LEC47: Population Genetics Flashcards

1
Q

population genetics is?

A

the application of genetic principles to entire populations or organisms

population = group of organisms of same species living in same geographical area

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2
Q

subpopulation?

A

may be within a population

allele frequencies can vary across subpopulations

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3
Q

what marks evolution of a population over time

A

changes in allele (genotype) frequency

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4
Q

allele frequncy?

A

proportion of **chromosomes **in a population carrying a particular allele at some locus

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5
Q

genotype frequency?

A

proportion of **individuals **in a population w/ a particular genotype at some locus

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6
Q

what does Hardy-Weinberg equilibrium state?

A

in a large population, allele frequency for autosomal traits will achieve and remain in a state of equilibirum after 1 generation of random mating

if you know the frequency of the allele in the population, you can estimate the frequence of the genotype in the population

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7
Q

what are population conditions for H-W equilibirum to work?

A

holds in a model population that’s

1) infinitely large or large enough to neglect errors,
2) mating occurs randomly,
3) there’s no advantage for any genotype,
4) no migration,
5) no new mutations

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8
Q

what is the formula of the H-W equilibrium? name the varibles

A

p = allele A

q = allele a

p2 = homozygous genotype AA

q2 = homogous genotype aa

2pq = htereozygous genotype Aa

p+q = 1

p2 + 2pq + q2 = 1

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9
Q

what does H-W say about allele frequencies?

A

allelic frequencies will remain constant over time if certain conditions are met:

random mating

absence of distributing forces like migration, mutation, and selection in a given gene

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10
Q

what can cause deviation from H-W equilibrium expected frequencies?

A

1) genotyping errors
2) selection
3) genetic drift
4) non-random mating
5) population structure

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11
Q

why does natural selection occur? what does it cause?

A

drives evolution of adaptive traits

occurs as result of fact that more organisms can survive and reproduce

thus selection, propagation, reproduction of genotypes that confer enhanced ability to survive and reproduce

if an allele confers ability to survive, it is reproduced over time

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12
Q

does natural selection work w/ H-W equilibrium

A

no

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13
Q

are humans exempt from natural selection?

A

no

think - 30% of pregnancies end by spontaneous abortion of embryos & fetuses, = **mortality selection **

& of those who marry, ~10% won’t have children, = fecundity selection

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14
Q

what is genetic drift?

A

in each generation, some individuals may by chance leave behind a few more descendents (& genes) than others

genes of next generation will be genes of those “lucky” individuals, not the healthier/”better” individuals

happens to all populations

is an entirely random process, unlike natural selection

does not produce adaptations

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15
Q

what are founder effects

A

genetic drift means population can have high frequency of a gene that causes disease, if its present in that population and there isnt mixing

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16
Q

what is stabilizing vs directional selection? what causes each?

A

selective pressures can act on traits to favor intermediate phenotypes, = stabilizing selection, and to discriinate against intermediate phenotypes, = disruptive selection, or to favor extreme phenotypes, = directional selection

17
Q

how does natural selection in humans occur

A

mortality in utero

illnesses prior to sexual maturity

non-reproduction due to fertility problems or choice

18
Q

what is birth weight an example of re: natural selection

A

extremes selected against

19
Q

what’s coat color an example of re: natural selection

A

intermediate coat color isnt as favorable as dark/light depending on environment, diurnal vs. nocturnal

20
Q

what are domesticated animal habits an example of re: natural selection

A

speed can be adventageous - greyhound breeding

21
Q

what is nonrandom mating

what does it cause

how does it occur

A

source of devaition from H-W in humans

occurs as result of assortative mating from non-random mate selection choices on bases of physical or cultural characteristics

inbreeding also results in positve assortative effects on gene pool

22
Q

assortative mating means

A

people non-randomly choose their mates

based on size, cultural characteristics

23
Q

what causes inbreeding

when does it occur

what is its effect on genotype

A

caused by restricted mobility often

more pronounced in small populations

increases homozygosity

high risk of recessive diseases

can cause evolution of subpopulations

24
Q

if sample is drawn from 2 or more populations, what is effect on allele frequencies?

A

cannot apply H-W, which assumes samples came from single population

find higher-than-expected homozygosity

can create false-positive associations

25
Q

what does “out of africa” hypothesis say about allele frequencies

A

original population’s hoogeneous genome has changed to migrated population’s genome

due to adaptations as moved across world to: environmental effects, nutritional changes, cultural adaptations

26
Q

how does population stratification impact GWAS studies

A

source of error in GWAS

get unequal distribution of alleles in study pop. may result from

1) sample made up of more than 1 distinct population
2) sample made up of individuals w/ differening levels of admixture

27
Q

if cases and controls in GWAS aren’t well matched ancestrally, what can happen?

A

1) unequal distribution of non-disease-related alleles btwn cases & controls
2) any allele more common in population w/ increased risk of disease may appear to be associated w/ disease

28
Q

what is an AIM?

A

ancestry-informative markers

polymorphisms that exhibit substantially diff frequencies btwn populations from diff geographical regions

can use AIMS to estimate the geographical origins of the ancestors of an individual, determine what proportion of ancestry is derived from each geographical region

15 million SNPs from which AIMs can be selected

29
Q

what does the int’l HapMap show

A

SNPs are not inherited individually; rather, correlate w/ each other & are inherited in blocks

30
Q

what is linkage disequilibrium

A

the non-random association of alleles at 2 or more loci

aka 2 SNPs being inherited together rather than independently

measured on scale of 0 to 1

31
Q

what are the measures for LD

A

D and r2

r2 is correlation btwn SNPs, preferred measure

when D and r2 >0.8, 2 SNPs are in LD and typing 1 SNP provides info on other SNPs

if D and r2 = 0, typing 1 SNP provides no info on the other SNP

32
Q

what is association between newness of a population and haplotide blocks?

A

newer population = longer hap blocks (higher LD)

older population (african) = shorter hap blocks (lower LD) - have the least homogeneity

33
Q

must all SNPs be tested in GWAS?

A

no

variation is inherited in groups/blocks

so can test SNPs by tagging SNPs, impute missing genotypes from neighboring SNPs

34
Q
A