 26

• morphological (eg. snail colour polymorphism): more actively observing outside
• cytological (eg. chromosome inversions): more microscopic

Question 27

which school (classical, balance) with which study (morphological, cytological)

Answer 27

morphological: more balance school (outside)

cytological: more classical school (inside)

Question 28

what TYPE of experiment was used for quantitative genetic evidence (continuous polygenic traits) for the existence of genetic variation?

Answer 28

selection experiments involving artificial selection

Question 29

artificial selection

Answer 29

involves controlled breeding of individuals with particular traits for many generations

Question 30

what were the 2 experiment examples for artificial selection; 2 evolutionary responses of continuous traits examples/experiments?

Answer 30

selection response for bristle number in fruit flies and selection response in maize

Question 31

is artificial selection a continuous selection? and why does it stop?

Answer 31

Artificial selection is a continuous process; however, it reaches a point where it stops. Some of the reasons why it stops are: All individuals in a population have developed homozygous alleles for a specific trait. The process of natural selection hinders further changes in a particular characteristic.

eg. in the bristle number in fruit flies artificial selection experiment; the red arrow indicates where they stopped selecting for more bristles and bristle number started going down
* there was still plenty of genetic variation available even after all of that selection and it seems like natural selection in this lab line favored not having that many bristles because it was returning back to going towards the original number of bristles

Question 32

does strong response to selection on a quantitative trait imply that there was a lot or barely any heritable variation to begin with?

Answer 32

strong response to selection on a quantitative trait implies that there was a lot of heritable variation to begin with

in terms of the bristle number in fruit flies artificial selection experiment:
so just like Darwin was arguing about domestication, this implies there was tons of heritable variation in population for bristle number as a starting point. the fact that you get a strong response to selection means that there must have been a bunch of genetic variation in the starting population

also seen in the maize exp:
so again the fact that we can select and get a strong response to selection means/ implies a lot of this variation that we see is heritable and it can experience this response and lead to evolutionary change
- where the selection relaxed = go in different directions (for high oil in a positive trend, when relaxed it started to go down then resumed to go up) (for low oil in a negative trend, when relaxed it started to go up)

Question 33

from the 2 experiments of artificial selection, the evolutionary responses of continuous traits…
1. demonstrates…
2. due to…

Answer 33

1. demonstrates existence of heritable variation in fitness-related phenotypes
2. due to many underlying genes (an open question is; what was maintaining this variation? are these due to many alleles that we’re at intermediate frequency because selection is actively maintaining variation or is it more a mutation selection balance? is there a single optimal phenotype and then new mutations are coming in and reducing the fitness and creating this genetic variations?)

Question 34

what are the results of artificial selection experiments on quantitative traits?

Answer 34

• selection responses demonstrate that ABUNDANT GENETIC VARIATION exists for polygenic quantitative traits
• BUT often NO INFO ON P and H as key population genetic parameters
  (so these experiments highlight there’s lots of genetic variation, but they don’t actually solve the original puzzle of what’s maintaining that genetic variation in populations)
• also: comparative studies difficult as trait traits studied often are group specific

Question 35

allozymes

Answer 35

different allelic forms of the same protein

Question 36

protein electrophoresis MONOMORPHIC GENE

Answer 36

everyone is homozygous for one allele
eg. the fast allele (FF FF FF)

Question 37

protein electrophoresis POLYMORPHIC GENE

Answer 37

there’s 3 difference allele: mid allele, slow allele, and fast allele. each of us can have 1 (1 band) or 2 (2 bands) copies of allele but no more than 2 copies. but we can have heterozygotes, homozygotes, and 3 different alleles segregating for example:

FF FS SS MM FM MS FF FS (some have 1 band some have 2 bands)

Question 38

what are the advantages of studies of enzyme polymorphism (5)?

Answer 38

• many loci can be examined
• can be used in nearly any organism
• loci co-dominant, heterozygotes can be identified
• variation examined close to DNA level
• provides genetic marker loci for other studies (and allows us to use genetic markers for many purposes)

other words (for top 3):
now we could study many genes, and we could do it in nearly any organism, we can look at whether individuals are heterozygous or homozygous directly rather than Mendel had to infer that there were some heterozygotes or do crosses to figure that out

Question 39

what is the 3rd possibility that answers the “what maintains the genetic variation?:1. mutation-selection balance 2. selection maintaining variation” question and how was this 3rd option found?

Answer 39

3. selectively neutral variation (found a 3rd option after the allozyme study using the electrophoresis seeing that there’s genetic variation everywhere so natural selection might be favouring genetic variation so balance school wins right? turns out there’s a 3rd possibility which is that maybe a lot of this genetic variation is not influencing fitness at all)

• different TYPES DO NOT DIFFER IN THEIR FITNESS relative to one another
• new mutations neither eliminated nor retained by selection

if you have new neutral mutation coming in all the time, they’re only subject to mutation and genetic drift. so a lot of these mutations might get lucky and become more common and then they’re just subject to sort of chance factors. and so maybe the different types often do not differ in fitness in survival relative to each other and so the new mutations are not eliminated or retained but they’re just subject to genetic drift

Question 40

what is the neutral theory? and what did it suggest?

Answer 40

most molecularly variations may be selectively neutral
- negative selection rapidly eliminates detrimental mutations
- positive selection rapidly fixes beneficial mutations
- the only mutations left to create genetic variation are selectively neutral

maybe they’re rapidly eliminated, so they’re not contributing much to genetic variation. and yes there’s adaptation, positive selection does happen, or we can’t explain the fate of organisms to their environment. but that happens rarely and rapidly so it’s transient. so it’s not contributing to variation either. and then the variation that’s left contributing to most of the genetic variation in evolution might be selectively neutral

suggested that maybe a lot of this genetic variation that we’re looking at does not affect survival and reproduction but it’s neutral with respect to fitness

Question 41

looking at genetic variation at the DNA level, you can get (2):

Answer 41

• DIRECT interference of genetic differences
• GENETIC CODE for genes can distinguish changes that alter protein from those that don’t

Question 42

genetic drift happens more strongly/weaker in small populations than large populations and therefore smaller populations are expected to have ____ amount of genetic diversity than large populations

Answer 42

genetic drift happens more STRONGLY in small populations than large populations and therefore smaller populations are expected to have LOWER amount of genetic diversity than large populations

Question 43

from the DNA variation in Maize vs Teosinte example, what’s the relation of genetic drift and the founder event/ bottleneck

Answer 43

corn has reduced genetic diversity compared to its wild ancestor teosinte
- a consequence of population BOTTLENECK(S) during domestication (founder event)

selection on some genes reduced diversity further than expected by genetic drift from the founder event

Question 44

in the comparison of genetic variation in Arabidopsis lyrata wild plants across countries, regions that were recently glaciated have lower or higher DNA diversity?

Answer 44

LOWER

genetic drift following recolonization

Question 45

human genetic variation and colonizationin relation to East Africa