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Flashcards in LEC47: Population Genetics Deck (34)
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population genetics is?

the application of genetic principles to entire populations or organisms

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



may be within a population 

allele frequencies can vary across subpopulations


what marks evolution of a population over time

changes in allele (genotype) frequency


allele frequncy?

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


genotype frequency?

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


what does Hardy-Weinberg equilibrium state?

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



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

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


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

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


what does H-W say about allele frequencies?

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


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

1) genotyping errors 

2) selection

3) genetic drift 

4) non-random mating 

5) population structure


why does natural selection occur? what does it cause?

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


does natural selection work w/ H-W equilibrium



are humans exempt from natural selection?


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

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


what is genetic drift?

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


what are founder effects

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


what is stabilizing vs directional selection? what causes each?

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


how does natural selection in humans occur

mortality in utero 

illnesses prior to sexual maturity 

non-reproduction due to fertility problems or choice


what is birth weight an example of re: natural selection

extremes selected against


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

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


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

speed can be adventageous - greyhound breeding


what is nonrandom mating

what does it cause

how does it occur

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


assortative mating means

people non-randomly choose their mates

based on size, cultural characteristics 


what causes inbreeding

when does it occur

what is its effect on genotype

caused by restricted mobility often

more pronounced in small populations 

increases homozygosity

high risk of recessive diseases

can cause evolution of subpopulations


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

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

find higher-than-expected homozygosity 

can create false-positive associations


what does "out of africa" hypothesis say about allele frequencies

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



how does population stratification impact GWAS studies

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 



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

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 



what is an AIM?

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


what does the int'l HapMap show

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


what is linkage disequilibrium

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


what are the measures for LD

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


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

newer population = longer hap blocks (higher LD)

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


must all SNPs be tested in GWAS?


variation is inherited in groups/blocks 

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


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