Exam 4: Chapters 20-21 Flashcards

Population Genetics

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1
Q

What does population genetics study? What is it?

A

The transmission of genetic variation in populations
- An extension of Mendel’s basic principles
- Tool to learn about biological function, evolutionary mechanisms, and human history

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2
Q

What is a population?

A

A group of interbreeding individuals of a single species living in the same time and place

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3
Q

What is a gene pool?

A

The total of all alleles carried in all members of a population

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4
Q

What is a sample?

A

A number of individuals used to make inferences about the entire population

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5
Q

What is phenotypic frequency?
What is genotypic frequency?
Example?

A

Pheno: Proportion of individuals in a population that have a particular phenotype
Geno: Proportion of individuals in a population that carry a particular genotype
Ex. population of 20, gene with 2 alleles (A and a)
12 (AA), 4 (Aa), 4 (aa)
Pheno frequency: A_ = 16/20 = 0.8 aa = 4/20 = 0.2
Geno frequency: AA = 12/20 = 0.6, Aa = 4/20 = 0.2, aa = 4/20 = 0.2

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6
Q

What is allelic frequency? How is it calculated?

A

Proportion of gene copies in a population that are of a given allele type

Ex. 20 people, 40 alleles
12 AA –> 24 A alleles
4 Aa –> 4 A alleles and 4 a alleles
4 aa –> 8 a alleles
Frequency of A = (24+4)/40 = 0.7
Frequency of a = (8+4)/40 = 0.3
or
Frequency of A = f of AA + 1/2 f of Aa
Frequency of a = f of aa + 1/2 f of Aa

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7
Q

What are Hardy-Weinberg equilibrium five assumptions?* What is the HWE?

A

1) The population has an infinite number of individuals
2) Individuals mate at random
3) No new mutations appear
4) No migration into or out of the populations
5) Genotypes have no effect on ability to survive and transmit alleles to the next generation
HWE: allele and genotype frequencies will not change unless one of the above conditions is violated
(Independently developed by these men in 1908)

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8
Q

What are the two important outcomes of sexually reproducing diploid organisms with equal segregation and random mating? (Under the HWE)

A

1) Allelic frequencies should be same in adults as in gametes
2) Allele frequencies in gametes can be used to calculate expected genotype frequencies in zygotes in the next generation (predicting genotype frequencies in next generation)

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9
Q

How can the Hardy-Weinberg proportions be expressed as a binomial equation?

A
  • in HWE: p^2 + 2pq + q^2 = 1 (AA + Aa + aa = 1)
    p = allelic frequency (A) - dominant
    q = allelic frequency (a) -recessive
  • Graph: one set of allele frequencies corresponds to one set of genotype frequencies
    p + q = 1 (allele frequencies)
    p^2 cannot be phenotypically distinguishable from pq
  • largest value for heterozygous: 50/50 p/q frequencies
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10
Q

What happens to a population not at HWE?

A
  • one generation of random mating can reshuffle alleles into equilibrium (back to HWE)
    – allele frequency remains constant
    – genotype frequency changes
    (except for sex-linked traits, that take a little longer)
    Ex:
  • Generation 1: b (blue eye allele) = 0.5 - all Bb with brown eyes
  • Generation 2: b (blue eye allele) = 0.5 - 25% BB, 50% Bb, 25% bb (p^2, 2pq, q^2)
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11
Q

What happens with sex-linked genes and HWE?

A

(X-linked)
- these genes require several generations to reach HWE
- first generation 100% males aY & females AA, second 100% AY and Aa, then oscillate: takes 6 generations or so to equilibrate at HWE
* important in endangered species

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12
Q

How does humans relate to HWE?

A
  • many human loci are near HWE
  • random mating may seem unrealistic, however, humans are not mating based on a specific genotype
  • many loci do not affect phenotype and are used in solving crimes and identifying human remains
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13
Q

What are the geographic differences in proportions of blue eyes in Europe?

A
  • HWE predicts allele frequencies are forever unchanging: they should be the same everywhere (NOT what we see)
  • Blue-eyes recessive to brown and arose 6,000-10,000 years ago
  • Trait common in Europe but rare outside of Europe
  • Globe is not evenly distributed with the OCA2 eye color gene
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14
Q

What does Hardy-Weinberg provide for modeling population deviations?

A

A starting point/foundation
- Natural populations rarely meet simplified assumptions of H-W
– New mutations at each locus arise occasionally
– No population infinitely large
– Migrates of small groups of individuals does occur
– Mating not random
– Genotype-specific differences in fitness
- H-W use: estimating population changes through a few generations: not as useful for predicting long-term changes

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15
Q

What is the Monte Carlo simulations?

A
  • A method to model long-term changes in allele frequencies
  • Uses computer program to model possible outcomes of randomly chosen mating over a designated number of generations
    – Starting population: defined number of individuals homozygous and heterozygous
    – mating pairs chosen through random-number generating program
    – Offspring genotypes of each generation based on probabilities
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16
Q

What happens at each generation in a Monte Carlo simulation? Then what?

A
  • At each generation:
    – Total offspring number and parental population size are equal
    – Parental generation is discarded and offspring serve as parents of next generation (works for humans)
  • Multiple, independent simulations are performed
  • Each simulation represents a possible pathway of genetic drift
    – change in allele frequencies as a consequence of randomness in inheritance due to sampling error from one generation to the next
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17
Q

What do we see in Monte Carlo and genetic drift?

A
  • There are different sizes of genetic drift
  • 6 Monte Carlo simulations run with two initial populations of heterozygous individuals and
  • in these simulations there was no selection
  • Smaller population leads to greater genetic drift (allele may fall out/be lost {bottom of chart} and or become fixed {top of chart})
  • Larger population leads to less genetic drift
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18
Q

What is fixation, what causes it, and how long does it take?

A
  • Fixation: when only one allele in a population has survived and al individuals are homozygous for that allele
    – no further change can occur (without migration)
  • At each generation, changes in allele frequencies are relatively small
  • Over many generations, there can be large changes in allele frequency
  • Populations with 2 alleles of equal frequencies: median number of generations to fixation is roughly equal to the total number of gene copies in breeding individuals
    (Population of 10, median fixation time 20 generations)
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19
Q

What accelerates genetic drift?

A

1) Founder effects: a few individuals separate from a larger populations and establish a new population
2) Population bottlenecks: large proportion of individuals die (ie from environmental disturbances)

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20
Q

How do mutations affect a population?

A
  • Mutations introduce new genetic variation
  • Mutations: variant DNA sequence in individual genome that was not present in either parent
    – Deleterious: disrupt important functions
    – Beneficial: provide selective advantage (no current example)
    – Neutral: no benefit nor harm
21
Q

What is molecular clock?

A
  • Mutations accumulate in populations at fairly constant rate over time
  • DNA differences between organisms can be used to estimate how long ago they shared a common ancestor
22
Q

What is fitness? How is it measured? What are the two basic components?

A

An individual’s relative ability to survive and transmit its genes to the next generation (statistical measurement)
- cannot be measured in individuals in a population
- measures in all individuals of same genotype in a population
- two basic components: viability & reproductive success

23
Q

What is natural selection?

A

The process that progressively eliminates individuals whose fitness is lower
- Individuals whose fitness is higher become the parents of the next generation
- Occurs in all natural populations: results in decreased genetic diversity
- it acts on fitness differences to alter allele frequencies
- Always narrowing genetic base
(Violates HWE)

24
Q

How does natural selection interact with a lethal recessive allele?

A
  • Causes death before reproduction
  • Alleles fall out of population slowly because recessive
25
Q

How does Monte Carlo model natural selection?

A
  • population = 500 (1 Rr, 499rr)
    six simulations:
  • 3 simulations R allele goes extinct in <100 generations
  • 3 simulations R allele moves to fixation
26
Q

How does fitness and different environments relate?

A
  • H. sapiens migrated out of northeast Africa 70,000 yrs ago
  • Exposure to UV decreases with increasing distance from equator
    – affects vit D production & skin cancer incidence
    – closer to equator dark skin protects against skin cancer
    – father from equator lighter skin allows more UV for sufficient vit D production
  • Skin pigmentation is a complex quantitative trait determined by alleles at many genes
  • Alleles of several genes show strong associations with different populations around the world
27
Q

What are two alleles for skin pigmentation?

A
  • KITLG: many in Africa (not seen in South America)
  • SLC24A5: many in Africa as well as China, East Russia, and (some) in central and south America
28
Q

What is an example of natural selection in pesticide resistance?

A
  • Large-scale use of DDT & other synthetic insecticides began 1940s
    – DDT nerve toxin in insects
    – dominant mutations in single gene confer resistance through detoxification of DDT
    – with DDT strong selection pressure shifts advantage to the homozygous dominant genotypes
  • 1984: >450 species mites & insects became resistant
29
Q

What changed in the genotype frequencies in mosquitoes in response to DDT?

A
  • In Bangkok: 1964-1967
  • R dominant, resistance allele
  • r susceptibility allele
  • RR means resistance with fitness cost: it increased during use of DDT and then decreased with the absence of insecticide due to negative selection
30
Q

What influences complex traits?

A
  • multiple genes (not independent so)
  • allele interactions
  • variation in environment (ie nutrition)
  • interaction between alleles and environment
31
Q

What is a goal of quantitative analysis of trait variation? What are the factors causing it?

A
  • one goal of quantitative analysis: separate genetic effects from environmental effects
  • Factors causing continuous variation of quantitative traits
    – number of genes determining trait
    – genetic and environmental factors affecting penetrance and expressivity of the genes
32
Q

How do dandelions show the effects of genes and the environment?

A
  • Affecting length of stem at flowering
    1) look at environmental variance (VE)
  • most seeds from mitotic division: all seeds from single parent are genetically identical (any differences because of environment)
  • grow in variable environment (hillside)
    2) look at genetic variance (VG)
  • environment constant by greenhouse
    3) Determine total phenotypic variance (VP)
  • grow genetically diverse seeds on hillside
  • VP = VG+VE
    *Width of curve at bottom tells us how much variance expect from factor
33
Q

What is heritability?

A

The proportion of total phenotypic variance (VP) that is ascribable to genetic variation (VG)
- Broad sense or narrow sense

34
Q

What is broad sense?

A

Broad sense H^2 = (VA+VD+VI)/(VA+VD+VI+VE) = VG/VP
- Measured only when comparing identical twins to each other

35
Q

What equations are good to know for population genetics?

A

VP = VE + VG
VG = VA + VD + VI
VA = variance due to additive (2+ allele effects added together) genetic effects
VD = variance due to dominance effects
VI = variance due to loci interaction

36
Q

What are the aspects of comparing parents and offspring in population genetics?

A
  • Only one allele at any given locus is shared (only one can be present)
  • Combinations of alleles at other loci also differ
  • Comparisons of parents and offspring represent additive variance (VA)
37
Q

What is narrow sense?

A

Narrow sense h^2 = VA/(VA+VD+VI+VE) = VA/VP
- Looks at the additive variance
more useful for making predictions

38
Q

What is genetic relatedness?

A

The average fraction of common alleles at all genetic loci shared by relatives

39
Q

What are geneticists seeking in population genetics?

A
  • to influence traits in a certain direction
  • mean of parents to offspring may be a heritability (h^2) of 0-1
    1: what select in parents is showing up in offspring
    0: what is selected in parents is not showing up in offspring at all - variance more effected by environment
    (typically falls somewhere in between)
    *Genetic selection success depends on narrow sense heritability
40
Q

How is heritability seen in Darwin’s finches?

A
  • bill depth
  • correlation between beak size of offspring and the average of the parent’s beaks size (slop of line is 0.82 = 82% due to additive genetic variance)
41
Q

What would happen Darwin’s finch population had no environmental or no genetic effects?

A
  • No Environment effect: heritability = 1.0 (45* slope)
  • No Genetic effect: heritability = 0
42
Q

What is seen in the traits of two children raised in the same family if heritability is 0.0 or 1.0?

A

0.0: No differences would be seen between monozygotic, dizygotic, or unrelated by adoption
1.0: differences would be observed to extent of difference varies with trait frequency in the population

43
Q

How can geneticists use heritability information?

A

To influence traits
- Selection differential (S): difference between value for this trait in the parents and entire population (breeding and non-breeding)
- Response to selection (R): the amount of change in the mean value of a trait that results from selection
R = h^2S

44
Q

What are QTLs?

A

Quantitative trait loci: genes that contribute to complex traits

45
Q

What are two approaches for mapping QTLs?

A

Depends on producing individuals with different genetic compositions
1) Direct QTL mapping: requires crosses between individuals that differ in the phenotype of interest
2) Association mapping: takes advantage of the history of a random breeding population

46
Q

What are the aspects of direct QTL mapping?

A
  • looks for joint segregation of the phenotype and genetic markers
    Rough mapping:
  • cross individuals showing two extremes of a phenotype
  • identify DNA markers (SNPs, insertions, deletions, SSRs) that segregate with the phenotype
  • markers strongly correlated with phenotype are likely to be near genes that influence the trait
47
Q

How is rough mapping genes involved in tomato fruit size?

A
  • Start: isogenic (homozygous) large (l) and small (p) tomato strains
  • BC1 generation: many sizes due to variation at many genes
  • At each gene the backcross generation consists of p/l and l/l individuals
  • Genotypes and measured weight of hundreds of tomatoes
  • Differences in mean weight of l/l and p/l for a given marker indicated the marker is linked to a QTL
    (marker tells use when the gene is present - better if in gene, select for marker to influence phenotype)
48
Q

What are GWAS and what do they do?

A

Genome-Wide Association Studies: identifies genes that control only a fraction of the total trait variation
- most variation has occurred recently due to population growth
- recent variation hasn’t spread widely around the globe
- acquisition of huge amount of data is necessary