LEC47: Population Genetics

Question 1

population genetics is?

Answer 1

the application of genetic principles to entire populations or organisms

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

Question 2

subpopulation?

Answer 2

may be within a population

allele frequencies can vary across subpopulations

Question 3

what marks evolution of a population over time

Answer 3

changes in allele (genotype) frequency

Question 4

allele frequncy?

Answer 4

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

Question 5

genotype frequency?

Answer 5

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

Question 6

what does Hardy-Weinberg equilibrium state?

Answer 6

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

Question 7

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

Answer 7

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

Question 8

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

Answer 8

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

Question 9

what does H-W say about allele frequencies?

Answer 9

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

Question 10

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

Answer 10

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

Question 11

why does natural selection occur? what does it cause?

Answer 11

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

Question 12

does natural selection work w/ H-W equilibrium

Answer 12

no

Question 13

are humans exempt from natural selection?

Answer 13

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

Question 14

what is genetic drift?

Answer 14

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

Question 15

what are founder effects

Answer 15

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

Question 16

what is stabilizing vs directional selection? what causes each?

Answer 16

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

Question 17

how does natural selection in humans occur

Answer 17

mortality in utero

illnesses prior to sexual maturity

non-reproduction due to fertility problems or choice

Question 18

what is birth weight an example of re: natural selection

Answer 18

extremes selected against

Question 19

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

Answer 19

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

Question 20

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

Answer 20

speed can be adventageous - greyhound breeding

Question 21

what is nonrandom mating

what does it cause

how does it occur

Answer 21

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

Question 22

assortative mating means

Answer 22

people non-randomly choose their mates

based on size, cultural characteristics

Question 23

what causes inbreeding

when does it occur

what is its effect on genotype

Answer 23

caused by restricted mobility often

more pronounced in small populations

increases homozygosity

high risk of recessive diseases

can cause evolution of subpopulations

Question 24

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

Answer 24

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

find higher-than-expected homozygosity

can create false-positive associations

Question 25

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

Answer 25

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

Question 26

how does population stratification impact GWAS studies

Answer 26

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

Question 27

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

Answer 27

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

Question 28

what is an AIM?

Answer 28

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

Question 29

what does the int’l HapMap show

Answer 29

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

Question 30

what is linkage disequilibrium

Answer 30

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

Question 31

what are the measures for LD

Answer 31

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

Question 32

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

Answer 32

newer population = longer hap blocks (higher LD)

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

Question 33

must all SNPs be tested in GWAS?

Answer 33

no

variation is inherited in groups/blocks

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