lec16: evolutionary significance of genetic variation

Question 1

Recap of theory of evolution: what are Darwin’s key ingredients for evolution by natural selection?

Answer 1

The essence of Darwin’s theory is that natural selection will occur if 3 conditions are met:
1. variation within a population
2. inheritance; has to be heritable
3. fitness/ a struggle for existence; differential survival and reproduction

Question 2

variation

Answer 2

individual variation in a population

Question 3

heredity

Answer 3

progeny resemble their parents more than unrelated individuals

Question 4

fitness

Answer 4

some forms are more sucessful at surviviing and breeding than others in a given environment
- natural selection

Question 5

which one of the 3 (variation,heredity, fitness) is MORE related to genetics?

Answer 5

1. variation
2. heredity

Question 6

where does heritable variation come from (3)?

Answer 6

1. mutation
2. segregation and independent assortment
3. recombination

Question 7

which one of the 3 (mutation,segregation and independent assortment, and recombination) is related to Mendel’s law?

Answer 7

segregation and independent assortment

Question 8

(1) mutation

Answer 8

a stable change in the DNA sequence of an organism

Question 9

(1) mutation occurs at a ___ rate. it varies in ways that are ___ ____. (2) explain.

Answer 9

mutation occurs at a LOW rate. it varies in ways that are PARTIALLY PREDICTABLE.
all mutations occur via mistakes in the DNA sequences, during DNA replication or in a cell if it experiences damage

Question 10

what are the 3 different possible effects of mutation? briefly explain each.

Answer 10

1. neutral: no affect on fitness but can still be introduced into the population
2. deleterious/ harmful (weakly detrimental up to lethal): reduce the organism’s fitness ability but natural selection should be acting to remove them from the population
3. beneficial: benefit fitness = natural selection should be acting for them to increase in frequency/pop

Question 11

characteristics of mutation:
mutation is an inevitable or evitable phenomenon? explain

Answer 11

it’s inevitable despite cellular mechanisms to correct errors during DNA replication. we’ve evolve many mechanisms to reduce the rate of mutation but never to 0, mistakes always occurs.

Question 12

characteristics of mutation:
is mutation directed or not directed toward an outcome by the organism or by the environment? explain

Answer 12

not directed.
1. it is random with respect to effects on fitness
2. not “summoned” to make things better
3. emphasized the difference in lamarck’s and darwin’s theory where mutation is not directed adaptively by environnment

Question 13

characteristics of mutation:
T or F: the rate does not depend on the type of mutation.
can it vary?

Answer 13

F: it does depend on the type of mutation. can also vary among genes

Question 14

characteristics of mutation:
can environment affect mutation rate? explain

Answer 14

YES eg. mutagens or high temperature. it an cause a greater or lesser rate of DNA damage but it’s not directing the organism some adaptive mutation but environment can play a role.

Question 15

what are the 4 types of mutations in relation to the structure of DNA?

Answer 15

1. point mutations
2. insertions/deletions (“indels”)
3. changes in repeat number
4. chromosomal rearrangements (eg. inversions)

Question 16

1. point mutations

Answer 16

single nucleotide mutation. changing one base pair of a DNA sequence

Question 17

2. insertions/deletions (“indels”)

Answer 17

inserting or deleting a base into or out of the DNA sequence

Question 18

3. changes in repeat number+ do these regions shave a higher or lower mutation rate than other parts of the genome + why?

Answer 18

in a DNA sequences with repeated nucleotide group, eg. another repeated group added
- these regions often have higher mutation rates than other parts of the genome because they are more error prone

Question 19

4. chromosomal rearrangements (eg. inversions)

Answer 19

flipping the DNA sequence

Question 20

how did they identify a new mutation by using humans and baboons?

Answer 20

• by estimating the rate of mutations of both humans and baboons.
• sequence the genome and then looking for differences in the DNA sequence of the offspring that aren’t found in either parent; the changes that occur in the kids absent from the parent which is the mutation that is categorized. then looked at the next generation to make sure these new changes were actually passed on. so the 3 generations and extra sequencing were aimed at distinguishing error from true mutational events.

extra note:
number inside: how many times these individual’s genome was sequenced. other word, amount of DNA sequencing
* sequencing the same individual’s genome over and over again because individual mutation is very rare and so it can be important to distinguish errors in technology in sequencing from real mutation
* so the repetition accurately distinguish technological errors from actual mutations

Question 21

what is the rate of new mutation in humans/population? what does it tell us?

Answer 21

for the entire human population, every base pair in the genome mutated about 97 times over on average. so although individually mutation is rare with a large enough genome and a large enough population, all mutations are being introduced over generations

Question 22

T or F: mutation rate varies between species.

Answer 22

true. eg. found a different mutation rate between humans and baboons. humans have over twice the rate of mutations than baboons.

Question 23

are mutation rates generally higher in females?

Answer 23

wrong. it’s generally higher in males and we get more mutations from our fathers than our mothers.

Question 24

explain the mutation effect on pehnotype and fitness in relation to the structure of genomes.

Answer 24

• less likely to have an effect on phenotype and fitness than if we have a mutation within a gene specially if that mutation within a gene causes a change in the amino acid sequence
• a single amino acid can be encoded by multiple different codons. what does that mean for mutation and evolution? there are cases where we have many different point mutations such as this one (3rd red arrow) that does not change the amino acid sequence. we still have a phenylalanine amino acid even though there was a change in DNA whereas here (2nd arrow) we have a point mutation that changed the amino acid which is more likely to affect phenotype and fitness than the 3rd arrow as it’s not leading to a change in the protein sequence

Question 25

what type of mutation is arrow 3? explain

Answer 25

neutral mutations. Examples include silent point mutations. They are neutral because they do not change the amino acid s in the proteins they encode

Question 26

T or F: single mutations can’t cause profound effects on traits.

Answer 26

F: it can for example a gene mutation that happened in an ant where legs appeared and grew out of their head

Question 27

T or F: Less obvious mutations also can be profound for fitness and evolution

Answer 27

true

Question 28

what is the most common enzyme deficiency in humans and what can it cause and protect?

Answer 28

G6PD deficiency
- can cause severe anemia due to red blood cell breakdown (with certain food)
- also protects against malaria

so it can confer some sort of benefit depending on the environment while also causing a form of anemia

Question 29

explain the process of mutations in G6PD: DNA, protein, and phenotype

Answer 29

• amino acid replacement mutations in the coding sequence of G6PD causing disease in A- allele
• DNA.. (nucleotide being replaced; point mutation - the changes = higher risk of anemia but also greater malaria resistance)
• Protein… (changes the protein)
• phenotype… where
  B : fully active enzyme (no anemia, high malaria susceptibility)
  A- : risk of anemia and malaria resistance due to reduced enzyme activity

Question 30

explain the fitness distribution for new mutants: experiments with yeast (look at slide)

Answer 30

note: the fitness is the growth rate of that mutant type compared to the unmutated type

Question 31

____ is the ultimate source of genetic variation. ___ helps increase genetic variation too. now we’ll be talking about the principles of inheritance as Mendel discovered them.

Answer 31

(1) mutation (2) inheritance

Question 32

moving to (2) segregation and independent assortment. heredity before Mendel: before Mendel, how did we think inheritance worked? Organisms resemble their parents, but how? (2 cases; 1700s and 1800s)

Answer 32

1. preformationist; spermists/ ovists believed only one parent contributed to inheritance giving its intact material to the next generation
2. theory of blending inheritance: postulated that factors from both parents mix together irreversibly (mix like paint - blue+yellow = green - to give the offspring)

Question 33

why was the theory of blending inheritance a problem for evolution by natural selection?

Answer 33

after we got the green colour, the next generation will also be green. meaning it loses the genetic variation that was there in the parents.

blue variant mating with all of these yellow parents the offspring will be green and if they keep back crossing these yellow types, you’re going to lose that new beneficial type; if blue was favoured, it’s going to disappear in the first couple generations; that presents a problem with evolution by natural selection

Question 34

Mendel (understanding the nature of particulate inheritance): what did he use for his controlled experiment?

Answer 34

used controlled experiments and used peas where he studied traits and phenotypes that were varying and studied what happened over multiple generations

Question 35

as talked about the predicted experiment where blending inheritance was believed and proved wrong by Mendel. What did Mendel’s experiment actual results were?

Answer 35

P: G x Y (hybrid cross of pure-breeding lines)
F1: Y Y Y Y (self-fertilized
F2: G Y Y Y Y (3/4 Y and 1/4 G) –> 3:1 ratio of the dominant to the recessive phenotype

Question 36

what are the 4 key conclusions from Mendel’s pea experiments? explain each.

Answer 36

1. rather than being like paint mixing, inheritance is determined by discrete particles - genes
2. each diploid organism carries 2 copies of each gene
   - alleles can exhibit DOMINANCE/ RECESSIVITY
3. gametes fuse to make offspring
   - sperm/ pollen with egg/ ovule
   - gametes contain only one allele per gene (so there’s a random choice of your dad’s copy or your mom’s copy when gametes form)
4. offspring inherit one gamete from each parent at RANDOM
   - one allele per gene at random from each parent

Question 37

which of the 2 conclusions are in relation to Mendel’s law of segregation? explain

Answer 37

3 and 4 - is why we get genetic variation in sexual diploid populations; parents aren’t jsut passing on their genome intact to the next generation, there’s a random sampling of gametes from both parents

Question 38

what does the segregation plus independent assortment state?

Answer 38

The law of independent assortment states that the allele of one gene separates independently of an allele of another gene.
- parent 1 (2 chromosomes) goes through meiosis and produces 4 gametes and same for parent 2
- with parent 1 and parent 2, the result is 16 different combinations in offspring (a variation in the offspring)

math
- 2 sets of chromosomes = 2^2 = 4 possible combination of gametes
- 4 sets of chromosomes from parent 1+ parent 2 = 2^2 x 2^2 = 16 possible zygote combinations
- humans: 23 sets of chromosomes: 2^23 = 8.4 million different combinations

Question 39

therefore, does segregation plus independent assortment of chromosomes generate diversity or not?

Answer 39

yes

Question 40

so why are we not all genetically identical to our siblings?

Answer 40

because of Mendel’s laws of segregation and independent assortment where every gamete is a random sampling of the 2 possible alternative chromosomes and that’s being done over and over again across chromosomes

Question 41

T or F: although mutation is the ultimate source of genetic variation, Mendel’s laws of segregation and independent assortment is also an important source of genetic variation

Answer 41

T

Question 42

moving to (3) recombination during meiosis further contributes to variation. explain

Answer 42

Recombination in meiosis. Recombination is a process by which pieces of DNA are broken and recombined to produce new combinations of alleles. This recombination process creates genetic diversity at the level of genes that reflects differences in the DNA sequences of different organisms.

• don’t inherit either our mom’s mom chromosome, or mom’s chromosome, or our mom’s dad’s chromosome intact during segregation and independent assortment, but during meiosis there’s this process of recombination occurs where there’s a shuffling up of maternal and paternal segments of the chromosome during meiosis
• do don’t just say my mom’s mom’s chromosome 3 intact, i have a mixture where it’s mostly my mom’s mom chromosome but a bit of my mom’s dad’s chromosome in there as well

Question 43

T or F: a key point and result from Mendel’s analysis is the distinct between genotype and genome

Answer 43

false. it’s between genotype and phenotype in which their relationship is important to consider.

Question 44

genotype

Answer 44

genetic constitution of an organism
- defined in relation to a particular gene or gene combinations
- eg. Aa, AaBB

so that’s like their DNA sequence or when we think about Mendel we put it in terms of big A and little A alleles, underlying those alleles is sequence in the DNA and the phenotypes

Question 45

phenotype

Answer 45

feature of the organism as observed
- used when discussing a trait of an organism that varies
- eg. size, fur colour, enzyme activity, mRNA expression level

Question 46

genome

Answer 46

the entire organism’s DNA
- includes genes and non-coding regions

Question 47

simple mendelian genetic POLYMORPHISMS

Answer 47

“having multiple forms”

• polymorphisms meaning there’s variation in the population and it relates to differences in the genetic basis.
• eg. the patterns and shape on a king snake is diff from another one
• common in nature
• this is a direct correspondence between trait (phenotype) and its genetic basis (genotype)
• “simple” because easy to track selection and evolution of that variation where there is a “this type” or “this type”

Question 48

Explain the phenotypic variation in human height; what is it trying to prove ? what does this say about Mendel?

Answer 48

• there are many types of phenotype that doesn’t follow Mendel’s discrete trait variation.
• height is highly heritable BUT doesn’t only have 2 types (you’re not tall or short), there is a CONTINUUM
• mendel was just studying the simple traits where you have one vs the other discrete phenotype
• MOST TRAIT VARY CONTINUOUSLY not with discrete categories

Question 49

discrete/ discontinuous traits + the ex provided above

Answer 49

• simple “Mendelian” genetics
• eg. blue vs red
• ex: king snake

Question 50

continuous/ complex/ quantitative traits + the ex provided above

Answer 50

• complex inheritance
• eg. blue, blue-green, green (different shades of green), green-yellow, yellow ….
• ex: human height

can also apply to diseases where it can vary in severity

Question 51

explain the relation between gene number and phenotypic variability in terms of: what are the affects.

Answer 51

• 1 gene: very discrete variation
• 2 gene: a distinct variation but yet a more continuous variation
• 4 genes you get a continuous variation

what if we had 400 or 4000 genes all across the genome influencing the trait. you can imagine variation in many genes in our genome might influence a trait like human height. so if we have many genes and the variation each has a small affect on the phenotype then we can connect Mendel’s law with continuous inheritance and Darwin’s theories

Question 52

are the simple connections between genotype and phenotype extremely usual or unusual?

Answer 52

unusual such as eye colour

Question 53

what are the 2 big factors that affect quantitative (continuous) traits? explain each

Answer 53

• complex polygenic (=many genes) inheritance (they are polygenic meaning the genetic basic is determined by many genes often of small effect all across the whole genome)
• environmental interactions (plays an important role in influencing the phenotype of quantitative traits as well; eg. where they land to germinate the seedling might affect how much nutrients they receive)

genome –> gene A, B, C, D… \
==> phenotype
env. –> factor 1, 2, 3, 4… /

Mendel’s laws still apply to each one of these individual genes but the complexity arises because you have many genes contributing along with the environment to this trait variation

Question 54

discrete or a continuous variation:
1. quantitative genetics
2. mendelian genetics

Answer 54

1. continuous
2. discrete where (has simple mendelian genetics: all genetics are mendelian but we can study discrete variation with this more simplified thinking of mendels, laws of segregation and independent assortment, dominance and recessiveness)

Question 55

discrete or a continuous variation:
genes of major effect, dominance and recessiveness

Answer 55

discrete

Question 56

discrete or a continuous variation:
many genes each with alleles of small effect, important environmental effects

Answer 56

continuous

Question 57

discrete or continuous variation:
selection response as change in average trait value

Answer 57

continuous where:
where we have to consider the role of many genes of small effect, so it’s harder to find those causal genes and the important role of the environment and we can still track evolution by natural selection under this case as emphasized in the new evolutionary synthesis, but it’s more tracking quantitatively the change in phenotype over time

Question 58

discrete or continuous variation:
spread of alleles, change in allele frequency

Answer 58

discrete where: (there we have genes of major effect and we can think about the spread of 1 allele, whether it’s beneficial or deleterious, and we can track the change in the frequency of the allele through time)