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Foundational genetic > Quantitative & Population Genetics > Flashcards

Quantitative & Population Genetics Flashcards

1
Q

Quantitative Genetics : why it’s important

A

“Understanding the inheritance of complex traits is one of the most important challenges facing geneticists in the twenty-first century“

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2
Q

quantitative trait

A

A measurable phenotype governed by complex genetic and environmental conditions that shows a continuous range.
• Quantitative (complex) traits do not show simple Mendelian inheritance ratios
-Quantitative traits are described by a frequency distribution (normal) and require precise measurement

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3
Q

Not all polygenic traits show continuous variation

A

Meristic traits
Phenotypes described by whole numbers. Pea pod with 3, 4, 5, 6 peas, but not 4.5 peas
Threshold traits
For example, Type II diabetes. Two phenotypes present or absent

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4
Q

Statistics for Quantitative Genetics nomalcuture

A

_
X : average value from samples measured
μ : average value entire population
Vx: variance
o: standard deviation

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5
Q

Calculate the mean

A

X=ΣX/n

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6
Q

Calculating the variance

A

_
Vx=Σ(X−X)^2
(n−1)
X is individual value
_
X is the population mean
n is the number of sample

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7
Q

Calculating the standard deviation

A

square root of variance

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8
Q

Nature vs. Nurture

A
  • the gene and environment can influence the phenotype
  • A genotype may be superior only under certain conditions
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9
Q

How to examine if a trait is genetically influence

A
  • comparing pedigrees
  • Twin studies
  • Create different inbred strains or lines aka homozygous (many generations of brother-sister matings, or self fertilization)
  • Selection, only allow individual of a trait with certain criteria to interbreed with each other
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10
Q

Calculate for Total Phenotypic Variance

A

Broad Sense Heritability (H^2)
H^2= Vg/(Vg + Ve)
• The part of the phenotypic variance that is due to genetic differences among individuals in a population.
• It is ‘broad sense’ as it encompasses several different ways that genes contribute to variation

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11
Q

Calculate for Total Phenotypic Variance of each inbred homozygous

A
  • First cross the two to create a F1, record their data
  • Cross the F1 together for F2, record the data
  • The average of the two homozygous and F1 variance is Ve (enviromental variant)
  • Vp of F2 is its phenotypic variant (Vp)
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12
Q

Narrow-sense heritability (h2) for additive trait

A

VPhenotypic = VAdditive + VDominance + VEnvironmental
h2= The proportion of total phenotypic variance due to additive genetic variance.
h2+ Vadditive/Vpopulation
• We can measure h2using
i) Correlations between parents and their offspring
ii) Measuring response to selection

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13
Q

Narrow-sense heritability Measuring response to selection

A 
Selection differential (S) = deviation between the mean of the selected plants and the mean of the population
Selection response (R) = deviation of the population mean, and the mean of selected offspring
Breeders equation : h^2= R/S
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14
Q

How can we identify the genes causing quantitative phenotype

A
  • available if the genetic marker for the gene is know
  • cross breed the two homozygous together
  • perform futher backcross
  • identify the effect of gene toward the polygenetic trait at different marker
  • Distinct distributions for genotypic classes at a marker locus signal the location of a QTL (quantitative trait locus) near the marker
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15
Q

Population Genetics

A
  • All alleles of every gene in a population make up the gene pool. Only individuals that reproduce contribute to the gene pool of the next generation.
  • Population geneticists study the genetic variation within the gene pool and how it changes over time.
  • “Population genetics analyses the amount and distribution of genetic variation in a population and the forces that control this variation”
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16
Q

Use of population genetic

A

DNA forensics
Conservation
tracking migration and lineage

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17
Q

What is a population?

A

• A group of individuals of the same species that can interbreed

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18
Q

Subpopulation

A
  • A large population is usually composed of smaller groups called subpopulations
  • Subpopulations are often separated by geographic barriers
  • Members of the same subpopulation are more likely to breed with year other
  • Subpopulations are sometimes referred to as ‘local populations’ or demes
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19
Q

population dynamic

A

-different aspect population can can from one generation to the next
-• Size
• Geographic location (monarch butterflies)
• Genetic composition
• Population geneticists use mathematical theories that predict how the gene pool will change in response to fluctuations

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20
Q

method for Detecting variation

A
  • Visible phenotypes
  • Chromosomal karyotypes (change in chromosomal number )
  • Immunological markers (blood type)
  • Protein gel electrophoresis
  • Microsatellite markers
  • DNA sequencing (indel, snp)
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21
Q

Detecting VariationMicrosatellite DNA kakapo case

A

The kākāpōis a critically endangered New Zealand parrot found on a few on predator-free islands. In 1995, there were only 51 individuals.
Microsatellite DNA markers were used to compare relatedness between individuals to try and establish suitable breeding pairs.
Today there are more than 150 individuals and this conservation effort was helped with population genetics.

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22
Q

what is genetic diversity and how to calculate it

A 
Gene diversity (GD) is the probability that two alleles drawn at random from the gene pool will be different
Gene diversity = 1-Sum Pi^2
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23
Q

Nucleotide diversity

A

Average gene diversity across all nucleotide sites in a gene (variant & invariant)
• When comparing two copies of a gene, most nucleotide sites are identical. Therefore, nucleotide diversity is typically very low.
• Often, we find little DNA variation within a protein coding gene from a single species.
• Identical DNA sites or bases among individuals are referred to as fixed sites, or invariant sites.

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24
Q

Nucleotide variation at the X-linked G6PD gene in humans

A

A segment of G6PD was sequenced from 47 men of African or non-African descent
Allele A- : poor activity, hemolytic anemia, some protection from malaria
Allele A+ : moderate activity
Allele B : high activity

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25
Q

Hardy-Weinberg assumtion

A
  • Random mating
  • Infinite population size
  • No selection
  • No migration
  • No subpopulations
  • No mutation
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26
Q

Hardy-Weinberg law

A 
p= f A/A +1/2 Aa = frequency of A 
p= f a/a +1/2 Aa = frequency of a 
1= P^2 + 2pq + Q^2
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27
Q

Using Hardy-Weinberg law to see if the frequency matches expected

A

First, calculate the frequency of each alleles
Then, find out the expected frequency of each genotype and number of expected
using chi square test to find out

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28
Q

Chi square test

A

Sum (O-E)^2/E
the degree of freedom is number of genotype-number of alleles

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29
Q

H-W: The three allele extension

A

Hexp= 1 – (p2 + q2 + r2) = 2pq + 2pr + 2qr
P2+Q2+R2+PQ+PR+QR=1

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30
Q

Hardy-Weinberg Law in real life

A

• Under Hardy-Weinberg equilibrium, allele frequencies remain the same from one generation to the next (assumes infinite populations size)
-• However, real populations are finite and frequencies may change
• The change in allele frequencies between generations due to sampling error is random genetic drift, or drift
• Natural selection can also change allele frequencies

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31
Q

Consequences of genetic drift

A

• Random genetic drift is a chance event
• Drift can have large impacts on small population sizes
• Slightly deleterious alleles can may become fixed in small populations due drift
• Similarly, beneficial mutations can also be fixed or
lost by drift

32
Q

probability of gene loss

A

alleles/2n= (alleles frequency x n) : 2n

33
Q

Effective population size, Ne

A
  • Not all individuals in a population contribute to the next generation
  • Ne is the effective population size: the number of individuals in a population having an equal probability of contributing gametes to the next generation. The effective population size can explain the rate at which genetic diversity can change in a real population due to genetic drift and inbreeding.
34
Q

Effective population size formula

A

Ne= 4(Nm x Nf) : (Nm+Nf)

35
Q

Effective population size over generation

A

Ne can also be calculated over multiple generations (t), when actual population sizes (N) are known.
Ne= 1: 1/t (1/n1 + 1/n2 + 1/nt)

36
Q

Population bottleneck

A
  • The reduction in population size over one or consecutive generations is considered a ‘bottleneck’.
  • This can result from natural disasters, habitat loss or predation, but also from fluctuations in food abundance
  • As bottlenecks reduce population size, genetic drift can have a larger influence
37
Q

Domestication Bottlenecks

A
  • Crop domestication reduces genetic variation, however, this may occur over a long period of time
  • Modern crops have less diversity than ancestral varieties
  • Breeding programs can introgress traits (disease resistance, environmental tolerance)
38
Q

Founder Effect Human dispersal out of Africa

A

Mitochondrial haplotypes can be used to trace human origins to Africa
• Human populations have different levels of genetic diversity
• Highest genetic diversity in Africa
• Lowest diversity in this dataset is among Native Americans
• ‘Microsatellite heterozygosity’ measured from 783 loci
• ‘Haplotype heterozygosity’ measured across 20 kb

39
Q

How do populations obtain ‘multiple alleles at a genetic locus

A

Migration
Hybridization
Mutation

40
Q

Germline vs. somatic mutations

A

Germline:
- occur in a germ cell, the offspring carries all the mutation
-It can be pass on (half the gamete carry the mutation)
Somatic:
-occur in a cell, affecting all of the daughter cell
-does not pass on the the next generation

41
Q

mutation rate

A

probability that an allele changes to a different allelic form in one generation.
-denoted by the greek letter u

42
Q

How can we determine mutation rates

A

How can we determine mutation rates?

  1. Mutation accumulation lines
  2. Sequencing viral genomes
  3. Family trios
43
Q

Mutation Accumulation (MA) lines

A

• Founding yeast colony split into 145 strains
• Each strain grown for approximately 2,000 generations
• Sequence parental and derived strains and count mutations
-the larger the genome size the higher the muation rates is

44
Q

Sequencing viral genomes

A
  1. Sequencing viral genomes
    • Human Immunodeficiency Virus mutation rates: 3 x 10-5 errors per base
    • However, this only includes virus particles that are still able to replicate
    • Cuevas et al. (2015) developed a strategy to measure natural mutation rates
    9.3 x 10^−5 Circulating virus, able to replicate (44x lower mutation rate)
    4.1 x 10^-3 Mutation rates in virus unable to replicate due to premature stop codons
45
Q

Family trios

A
  • Using parent DNA sequence to identify any new mutation in the offspring
  • It had been found that the number of mutation increase with the father’s age
46
Q

mutation rates over time

A 
Pt= Po (1 - μ)^t 
Po= initial frequency of A1 
Pt= frequency of A1after t generations 
μ= mutation rate
47
Q

Some assumtion for calculating mutation over time

A
  • infinite pop
  • No selection
  • The mutation is recurrent at a constanct rate and there is no recurision
48
Q

calculation for new mutation per generation, frequency of fixation due to drift and rate of substitution

A

2Nμ New mutations enter a population each generation
1/2N The frequency at which genetic drift replaces a new allele with an old allele
k= μ the rate of substitution of neutral alleles

49
Q

The molecular clock

A
  • Fossil records can be used to estimate most recent common ancestors.
  • As species diverge, DNA sequences become increasingly different
  • We can also use the number of neutral substitutions in a gene to estimate species divergence times
50
Q

What is a neutral site

A

A mutation in an area that have no benefit or disadvantage

51
Q

Calculate of generation between common ancestor

A

Calculate the number of neutral substitutions in a gene between two species
Neutral difference/ total of base pair = divergence
t=d/2k

52
Q

Hardy and calculation for recessive disease

A

square of the frequency

53
Q

Identical by descent (IDB)

A

Definition: Two copies of a gene or allele that can be traced back to a common ancestor.

54
Q

The inbreeding coefficient, F

A

Definition: The probability that two alleles in an individual can be traced back to the same copy in a common ancestor

55
Q

Ptolemaic dynasty of Egypt

A
  • Many consanguineous matings(double horizontal lines)
  • Inbreeding increases homozygosity and decreases heterozygosity
56
Q

Calculate of an inbreeding close loop

A

F1= (1/2)^n
n is the number of generation

57
Q

Calculate of an inbreeding sibling loop

A

F1= (1/2)^n(1+Fa)
Fa is the inbreeding coaficient of the ancestor

58
Q

Properties of inbreeding

A
  • alleles frequencies does not change
  • genoptype frequencies change: increase in homozygousity and decrease in heterozygousity
59
Q

calculate Number of Homozygous Recessives per 10,000 Individuals due to inbreeding

A

fa/a= q2+ pqF
f is the inbreeding coefficient

60
Q

Three principle of natural selection

A
  1. Variation: A population of a species contains individuals that vary in morphology, physiology and behaviour.
  2. Heredity: Offspring resemble their parents more than they resemble unrelated individuals
  3. Selection: Some forms are more successful at surviving and reproducing than other forms in a given environment.
    Frequencies of characteristics (phenotypes) will change over time within a population or species, depending on the environment
61
Q

Natural selection:
DNA variation and phenotypes

A
  • Within a population, we see genetic variation in DNA sequences. Distinct alleles may cause differences in protein function
  • Some alleles may encode proteins that enhance an individual’s survival or reproductive capacity (beneficial alleles = more likely to survive and reproduce)
  • Over the course of many generations, allele frequencies of many different genes may change through natural selection and this significantly alters the characteristics of a species
  • The net result of natural selection is a population that is better adapted to its environment and/or more successful at reproduction
62
Q

effect of natural selection

A

-Promotes adaptation to existing or new environments
Buffers the species against the effects of migration, mutation and genetic drift
Explains diversity as it promotes the adaptation of various phenotypes to different environments

63
Q

The selection coefficient

A

W= relative fitness
S = Selection coefficient
S=1−w
w=1−s

64
Q

method for assessing fitness, component of fitness

A

in the exmaple, fecundity (no of embryo produce) and viability% (survived)

  • calculate the total number of survived offspring per genotype. the highest is the fitness (1)
  • W= offspring survived/ best fitness survived
65
Q

assessing fitness Departures from Mendelian expectations in laboratory crosses

A
  • Calculate the number of offspring expected to have of each phenotype based on mendelian ratio
  • divide actual number against expected, the highest result is the fittess
  • W= BA/BA of fittest
66
Q

inbreeding coefficient of different relationship

A

-unrelated; 0
-brother sister: 1/4
-Half sib: 1/8
-First cousin” 1/16
second cousin: 1/64

67
Q

Case study of pepper moth

A
  • Illustrate the effect of natural selection
  • two phenotype: black and pepper
  • pepper is selected agaisnt due to industrial revolution turning tree trunk black
  • When pollution is reduced and tree become white again, increase in pepper moth and decrease in black
68
Q

General Selection Model

A

• Natural Selection will favour specific genotypes
• GSM can be used to explain how allele frequencies change when selection act
1. The population size is large
2. Mating is random
3. No new alleles are introduced by mutation
4. No migration
5. One locus, two alleles
6. Relative fitness values are constant over generations

69
Q

Calculate the contribution of each genotype toward the next generation

A

Pw, the sum of Pw is the total contribution toward the next generation
P= the ratio of the population of that genotype, w is relative fitness
total contribution is denoted by w^-

70
Q

Calculate the frequency of A and a in the next generation p1

A
71
Q

Calculate the frequency of A and a in the next generation p2 under selection fitness

A
72
Q

Allele frequencies change under the force of natural selection

A
  • When the mutation is dominant,selection is inefficient at purging the unfavoured recessive allele.They can persist in the heterozygous state
  • Favored recessive alleles arethe opposite. They rise slowly and become fixed, removing unfavoured allele from the population
73
Q

Experimental design to test the
hypothesis

A

Step 1 mark all the carbonia and typical moth with a paint brush

2/ release the same number of moth in each phenotype

3/affter a few day recapture the moth using mecury vapor light

4/ make observation about the moth in the wild

74
Q

The data from the moth obsevation

A

Unpolluted woods :
• dark Carbonariaform eaten more frequently (43:15, ~3:1 ratio)
• fewer Carbonariarecaptured
Polluted woods :
• light Typicaform eaten more frequently (26:164, ~1:6 ratio)
• Fewer Typicarecaptured

75
Q

The balance between mutation & selection

A

Equilibrium
The increase in allele frequency due tomutation exactly balances the decrease in the allele frequency due to selection

76
Q

Equilibrium frequency, q^ of a deleterious recessive alleles

A

q^=sqr(u/s)
q^ is equilibrium
u is mutation rate
s is selection coefficient
The increase in allele frequency due to mutation exactly balances the decrease in the allele frequency due to selection

77
Q

Equilibrium frequency of a partially dominant allele

A

q^=u/hs
q^ Equilibrium
u Mutation rate
s Selection coefficient
h Degree of dominance of the deleterious allele

Foundational genetic (15 decks)

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