Population genetics Flashcards
1
Q
What are uses of population genetics?
A
• Forensic genetics
o Paternity testing
o Crime scenes
• Conservation genetics
• Management of pesticide and antibiotic resistance
o Natural selection resulting
• Origins of people and populations of animals
2
Q
Why is conservation genetics important?
A
• Design of captive breeding programs so that genetic variability is maintained
• Mating structures in endangered populations
o Minimum viable population size maintenance-
50 for a captive population
500 for a wild population
• Resolving taxonomic uncertainties
• Source populations for recovery programs
• Paternity testing and forensics
3
Q
What is a polymorphism?
A
• Polymorphism- existence of two or more allelic forms
4
Q
What is monomorphic?
A
• Monomorphic- only one allelic form
5
Q
What is an allozyme?
A
• Allozyme- variations in form of a metabolic enzyme
6
Q
What is vertebrate allozyme polymorphic loci percentage?
A
15-30%
7
Q
What is invertebrate allozyme polymorphic
A
30-40%
8
Q
What is a plant allozyme polymorphic loci percentage?
A
25%
9
Q
What is vertebrate heterozygosity percentage?
A
5-8%
10
Q
What is invertebrate heterozygosity percentage?
A
7-15%
11
Q
What is plant heterozygosity percentage?
A
7%
12
Q
How does evolution proceed?
A
• Evolution proceeds by the differential reproduction of genotypes
13
Q
How does selection and variation interact?
A
• Expect variation to be eliminated by selection
14
Q
What is the interaction between selection and evolution?
A
• Selection is pushing populations in one direction, while evolutionary forces are pushing populations in another direction to maintain variability
15
Q
Why do lethal alleles still exist in a population?
A
• Natural selection can be weak if lethal allele kills you after reproductive age, hence why deleterious alleles are maintained in the population
16
Q
Where does new genetic variation come from?
A
- Mutation
- Migration
- Sexual reproduction
17
Q
How does mutation introduce new genetic variation?
A
o Original variation from mutation
o Slow process
o pn=p0e^(-nu)
Let the mutation rate from allele a to allele A be u
pn is the frequency of allele A at time n
p0 is the frequency of allele A at time 0
18
Q
How fast are mutation rates?
A
o Mutation rates are:
Very slow- do not contribute much to genetic variability but is root of all genetic variability
19
Q
How do sexual species generate variability?
A
o Sex generates variability
Sexual species
• Crosssing over and sexual reproduction produces high heterozygosity and shuffling of exons
• Genetically variable
20
Q
How do asexual species generate variability?
A
Asexual/clonal species
• Variation arises only through mutation
• Amount of variation and the rate of evolution is lower in asexual species
• Asexual species are very similar to each other
21
Q
What can gene duplication result in?
A
- Natural selection can only act on existing DNA sequences
* Gene duplication can allow for new gene function and permits evolutionary change
22
Q
What can duplicated/repeated sequences resulting from gene duplication be?
A
• Duplicated/ repeated sequences can:
o Retain original function
o Acquire new functions
o Lose function in some duplicates
23
Q
What are pseudogenes?
A
• Pseudogenes-segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability
24
Q
What are gene families, when are they switched on and where do they come from?
A
o May cooperate to produce gene products
o Various versions switched on in different tissues and different lifestages
25
What is myoglobin?
Myglobin- oxygen storage in muscles- most ancient and can be found in plants
26
Describe when the alpha-globin family evolved and where it evolved from?
Beta-globin and alpha- globin family
| • Alpha-globin family diverged from the beta-globin family around 450000000 when first fishes emerged
27
Why is haemoglobin expressed differently in the foetus vs the adult?
Haemoglobins- blood
| • Different haemoglobin in foetus vs adult because oxygen obtained from different places
28
How many gene families are known in humans?
o 100 gene families known in humans
29
How is allele frequency change described?
```
Allele frequency change is described by:
∆p=pq (WA-Wa)/W
p is the frequency of A allele
q is the frequency of a allele
Where WA is the fitness of the A allele
Where Wa is the fitness of the a allele
Where W is the mean fitness of the population
Whenever Wa is not equal to WA, then Δp is not equal to 0
```
30
How can polymorphisms be maintained?
```
• Polymorphisms can be maintained through:
o Frequency dependent selection
o Neutral fitness
o Variable environments
o Heterozygous advantage
```
31
What is frequency dependent selection? Describe the two different types of it
o Frequency dependent selection
Frequency-dependent selection is an evolutionary process by which the fitness of a phenotype or genotype depends on the phenotype or genotype composition of a given population.
• Positive frequency-dependent selection, the fitness of a phenotype or genotype increases as it becomes more common in a population.
o Good for language and mating calls- common communication in a population is important
• Negative frequency-dependent selection, the fitness of a phenotype or genotype decreases as it becomes more common in a population. This is an example of balancing selection
o Good for predator avoidance.
32
What is neutral fitness?
o Neutral fitness
| Two alleles may have identical fitness
33
What is cline?
Cline- where allele frequency changes with some sort of environmental gradient e.g. temperature or saltiness
34
What is a balanced polymorphism and how is it maintained?
When polymorphisms are maintained by a heterozygote advantage this is known as balanced polymorphism
• When heterozygote is better than homozygote wild type or homozygote recessive, maintains potentially deleterious allele in the population, which maintains balanced polymorphisms
35
What forces maintain heterozygosity?
There is a synthesis of forces maintaining heterozygosity
• Genetic drift
• Mutations from one allele to another
• Balanced polymorphism
36
What is the possible heterozygote advantage of sickle cell anemia and in what population is it maintained in?
Possible heterozygote advantage: Resistance to malaria
| Relatively common in these populations: Africans
37
What is the possible heterozygote advantage of tay sacs and in what population is it maintained in?
Possible heterozygote advantage: Intelligence
| Relatively common in these populations Ashkenazim jews
38
What is the possible heterozygote advantage of diabetes and in what population is it maintained in?
Possible heterozygote advantage: famine resistance
| Relatively common in these populations: Australian aborigines
39
What is the possible heterozygote advantage of cystic fibrosis and in what population is it maintained in?
Possible heterozygote advantage: Typhoid resistance
| Relatively common in these populations: Europeans
40
What is the equation for the Hardy-Weinberg equilibrium frequencies?
• Frequency of allele X: p
• Frequency of allele x: q
• Probability of two alleles being in a genotype- multiple frequency of alleles together
• 1=p^2+2pq+q^2=(p+q)^2
o Hardy Weinberg law- frequency of an allele stays the same from generation to generation
41
What is the Hardy-Weinberg law?
• In a large population and in the absence of mutation, selection or migration, allele and genotype frequencies remain constant from one generation to the next
42
What is the Walhund effect?
• Walhund effect-
o If have 2 populations with very different genotype frequencies, if mix these two and sample combined population, it will be out of Hardy-Weinberg equilibrium
o Causes a deviation of expected genotype frequencies from that predicted
o Detected as a deficit of heterozygotes
43
What is the equation for frequency?
• Frequency= Sample/Total
44
For Hardy-Weinberg questions, if faced with an example giving genotypes and observed numbers, what is the process to solve such a question?
1. Work out total number of allele X
2. Work out total number of alleles in a population
3. Divide total number of allele X by total number of alleles in population to find frequency
4. To find frequency of other allele, do 1-X
5. Work out expected frequencies of each genotype by squaring frequency if looking at homozygotes or multiplying the allelic frequencies by each other and 2 for heterozygotes
6. Multiply genotype frequencies and multiple by total population number
7. Compare expected vs observed numbers by doing a standard chi-square test
a. Don’t round results- keep 2 decimal places afterwards
b. Degrees of freedom for Hardy-Weinberg:
i. n-1-1
1. First -1 is for doing the test
2. Second -1 is for the assumptions made during the test: we estimated p/q values
45
What are perturbations that disrupt the hardy-weinberg equilibrium caused by?
```
• Perturbations caused by:
o Migration
o Selection
If one of the genotypes is lethal, then allele frequencies in population will change over evolutionary time
o Genetic drift
o Mutation
o Assortative mating
```
46
What is genetic drift and what is the impact that it can have?
o Genetic drift
If have small population, matings can be dominated by one individual, which can cause changes in allele frequencies
Genetic drift leads to:
• Loss of heterozygosity
• Eventual fixation
o One allele is lost in the population, and the other allele will become prevalent in the population
Low heterozygosity in a population suggests recent founder affect or local inbreeding
Small populations will often lose alleles by random chance
Problems for zoo populations: desirable alleles are lost
47
How do you compute expected allele frequencies under selection against a lethal allele?
```
• Equation:
o qn=q0/(1+nq)
qn-frequency in n generations
q0-initial frequency of lethal allele
n- generation number
q- frequency of lethal allele
```
48
Why does the lethal allele frequency asymptote?
• Lethal allele frequency asymptotes because heterozygous carriers- selection becomes very weak when allele is at low frequency because it is hidden in heterozygous carriers
o Frequency goes down 1/(n+1) per generation
o As alleles become more rare, selection is less effective
49
What is the founder effect?
Founder effect
• Population of founder will have different allele frequencies than population the founder came from
• Genotype of founder will strongly affect genotypes of rest of population
50
What is the equation to find the number of generations it takes for lethal allele frequency to go from one point to another?
To find the number of generations it takes for lethal allele frequency to go from one point to another, use t=(1/qn) -(1/q0)
51
What is inbreeding?
• Inbreeding- defined as the mating of relatives.
52
How can inbreeding occur?
o Can occur by:
Low population size
Artificial use to fix traits
Mating within group
53
What are the effects of inbreeding?
o Effects of inbreeding are:
Random genetic drift- allele frequencies become erratic
Causes differentiation between subpopulations -populations separate genetically
Uniformity within subpopulations
Increase in homozygosity
54
What are the uses of inbreeding?
o Uses of inbreeding
| To fix desirable traits in agriculture and animals
55
What are the undesirable effects of inbreeding?
o Undesirable effects of inbreeding
It can increase frequency of undesirable alleles so that individuals in population become less fit
Reduces fecundity
Causes expression of undesirable alleles as they become homozygotes
56
What is the coefficient of inbreeding and how do you calculate it?
• Coefficient of inbreeding- number used to describe how inbred an individual is
o F= average probability that two alleles in one individual are identical by descent from common ancestor
o Coefficient calculations
F= Σ (1/2)n
• n is the number of individuals from one parent to the other parent
• Do this for both parents
57
What is the coefficient of inbreeding for full siblings?
1/4
58
What is the coefficient of inbreeding for first cousins?
1/16
59
When does self-fertilisation commonly occur and what is its effect on heterozygosity and allele frequency?
• Fixes traits extremely quickly
• Common in plants (fertilisation occurs within the flower)
• Heterozygosity is halved each generation
o Self-fertilisation splits a population into a series of homozygous lines
o Self-fertilisation does not alter original allele frequency
60
What is infant mortality percentage in unrelated mating scenarios?
• Unrelated mating- 3.5% infant mortality
61
What is infant mortality percentage in second cousin mating scenarios?
• Second cousin mating- 3.8% infant mortality
62
What is infant mortality percentage in 1 1/2 cousin mating scenarios?
• 1 ½ cousin mating- 6.06% infant mortality
63
What is infant mortality percentage in first cousin mating scenarios?
• First cousin mating- 5.68% infant mortality
64
Are incest taboos culturally derived or genetically derived? Provide evidence
• Israeli Kibbutz
o Parents tried to get children in their own family groups to mate with each other, but children did not really want to
o Suggests a genetic aversion to incest instead of cultural
• Many small communities have systems of marriage that designed to reduce inbreeding
o Aboriginal cultures exchange brides and bachelors between tribal groups
65
What is the coefficient of relatedness and how is it calculated?
• Coefficient of relatedness (r) = probability that two alleles are identical by descent in two different individuals
o Instead of counting individual numbers, count line number between two targets
o r= Σ (1/2)n
n= number of steps (arrow heads) from one individual to the other
66
What is the coefficient of relatedness of identical twins?
1
67
What is the coefficient of relatedness of parent offspring?
0.5
68
What is the coefficient of relatedness of brother sister?
0.5
69
What is the coefficient of relatedness of half siblings?
0.25
70
What is the coefficient of relatedness of cousins?
0.25
71
What is inclusive fitness?
• Inclusive fitness= personal fitness+ 1/r(fitness of relatives)
72
What is the basis of maternal and paternal care?
• Genes that will reduce personal fitness can spread if they greatly increase the fitness of relatives
o Basis of maternal and paternal care
73
What is inbreeding depression and what does it result in?
• Inbreeding depression
o Mate two relatives together so offspring are homozygous, then offspring have less vigour (reproductive success) than either of the parents
o Decrease in growth, fertility and survival following inbreeding and an increase in homozygosity
74
How do you obtain hybrid vigour and what is it?
• Hybrid vigour
o Cross two inbred lines, there will be increased vigour in offspring
o Will now be heterozygous at every locus
o Heterosis- heterozygosity increases fertility
o Increase in vigour, usually after crossing inbred lines
75
What are the two theories as to why heterozygosity increases fertility?
• Davenport (1908)- Dominance of linked factors
o Favourable alleles are dominant
o Crossing inbred lines produces more heterozygous loci
More loci carrying dominant allele
• East (1936)- Overdominance
o Heterozygote is superior
76
Describe why inbreeding depression is a major concern in some endangered species and not so much for others. Give examples.
• Inbreeding depression is of major concern in domestic animals, humans and endangered species
• Inbreeding reduces survival of infants
o Sumatran tiger- 0.03% reduction in survivability of offspring per inbreeding unit
These are naturally inbreeding
o Brown lemur- 90% reduction in survivability of offspring per inbreeding unit
Lives in large groups- have to be heterozygous and suffer greatly if mate with relatives
77
Why is it important to maintain heterozygosity?
• Importance of maintaining heterozygosity
o Reduced heterozygosity indicates inbreeding and leads to reduced population viability
o Assumption is probably correct- heterozygosity is low in many species with low population size
78
What is effective population size (Ne)?
o Average number of individuals that contribute genes to succeeding generations
79
How can effective population size be increased?
```
o Ne can be increased by
Having a large population
Avoiding sibling mating
All individuals contribute to the next generation
Reduce variance in population size
```
80
What is census/actual population size?
• Census/actual population size- number of individuals in the population
81
Is effective population size higher or lower than actual population size and why?
• Effective population size is lower than actual population size as many of the individuals will be too young, too old, unsuccessful or too scared to breed
82
Why do we want to maximise effective population size when managing a population?
To reduce inbreeding
83
What is minimum effective population size?
• Minimum effective population size
o If one or two individuals dominate reproduction, the effect population size Ne is a lot lower than actual population size
o 50 for a controlled population, 500 for a wild population minimum effective population size
84
What is the census population size of the northern hairy-nosed wombat?
240 animals
85
What is the census population size of the sticknest rat and what is its endangered status?
• Sticknest rat: 3000-4000 (increasing)
| o Being pulled off endangered species list
86
What is the location of the rufous hare-wallaby?
• Rufous hare-wallaby (mala)- extinct on mainland. Confined to two small islands off western Australia
87
Describe the diffficult decision that conservation specialists have to make regarding allocation of conservation money and give an example
• Black-eared monorina melatonis
o Large honey eater of Victoria’s mallee country
o Rare
• Yellow-throated miner Manorina flavigula
o Common form of cleared country
• These two species look similar and can hybridise together
• Conversation specialists look at hybridization abilities between species and prioritise spending on conservation of diverse species
88
What are qualitative traits and how can their phenotype be determined?
• Qualitative traits
o Controlled by a few genes of large effect
o Phenotype can be determined by simple crossing experiments
89
What are quantitative traits and can their phenotype be determined?
o Controlled by many genes and alleles of small effect
o Environmental factors likely to contribute to phenotype
o Crossing experiments will not reveal simple allelic segregations
o Quantitative traits vary over a range
90
Describe a statistical description of quantitative traits
o Quantitative traits are described by a frequency distribution
A mean is the average
• Mean of normal curve is its peak
Variance is a measure of spread
Standard deviation is square root of variance
91
What is the formula for spread?
• Spread= (Σ(mean-score)2)/Number of observations
92
Describe how the genetic basis for corolla length in tobacco was determined and confounds of these results
• Genetic basis for quantitative traits- corolla length in tobacco
o Got 2 lines of tobacco- one with a really long corolla and a short one
o Crossed them to get intermediate F1
o Then intercrossed F1 and produced inbred lines from them
o They then separated back again
• East demonstrated that:
o Corolla length is controlled by about 5 genes
Assume each locus adds 1 cm
There are 35= 243 different genotypes
• 3 different genotypes (2 alleles) and 5 loci
o Underestimate- more than 2 alleles at each locus
o Environmental factors contribute to corolla length
93
What are the steps of biometrical genetics?
* Use statistics to describe genetic variance (means and variances)
* Partition phenotypic variance into contribution from genes and environment
* Predict response to selection (the breeder’s equation)
94
How do you partition phenotypic variance during biometrical genetic analysis? What is the formula for it?
o Phenotype= Genotype+ environment
o Genetic model for partitioning phenotypic variance:
Vp=Vg+ Ve+ (Ve*Vg)
• Where Vp is phenotypic variance
• Where Vg is genotypic variance
• Where Ve is environmental variance
• Where Ve*Vg is genotype by environmental interaction
o A good genotype in one place will not be the best in all places
o A genotype may be superior only in certain conditions
95
How do you estimate Vg?
Vg
• Take population and grow it in controlled, uniform environment
• Any variability present would be due to genetic variability
96
How do you estimate Ve?
Ve
• Take inbred populations and grow in different environments
• Any variability present is due to environmental variability
97
What is the heritability quotient?
o Heritability quotient
h2= (Vg/Vg+Ve)= Vg/Vp
• h2- a measure of how well differences in people’s genes account for differences in their traits
• Heritability vary between 0 and 1
98
Describe the Vg, Ve and heritability quotient of height of blue gums
Vg=high
Ve= high
Heritability= Moderate
99
Describe the Vg, Ve and heritability quotient of wing vein angles in insects
```
Vg= high
Ve= low
Heritability= very high
```
100
Describe the Vg, Ve and heritability quotient of birth number in humans
```
Vg= low
Ve= low
Heritability= low
```
101
Describe the Vg, Ve and heritability quotient of social maturity in children
```
Vg= low
Ve= high
Heritability= very low
```
102
What is narrow sense heritability? What is the effect of narrow sense heritability and what does it include/not include?
o Narrow sense heritability- defined as the proportion of trait variance that is due to additive genetic factors
o Selection can only change allele frequencies
o To predict response to selection we must only consider the additive effects of genes
o Not inbreeding or hybrid vigour
Inbreeding depression is not transmitted to next generation
o Can change alleles a population caries but not its breeding structure
103
What is broad sense heritability?
• Broad sense heritability- defined as the proportion of trait variance that is due to all genetic factors including dominance and gene-gene interactions
104
What is the breeder's equation?
• R=h^2s
o R= response to selection
o h^2= narrow heritability
o s= selection differential (the proportion of individuals selected)
105
Is heritability fixed across populations?
* Heritability is not a fixed character
| * Heritability only refers to a particular population and environment
106
Can heritability be extrapolated to other environments
•Cannot extrapolate high heritability to other environments
107
Is a phenotype heritable if there is no phenotypic variance? Why/why not?
* If there is no phenotypic variance, then you cannot have selection and therefore the phenotype is not heritable
* If a trait is heritable we know that there are several genes that influence the trait
108
What is the equation for heritability? How does this equation work?
• Heritability= 2(rMZ-rDZ)
o Correlation coefficient of monozygotic twins: rmZ
o Correlation coefficient of dizygotic twins: rDZ
• If a trait is heritable, then dizygotic twins would be correlated but not as much as monozygotic twins (assuming the dizygotic twins and monozygotic twins share the same environment)
109
Why do traits related to fitness of an individual have low heritability?
• Traits related to fitness of an individual have low heritability as if you have phenotype that causes you to have low fitness, then will be eliminated from the population
o Genes have been taken out of the population by natural selection
110
What are four approaches to identifying genes influencing physiology or behaviour in eukaryotic organisms?
o Expression profiling (e.g. microarray, RNA sequencing)
o Quantitative trait loci (QTL) mapping
o Candidate genes
o Genome-wide association studies
111
What is the use of expression profiling?
Can be used to determine the expression of all of the genes in a tissue or an individual
112
Describe briefly how a microarray is performed
1. Genes on microscope slide which have a tag for each gene
o Genes are replicated and in different directions
2. RNA extracted from individual with one phenotype and other RNA extracted from individual with another phenotype
3. Convert these RNAs to cDNA
4. Put marker on cDNA
5. Wash it on the slide
6. If cDNA homologous to a gene on slide, then it will stick to slide
7. Plot genes in graph with differential expression on x axis and log odds on the y scale
8. Confirm results by real time quantitative PCR
113
Describe briefly how RNA sequencing is performed
1. Take animals which differ in phenotype
2. Extract their respective RNA
3. Convert to cDNA
4. Sequence the cDNA
5. Read the cDNA and see which genes are being expressed in particular individual
114
Describe how quantitative trait loci mapping is performed
1. Cross two breeding lines that differ very strongly for a trait of interested
2. Produce heterozygotes
3. Backcross F1 heterozygotes to one of the parents
4. Produce backcross progeny: some will be homozygous and other heterozygous
5. Segregate backcross progeny based on expressed trait
6. Look for markers that segregate with allele of interest
7. Genotype these progeny and see if marker is frequently associated with allele which produces trait of interest
o If it is not, then marker is a far distance away from the allele of interest and hence is useless due to increased recombinant rate
o If it is, then marker is a close distance from the allele of interest and hence is useful
115
What are the requirements for quantitative trait loci mapping?
1. Two strains that differ strongly for the trait of interest
2. A saturated genetic map
116
What is the problem of the multiple comparisons used in quantitative trait loci mapping and how can it be resolved?
1. If analyse a wide range of markers with a p=0.05, then there will be a lot of significant marker-allele associations made when in fact these are not significant
2. Need to set significance threshold very low (p<0.001)
117
What is interval mapping and how is it performed?
1. Uses information from linkage map
2. Seeks pair of linked markers that show evidence of a QTL between them
3. If gene that affects trait is closer to one marker than the other, the close marker will have increased signal compared to the other marker
4. If gene that affects trait is in the middle of two markers, then the two markers will have equal weak signal
5. Use to associate where genes are in between two markers
118
How is an LOD score calculated and what it is?
1. Logarithm of odds ratio
| o =log10((Probability that a QTL exists between 2 markers)/ (Probability that a QTL does not exist))
119
How is candidate gene analysis performed?
List of candidate genes
Design PCR primers for these genes within the target species
Compare differential gene expression with RT-PCR
120
What is a GWAS (genome-wide association study) and what is a requirement of it?
Observational study of a genome-wide set of genetic variants in different individuals to see if any variant (SNP) is associated with a trait
Need a population where phenotype is common, where some have it and some do not and find markers associated with phenotype
121
What is gametic disequilibrium?
Gametic disequilibrium- the non-random association of alleles at different loci in a given population
1. Recombination is rare over short distances-> haplotypes preserved for many generations
122
What is quantitative trait locus?
• Quantitative trait locus-a section of DNA that correlates with variation of a quantitative trait in the phenotype of a population of organisms
123
List some examples of behaviour that are strongly genetically influenced
* Colony structure in fire ants
* Foraging behaviour in fruit flies
* Promiscuity in volves
124
Describe how colony structure in fire ants is genetically influenced by describing
- Two types of ant forms and their locations
- Consequence of each genotype
- Function of the allele that produced behavioural consequence
o Two forms of ants
Monogyne -Gp-9 worker phenotype BB
1. Argentina
2. One queen per nest
3. BB queens found their own colonies
o Big ants full of fat that found their own monogyne queens
Polygyne- Gp-9 worker phenotype of Bb or bb
1. Invasive in US
2. Multiple queens per nest
3. Polygyne queens are feeble and week
o Bb queens do not found their own nest-> don’t have their enough fat but do join a polygyne nest
o BB queens in polygyne nests get killed by bb workers
o bb queens are unviable (too small and feeble to found colony) and will soon die
o Gp-9 encodes a pheromone receptor
Expression of genes associated with Gp-9 genotype are overrepresented on the social chromosome (chromosome 16)
125
Describe how foraging behavviour in fruit flies is genetically determined
o for genotype
o Rovers (30% of population)-> forR/forR or forR/fors
Roving is dominant to sitting
o Sitters-> fors/fors
o Stems from difference at one locus (of 13,000)
o for gene encodes an enzyme (kinase) involved in signal transduction
o Homologues of for gene control foraging behaviour in creatures including nematodes, honey bees and humans
126
Describe how promiscuity in voles is genetically determined
• Promiscuity in voles
o Promiscuous mountain voles
Vasopression 1 Receptor gene (V1aRs)-> promiscuous
o Monogamous prairie voles
V1aRL-> monogamous
o If gene has high expression, then feel happier when receiving affection
127
Describe where the CRISPR set up comes from and how it worked in its original organism
• Comes from E.Coli.
o DNA includes spacer DNA (17-20 nucleotides) that matches with viral bacteriophage DNA-> history of old infections so that cell will not be infected again
o Genes associated with CRISPR are cas genes
o Cas genes make cas proteins-
Helicases
Nucleases
o Immune system for bacteria to fight bacteriophage
o When bacteriophage injects DNA, it would normally hijack the cell and become imbedded in genome, and eventually make bunch of bacteriophages and kill the cells
o if there is immune system, bacteria will transcribe and translate Cas9 proteins as well as translate its spacer crRNA which will fit into Cas9 protein
This will allow for invading bacteriophage DNA to be broken apart before it can infiltrate the genome
o If there is an immune system but no spacer that matches the attack, then CRISPR/Cas9 system will create Cas1 protein which will break apart attacking DNA and copy it into the CRISPR system
128
What is required in the CRISPR/Cas9 system?
• CRISPR/Cas9 system
o Cas9 protein
Produces double stranded DNA cut and inactivates cut gene
o gRNA
crRNA- spacer segment that matches up with viral DNA or matches up with desired DNA
tracrRNA- holds CRISPR RNA in place
o Desired DNA for HDR mechanisms to replace double stranded break
129
What is a gene drive and what is their purpose?
• A gene drive is selfish genetic elements that use a variety of mechanisms to ensure they are transmitted to subsequent generations at greater than expected frequencies
o Systems that promote inheritance of a particular genetic variant to increase its frequency in a population in the absence of natural selection
130
What does a gene drive do and result in?
• Promotes super-mendelian inheritance (100% of parent DNA transmitted instead of 50%)
o Gene drives distort normal patterns of inheritance
o Results in offspring population with unequal representation of parental alleles, biased in favour of the distorting allele
131
How are gene drives occuring/produced?
• Can be naturally occurring
o Naturally occurring drives can propagate through a population despite negative effects on fertility or viability
• Can be engineered using CRISPR in germline cells as CRISPR will get passed on to other generations
o CRISPR gene drive
Transgenic organism carries a drive cassette encoding Cas9 and a gRNA
In most cases, one allele of the targeted locus is converted to a drive allele through homologous recombination with the vector bearing the drive cassette
The second wild-type allele is then converted to a drive allele by Cas9 and gRNA expressed from the initial drive allele
132
What is a potential use for gene drives?
• Can be used to suppress or locally eliminate populations by disrupting recessive genes needed for fertility by making offspring infertile or by biasing the sex ratio towards males
133
What are obstacles to efficient propagation of CRISPR gene drives?
* Naturally varying SNPs in the PAM, seed or outer protospacer in wild populations could impair or eliminate recognition and subsequent cleavage
* Variation could also be introduced by nonhomologous end joining mediated repair of Cas9 generated double stranded breaks and subsequent modification of the target sequence via indel
* Inbreeding- there is reduced likelihood that organisms carrying the drive will mate with the target wild population
* Low mating fitness of the drive-bearing organisms
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What are the pros of eradicating pests or invasive species?
- Protect endemic species-> restore native environments by eliminating invasive species
- Save endangered native species from predators
- Environmental restoration
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What are the cons of eradicating pests or invasive species?
- Eliminating a species could cause unintended ecological change
- Species are pests only in certain contexts
- Temporary
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What are the risks of using gene drives?
- Gene drive could fail due to emergence of inactivating mutations
- Breeding with another species and spreading the gene drive to another species but unlikely to happen -> gene flow
- Spill-over to other populations -> spread of gene drives from one country to another and eradicate an invasive species in one country and the native population in its original country
- Could evolve outside of our control and change an entire species
- Only works in sexual species and in those with fast reproductive cycle
- Some governments may use them without the permission of others, which could alter the global ecosystem and cause distrust
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What are the benefits of using gene drives?
- Cheap (once initial investment is made)
- Targeted to species
- Self-propagating
- Effective (assumed to be)
- Not poisons so animals don’t suffer
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What are suitable applications for gene drive technology and examples of these?
• Invasive species
o Predator free 2050- New Zealand
Eradicate mammals (rats, stoats, possums) from NZ
o Invasive European wasps
• Disease vectors
o Mosquitoes
Eradicate species that transmit Malaria, dengue fever
Engineer mosquito to be resistant to/unable to transmit the disease
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What is the gene drive daisy chain system?
* Daisy chain- building an inherently local drive system
* Daisy drives are where the drive components are separated into a linear chain, each component of which must be present for drive propagation
* Each element in the daisy chain functions as a form of genetic fuel: they are sequentially spent over generations of mendelian inheritance until the drive runs out and stops
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Describe the two component daisy gene drive system and a disadvantage of it
• Simplest daisy drive is a two-component system
o Drive cassette (component 1) only propagates through a population when an unlinked, non-driving component (component 2) is also present
o However, these daisy drives are unlikely to be an effective way to alter a population when released in large numbers
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Describe the three component daisy gene drive system and a disadvantage of it
• In a 3-component daisy drive, non-driving component 3 would drive component 2 which would in turn drive component 1 (the drive cassette)
o Addition of a single component ensures that the drive persists for a longer period in the population but is still eliminated after many generations
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What are the risks of using daisy gene drive systems?
• Whilst it is a safer alternative, there is still a potential risk:
o Any recombination event that puts a gRNA from an upstream component of the drive into linkage with a downstream component would create a self-sustaining drive that would be in principle capable of uncontrolled spread in the absence of resistance
